Enrichment Culture Research Articles

Evaluation of Monascus purpureus fermentation in dairy sludge-based medium for enhanced production of vibrant red pigment with minimal citrinin content.

This study aimed to explore the production of red pigment from Monascus purpureus in waste culture medium and its potential health benefits. Subsequently, the M. purpureus cultivated in a medium containing dairy sludge as waste, the extracted pigment was purified, and subjected to various analyses, including liquid chromatography mass spectrometry (LCMS) and nuclear magnetic resonance (NMR) to verify its purity, high-pressure liquid chromatography (HPLC) to measure the citrinin levels, microbial, and antioxidant activity. Finally, fermentation was conducted in a batch system using a fermenter. M. purpureus was grown in a medium composed of dairy sludge, monosodium glutamate, and glucose, resulting in a biomass yield of 26.15 g/L. After extraction and purification, the sample yielded 4.85 g of dry color. Analysis confirmed the purity of the pigment by LCMS and NMR and revealed low citrinin levels by HPLC. In the fermenter, the sample obtained from enriched culture conditions displayed the highest concentration of monascorubramine, maximum specific growth rate of 0.029/1/h, a cell yield (Yx/s) of 0.29 g/g, and a production efficiency of 65% for M. purpureus. The produced pigment sample showed potential for use in the food industry due to its low citrinin content and high concentration of red pigment.

Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.

Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3--N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3--N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.

Simultaneous devulcanization and denitrification: a novel approach for valorization of both ground tire rubber and nitrate-containing wastewater.

This study focused on a new approach for valorization of both ground tire rubber (GTR) and nitrate-containing wastewater via simultaneous devulcanization and denitrification. Initially, sulfur-based autotrophic denitrifiers were successfully enriched from three different seed sludge sources, biological nutrient removal (BNR) sludge, anaerobic digester sludge and BNR sludge of a leather organized industrial zone WWTP. Average nitrate removal efficiencies were 96-98%. Biological devulcanization (biodevulcanization) of GTR was later investigated with these enriched cultures. Results revealed that biodevulcanization was only achieved with the culture enriched from BNR sludge of the leather organized industrial zone WWTP, as 3.9% sulfur removal (desulfurization efficiency). Metal sulfate precipitation was speculated to cause an underestimation of the desulfurization ratio. Fourier-transform infrared spectroscopy (FTIR) results demonstrated a decrease in the intensity of the C-S bonds and an increase in intensity of S-O bonds in treated GTR samples. This was attributed to the oxidation of sulfidic crosslinks, i.e. verification of biodevulcanization. This study indicated that simultaneous biodevulcanization and denitrification could be a promising process for valorization of both GTR and nitrate-containing wastewater which in turn would support circular economy and sustainable development.

Bacterial microbiota associated with raw plant-based meat analogue products and their influences on selective enrichment for Escherichia coli O157:H7

Towards fostering a more sustainable food production system in face of the climate change challenge, alternative protein meat-substitute products that are plant-based and free of animal by-products have been gaining attractions from both food manufacturers and consumers. With these so-called plant-based meat analogues (PBMAs) becoming increasingly available at supermarkets, there is very little known about their microbial properties. In this short report, we characterized the bacterial composition of raw plant-based ground meat imitation retail products using 16S rRNA gene amplicon sequencing. Despite the observed bacterial community dissimilarity between sample brands, a total of 18 shared genera (dominated by Bacilli and Gammaproteobacteria classes) were identified as the core constituents of the bacterial microbiota of these PBMA products. Within the scope of food safety testing, to gain insights on the dynamics of the enrichment process for E. coli O157:H7 in accordance with the Health Canada reference method MFHPB-10, bacterial taxonomic analyses were conducted at different stages of the prescribed cultural procedures. Using both control and E. coli O157:H7-inoculated PBMA samples it was revealed that, independent of the presence of E. coli O157:H7, off-target bacteria of the Clostridium sensu stricto 1 genus were significantly enriched from the uncultured samples. Additionally, the abundance of Hafnia-Obesumbacterium bacteria in the PBMA samples was also increased in the enrichment products, but only when E. coli O157:H7 was absent. Consistent with the spread-plating results indicating that the inoculated E. coli O157:H7 cells were capable of reaching a high density (>108 CFU/ml) in the resultant enrichment cultures, the significant enrichment of bacterial 16S rRNA gene sequences belonging to the targeted genus of Escherichia, but not Hafnia-Obesumbacterium. This further highlights the competitive nature of the selective enrichment for E. coli O157:H7 against specific background bacteria associated with the PBMA products.

