Native Microorganisms Research Articles

Native microorganisms for sustainable dye biodegradation in wastewaters from jeans finishing.

The textile mill is one of the most water-consuming industries. Wastewater production is very high, and among the main generated pollutants are dyes. In particular, jeans finishing, which is performed all over the world, generates wastewater with indigo dye that has to be eliminated before discharge. This work studies the biological treatment of this type of wastewater using native microorganisms, i.e., without the need for external seed sludge to start-up the process. Two strategies for starting up the biological treatment using laboratory sequencing batch reactors have been compared: the addition of seed sludge from a biological reactor of a wastewater treatment plant and the non-addition of seed sludge, which means that native microorganisms (those in wastewater coming from the industry facilities) are responsible for COD and color degradation. Special attention is paid to biomass shift in both reactors, analyzing both bacterial and fungal populations. Results yielded more than 90% of COD and color removal after 25days in both reactors. MLSS increased in both reactors during the operation, reaching very similar values (around 1840mg/L). Rozellomycota was the predominant phylum in the reactors. Concerning bacteria, Planctomycetota abundance increased considerably in both reactors, which shows the important role of these bacteria in the treatment. It can be concluded that the lower bacterial diversity in the native population in comparison with the seeded sludge was shifting to a higher microbial diversity during the process, achieving a similar microbial population in reactors. It implies that it is not necessary to either work with isolated cultures or seeded sludge, which leads to a simpler and more sustainable solution for textile wastewater treatment in areas all over the world.

Regulation of MareA Gene on Monascus Growth and Metabolism Under Different Nitrogen Sources.

Monascus is a widely used natural microorganism in our country, which can produce useful secondary metabolites. Studies have shown that the nitrogen source directly affects the growth, reproduction, and secondary metabolites of Monascus. As a global transcriptional regulator of nitrogen metabolism, MareA gene is involved in the regulation of secondary metabolism. In this study, we found the MareA gene that is highly homologous to the AreA gene sequence, and used MareA to obtain ΔMareA and OE-MareA. Three strains were cultured with glutamine, urea, NaNO3, and (NH4)2SO4 nitrogen sources. The Monascus pigments and related genes were analyzed by solid-state fermentation under different nitrogen sources. The results showed that the pigment production of the ΔMareA decreased, but the OE-MareA did the opposite. The secondary metabolites of the three strains were analyzed by HPLC and expression level of pigment biosytnthesis gene was determined by RT-qPCR. The relative expression levels of four key Monascus pigment genes in ΔMareA were significantly upregulated in mppE gene, but downregulated in MpPKS5, mppG, and mppD genes. Monascus pigment genes were increased in OE-MareA. In terms of growth regulation, the expression of VosA and LaeA genes was significantly reduced in ΔMareA, while OE-MareA significantly promoted the expression of GprD genes. The pigment production and gene expression in ΔMareA were significantly lower than that of C100, while the opposite was true of OE-MareA when NaNO3 was added to the culture medium. In conclusion, MareA gene had different regulatory effects on Monascus growth and pigments metabolism under different nitrogen sources.

Investigation of the effect of urease bioadditives on porosity and water absorption of cement composites

The results of the application of the biomineralization process in concrete to improve concrete properties such as porosity and water absorption are presented. As a result of the research, an assessment of the activity of various bioadditives based on the Bacillus subtilis strain and isolates isolated from samples of chernozem soil of the Yelets district of the Lipetsk region was given.It was found that the immobilized bacteria slightly differ from the native form in terms of urease activity, however, when stored for more than 50 days. they maintain their activity at a high level, and native microorganisms lose their ability to function, reducing urease activity by 10 times practically to minimum values. It was also revealed that when using Portland cement of various types, there is a decrease in water absorption up to 30%, and porosity decreases up to 40%.The use of different types of fine aggregate also affects porosity, so when using the same parts of sand P1 and P2, porosity is lower than with a homogeneous fine aggregate.It was also noted that all samples had increased strength characteristics – compressive strength and bending strength by 15–25%, respectively. Thus, the use of bioadditives is optimal to achieve improved concrete characteristics.

