Culturable Bacteria Research Articles

Microbial Indoor Air Quality Within Greenhouses and Polytunnels Is Crucial for Sustainable Horticulture (Malopolska Province, Poland Conditions)

Sustainable horticulture is crucially based on the greenhouse production of vegetables under controlled conditions. In this study, we wanted to learn how cultivated plants may impact indoor air quality and whether the workers can be exposed to bioaerosols in a similar way in these settings. The study objective was to test the hypothesis that the microbial concentrations, distribution of bioaerosol particle sizes, and composition of the airborne microbiome are specific to greenhouses, polytunnels, and open-air sites. The air samples were collected to assess the concentration of total culturable bacteria (TCB), fungi, actinomycetes, and β-haemolytic bacteria and for the identification of bacterial and fungal strains. Higher concentrations of TCB and fungi were found in the greenhouse (log 3.71 and 3.49 cfu m−3, respectively) than in polytunnels (log 2.60–2.48 and 2.51–2.31 cfu m−3, respectively) during the vegetation of cucumbers. These airborne microbes were represented by a significant contribution of the respirable fraction with a distinct contribution of fine particles in size below 4.7 µm. Cultivation of cucumbers resulted in the higher emission of airborne microorganisms in contrast with growing herbs such as oregano and basil. In total, 35 different bacteria and 12 fungal species, including pathogenic or allergenic agents, were identified within the studied sites. The workers can be exposed to increased concentrations of TCB and fungi in the greenhouse during the plant vegetation. It might be recommended to properly manage greenhouses and polytunnels, dispose of dust sources, and maintain appropriate ventilation to sustain relevant air quality.

Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation.

Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome. Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation. In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract.

Impact of Water Ionic Chemistry on Kombucha Fermentation

Kombucha is made by using a symbiotic culture of bacteria and yeast (SCOBY) to ferment sweetened tea. This fermentation produces a beverage with a unique aroma and acidic flavor. Kombucha has recently gained popularity in the United States and has been reported to have numerous health benefits. While there is a wide variation in kombucha composition, little is known about the impact water’s chemistry has on the fermentation and the resulting kombucha. Brewing water for kombucha was altered using the following ions: bicarbonate, chloride, calcium, magnesium, and sulfate at different concentrations. Pre-(tea) and post-(kombucha) fermentation (kombucha) products were analyzed for total acidity, pH, free amino nitrogen (FAN), total phenols, antioxidants, and biological components. A one-way ANOVA was run to determine statistical (p < 0.05) differences between the characteristics analyzed. Statistical differences were observed between the different water chemistry ions for all of the characteristics analyzed. Further investigation into the impact water chemistry has on flavor analysis is required. The information obtained from this research can be used to help producers to make kombuchas with an optimized chemical profile and improved antioxidant potentials.

Manipulation in root-associated microbiome via carbon nanosol for plant growth improvements

BackgroundModulating the microbiome with nanomaterials has been proposed to improve plant growth, and reduce reliance on external inputs. Carbon Nanosol (CNS) was attracted for its potential to improve plant productivity. However, the mechanism between CNS and rhizosphere microorganisms remained largely elusive.ResultsHere, we tried to systematically explore the effects of CNS (600 and 1200 mg/L by concentration) on tobacco growth, soil physical properties, and root-associated microbiome. The influence of CNS on soil physicochemical properties and plant growth was significant and dose-dependent, leading to a 28.82% increase in biomass accumulation by 600 mg/L CNS. Comparison between the CNS-treated and control plants revealed significant differences in microbiome composition, including 1148 distinct ASVs (923 bacteria and 225 fungi), microbiome interactions, and metabolic function of root-associated microbiomes. Fungal and bacterial communities had different response patterns for CNS treatment, with phased and dose-dependent effects, with the most significant changes in microbial community structure observed at 1200 mg/L after 10 days of treatment. Microbial networks of CNS-treated plants had more nodes and edges, higher connectivity, and more hub microorganisms than those of control plants. Compared with control, CNS significantly elevated abundances of various bacterial biomarkers (such as Sphingomonas and Burkholderia) and fungi biomarkers (including Penicillium, Myceliophthora, and Talaromyces), which were potential plant-beneficial organisms. Functional prediction based on metagenomic data demonstrated pathways related to nutrient cycling being greatly enriched under CNS treatment. Furthermore, 391 culturable bacteria and 44 culturable fungi were isolated from soil and root samples. Among them, six bacteria and two fungi strains enriched upon CNS treatment were validated to have plant growth promotion effect, and two fungi (Cladosporium spp. and Talaromyces spp.) played their roles by mediating volatile organic compounds (VOCs). To some extent, the driving and shaping of the microbiome by CNS contributed to its impact on plant growth and development.ConclusionOur results revealed the key role of root-associated microbiota in mediating the interaction between CNS and plants, thus providing valuable insights and strategies for harnessing CNS to enhance plant growth.Graphical