Alkalothermophilic Iron-Reducing Bacteria of the Goryachinsk Thermal Water Basin

A study of iron-reducing prokaryotes that use the poorly crystalline mineral ferrihydrite as an electron acceptor revealed their widespread occurrence on the planet. However, the ability of iron reducers to develop under polyextreme conditions (at elevated values of pH and temperature) has not been previously demonstrated. To confirm the existence of alkalothermophilic iron reducers, we studied the water and sediment samples from the Goryachinsk nitrogen-rich thermal water basin. These springs are associated with young tectonic fractures in the Baikal rift zone; their water is characterized by low salinity, alkaline pH (8.8‒9.2) and temperature of 53‒55°C. Enrichment cultures reducing synthesized ferrihydrite were obtained by adding this mineral to the water and sediment samples from the Goryachinsk thermal springs, followed by anaerobic incubation at 50 and 55°C. The 16S rRNA gene profiling of the water and sediment samples and of the primary enrichment cultures revealed high taxonomic diversity, almost exclusively represented by bacterial taxa. Subsequent transfers with ferrihydrite and organic acids or hydrogen as electron donors resulted in stable enrichment cultures of organo- and lithotrophic alkalothermophilic iron reducers. Members of the genus Parvivirga, one of the first cultured representatives of the OPB41 group (now the order Anaerosomatales, phylum Actinomycetota), constituted 30 to 50% of the total abundance.

Impact of glyphosate on soil bacterial communities and degradation mechanisms in large-leaf tea plantations

This study investigated the impact of glyphosate on bacterial communities and their degradation mechanisms in large-leaf tea soil, through exposure microcosm and enrichment culture experiments. Soils from three tea gardens in Yunnan, China, were used: two glyphosate-free (JM and KL) for microcosm study and one long-term exposed (G2) for enrichment culture experiment. The results revealed a two-phase degradation process with half-lives of 12.7 to 268 days, while the metabolite AMPA was notably persistent. The acidic conditions and high organic content of tea soils may retard glyphosate microbial availability and degradation. Glyphosate initially stimulated bacterial growth but led to abundance declines with prolonged exposure. It tended to enhance bacterial diversity at lower doses. Network complexity increased in JM soil where strong adsorption moderated glyphosate exposure, yet decreased in KL soil where weak adsorption enabled greater microbial-glyphosate interactions. Community structure analysis revealed soil-specific responses, with decreased Proteobacteria in JM soil and Actinobacteria in KL soil, while several phyla including Proteobacteria, Acidobacteriota, Chloroflexi, Myxococcota, and Verrucomicrobiota showed increased abundance. PICRUSt2 analysis indicated enhanced biosynthesis and cell growth pathways, while carbohydrate metabolism, nitrogen metabolism, and xenobiotics biodegradation pathways were reduced. LEfSe analysis identified potential degrading biomarkers primarily from Proteobacteria, Acidobacteriota, Myxococcota, Chloroflexi, and Actinobacteriota, suggesting their putative role in degradation. The enriched consortium G2 efficiently degraded 400mg/L glyphosate within 7 days, with notable increases in Afipia, Dokdonella, and Cohnella abundance. This study provides insights into bacterial interactions with glyphosate in tea soils, suggesting strategies for contamination mitigation and environmental restoration.