Whole UVCB Tests Can Yield Biotic and Abiotic Degradation Kinetics of Known and Unknown Constituents for an Enhanced UVCB Degradation Profile

The green transition and move towards safe and sustainable-by-design chemicals entail the need for new methods to study the biodegradability of UVCBs (substances of Unknown or Variable composition, Complex reaction products and Biological materials). Standard simulation biodegradation tests have been developed for single substances and are generally not applicable for UVCBs. The aims of this study were (1) to combine a whole UVCB biodegradation test with a sensitive constituent specific analytical technique, (2) to measure biotic and abiotic degradation of known and unknown UVCB constituents and (3) to determine the impact of a WWTP discharge on the constituent specific biodegradation in stream water. Lavender oil and black pepper oil are of significance in the perfume and cosmetics industries and served as model UVCBs. Stream water sampled upstream and downstream of a wastewater treatment plant (WWTP) discharge point was used as inoculum (i.e., naturally and wastewater adapted bacterial consortia). Tests were conducted in gastight headspace vials and automated Arrow Solid Phase Microextraction GC-MS-scan was applied on unopened vials. Peak area ratios between biotic test systems and abiotic controls were used to determine primary biodegradation kinetics, and freshly spiked analytical references to separate biotic from abiotic degradation. Biodegradation half-times were below 20 days for all known (8-12) and unknown constituents (>78) in the essential oils. Dual column GC-MS analysis produced a level 2 identification of 16 unknown lavender constituents. Biodegradation kinetics were similar in inoculum taken before and after the WWTP outlet, confirming that native stream microorganisms were competent degraders.

Impact of Bacillus Inoculation on Rhizosphere Bacterial Community Structure: A Review

The rhizosphere is a specialized zone where plant roots interact with the soil microbiome. Among various beneficial microbes, the genus Bacillus stands out due to its diverse functionalities and potential to boost plant growth and resilience. Bacillus is a key genus of plant growth-promoting rhizobacteria (PGPR) known for enhancing nutrient availability, producing phytohormones, and inducing plant resistance to pathogens. Inoculating Bacillus species into the rhizosphere can significantly alter the bacterial community's structure and composition. These alterations are driven by the competitive and cooperative interactions between Bacillus and the native rhizosphere microorganisms. Incorporating soil microorganisms into the host plant's beneficial bacterial community improves soil nutrient cycling and nutrient use efficiency. Using microbial inoculants is an effective strategy to address crop succession challenges, enhance microbial community structure, and improve soil fertility, thereby promoting crop growth. This review thoroughly examines the current understanding of how Bacillus inoculation impacts rhizosphere bacterial community structure.

Research review of antibacterial surfactants

The COVID-19 outbreak a pandemic since 11 March 2020, drastic measures to stop the spread of the pandemic have been carried out around the world. Since then, many people have paid more attention to hygiene as well as antibacterial. There are a large number of microorganisms in nature, which have great harm to people, animals, and plants, affecting people’s health and even threatening life. Nowadays, there has been growing interest in antimicrobial surfactants, and many investigators have recently turned to studying antibacterial surfactants. However, medical disinfection can be irritating to human skin and have other disadvantages. In this review, I provide a summary of the current state of the research on different antibacterial surfactants.

Semiconducting minerals participated extracellular electron transfer in red soil of Ningxia Plain, China