A transformer-based deep learning model for identifying the occurrence of acute hematogenous osteomyelitis and predicting blood culture results

BackgroundAcute hematogenous osteomyelitis is the most common form of osteomyelitis in children. In recent years, the incidence of osteomyelitis has been steadily increasing. For pediatric patients, clearly describing their symptoms can be quite challenging, which often necessitates the use of complex diagnostic methods, such as radiology. For those who have been diagnosed, the ability to culture the pathogenic bacteria significantly affects their treatment plan.MethodA total of 634 patients under the age of 18 were included, and the correlation between laboratory indicators and osteomyelitis, as well as several diagnoses often confused with osteomyelitis, was analyzed. Based on this, a Transformer-based deep learning model was developed to identify osteomyelitis patients. Subsequently, the correlation between laboratory indicators and the length of hospital stay for osteomyelitis patients was examined. Finally, the correlation between the successful cultivation of pathogenic bacteria and laboratory indicators in osteomyelitis patients was analyzed, and a deep learning model was established for prediction.ResultThe laboratory indicators of patients are correlated with the presence of acute hematogenous osteomyelitis, and the deep learning model developed based on this correlation can effectively identify patients with acute hematogenous osteomyelitis. The laboratory indicators of patients with acute hematogenous osteomyelitis can partially reflect their length of hospital stay. Although most laboratory indicators lack a direct correlation with the ability to culture pathogenic bacteria in patients with acute hematogenous osteomyelitis, our model can still predict whether the bacteria can be successfully cultured.ConclusionLaboratory indicators, as easily accessible medical information, can identify osteomyelitis in pediatric patients. They can also predict whether pathogenic bacteria can be successfully cultured, regardless of whether the patient has received antibiotics beforehand. This not only simplifies the diagnostic process for pediatricians but also provides a basis for deciding whether to use empirical antibiotic therapy or discontinue treatment for blood cultures.

Improvement Schemes for Bacteria in MICP: A Review

Biomineralization is a common phenomenon in nature, and the use of microbial-induced calcium carbonate precipitation (MICP) technology for engineering construction is a successful attempt to utilize natural biological phenomena, which has become a hot topic of current research. There are many factors affecting MICP, such as bacterial properties and external environmental factors. Many scholars have carried out a lot of research on these factors, but even under appropriate conditions, the MICP process still has the problem of low efficiency. According to different engineering, the tolerance and effect of bacteria in different environments are also different. At the same time, the cultivation and preservation of bacteria will also consume a large amount of raw materials, which is far more significant than the cost of engineering construction. The efficiency and cost limit the large-scale application of this technology in practical engineering. In response to these problems, researchers are exploring new ways to improve the efficiency of MICP technology. Based on the bacteria used in MICP, this paper explores the mechanism of bacteria in the process of MICP and reviews the improvement of bacteria from the perspective of efficiency improvement and economy.

Evaluation of a microfluidic-based point-of-care prototype with customized chip for detection of bacterial clusters.

Especially in medical facilities, where morbid people are nursed in close distance to each other, pathogenic bacteria can accumulate and spread. To contain such infection clusters, usually time- and labor-intensive large-scale screening assays are conducted, where patients and patient-side surfaces are sampled, and PCR or whole-genome sequencing analyses are conducted to confirm or deny cluster affiliation of cultivated bacteria. Hence, fast solutions with easy application are required to complement the current state-of-the-art technology for cluster surveillance. Here, we developed a fully automated microfluidic point-of-care prototype that identified bacterial cluster isolates within 70 min from bacterial solutions, including swab eluates. The system requires only low hands-on time and can be applied apart from laboratory infrastructures near the patient, which considerably reduces the time from sampling to result. This ensures fast implementation of hygiene measures and quick containment of the infection cluster, which would enhance patients' safety and outcome.

