Search Results (142)

Fusarium wilt causes substantial losses in many crops, and Penicillium rubens strain 212 (PO212) is a well-established biological control agent effective against several soil-borne pathogens, including the causal agents of Fusarium wilt. Before its widespread use, it is essential to assess whether applying PO212 may affect indigenous soil microbial communities. To address this, two open-field tomato trials were conducted to evaluate spatial and temporal changes in non-target soil fungal communities following the application of PO212. Fungal community profiles were monitored over one year using PCR–DGGE of fungal rDNA, and representative DGGE bands were sequenced for taxonomic confirmation. Community structure and variability were analysed using cluster analysis (UPGMA and Neighbor-Joining) and analysis of molecular variance (AMOVA) to determine the effects of treatment, sampling date, and soil depth. PO212 application did not significantly altered the composition or diversity of indigenous soil fungal communities. DGGE banding patterns and diversity indices were similar between treated and untreated soils throughout the study period. Observed community changes were driven primarily by temporal (seasonal) variation, with samples collected at 365 days clustering separately from earlier sampling dates for both treatments. AMOVA confirmed that sampling date, rather than PO212 treatment, explained most of the variance in community composition (p < 0.05). Although PO212 persisted in soil, fluctuations in other fungal populations were minor and within the range of natural seasonal variability. Overall, field application of PO212 did not disrupt indigenous soil fungal communities, supporting its environmental safety as a biocontrol agent for managing Fusarium wilt. Full article

A high-load partial nitrification reactor (HLPNR) was operated to treat high-ammonia wastewater by varying the hydraulic retention time (HRT). The associated shifts in the microbial community were analyzed using PCR-DGGE and high-throughput sequencing. The results indicated that the reactor achieved a maximum nitrogen loading rate (NLR) of 10.14 kg·N/(m³·d) at an HRT of 1.5 h, with a nitrite accumulation rate (NAR) of 86%. PCR-DGGE analysis revealed Proteobacteria and Nitrosomonas as the dominant phylum and genus, respectively, whose relative abundances varied significantly with HRT. Specifically, the relative abundance of Nitrosomonas sp. G1 increased from 15% to 40%, indicating that the abundances of Proteobacteria and Nitrosomonas were directly related to the load of the HLPNR. High-throughput sequencing revealed a marked decline in both the diversity and abundance of the HLPNR’s microbial community under conditions of reducing load. The dominant genus changed; however, the stability of the HLPNR was not destroyed. It can be inferred that the stability of the HLPNR primarily depended on the enrichment of key functional bacteria rather than on the overall microbial community composition. Full article

The rapid expansion of the meat duck industry in China has intensified environmental challenges, particularly those related to managing high-moisture duck manure. Fermentation bed systems, utilizing rice husks as a primary substrate, offer a sustainable solution by promoting waste decomposition and improving animal welfare. This study investigated microbial diversity in rice husk-based fermentation bed materials across different usage durations to assess their ecological feasibility. Samples were collected from a duck farm in Linyi, China, after one, three, five and seven batches of duck rearing (21 days per batch). Microbial communities were analyzed using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE), followed by cluster analysis, principal component analysis (PCA) and sequencing of recovered DGGE bands. The results revealed significant shifts in microbial composition, with low similarity (18% overall) and distinct abundance patterns among groups. Bacteroidetes abundance increased with prolonged usage, while Staphylococcus aureus was only detected in the first batch. A total of 32 sequenced bands identified dominant phyla, including Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. Group 4 (seven batches) exhibited the highest microbial diversity and richness (Shannon index: 2.68; mean abundance: 16.33 bands), which was attributed to organic matter accumulation and nutrient release during fermentation. These findings demonstrate that rice husk-based fermentation beds maintain robust microbial diversity over time, effectively supporting waste degradation and duck health. We conclude that rice husks are a viable, eco-friendly substrate for waterfowl fermentation bed systems, with periodic microbial supplementation recommended to enhance long-term efficacy. This work provides critical insights for optimizing sustainable livestock farming practices. Full article