Impact of TiO2, ZnO, and Ag nanoparticles on anammox activity in enriched river Nile sediment cultures: unveiling differential effects and environmental implications

BackgroundThe increasing use of nanoparticles (NPs) necessitates investigation of their impact on wastewater treatment processes, particularly anammox, a critical biological nitrogen removal pathway. This study explored the effects of short-term exposure to TiO2, ZnO, and Ag-NPs on anammox activity in enriched cultures derived from River Nile sediments.Materials and methodsAnammox bacteria were identified and enriched, with activity confirmed through 16S rRNA and hydrazine oxidoreductase (hzo) gene amplification and sequencing. Activity assays demonstrated efficient ammonium removal by the enriched culture. Subsequently, the impact of different sized and concentrated NPs on anammox activity was assessed.ResultsXRD analysis confirmed NP behavior within the microcosms: TiO2 transformed, ZnO partially dissolved, and Ag remained ionic. hzo gene expression served as a biomarker for anammox bacterial activity. Interestingly, 100 nm TiO2-NPs up-regulated hzo expression, potentially indicating a non-inhibitory transformed phase. Conversely, ZnO and Ag-NPs across all sizes and concentrations significantly down-regulated hzo expression, suggesting detrimental effects. Ag-NPs amended microcosms showed a significant reduction (79%) in hzo gene expression and a detrimental effect on bacterial populations. Overall, anammox activity mirrored hzo expression patterns, with TiO2 (21 and 25 nm, respectively) exhibiting the least inhibition, followed by ZnO and Ag-NPs.ConclusionThis study highlights the differential effects of NPs on anammox, with the order of impact being Ag > ZnO > TiO2. These findings provide valuable insights into the potential environmental risks of NPs on anammox-mediated nitrogen cycling in freshwater ecosystems.

Potential role of alginate in marine bacteria-yeast interactions.

The ability of microorganisms to decompose brown algae has attracted attention. This study aims to clarify the characteristics of marine microbial communities in which prokaryotic and eukaryotic microorganisms interact via the metabolism of brown algae carbohydrates. Amplicon-based microbiome analysis revealed the predominance of the genera Marinomonas and Vibrio in seawater and seaweed samples mixed with alginate and mannitol, which are the primary carbohydrates in brown algae. Three Vibrio species and Candida intermedia were isolated via alginate enrichment culture. Although C. intermedia did not utilize alginate as a nutrient source, the yeast grew in the spent alginate medium in which Vibrio algivorus had been cultured. Coculture with C. intermedia and the Vibrio isolates, especially V. algivorus, also enhanced the growth of the yeast on alginate. These results suggested that C. intermedia grew because of the supply of nutrients via alginate metabolism by Vibrio species. In the coculture medium, the amount of phosphatidylserine increased in the early phase but decreased with the growth of C. intermedia, indicating that phosphatidylserine secreted by Vibrio is involved in the putative mutualistic interaction. We examined whether such interaction is applicable to the production of useful substances and succeeded in lipid production by oleaginous marine yeast Yarrowia lipolytica through coculture with V. algivorus. Our study suggested the potential of mutualistic interaction via degradation of alginate by marine Vibrio for production of industrially useful substances in yeast cells.IMPORTANCEIn this study, we analyzed the microbiome of seawater and seaweed in the presence of brown algae carbohydrates and reconstructed the putative mutualistic relationship of marine Vibrio and Candida intermedia mediated by metabolism of brown algae in the ocean.

Verrucomicrobia of the Family Chthoniobacteraceae Participate in Xylan Degradation in Boreal Peat Soils.