Addressing underestimation of waterborne disease risks due to fecal indicator bacteria bound in aggregates.

This study aims to identify and address significant limitations in current culture-based regulatory methods used for monitoring microbiological water quality. Specifically, these methods' inability to distinguish between planktonic forms and aggregates containing higher bacterial loads and associated pathogens may lead to a severe underestimation of exposure risks, with critical public health implications. We employed a novel methodology combining size fractionation with ALERT, an automated rapid method for comprehensive quantification of culturable fecal indicator bacteria (FIB). Our findings reveal a substantial and widespread presence of aggregate-bound indicator bacteria across various water matrices and geographical locations. Comprehensive bacterial counts consistently exceeded those obtained by traditional methods by significant multiples, such as an average of 3.4×at the Seine River 2024 Olympic venue, and occasionally up to 100×in irrigation canals and wastewater plant effluent. These results, supported by microscopic and molecular analyses, underscore a systematic bias in global water safety regulatory frameworks. Our research demonstrates the inadequacy of traditional culture-based techniques in assessing microbiological risks posed by aggregate-bound FIB and associated pathogens, particularly in water matrices affected by FIB-rich fecal particles from recent sewer overflows or sediment, which can carry higher infectious risks. Incorporating comprehensive FIB analysis techniques, including molecular methods and rapid culture-based approaches as shown in this study, offers a promising and effective solution to these risk assessment limitations.

Protective immune-response of Aeromonas hydrophila phage lysate in crucian carp against direct virulent challenge with A. hydrophila-TPS

Aeromonas hydrophila was a common opportunistic pathogen that was widely found in various aquatic environment and could cause multiple infections in humans and animals. The haemorrhagic septicemia and bacterial enteritis in fish triggered by this pathogen led to significant losses in the aquaculture industry. In this study, we aimed to develop a phage lysate vaccine by lysing the A. hydrophila-TPS strain using phage PZY-Ah, which was previously isolated and preserved in the laboratory. First, we focused on optimizing phage lysis conditions, including different host bacteria culture time, phage lysis time, and phage to bacterial ratios. The optimal conditions were established as follows: culturing the A. hydrophila-TPS strain for 6 h, adding phage at a ratio of 1:10, and mixing for 4 h, which resulted in maximum lysis of the host bacteria. Subsequently, we assessed the immune responses of groups receiving formaldehyde-inactivated vaccines compared to those receiving various concentrations of the phage lysate vaccine. Both the TPS-phage lysate and formaldehyde-inactivated vaccine groups exhibited increased levels of specific immune enzymes (ACP, AKP, LZM, SOD, CAT) and cytokines (IL-1β, TNF-α and IFN-γ) in serum, as well as enhanced humoral immunity (IgM, C3 and C4) in crucian carp. Furthermore, challenge tests conducted post-immunization demonstrated that the high concentration of the TPS strain-lysate vaccine group (1 × 108 CFU/mL) achieved the highest immune protection rate at 88.89 %. Overall, the development of the TPS-phage lysate vaccine significantly enhanced the immunity of crucian carp, providing a higher level of protection and establishing a foundation for the research and development of phage-based aquatic vaccines.

Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium

Despite previous culture-independent studies highlighting the prevalence of the order Burkholderiales in deep-sea environments, the cultivation and characterization of deep-sea Burkholderiales have been infrequent. A total of 243 deep-sea bacterial strains were isolated from various depths in the Northwest Pacific Ocean, with 33 isolates (13.6%) from a depth of 4000 m classified into Burkholderiales. Herein, we report the isolation and genome characteristics of strain SAORIC-580T, from a depth of 4000 m in the Northwest Pacific Ocean. The strain showed a close phylogenetic relationship with Limnobacter thiooxidans CS-K2T, sharing 99.9% 16S rRNA gene sequence identity. The complete whole-genome sequence of strain SAORIC-580T comprised 3.3 Mbp with a DNA G+C content of 52.5%. Comparative genomic analysis revealed average nucleotide identities between 79.4–85.7% and digital DNA-DNA hybridization values of 19.9–29.5% when compared to other Limnobacter genomes, indicating that the strain represents a novel species within the genus. Genomic analysis revealed unique adaptations to deep-sea conditions, including genes associated with phenol degradation, stress responses, cold adaptation, heavy metal resistance, signal transduction, and carbohydrate metabolism. The SAORIC-580T genome was found to be more abundant in the deep sea than at the surface in the trenches of the Northwest Pacific Ocean, suggesting adaptations to the deep-sea environment. Phenotypic characterization highlighted distinct differences from other Limnobacter species, including variations in growth conditions, enzyme activities, and phenol degradation capabilities. Chemotaxonomic markers of the strain included ubiquinone-10, major fatty acids such as C16:0, C16:1, and C18:1, and major polar lipids including phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on the polyphasic taxonomic data, it is concluded that strain SAORIC-580T (= KACC 21440T = NBRC 114111T) represents a novel species, for which the name Limnobacter profundi sp. nov. is proposed.

Membrane-based preparation for mass spectrometry imaging of cultures of bacteria.

The study of the dialogue between microorganisms at the molecular level is becoming essential to understand their relationship (antagonist, neutral, or beneficial interactions) and its impact on the organization of the microbial community. Mass spectrometry imaging (MSI) with matrix-assisted laser desorption/ionization (MALDI) is a technique that reveals the spatial distribution of molecules on a sample surface that may be involved in interactions between organisms. An experimental limitation to perform MALDI MSI is a flat sample surface, which in many cases could not be achieved for bacterial colonies such as filamentous bacteria (e.g., Streptomyces). In addition, sample heterogeneity affects sample dryness and MALDI matrix deposition prior to MSI. To avoid such problems, we introduce an additional step in the sample preparation. A polymeric membrane is interposed between the microorganisms and the agar-based culture medium, allowing the removal of bacterial colonies prior to MSI of the homogeneous culture medium. A proof of concept was evaluated on Streptomyces ambofaciens (a soil bacterium) cultures on solid media. As the mycelium was removed at the same time as the polymeric membrane, the metabolites released into the medium were spatially resolved by MALDI MSI. In addition, extraction of the recovered mycelium from the membrane confirmed the identification of the metabolites by ESI MS/MS analysis. This approach allows both the spatial distribution of metabolites produced by microorganisms in an agar medium to be studied under well-controlled sample preparation and their structure to be elucidated. This capability is illustrated using desferrioxamine E, a siderophore produced by S. ambofaciens.

Diversity, growth promoting potential and anti-fungal properties of culturable endophytic bacteria isolated from Condonopsis pilosula roots

Diversity, growth promoting potential and anti-fungal properties of culturable endophytic bacteria isolated from Condonopsis pilosula roots

Bioaerosol emission and exposure risk from a wastewater treatment plant in winter and spring

The potential health risks posed by bioaerosols containing pathogens originating from wastewater treatment plants (WWTPs) have gaining intensive attention. This study designated sampling locations within a WWTP situated in Xi'an, a major city in northwest China. The airborne bacterial concentration, taxonomic composition, and the associated health risks were analyzed in the aeration tanks with bottom microporous aeration system. The Anaerobic-Anoxic-Oxic (AAO) tank emitted significantly higher culturable bacteria (1.58×104 CFU m−3 in spring, 6.69×103 CFU m−3 in winter) compared to Double-ditch (DE) oxidation ditch and aerated grit chamber (AGC) chamber, aligning with 16S rDNA quantification results. The bacterial concentrations are higher in spring than that in winter, with the AAO tank posing the highest exposure risk during the spring season. The dominant genera in the air samples include Cutibacterium, Lawsonella, Acinetobacter, Pseudomonas, and Aeromonas. Among the identified genus, 139 bacterial genera were identified as potential human pathogens like Neisseria, Moraxella, Haemophilus, Escherichia-Shigella and Streptococcus. These pathogens further elevate exposure risks from WWTP bioaerosols. This study provides relevant information on the seasonal health risk variations tied to bioaerosol emissions from diverse aeration tanks with bottom microporous aeration system in the mega city of northwest China, emphasizing the imperative to enhance the management and control measures for bioaerosols originating from the AAO tank.