In recent years, exploring interactions between sunlight, semiconducting minerals and microorganisms in nature has attracted great attention. However, relatively little research has been conducted on the interaction between minerals and microorganisms in the plain areas of the Yellow River Basin under sunlight. In this study, the mineral composition and microbial community of red soil from the Ningxia Plain, China were analyzed. X–ray diffraction (XRD) results showed that red soil contained semiconducting minerals such as birnessite, hematite and goethite. 16S rRNA analysis found that electroactive microorganisms such as Proteobacteria, Firmicutes and Actinobacteriota were enriched in in–situ microbial community of red soil. Afterwards, electrochemical tests such as linear sweep voltammetry (LSV) and I–t curves, indicated that red soil exhibited good semiconducting properties under light irradiation. Finally, a dual chamber system and electrochemical techniques were used to explore the electron transfer relationship between red soil and microorganisms. The open circuit voltage (350 mV) and maximum power density (1242.72 mW/m2) of red soil cathode system were significantly improved compared to blank graphite electrode, indicating that red soil could serve as electron acceptors for microbial extracellular respiration. Red soil electrode in live bacteria exhibited the highest photocurrent density (0.29 μA/cm2) and the lowest charge transfer resistance (Rct) (223 Ω) under light conditions, indicating that red soil accelerated the rapid transfer of electrons, reduced polarization loss, and enhanced extracellular electron transfer (EET) process under light conditions. This study demonstrated that the participation of semiconducting minerals in microbial EET processes under sunlight in the Ningxia Plain, China.

Atomically dispersed iron sites from eco-friendly microbial mycelium as highly efficient hydrogenation catalyst

Iron, one of the most abundant elements on earth and an essential element for living organisms, plays a crucial role in our daily metabolism. In the field of catalysis, the development of high-performance catalysts based on less toxic iron element is also of significant importance for green chemistry and a sustainable future. To construct Fe-based heterogeneous catalysts with excellent hydrogenation performance, precise modulation of the atomic coordination structure is a key strategy for enhancing catalytic activity. In this study, we present an in-situ coating method for applying a zeolitic imidazolate framework (ZIF) onto the surface of fungal hyphae. The asymmetric coordination structure of Fe1-N3P1 was precisely tailored by utilizing the phosphorus source from the fungus and the nitrogen source in the ZIFs. Detailed characterizations and density functional theory calculations revealed that the incorporation of ZIFs not only increased the specific surface area of catalysts, but also facilitated the dispersion of Fe2P nanoparticles into the Fe1-N3P1 center, making the lowest reaction energy barrier and resulting in the best performance for nitrobenzene hydrogenation when compared to the Fe2P nanoparticles and clusters. This research introduces a novel design concept for constructing asymmetric monoatomic configuration based on the inherent characteristics of natural microorganisms and the exogenous porous coordination polymers.

Determining Marine Biodegradation Kinetics of Chemicals Discharged from Offshore Oil Platforms─Whole Mixture Testing at High Dilutions Increases Environmental Relevance.

Offshore oil platforms discharge enormous volumes of produced water that contain mixtures of petrochemicals and production chemicals. It is crucial to avoid the discharge of particularly those chemicals that are persistent in the marine environment. This study aims to (1) develop a biodegradation testing approach for discharged chemicals by native marine microorganism, (2) determine how dilution affects biodegradation, and (3) determine biodegradation kinetics for many discharged chemicals at low and noninhibitory concentrations. Produced water from an offshore oil platform was diluted in the ratio of 1:20, 1:60, and 1:200 in seawater from the same location and incubated for 60 days at 10 °C. Automated solid-phase microextraction GC-MS was used as a sensitive analytical technique, and chemical-specific primary degradation was determined based on peak area ratios between biotic test systems and abiotic controls. Biodegradation was inhibited at lower dilutions, consistent with ecotoxicity tests. Biodegradation kinetics were determined at the highest dilution for 139 chemicals (43 tentatively identified), and 6 chemicals were found persistent (half-life >60 days). Nontargeted analysis by liquid chromatography-high-resolution MS was demonstrated as a proof-of-principle for a comprehensive assessment. Biodegradation testing of chemicals in discharges provides the possibility to assess hundreds of chemicals at once and find the persistent ones.

