Search Results (16)

The Sjenica sheep stelja is a characteristic, traditional dry-cured meat product from Serbia with unique and recognizable sensory attributes. The methodology involved examining physicochemical measurements, followed by sensory evaluation and microbiological analyses, over a 120-day ripening period across three years and three different villages, as well as the correlation between chemical characteristics and the number of specific groups of bacteria. Results showed consistent quality parameters across producers and production periods, with notable variation in fat, protein, and ash content. Sensory evaluation confirmed that the product met the quality standards outlined in the Elaborate for the Protection of Geographical Indication, with minor differences in color, aroma, chewiness, and taste among samples. The microbiological analysis demonstrated the dynamic nature of microbial communities throughout maturation, including changes in the counts of aerobic mesophilic bacteria, Enterobacteriaceae, Pseudomonadaceae, lactic acid bacteria, and molds. Penicillium species, particularly P. nalgiovense and P. solitum, were consistently identified, while other fungal genera exhibited varying distribution patterns. The correlation analysis highlights the complex influence of chemical parameters on microbial dynamics throughout the aging process. These findings emphasize the influence of traditional production methods, regional variations, and chemical composition on the sensory quality and microbial safety of Sjenica Sheep Stelja, providing valuable insights for future research and quality control. Full article

Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in the Qinghai–Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were Tricharina gilva and Peziza lohjaoensis, and the microbial diversity of T. gilva-infected soil was higher than that of healthy soil, while the diversity of P. lohjaoensis-infected soil was lower. Interestingly, whether infected with T. gilva or P. lohjaoensis, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with P. lohjaoensis, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed Pseudomonadaceae, Terfezia, and Pedobacter, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with T. gilva, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included Hydrogenophaga, Sphingomonas, and Polaromonas, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with P. lohjaoensis than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with T. gilva than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of Morchella. Full article

Background/Objectives: Taxon-specific conserved signature indels (CSIs) exhibit a strong predictive ability of being found in other members of specific taxa/genera. Recently, multiple exclusively shared CSIs were identified for several newly described Pseudomonadaceae genera (viz. Aquipseudomonas, Atopomonas, Caenipseudomonas, Chryseomonas Ectopseudomonas, Geopseudomonas, Halopseudomonas, Metapseudomonas, Phytopseudomonas, Serpens, Stutzerimonas, Thiopseudomonas, and Zestomonas). This study examines the potential applications of these CSIs for identifying other Pseudomonas spp. (strains) related to these genera. Methods: This work utilized the AppIndels.com server, which uses information regarding the presence of known taxon-specific CSIs in a genome for predicting its taxonomic affiliation. For this purpose, sequence information for different CSIs specific for the Pseudomonadaceae species/genera were added to the server’s database. Results: The AppIndels server was used to predict the taxonomic affiliation of 1972 genomes of unclassified Pseudomonas spp. (strains/isolates). Based upon finding a significant number of CSIs matching a specific taxon, the AppIndels server made positive predictions regarding the taxonomic affiliation of 299 examined genomes into the following clades/genera: Pseudomonas sensu stricto clade (46), Pseudomonas aeruginosa (64), Ectopseudomonas (46), Chryseomonas (32), Stutzerimonas (31), Metapseudomonas (22), Aquipseudomonas (21), Phytopseudomonas (17), Halopseudomonas (9), Geopseudomonas (4), Thiopseudomonas (3), Serpens (2), and Caenipseudomonas and Zestomonas (1 each). Phylogenetic studies confirmed that the taxonomic predictions by the server were 100% accurate. Conclusions: Our results demonstrate that the CSIs specific for Pseudomonadaceae species/genera, in conjunction with the AppIndels server, provides a novel and useful tool for identifying other species/strains affiliated with these species/genera. Phylogenetic studies suggest that many examined Pseudomonas strains constitute novel species in the indicated genera. Full article

The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km² between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km². It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve’s natural ecosystems. Full article