This study evaluates the potential of biorefinery and dairy wastewater as substrates for electricity generation in double chamber Microbial Fuel Cells (DCMFC), focusing on their microbial taxonomy and electrochemical viability. Taxonomic analysis using 16S/18S rDNA-targeted DGGE and high-throughput sequencing identified Proteobacteria as dominant in biorefinery biomass, followed by Firmicutes and Bacteriodota. In dairy biomass, Lactobacillus (77.36%) and Clostridium (15.70%) were most prevalent. Biorefinery wastewater exhibited the highest bioelectrochemical viability due to its superior electrical conductivity and salinity, achieving a voltage yield of 65 mV, compared to 75.2 mV from mixed substrates and 1.7 mV from dairy wastewater. Elevated phosphate levels in dairy wastewater inhibited bioelectrochemical processes. This study recommends Biorefinery wastewater as the most suitable purely organic substrate for efficient bioelectricity generation and scaling up of MFCs, emphasising the importance of substrate selection for optimal energy output for practical and commercial viability. Full article

In this study, Caciocavallo, a typical cheese produced in Sicily Island (Italy), was obtained from the milk of dairy cows fed with and without enriched olive cake (ECO and CTR, respectively) in order to evaluate nutritional, microbiological, volatile, and sensory differences in cheeses. ECO cheese showed greater (p < 0.05) MUFA and PUFA and polyphenols content and lower SFA content than CTR cheese. Microbiological analyses revealed the absence of Salmonella, Listeria monocytogenes, Escherichia coli, and E. coli O157, and no significant differences in the viable counts of the remaining microbial groups analyzed, between samples. Thermophilic lactococci were more prevalent in ECO cheese. The implementation of a culture-independent method, such as PCR-DGGE analyses, revealed the presence of a more diverse microbial population in both cheeses. Regarding the volatile compounds profile, long-chain free fatty acids were more abundant in the ECO cheese, resulting in a healthier free fatty acid profile. This study also showed that, especially for their appearance and taste, consumers mostly appreciated the ECO cheese. The results show that using enriched olive cake could enhance the sustainability and the quality of Ragusano cheese, improving not only the health of its consumers but also positively influencing tastes and acceptability. Full article

In Vietnam, diarrhea, especially persistent diarrhea, is one of the most common diseases in children, while a significant proportion of cases are negative with pathogens; thus, there is an urgent need to understand gut bacterial dysbiosis. In this study, bacteria in the fecal samples of five healthy and ten diarrheal children were separated from other residues, then adopted to extract their metagenomic DNA for evaluating their diversity based on V3 and V6–V8 regions and the 16S rRNA gene by PCR-RFLP and PCR-DGGE. As a result, bacterial metagenomic DNAs with high quality, quantity and diversity were successfully extracted using a GeneJET kit and a chemical protocol. A sequence analysis of 73 representative DNA fragments from gels indicated a remarkable bacterial dysbiosis in all groups of diarrhea. Viral diarrhea was characterized by extremely reduced bacterial diversity with the blossom of Bifidobacterium and Streptococcus. Streptococcus was also the most abundant in persistent diarrhea. Beneficial bacteria that may play a role in the self- rebalance in intestinal bacterial communities, such as Bifidobacterium, Lactobacillus, and Enterococcus, were seen in all diarrheal groups, while Bacteroides and Akkermansia muciniphila were seen in the healthy group but absent in the diarrheal groups. This study provides additional evidence for a relationship between intestinal bacterial dysbiosis and diarrhea in children, emphasizing an increase in Streptococcus. Full article

To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the manure conditions, microbial community presence in manure, and their functions. Additional efforts are needed to understand the GHG emissions from manure and develop control strategies to minimize the biological GHG emissions from manure. To study the microbial shift during anaerobic processes responsible for GHG emission, we conducted a series of manure anaerobic digestion experiments, and these experiments were conducted in lab-scale reactors operated under various temperature conditions (28 °C, 36 °C, 44 °C, and 52 °C). We examined the third variable region (V3) of the 16S rRNA gene fingerprints of bacterial presence in anaerobic environment by PCR amplification and DGGE separation. Results showed that bacterial community was affected by the temperature conditions and anaerobic incubation time of manure. The microbial community structure of the original manure changed over time during anaerobic processes, and the community composition changed substantially with the temperature of the anaerobic process. At Day 0, the sequence similarity confirmed that most of the bacteria were similar (>95%) to Acinetobacter sp. (strain: ATCC 31012), a Gram-negative bacteria, regardless of temperature conditions. At day 7, the sequence similarity of DNA fragments of reactors (28 °C) was similar to Acinetobacter sp.; however, the DNA fragments of effluent of reactors at 44 °C and 52 °C were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 97%) and Tepidimicrobium ferriphilum (strain: DSM 16624) (similarity: 100%), respectively. At day 60, the analysis showed that DNA fragments of effluent of 28 °C reactor were similar to Galbibacter mesophilus (strain: NBRC 10162) (similarity: 87%), and DNA fragments of effluent of 36 °C reactors were similar to Syntrophomonas curvata (strain: GB8-1) (similarity: 91%). In reactors with a relatively higher temperature, the DNA fragments of effluent of 44 °C reactor were similar to Dielma fastidiosa (strain: JC13) (similarity: 86%), and the DNA fragments of effluent of 52 °C reactor were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 99%). To authors’ knowledge, this is one of the few studies where DGGE-based approach is utilized to study and compare microbial shifts under mesophilic and thermophilic anaerobic digestions of manure simultaneously. While there were challenges in identifying the bands during gradient gel electrophoresis, the joint use of DGGE and sequencing tool can be potentially useful for illustrating and comparing the change in microbial community structure under complex anaerobic processes and functionality of microbes for understanding the consequential GHG emissions from manure. Full article