Decay kinetics of human-associated pathogens in the marine microcosms reveals their new dynamics and potential indicators in the coastal waters of northern China

Pathogens in coastal waters cause infectious diseases and endanger public sanitation safety in humans and animals worldwide. To avoid these risks, timely detection of human-associated pathogens in waters is crucial. In this study, the decay kinetics of the molecular markers for human-associated pathogens, including enteric bacteria (Escherichia coli, Enterococcus, and Bacteroides), non-enteric bacteria (Staphylococcus aureus), crAssphage, and polyomavirus, were monitored over time at different temperatures and background microbes in seawater microcosms. The results indicated that temperature and native marine microbes were the main influential factors in attenuating bacterial pathogens. Remarkably, the effect of native microorganisms was more evidentially striking. Furthermore, Enterococcus was a more reliable and suitable fecal indicator bacterium than E. coli for the marine environment. The decay of crAssphage was like that of polyomavirus, indicating that it may be a good indicator of enterovirus in seawater. More importantly, the 16S amplicon sequencing data highlighted the decay kinetics of multiple bacterial pathogens in parallel with the dynamic changes of the whole bacterial communities. This study provides valuable information for public health risk management and a new approach to understanding the fate of bacteria in the coastal environment.

Insights into Women's health: Exploring the vaginal microbiome, quorum sensing dynamics, and therapeutic potential of quorum sensing quenchers

The vaginal microbiome is an important aspect of women's health that changes dynamically with various stages of the woman's life. Just like the gut microbiome, the vaginal microbiome can also be affected by pathologies that dramatically change the typical composition of native vaginal microorganisms. However, the mechanism as to how both vaginal endemic and gut endemic opportunistic microbes can express pathogenicity in vaginal polymicrobial biofilms is poorly understood. Quorum sensing is the cellular density-dependent bacterial and fungal communication process in which chemical signaling molecules, known as autoinducers, activate expression for genes responsible for virulence and pathogenicity, such as biofilm formation and virulence factor production. Quorum sensing inhibition, or quorum quenching, has been explored as a potential therapeutic route for both bacterial and fungal infections. By applying these quorum quenchers, one can reduce biofilm formation of opportunistic vaginal microbes and combine them with antibiotics for a synergistic effect. This review aims to display the relationship between the vaginal and gut microbiome, the role of quorum sensing in polymicrobial biofilm formation which cause pathology in the vaginal microbiome, and how quorum quenchers can be utilized to attenuate the severity of bacterial and fungal infections.

Biopreservation of Food Using Probiotics: Approaches and Challenges

Food preservation has received a paramount focus throughout history, prompting the use of various methods such as chemical additives, thermal treatments, and nonthermal approaches to prolong the shelf life of food. In this regard, biopreservation is emerging as a promising alternative owing to its eco-friendly nature and minimal toxicity effects. It involves harnessing natural microorganisms and their byproducts to enhance both the nutritional value and longevity of food products. This review delves into the role of probiotics and postbiotics in biopreservation, elucidating their beneficial impact on human health and their potential as ‘safe’ food preservatives. It covers a spectrum of pro/post-biotic organisms, including bacteria and yeast, alongside different types of biopreservatives, their mechanisms of action, and applications across diverse food categories. Furthermore, the review assesses the influence of biopreservation on food quality and sensory attributes. However, commercialization hurdles loom, particularly concerning safety and regulatory compliance, necessitating thorough scrutiny before widespread implementation.

Contribution of Proteorhodopsin to Light-Dependent Biological Responses in Hymenobacter nivis P3T Isolated from Red Snow in Antarctica.

Proteorhodopsin (PR) is a major family of microbial rhodopsins that function as light-driven outward proton pumps. PR is now widely recognized for its ecological importance as a molecule responsible for solar energy flow in various ecosystems on the earth. However, few concrete examples of the actual use of light by natural microorganisms via PR have been demonstrated experimentally. This study reveals one example of that in a cryophilic bacterium Hymenobacter nivis P3T isolated from red snow in Antarctica. The results demonstrate light-dependent biochemical and biological responses in H. nivis cells, such as the proton pump activity of H. nivis PR (HnPR), which leads to the production of proton motive force, cellular ATP production, and cell growth. In addition, the results of this study demonstrate the photochemical properties of a PR, namely, HnPR, in the membrane of a natural host bacterium. The photocycle of HnPR was much faster than other PRs even at 5 °C, indicating that the proton pump function of HnPR has adapted to the low-temperature environment of Antarctica. Although it is well-known that PR helps natural host microorganisms to use light energy, this study provides another concrete example for understanding the biological role of PR by demonstrating the link between the molecular functions of PR and the light-dependent biochemical and biological responses of a PR-bearing host.