This study aimed to provide foundational research for the biological control of postharvest avocado fruits anthracnose and establish a microbial system of postharvest avocado fruits. The high-throughput sequencing of avocado fruits from the anthracnose-infected and healthy groups was performed using Illumina NovaSeq second-generation sequencing technology. The results revealed that, except for Colletotrichum sp. strain 38#, there were differences in the bacterial community structure of avocados before and after infection, as determined through alpha and beta diversity analysis. Additionally, there were significant differences in the endophytic fungal community structure, allowing clear differentiation between the infected and healthy avocados. The endophytic bacterial community was primarily composed of 4 phyla and 10 genera, with the Bacteroidota phylum and Chryseobacterium genus demonstrating sensitivity to anthracnose pathogens, as evidenced by a decrease in their relative abundance after infection. The endophytic fungal community was characterized by 3 phyla and 10 genera. After infection, the relative abundance of 2 phyla (Anthophyta and Basidiomycota) and 7 genera (Eucalyptus, Candida, Kluyveromyces, Talaromyces, Oidiodendron, Nigrospora, and Pestalotiopsis) decreased, whereas the relative abundance of the Colletotrichum genus increased dramatically. The LEfSe (Linear discriminant analysis Effect Size) analysis indicated that significant biomarkers were more prevalent in endophytic bacteria than in endophytic fungi in the avocados. In endophytic bacteria, the key biomarkers included the Firmicutes phylum (Bacilli class), Proteobacteria phylum (Gammaproteobacteria class, Pseudomonadales order, Pseudomonadaceae family, and Pseudomonas genus), Flavobacteriales order, Weeksellaceae family, and Chryseobacterium genus. In endophytic fungi, the important biomarkers were Saccharomycetes class (Saccharomycetales order), Glomerellales order (Glomerellaceae family and Colletotrichum genus), and Botryosphaeriales order (Botryosphaeriaceae family and Lasiodiplodia genus). These results may provide a theoretical basis for the development of future biological agents for avocado anthracnose. Full article

The formation of mineral-protected organic carbon (MPOC) is a vital process for soil organic carbon (SOC) accumulation and stabilization, influenced by factors such as exogenous carbon (C) input and soil microorganisms. However, the dynamics of MPOC and soil microorganisms following exogenous C input, and the key microorganisms driving MPOC formation, remain poorly understood. To address this, we conducted exogenous C addition culture experiments to investigate changes in MPOC and soil microorganisms and identify the primary microorganisms influencing MPOC formation. We observed that the MPOC content in treated soils increased over time, ranging from 0.43 to 2.06 g kg⁻¹. MPOC showed a significant positive correlation with soil bacterial diversity and a significant negative correlation with fungal diversity. Soil samples contained 248 bacterial families and 189 fungal genera, with Oxalobacteraceae (7.42%) and unclassified_k__Fungi (24.82%) being the most abundant, respectively. Using FAPROTAX and FunGuild ecological function prediction methods, we analyzed soil bacteria and fungi functional profiles and abundances. We identified the main bacterial families influencing MPOC formation as Microbacteriaceae, Mycobacteriaceae, Pseudomonadaceae, Streptomycetaceae, and Xanthomonadaceae. The primary fungal genera were Cylindrocarpon, Leohumicola, Metarhizium, Neobulgaria, Neopestalotiopsis, Olpidium, and Tetracladium. These findings provide theoretical support for understanding microbial regulation mechanisms in soil C sequestration and emission reduction. Full article

Paenibacillus dendritiformis UJA2219 isolated from carrot produces broad-spectrum antibacterial activity. The aim of the present study was to determine the impact of partially-purified cell-culture extracts of strain UJA2219 on the microbial load and bacterial diversity of a homemade vegetable puree. The puree was challenged with an overnight culture of strain UJA2219 or with cultured broth extracts partially purified by cation exchange (CE) chromatography or reversed-phase (RP) chromatography and incubated for 7 days at temperatures of 4 °C or 25 °C. The best results were obtained at 25 °C with the RP extract, decreasing counts of the presumptive Enterobacteriaceae below detectable levels. The bacterial diversity of control and treated puree was studied by Illumina paired-end sequencing, using DNA extracted from the puree samples incubated at 25 °C for 24 h. The controls and the puree inoculated with the UJA2219 strain showed an almost-identical bacterial diversity profile, with Pseudomonadota (mainly Fam. Pseudomonadaceae -gen. Pseudomonas- and Enterobacteriace as the most abundant groups). The greatest differences in bacterial diversity were obtained in the puree treated with RP extract, showing a decrease in the relative abundance of Pseudomonadota (especially gen. Pseudomonas) and an increase of Bacillota (mainly of the genera Bacillus, Enterococcus and Lactococcus). Results from the study suggest that the antimicrobial preparations from strain UJA2219 have a potential for application in food biopreservation. Full article