Evaluating the Impact of Integrated Nutrient Management Practices on Land Productivity, Crop Residue Decomposition and Abundance of Soil Organisms in a Banana Plantation in Sri Lanka

The fertilization practices heavily influence the decomposition rate of organic materials added to soil. Hence, the nutrient management strategies that aim to improve crop yields may not necessarily support organic carbon accumulation in soil and overall soil fertility. This study investigated how land productivity, crop residue decomposition and diversity of soil organisms were affected by the combined use of chemical fertilizers (CF) and poultry manure (PM) in a banana plantation in Buttala, Sri Lanka. Banana yield, soil properties and decomposition of crop residues were studied in six treatments as, CF1+PM1, CF1+PM2, CF1+PM3, CF2 +PM1, CF2+PM2, and CF2+PM3. CF1 and CF2 correspond with 75% and 100% of recommended CF application rate. PM1, PM2 and PM3 correspond with PM application rates of 0, 2.5 and 5 kg/plant. Crop residue decomposition was assessed using litter bags containing two litter materials as banana pseudo-stem pieces and banana leaves and placed at two depths (surface and at 7.5 cm depth). Litter bags were recovered at 17, 31 and 45 days after placement (DAP) and weight loss of crop residues was determined. The application of poultry manure significantly increased (P<0.01) banana yield at first harvest and decreased (P<0.1) bulk density. Type of material and time of exposure to decomposition had significant effects (P<0.05) on litter decomposition but depth of placement and nutrient management strategy had no significant effect (P>0.05) on decomposition. By 45 DAP pseudo-stems were degraded more than leaves (67.47±13.99 % and 46.90±5.76 %, respectively). The abundance of culturable bacteria and cellulose decomposers in soil and the abundance of soil fauna in decomposing litter were significantly (P<0.1) increased with the PM application to soil. In conclusion, in the studied banana plantation, incorporation of PM in nutrient management increased land productivity and had positive impact on some soil properties, which are important determinants of soil fertility but did not register any effects on crop residue decomposition during the study period.

Molecular Diagnosis of Vaginal Microbiota Associated with Spontaneous Abortion in Women

Spontaneous abortion (SA) is a sever disease in which a women losses her foetus usually before 24 weeks of the pregnancy. About 10% -50% of pregnancy cases are run out with SA for reasons related with women's age and health. This condition occurrence may increases if the patient has a history of bacterial vaginosis. This study aimed at the characterization and isolation of vaginal microbiota generally and highlight on commensal bacteria becoming opportunistic when circumstances are favourable. From October to December 2022, about 100 samples were collected, 50 specimens from women with SA and 50 specimens from healthy pregnant outcomes (control). The high vaginal swabs samples were collected from Babylon Teaching Hospital for Maternity and Children and Imam Sadiq Teaching Hospital in Babylon, Iraq. To culture the samples, they were transported by media swab to laboratory. The culture of bacteria was done on 4 types of agar media: UTI chromogenic agar, MRS agar, MacConkey agar and blood agar. The first identification of bacteria was based on phenotypic traits of colonies, using manual biochemical tests and gram stain. Finally, the diagnosis was confirmed genetically by extracting bacterial genomic DNA for 20 of bacterial isolates under study and using PCR technique for 16S rRNA Loci gene and sequencing. The current study results showed difference in bacterial genera in women with SA compared with healthy women. It was also noted that embroilment of Enterococcus faecalis occurred in most cases of SA with an estimated percentage of 56% (28/50), thus defeating Escherichia coli by 32% (16/50) and 4% (2/50) for Klebsiella pneumonia and 4% (2/50) for Enterococcus gallinarum. In this study, some very rare bacteria species were identified including Acinetobacter junii at 2% (1/50) and Corynebacterium coyleae at 2% (1/50). While the percentage of bacteria associated with healthy women was: 30% (15/50) for E. faecalis, 26% (13/50) for E. coli, 18% (9/50) for K. pneumonia, 24% (12/50) for Staphylococcus epidermidis, and 2% (1/50) for Metabacillus niabensis (which was diagnosed for the first time in Iraq as well as the rest of the world in a clinical sample).