The potential of soil endemic microorganisms in ameliorating the physicochemical properties of soil subjected to a freeze-thaw cycle

Establishing soil biological crusts will result in the long-term restoration of ecosystems. Nonetheless, little research has been conducted to demonstrate the influence of soil endemic microorganisms on suppressing the adverse effects of freezing-thawing on soil properties. This current study evaluated the formation of biological crusts, the enhancement of physical and chemical characteristics of soil, and surface soil stability by inoculating native bacteria and cyanobacteria into the soil during a freezing-thawing cycle. The soil was collected from the Badranlou Region in North Khorasan Province, Northern Iran, and native bacteria and cyanobacteria were isolated, identified, chosen, and cultured. The native treatments of bacteria and cyanobacteria were then inoculated in individual bacteria, cyanobacteria, and combined inoculation of cyanobacteria and bacteria onto an experimental soil in six replications. After 60 days, they were subjected to freezing-thawing conditions to have maximum effect on the soil environment, and finally, the soil surface properties were statistically compared. The results of the significant effect (p<0.001) of inoculation treatments on the physical and chemical properties of the study soil revealed that the carbon, nitrogen, organic matter, phosphorus, potassium, and surface soil stability in bacterial treatment compared to the control treatment increased by 68, 39, 68, 17, 25, 99 %, respectively. While under cyanobacterial treatment, they rose by 83, 61, 83, 18, 73, and 172 %, respectively. The combination inoculation treatment of bacteria and cyanobacteria enhanced the study variables by 73, 66, 73, 25, 58, and 189 %, respectively. Compared to control plots, the soil bulk density in bacterial, cyanobacterial, and compound inoculation treatments was substantially reduced (p<0.001) by 9, 15, and 12 %, respectively. The soil stability, carbon, and organic matter were among the most essential properties of the soil, and they best showed the difference between the various treatments applied. It confirmed the region's potential restoration by inoculating native soil microorganisms.

Isolation of native microorganisms from Shengli lignite and study on their ability to dissolve lignite.

To more greenly and efficiently utilize the abundant lignite resources and explore the microbial degradation and transformation potential of lignite for its environmentally friendly and resourceful utilization, Shengli lignite from the Hulunbuir region of Inner Mongolia, China, was selected as the research subject. Through the dilution plating method and streaking method, 31 native microorganisms were successfully isolated from the Shengli lignite, including 16 bacteria and 15 fungi. After microbial coal dissolution experiments, it was found that certain microorganisms have a significant dissolving effect on lignite, with some bacterial and fungal strains showing strong dissolution capabilities. In particular, the bacterium SH10 Lysinibacillus fusiformis and the fungus L1W Paecilomyces lilacinus demonstrated the best coal-dissolving abilities, with dissolution rates both reaching 60%. The products of microbial dissolution of lignite were analyzed using gas chromatography-mass spectrometry (GC-MS) technology, identifying a variety of small molecular organic compounds, including alkanes, alcohols, esters, and phenols. The results of this study provide a new perspective on the biodegradation of lignite and lay the foundation for the development of new lignite treatment and utilization technologies.

Mannitol as a Growth Substrate for Facultative Methylotroph Methylobrevis pamukkalensis PK2.