The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10–30 cm (shallow = S) and 30–50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon–Weaver index (H′). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community. Full article

Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information. Full article

Circular economy recycling-derived fertilizers (RDF) have the potential to replace linear economy fertilizers such as unsustainable superphosphates. Here, effects of ash RDF treatments in Irish grassland cultivation were investigated in a simulated second growing season. Soil fertilized in a preceding pot trial with superphosphate (SP), poultry-litter ash (PLA) and sewage-sludge ash (SSA) at P concentration of 60 kg P ha⁻¹ and a P-free control (SP0) was reused in a microcosm trial. Lolium perenne was cultivated for 54 days in six replicates with a full complement of micro- and macro-nutrients other than P. PLA treatments provided higher dry weight shoot yields than SP0, while SSA and SP overlapped with SP0 and PLA. Most probable number (MPN) analysis showed that phosphonate- and phytate-utilizing bacterial abundance was significantly increased in PLA. Alkaline (phoD) phosphomonoesterase gene fragments were significantly more abundant (qPCR) in the ashes than the superphosphate or P-free control. Bacterial communities were significantly affected by the P application. Similarly, a significant separation of treatments was confirmed in a canonical correspondence analysis of the phoD-harboring community. The genera Streptomyces and Xanthomonas were significantly higher in abundance in the ash RDFs. These results demonstrated the potential benefits of ash RDF treatments as an alternative P source. Full article

This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices. Full article

Microorganisms colonizing modern water-based metalworking fluids (MWFs) have been implicated in various occupational respiratory health hazards to machinists. An understanding of the exposure risks from specific microbial groups/genera/species (pathogenic or allergenic) and their endotoxins and the need for strategies for effective, timely fluid management warrant real-time extended tracking of the establishment of microbial diversity and the prevailing fluid-related factors. In the current study, the microbial community composition, succession, and dynamics of a freshly recharged industrial semi-synthetic MWF operation was tracked in real-time over a period of 50 weeks, using a combination of microbiological and molecular approaches. Substantial initial bacterial count (both viable and non-viable) even in the freshly recharged MWF pointed to the inefficiency of the dumping, cleaning, and recharge (DCR) process. Subsequent temporal analysis using optimized targeted genus/group-specific qPCR confirmed the presence of Pseudomonads, Enterics, Legionellae, Mycobacteria (M. immunogenum), Actinomycetes, and Fungi. In contrast, selective culturing using commercial culture media yielded non-specific isolates and collectively revealed Gram-negative (13 genera representing 19 isolates) and Gram-positive (2 genera representing 6 isolates) bacteria and fungi but not mycobacteria. Citrobacter sp. and Bacillus cereus represented the most frequent Gram-negative and Gram-positive isolates, respectively, across different media and Nectria haematococca isolation as the first evidence of this fungal pathogen colonizing semi-synthetic MWF. Unbiased PCR-DGGE analysis revealed a more diverse whole community composition revealing 22 bacterial phylotypes and their succession. Surges in the endotoxin level coincided with the spikes in Gram-negative bacterial population and biocide additions. Taken together, the results showed that semi-synthetic MWF is conducive for the growth of a highly diverse microbial community including potential bacterial and fungal pathogens, the current DCR practices are inefficient in combating microbial reestablishment, and the practice of periodic biocide additions facilitates the build-up of endotoxins and non-viable bacterial population. Full article