The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type hemicelluloses represent one of the most actively decomposed peat constituents. The aim of this work was to characterize the microorganisms capable of hydrolyzing xylan under the anoxic conditions typical of peatland soils. The laboratory incubation of peat samples with xylan resulted in the pronounced enrichment of several phylotypes affiliated with the Verrucomicrobiota, Firmicutes, and Alphaproteobacteria. Sequencing of the metagenome of the enrichment culture allowed us to recover high-quality metagenome-assembled genomes (MAGs) assigned to the genera Caproiciproducens, Clostridium, Bacillus (Firmicutes), and Rhizomicrobium (Alphaproteobacteria), Cellulomonas (Actinobacteriota) and the uncultured genus-level lineage of the family Chthoniobacteraceae (Verrucomicrobiota). The latter bacterium, designated "Candidatus Chthoniomicrobium xylanophilum" SH-KS-3, dominated in the metagenome and its MAG was assembled as a complete closed chromosome. An analysis of the SH-KS-3 genome revealed potential endo-1,4-beta-xylanases, as well as xylan beta-1,4-xylosidases and other enzymes involved in xylan utilization. A genome analysis revealed the absence of aerobic respiration and predicted chemoheterotrophic metabolism with the capacity to utilize various carbohydrates, including cellulose, and to perform fermentation or nitrate reduction. An analysis of other MAGs suggested that Clostridium and Rhizomicrobium could play the role of primary xylan degraders while other community members probably took advantage of the availability of xylo-oligosaccharides and xylose or utilized low molecular weight organics.

The Effects of Model Insoluble Copper Compounds in a Sedimentary Environment on Denitrifying Anaerobic Methane Oxidation (DAMO) Enrichment.

The contribution of denitrifying anaerobic methane oxidation (DAMO) as a methane sink across different habitats, especially those affected by anthropogenic activities, remains unclear. Mining and industrial and domestic use of metals/metal-containing compounds can all cause metal contamination in freshwater ecosystems. Precipitation of metal ions often limits their toxicity to local microorganisms, yet microbial activity may also cause the redissolution of various precipitates. In contrast to most other studies that apply soluble metal compounds, this study investigated the responses of enriched DAMO culture to model insoluble copper compounds, malachite and covellite, in simulated sedimentary environments. Copper ≤ 0.22 µm from covellite appeared to cause immediate inhibition in 10 h. Long-term tests (54 days) showed that apparent methane consumption was less impacted by various levels of malachite and covellite than soluble copper. However, the medium-/high-level malachite and covellite caused a 46.6-77.4% decline in denitrification and also induced significant death of the representative DAMO microorganisms. Some enriched species, such as Methylobacter tundripaludum, may have conducted DAMO or they may have oxidized methane aerobically using oxygen released by DAMO bacteria. Quantitative polymerase chain reaction analysis suggests that Candidatus Methanoperedens spp. were less affected by covellite as compared to malachite while Candidatus Methylomirabilis spp. responded similarly to the two compounds. Under the stress induced by copper, DAMO archaea, Planctomycetes spp. or Phenylobacterium spp. synthesized PHA/PHB-like compounds, rendering incomplete methane oxidation. Overall, the findings suggest that while DAMO activity may persist in ecosystems previously exposed to copper pollution, long-term methane abatement capability may be impaired due to a shift of the microbial community or the inhibition of representative DAMO microorganisms.

Fungal Extracellular Enzymes from Aspergillus spp. as Promising Candidates for Extra-Heavy Oil Degradation and Enhanced Oil Recovery.