Marginal bone resection and immediate internal fixation in multidrug resistant chronic septic nonunions of lower limb long bones: a case series.

This study aimed to evaluate the efficacy of a combined treatment approach integrating extensive debridement, immediate internal fixation, and the Masquelet technique for the management of infected nonunion of long bones in the lower limbs caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. This retrospective case series was conducted at the Imam Khomeini Hospital Complex, Tehran, Iran, a tertiary-level academic referral centre. The study documented consecutive cases of patients presenting with infected nonunion of the tibia or femur, with a positive culture for MDR or XDR bacteria, treated between January 2019 and December 2022. Inclusion criteria were adults with a confirmed diagnosis of infected nonunion due to MDR or XDR bacteria, with exclusion criteria including patients with unrelated infections or allergies to the components of the treatment regimen. The primary outcomes measured were infection resolution and bone healing. The study cohort comprised 16 patients, predominantly male (87.5%) with an average age of 38.5 years. Methicillin-resistant Staphylococcus aureus (MRSA) was identified as the causative agent in 31.25% of the infections. Patients were followed for a period ranging from 12 to 26 months. The treatment protocol was uniformly applied across all cases. Successful bone union was observed in the majority of patients within 140 to 240 days following grafting. However, there were two instances where amputation was necessitated due to the failure to eradicate the infection. Complications arose in three cases during the follow-up period: two required re-debridement due to a recurrence of the infection, and one was subjected to bone transport owing to persistent nonunion. Notably, all cases that either failed or encountered complications were smokers. In this integrated approach, high rates of infection resolution and bone healing were achieved, suggesting this method as a viable option for these complex cases.

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.

Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides

Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil.

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1h in microcosms. Heating to 60°C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100°C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60°C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

Algal Growth and Morphogenesis-Promoting Factors Released by Cold-Adapted Bacteria Contribute to the Resilience and Morphogenesis of the Seaweed Ulva (Chlorophyta) in Antarctica (Potter Cove)

AbstractMacroalgae are found in a variety of marine vegetation ecosystems around the world, contributing significantly to global net primary production. In particular, the sea lettuce species, i.e., members of the genus Ulva (Chlorophyta), are located in many ecological niches and are characterized by excellent adaptability to environmental changes but depend on essential associated bacteria, which release algal growth and morphogenesis-promoting-factors (AGMPFs). Our work investigated the hypothesis that bacteria need to be stress-adapted to provide sufficient amounts of AGMPFs for the growth and morphogenesis of Ulva throughout its life cycle, even under severe environmental conditions. Our study thus aimed to understand which bacteria contribute to overcoming a variety of stressors in polar regions. Green macroalgae were collected from Potter Cove, King George Island (Isla 25 de Mayo), Antarctica, to study the associated microbiome and, subsequently, to identify AGMPFs releasing bacteria. Therefore, microbiome analysis was combined with morphogenetic bioassays and chemical analysis, identifying bacteria essential for algal growth under Antarctic conditions. Hereby, axenic cultures of Ulva compressa (cultivar Ulva mutabilis, Ria Formosa, Portugal), previously developed as a model system for bacteria-induced algal growth and morphogenesis, were inoculated with freshly isolated and cultivable Antarctic bacteria to determine their morphogenetic activity. The exploratory microbiome investigation identified numerous cold-adapted AGMPF-producing bacteria. Unlike the temperate-adapted bacterial strains originally isolated from the U.mutabilis holobiont, the cold-adapted isolates Maribacter sp. BPC-D8 and Sulfitobacter sp. BPC-C4 released sufficient amounts of AGMPFs, such as thallusin and still unknown compounds, necessary for the morphogenesis of the Antarctic Ulva even at 2 °C. Our results illustrate the role of chemical mediators provided by bacteria in cross-kingdom interactions under cold conditions within aquatic systems. The newly isolated bacteria will enable further functional studies to understand the resilience of the holobiont Ulva and might be applied in algal aquaculture even under adverse conditions. The study highlights the importance of eco-physiological assays in microbiome analysis.