Lignocellulose biomasses (LCB), including spent mushroom substrate (SMS), pose environmental challenges if not properly managed. At the same time, these renewable resources hold immense potential for biofuel and chemicals production. With the mushroom market growth expected to amplify SMS quantities, repurposing or disposal strategies are critical. This study explores the use of SMS for cultivating microbial communities to produce carbohydrate-active enzymes (CAZymes). Addressing a research gap in using anaerobic digesters for enriching microbiomes feeding on SMS, this study investigates microbial diversity and secreted CAZymes under varied temperatures (37 °C, 50 °C, and 70 °C) and substrates (SMS as well as pure carboxymethylcellulose, and xylan). Enriched microbiomes demonstrated temperature-dependent preferences for cellulose, hemicellulose, and lignin degradation, supported by thermal and elemental analyses. Enzyme assays confirmed lignocellulolytic enzyme secretion correlating with substrate degradation trends. Notably, thermogravimetric analysis (TGA), coupled with differential scanning calorimetry (TGA-DSC), emerged as a rapid approach for saccharification potential determination of LCB. Microbiomes isolated at mesophilic temperature secreted thermophilic hemicellulases exhibiting robust stability and superior enzymatic activity compared to commercial enzymes, aligning with biorefinery conditions. PCR-DGGE and metagenomic analyses showcased dynamic shifts in microbiome composition and functional potential based on environmental conditions, impacting CAZyme abundance and diversity. The meta-functional analysis emphasised the role of CAZymes in biomass transformation, indicating microbial strategies for lignocellulose degradation. Temperature and substrate specificity influenced the degradative potential, highlighting the complexity of environmental–microbial interactions. This study demonstrates a temperature-driven microbial selection for lignocellulose degradation, unveiling thermophilic xylanases with industrial promise. Insights gained contribute to optimizing enzyme production and formulating efficient biomass conversion strategies. Understanding microbial consortia responses to temperature and substrate variations elucidates bioconversion dynamics, emphasizing tailored strategies for harnessing their biotechnological potential. Full article

Traditional dairy products, especially cheeses, represent part of the cultural food heritage of many countries. In addition, these cheeses constitute microbiological “reservoirs”, of which many have been lost due to the introduction of the pasteurization of milk in the dairy industry. Increased awareness of the importance of microorganisms that make up the biodiversity of traditional cheeses, as well as the development of molecular methods in recent decades, have enabled efforts to identify and preserve them. Traditional Livno cheese is a full-fat hard cheese, considered one of the most famous traditional cheeses of Bosnia and Herzegovina and is seasonally produced from a mixture of raw sheep’s milk supplemented with cow’s milk. Often, Livno cheese has variable quality, due to microbial contamination and poor milk quality. In this study, traditional Livno cheese was studied during the ripening of cheeses produced by different producers during two seasons. Culture-dependent analyses were made during ripening using microbiological plating on suitable media. Likewise, culture-independent methods Denaturing Gradient Gel Electrophoresis (DGGE) and Automated Ribosomal Intergenic Spacer Analysis (ARISA) were used to elucidate the cheese microbiota. Results of analysis showed Lactococcus spp., Streptococcus spp., Lactobacillus spp., Pediococcus spp. and Leuconostoc spp. to be dominant species in traditional Livno cheese. However, when comparing the use of culture-dependent and culture-independent methods in the evaluation of Livno cheese microbiota, Enterococcus was not detected by culture-independent DGGE methods. The microbial population of both the milk and the environment determines the fermentation processes during cheese production and ripening, and thereby defines the quality of this cheese. The numbers of bacteria in the cheese were shown to be dependent on the manufacturer, the degree of ripening and the production season. Full article

Guadua angustifolia produces phenolic compounds, and this production may be influenced by the application of chemical, organic, and biological fertilizers. Currently, the effect of such fertilizers on the synthesis dynamics of this group of metabolites in bamboo is unknown. In this study, the total phenolic content (TPC) and total flavonoid content (TFC) in the leaves of plants fertilized with diammonium phosphate (DAP) and humus in combination with the biofertilizers Promofort^®, Azospirillum brasilense, Pseudomonas fluorescens, and Stenotrophomonas sp. were determined using colorimetric techniques across three sampling events (four, five, and seven months after planting). Additionally, an approximation of the bacterial profile of G. angustifolia roots was performed using the DGGE-PCR fingerprint technique. Through repeated measures ANOVA (rmANOVA), it was determined that there is no statistically significant three-way interaction between humus or DAP application, biological fertilizers, and time for either TPC or TFC. However, there were interactions between the sampling event and the application of biological fertilizers for both TPC and TFC, with the latter being promoted by the application of Promofort^®. Finally, NMDS analyses and heatmaps with hierarchical clustering showed that the composition and abundance of OTUs in the bacterial profile varied with fertilization type and increased over time. Full article