Heavy crude oil (HCO) and extra-heavy crude oil (EHCO) with high viscosity and density pose enormous challenges to the exploitation of oil reserves. While bacteria are increasingly used in biocatalytic upgrading of HCO and EHCO, less attention has been paid to the potential of fungi. The aim of this study was to ascertain the role of fungal extracellular enzymes from Aspergillus spp. In the biodegradation of EHCO and their application potential for enhanced oil recovery. A. terreus HJ2 and A. nidulans HJ4 with the ability to biodegrade HCO were previously isolated from bitumen enrichment cultures. Both strains grew well on EHCO agar plates supplemented with a small amount of soluble starch (0.2%) and yeast extract (0.3%). Extracellular enzymes from each strain separately, as well as mixtures of the enzymes, exhibited EHCO degradation activity, leading to redistribution of hydrocarbons with substantial formation of biogases and organic acids in a 7-day period. Enzymatic degradation resulted in decreased contents of resins and asphaltenes, accompanied by increased contents of saturates and aromatics. Gas chromatography-mass spectrometry revealed distinct redistribution patterns of n-alkane in the biotreated oil. Enzymatic degradation additionally caused considerable reduction in oil viscosity (by 12.7%) and heavy metal concentrations (Ni, by 44.1%; Fe, by 54.0%; V, by 31.6%). The results provide empirical evidence for the application potential of fungal extracellular enzymes from Aspergillus spp. in EHCO recovery and biocatalytic upgrading of EHCO.

Acid mine drainage bioremediation using bacteria enriched from the confluence zone between its flow and treated sewage

AbstractSediments from the confluence zone between an acid mine drainage stream and a water stream receiving the effluent from a municipal wastewater treatment plant were inoculated in a Postgate B medium base having methanol, glycerol, or ethanol as carbon source/electron donor, over a pH range between 2.00 and 6.00, aiming to obtain native cultures enriched in acidophilic/acid-tolerant sulfate-reducing bacteria. The most effective sulfate reduction observed in acidic conditions was in the enrichment cultures with methanol. Thus, the microbial consortium enriched in these conditions was further used in acid mine drainage bioremediation experiments at an initial pH of 4.50 and using different doses of nutrients medium base and methanol as carbon source/electron donor. The most promising results, with more than 99% removal of metals, were obtained in the mixture of 20% Postgate B medium base plus 80% acid mine drainage (v/v), which corresponds to 0.115% basal salts and 0.02% yeast extract (w/v). Metataxonomic analysis based on 16S rRNA gene sequences showed the presence of Desulfosporosinus spp. in all enrichment cultures, with the highest relative abundance in cultures at pH 4.00 with methanol. Furthermore, metataxonomic analysis in the acid mine drainage remediation tests revealed the presence of Desulfosporosinus spp. in all tested conditions. In addition, the study also revealed Clostridium members in all tests. Plus, their relative abundances were related to the dose of nutrient medium base and in balance with the abundances of Desulfosporosinus spp.

Defluorination of various perfluoro alkyl acids and selected PFOA and PFOS monomers by Acidimicrobium sp. Strain A6 enrichment cultures

Per- and polyfluoroalkyl substances (PFAS) have emerged as a diverse class of environmental pollutants, garnering increasing attention due to their various structural types and potential ecological impacts. The impact of select PFAS on environmental microorganisms and the potential for microbial degradation of certain PFAS are timely research topics. In this study, we conducted a series of batch incubation to investigate the effects of C4-C10 perfluoroalkyl carboxylic acids (PFCAs) and perfluorosulfonic acids (PFSAs), as well as linear and branched perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) monomers, on the Feammox reaction and Acidimicrobium sp. A6 (A6), a microbe known to degrade PFOA and PFOS. We explored the defluorination ability of A6 cultures with these PFAS, evaluating their response to varying chemical structures. While A6 cultures demonstrated the ability to degrade a wide range of PFAAs (11.5–56.9 % reduction over 120 days), challenges were noted with specific compounds like PFPeA and double-branched PFCAs and PFSAs, which also showed reduced ammonium removal. Additionally, exposure to the selected PFAS resulted in notable shifts in the microbial community within the A6 enrichment cultures, indicating a selective pressure that benefits certain strains (e.g., increased percentages of Acidimicrobium, Paraburkholderia, and Desulfosporosinus in several PFCA, PFSA and PFOA/PFOS monomers enriched cultures). These insights contribute to our understanding of microbial-PFAS interactions and are instrumental in developing bioremediation strategies for PFAS-impacted environments.