Biochemistry of carbon assimilation in aerobic methylotrophs growing on reduced C1 compounds has been intensively studied due to the vital role of these microorganisms in nature. The biochemical pathways of carbon assimilation in methylotrophs growing on multi-carbon substrates are insufficiently explored. Here we elucidated the metabolic route of mannitol assimilation in the alphaproteobacterial facultative methylotroph Methylobrevis pamukkalensis PK2. Two key enzymes of mannitol metabolism, mannitol-2-dehydrogenase (MTD) and fructokinase (FruK), were obtained as His-tagged proteins by cloning and expression of mtd and fruK genes in Escherichia coli and characterized. Genomic analysis revealed that further transformation of fructose-6-phosphate proceeds via the Entner-Doudoroff pathway. During growth on mannitol + methanol mixture, the strain PK2 consumed both substrates simultaneously demonstrating independence of C1 and C6 metabolic pathways. Genome screening showed that genes for mannitol utilization enzymes are present in other alphaproteobacterial methylotrophs predominantly capable of living in association with plants. The capability to utilize a variety of carbohydrates (sorbitol, glucose, fructose, arabinose and xylose) suggests a broad adaptability of the strain PK2 to live in environments where availability of carbon substrate dynamically changes.

Superiority of native soil core microbiomes in supporting plant growth

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

120. Zootechnical performance of fattening pigs and ammonia emissions and greenhouse gases: Effect of a selected natural micro-organism complex added to slurry in pig housing

120. Zootechnical performance of fattening pigs and ammonia emissions and greenhouse gases: Effect of a selected natural micro-organism complex added to slurry in pig housing

Directed evolution of material-producing microorganisms

Nature is home to a variety of microorganisms that create materials under environmentally friendly conditions. While this offers an attractive approach for sustainable manufacturing, the production of materials by native microorganisms is usually slow and synthetic biology tools to engineer faster microorganisms are only available when prior knowledge of genotype-phenotype links is available. Here, we utilize a high-throughput directed evolution platform to enhance the fitness of whole microorganisms under selection pressure and identify genetic pathways to enhance the material production capabilities of native species. Using Komagataeibacter sucrofermentans as a model cellulose-producing microorganism, we show that our droplet-based microfluidic platform enables the directed evolution of these bacteria toward a small number of cellulose overproducers from an initial pool of 40,000 random mutants. Sequencing of the evolved strains reveals an unexpected link between the cellulose-forming ability of the bacteria and a gene encoding a protease complex responsible for protein turnover in the cell. The ability to enhance the fitness of microorganisms toward a specific phenotype and to unravel genotype-phenotype links makes this high-throughput directed evolution platform a promising tool for the development of new strains for the sustainable manufacturing of materials.

Pulsed light treatment of whole white button mushroom (Agaricus bisporus): Kinetics and mechanism of microbial inactivation and storage study.

The whole white button mushrooms (WWBMs) are highly perishable due to susceptibility to microbial spoilage. This study explored the potential of pulsed light (PL) treatment for decontamination and shelf-life extension of WWBM. WWBM surface was inoculated with Escherichia coli, Listeria monocytogenes, and Aspergillus niger spores (8.1, 8.0, and 8.05log10CFU/g, respectively) and tested for inactivation against various PL intensities (fluence 0.13-0.75J/cm2). The kinetics and mechanism of microbial inactivation were explored, and shelf life was determined at 4, 20, and 37°C. Microbial inactivation increased with increasing PL intensity. PL-induced microbial inactivation was well explained by Weibull model with shape parameters (β-value) for E. coli, L. monocytogenes, A. niger, aerobic mesophiles, and yeast and mold as 0.87, 0.92, 0.91, 0.89, and 0.94, respectively. PL-treatment at 0.75J/cm2 resulted in >5-log cycle reduction in all inoculated and natural microorganisms. Exposure to PL led to collapse of cellular structure, ruptured cell wall, and leakage of cellular material in all microorganisms and spores along with alterations in nucleic acid and lipid bands. At 4°C, maximum shelf life of 5 days was achieved when WWBM was exposed at 0.75J/cm2. The WWBM retained 83.3% phenolics, 83.9% antioxidant capacity, and 77.4% vitamin D2 at 4°C while reducing the polyphenol oxidase and peroxidase activity by 89% and 79%. The degradation rate for quality parameters increased with storage temperature. The activation energy of the browning index affirmed it as the most sensitive quality attribute during storage. The study concluded the potential of PL treatment to prolong the shelf life of WWBM.