Genome sequence of Nitrosopumilus adriaticus CCS1 assembled from an ammonia-oxidizing enrichment culture.

We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related to Nitrosopumilus adriaticus NF5 but shows distinct genomic features compared to strain NF5.

P40 A challenging case of new systemic lupus erythematosus

Abstract Introduction The diagnosis of systemic lupus erythematosus (SLE) and its distinction from systemic infection can be challenging. We present a case of new systemic lupus alongside endocarditis, which illustrates this problem. Case description A previously well, 35-year-old male tarmacer of mixed ethnicity, presented with a three months’ history of general malaise, arthralgia and weight loss of 20kg. Two weeks prior to admission he developed progressive confusion, headaches and imbalance. Clinical assessment revealed a pyrexial patient in delirium without focal neurological signs, a faint maculopapular facial rash, symmetrical synovitis, very few nailfold infarcts, a systolic and diastolic murmur and sterile haemato-proteinuria. No history of IV drug abuse. Investigations showed elevated ESR 61, CRP 217, WBC 11.70 and procalcitonin 7.0. He had AKI stage 2 (eGFR 35 with a urinary protein/creat ratio 162; homogenous ANA (1:1280) with positive dsDNA and crithidia-luciliae binding. C3 and C4 suppressed (0.59 and 0.13, respectively); One blood culture prior to broad spectrum antibiotics was negative. Assuming the possibility of Libman-Sacks endocarditis, the attending acute stroke physician initially also treated with pulsed IV steroids, as well as antibiotics. Due to the delirium, key diagnostic tests were technically difficult, although a transthoracic ECHO showed moderately severe aortic and mitral regurgitation that were not felt to be typical for infective endocarditis by the attending cardiologist. The ITU team offered sedation and controlled ventilation to enable all necessary investigations: trans-oesophageal ECHO showed vegetations of aortic and mitral valve leaflets with perforations of single leaflets, resulting in severe acute aortic and mitral regurgitation; a renal biopsy showed class 3 lupus nephritis and an MRI/A Brain showed widespread cerebral foci of restricted diffusion imaging. Consultation with the regional cardiothoracic centre advised urgent transfer for double metal valve replacement, performed on Day 8 post admission. Surgical inspection confirmed an aortic root abscess, and enrichment culture of the native valve subsequently grew Staph. aureus. In addition to IV antibiotics for infective endocarditis, he was continued on steroid taper and commenced on MMF for lupus nephritis. Discussion It can be difficult to differentiate between infective endocarditis and Libman-Sacks endocarditis, especially when there are no existing risk factors. In cases like these antibiotics and steroids can be started at the same time. In our case, we had a young gentleman with no prior medical history who had multiple compounding factors and barriers to fully investigate. Because of his agitation, he required sedation and that allowed the team to perform life saving investigations (renal biopsy and TOE). He ended up having a double metal valve replacement within 8 days post-admission. Multidisciplinary team involvement and close collaboration was of crucial importance in this case to ensure a safe patient outcome. Key learning points • This case illustrates the need to vigorously chase the possibility of concurrent infection in severe new SLE. Close collaboration between multiple specialities to achieve this is key, especially when a patient lacks agency due to their illness.

Culturomics: A promising approach for exploring bacterial diversity in natural fermented milk

Natural fermented milk is an abundant source of microbial resources, some of which possess probiotic properties that can help prevent and treat human diseases. However, many potential probiotics have not yet been isolated using traditional pure-culture methods. Culturomics, a relatively novel approach, can be primarily employed to cultivate and identify previously unknown and uncultured bacteria. Nevertheless, their application in natural fermented milk remains limited. Therefore, the primary objective of this study was to evaluate the bacterial diversity in natural fermented milk and explore its microbial potential. For this purpose, we collected three natural fermented milk samples from Inner Mongolia and subjected them to enrichment culture in blood culture bottles for 14 d. Bacterial isolates were obtained from the samples at 0, 3, 7, and 14 days using two culture temperatures and four media, and full-length 16S rRNA gene sequencing was performed for each sample at each time point. The results revealed that 488 strains were isolated from three samples belonging to 3 phyla, 11 genera, and 27 species. The method using two culture temperatures (20 °C and 30 °C) and two media (MRS and RCM + Vb) yielded most of the isolates after 3, 7, and 14 days of enrichment culture. Furthermore, full-length 16S rRNA gene sequencing confirmed that this method significantly increased bacterial diversity in natural fermented milk. In conclusion, the culturomics method demonstrates great potential for the isolation of a greater number of bacterial species and is advantageous for further exploration of the diversity of culturable microorganisms in natural fermented milk.

Comparative Study of Mesophilic Biomethane Production in Ex Situ Trickling Bed and Bubble Reactors

Biomethane production via biogas upgrading is regarded as a future renewable gas, further boosting the biogas economy. Moreover, when upgrading is realized by the biogas CO2 conversion to CH4 using surplus renewable energy, the process of upgrading becomes a renewable energy storage method. This conversion can be carried out via microorganisms, and has attracted scientific attention, especially under thermophilic conditions. In this study, mesophilic conditions were imposed using a previously developed enriched culture. The enriched culture consisted of the hydrogenotrophic Methanobrevibacter (97% of the Archaea species and 60% of the overall population). Biogas upgrading took place in three lab-scale bioreactors: (a) a 1.2 L bubble reactor (BR), (b) a 2 L trickling bed reactor (TBR) filled with plastic supporting material (TBR-P), and (c) a 1.2 L TBR filled with sintered glass balls (TBR-S). The gas fed into the reactors was a mixture of synthetic biogas and hydrogen, with the H2 to biogas CO2 ratio being 3.7:1, lower than the stoichiometric ratio (4:1). Therefore, the feeding gas mixture did not make it possible for the CH4 content in the biomethane to be more than 97%. The results showed that the BR produced biomethane with a CH4 content of 91.15 ± 1.01% under a gas retention time (GRT) of 12.7 h, while the TBR-P operation resulted in a CH4 content of 90.92 ± 2.15% under a GRT of 6 h. The TBR-S operated at a lower GRT (4 h), yielding an effluent gas richer in CH4 (93.08 ± 0.39%). Lowering the GRT further deteriorated the efficiency but did not influence the metabolic pathway, since no trace of volatile fatty acids was detected. These findings are essential indicators of the process stability under mesophilic conditions.

Isolation and characterization of a resistance Bacillus subtilis for soil stabilization and dust alleviation purposes

Dust poses environmental, geological, health, and economic concerns, and microorganisms can help mitigate these adverse consequences by improving soil properties. Microbial calcium carbonate precipitation (MICP) has been found to be an efficient strategy for increasing soil strength, reducing soil porosity, and preventing erosion; however, severe environmental conditions such as pH and high temperatures may impede this process. To identify the best strain for MICP, 60 bacteria strains were obtained from arid soils using the enrichment culture technique. They were tested for the capacity of calcium carbonate deposition and biocement synthesis in stress environments. Phenotypic characterization indicated that the majority of the bacterial isolates were gram-positive and rod-shaped, with strong catalase and oxidase enzyme activity. Furthermore, MALDI-TOF MS identification revealed that the isolates were from the Bacillus and Pseudomonas genera. Scanning Electron Microscopy (SEM), Energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD) were used to analyze the microstructures and composition of bacterial cement. The results represented that B. subtilis isolate S56 has a higher production yield and forms distinctive calcite crystals as a result of fast urease synthesis. B. subtilis isolate S56 can be applied in situ to reduce soil erosion and dust pollution. This study reveals the potential of the B. subtilis S56 strain for soil consolidation and dust prevention in harsh environments and has the prospect of promoting its application in desertification control and ecological restoration.

Improved chickpea growth, physiology, nutrient assimilation and rhizoremediation of hydrocarbons by bacterial consortia.

Soil pollution by petroleum hydrocarbons (PHCs) reduces yield by changing the physico-chemical properties of soil and plants due to PHCs' biotoxicity and persistence. Thus, removing PHCs from the soil is crucial for ecological sustainability. Microbes-assisted phytoremediation is an economical and eco-friendly solution. The current work aimed to develop and use bacterial consortia (BC) for PHCs degradation and plant growth enhancement in hydrocarbon-contaminated soil. Initially, the enriched microbial cultures (that were prepared from PHCs-contaminated soils from five distinct regions) were obtained via screening through microcosm experiments. Afterward, two best microbial cultures were tested for PHCs degradation under various temperature and pH ranges. After culture optimization, isolation and characterization of bacterial strains were done to construct two BC. These constructed BC were tested in a pot experiment for hydrocarbons degradation and chickpea growth in PHCs contaminated soil. Findings revealed that PHCs exerted significant phytotoxic effects on chickpea growth and physiology when cultivated in PHCs contaminated soil, reducing agronomic and physiological traits by 13-29% and 12-43%, respectively. However, in the presence of BC, the phytotoxic impacts of PHCs on chickpea plants were reduced, resulting in up to 24 - 35% improvement in agronomic and physiological characteristics as compared to un-inoculated contaminated controls. Furthermore, the bacterial consortia boosted chickpea's nutritional absorption and antioxidant mechanism. Most importantly, chickpea plants phytoremediated 52% of the initial PHCs concentration; however, adding BC1 and BC2 with chickpea plants further increased this removal and remediated 74% and 80% of the initial PHCs concentration, respectively. In general, BC2 outperformed BC1 (with few exceptions) in promoting plant growth and PHCs elimination. Therefore, using multi-trait BC for PHCs degradation and plant growth improvement under PHCs stress may be an efficient and environmentally friendly strategy to deal with PHCs pollution and toxicity.

Study of biotechnological potential of hydrocarbon-oxidizing bacteria from oil-contaminated soils of the Uzen oil field

Background: Oil-contaminated soils are one of the significant environmental concerns in Western Kazakhstan. Cleaning soils from oil contamination is becoming extremely important. Biological soil treatment, which uses hydrocarbon-oxiding bacteria for microbiological remediation, is a more environmentally friendly and delicate method of soil treatment than any other currently used technology (physical, chemical, biological). One of the important aspects of microbiological remediation is the use of bacteria endomimic to the treated soil. This guarantees the most effective soil purification, as the bacteria perform in relatively optimal conditions for themselves. The soil of the Mangistau region, especially the coastal regions, is distinctive due to its high mineralisation and low moisture content, which have helped to form a specific microflora that is adapted to these conditions. Aim: The study aims to search and isolate highly effective hydrocarbon-oxidizing bacteria that are native to highly mineralized soils of the Uzen oil field. Materials and methods: The research employs a variety of analytical techniques, including water chemistry analysis and infrared spectrometry, as well as the microbiological culture of aerobic bacteria on liquid and dense media in environments (temperature and salinity) that closely resemble their native ecotopes. Results: Four enrichment cultures of hydrocarbon-oxidizing bacteria were obtained, and three pure cultures of oil-oxidizing bacteria were isolated. Their hydrocarbon-oxidizing efficiency has been studied. On the basis of heavy, extremely viscous paraffinic oil from the Uzen field, their hydrocarbon-oxidizing efficiency was examined. Conclusion: In this study, active enrichment cultures of halophilic hydrocarbon-oxidizing bacteria as well as active accumulative cultures of halophilic and moderately thermophilic aerobic bacteria were obtained. These bacteria are capable of oxidising a wide range of hydrocarbons, including high-molecular polycyclic and sulfur-containing compounds. Their high biotechnological potential will be studied in further studies.