High hydrostatic pressure (HP) is a promising method to improve the microbiological quality of sous-vide foods. Monitoring the composition and behavior of the microbial communities in foods is of most importance for the production of high-quality and safe products. High-throughput sequencing (HTS) provides advanced approaches to determine food’s microbial community composition and structure. The aim of the present study was to determine the impact of different HP treatments on the microbial load and bacterial diversity of sous-vide Atlantic cod. Sous-vide cooking at 57.1 °C for 30 min followed by HP treatment at 500 MPa for 8 min reduced viable cell counts (total aerobic mesophiles) in the cod samples below detectable levels for 45 days of storage under refrigeration. In a second trial with cod cooked sous-vide at 52 °C for 20 min followed by HP treatments at 300 or 600 MPa (with HP treatment temperatures of 22 °C or 50 °C for 4 or 8 min, depending on treatment), only the treatments at 600 MPa delayed bacterial growth for at least 30 days under refrigeration. The optimal HP conditions to improve the microbiological quality of sous-vide cod cooked at low temperatures were obtained at 600 MPa for 4 min at a pressurization temperature of 50 °C. Bacterial diversity was studied in cod cooked sous-vide at 52 °C for 20 min by HTS. In the absence of HP treatment, Proteobacteria was the main bacterial group. A succession of Pseudomonadaceae (Pseudomonas) and Enterobacteriaceae was observed during storage. Firmicutes had low relative abundances and were represented mainly by Anoxybacillus (early storage) and Carnobacterium (late storage). The HP-treated sous-vide cod showed the greatest differences from controls during late storage, with Aerococcus and Enterococcus as predominant groups (depending on the HP conditions). The application of HTS provided new insights on the diversity and dynamics of the bacterial communities of sous-vide cod, revealing the presence of bacterial genera not previously described in this food, such as Anoxybacillus. The significance of Anoxybacillus as a contaminant of seafoods should be further investigated. Full article

Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils. Full article

The root microbiota contributes to the plant’s defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08–61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota. Full article

Chlorine-containing organic compounds are important industrial solvents but are severely toxic to humans and the environment. Because of their stability and dense non-aqueous phase, they barely biodegrade when released into soil and groundwater systems and may significantly impact the soil environment. One bioremediation approach, biostimulation, adds rate-limiting nutrients to the soil to promote biodegradation processes, but the link remains unclear between stimulated microbial communities and nutrient inputs in anaerobic environments. This study evaluated changes to soil microbial communities in 1,2-dichlorobenzene (1,2-DCB)-contaminated soil under diverse carbon (C) and nutrient conditions. The experiments used anaerobic microcosms that were amended with various C and nutrient sources, and the analysis employed real-time PCR and next-generation sequencing. The results reveal that methanogens may have high resistance to 1,2-DCB in oligotrophic conditions. However, bacteria such as Pseudomonas, Sphingomonas, and some uncultured genera in the Xanthomonadaceae, Pseudomonadaceae, and Bacillales families can resist high 1,2-DCB concentrations when N and P sources are available. These results indicate that external N and P sources are important for stabilizing soil microbial communities and their processes in contaminant sites. Full article

The aim of this study was to analyze the microbiome of carrot (Daucus carota subsp. sativus) subjected to minimal pre-treatment (rinsing in organic acid solution) and packaging in a high-oxygen modified atmosphere, and then stored for 17 days under refrigeration conditions (4 °C). The highest levels of bacteria in the carrot microbiome were characterized, at almost 78%, by bacteria belonging to the Enterobacteriaceae and Pseudomonadaceae families. Rinsing in a solution of ascorbic and citric acids resulted in the improvement of microbiological quality in the first day of storage. However, the use of a high-oxygen modified atmosphere extended the shelf life of the minimally processed product. Compared to carrots stored in air, those stored in high oxygen concentration were characterized by a greater ratio of bacteria belonging to the Serratia and Enterobacter genera, and a lower ratio belonging to the Pseudomonas and Pantoea genera. Moreover, the β-biodiversity analysis confirmed that the oxygen concentration was the main factor influencing the differentiation of the metabiomes of the stored carrots. The bacterial strains isolated from carrots identified by molecular methods were mostly pathogenic or potentially pathogenic microorganisms. Neither the minimal pre-treatment nor packaging in high-oxygen atmosphere was able to eliminate the threat of pathogenic bacteria emerging in the product. Full article

In the context of global warming and increasing wildfire occurrence, this study aims to examine, for the first time, the changes in multi-level biodiversity and key soil features related to soil functioning in a burned Mediterranean beech forest. Two years after the 2017 wildfire, changes between burned and unburned plots of beech forest were analyzed for plant communities (vascular plant and cover, bryophytes diversity, structural, chorological, and ecological variables) and soil features (main chemical properties, microbial biomass and activity, bacterial community composition, and diversity), through a synchronic study. Fire-induced changes in the micro-environmental conditions triggered a secondary succession process with colonization by many native pioneer plant species. Indeed, higher frequency (e.g., Scrophularia vernalis L., Rubus hirtus Waldst. and Kit. group, and Funaria hygrometrica Hedw.) or coverage (e.g., Verbascum thapsus L. subsp. thapsus and Digitalis micrantha Roth ex Schweigg.) of the species was observed in the burned plots, whereas the typical forest species showed a reduction in frequency, but not in cover, except for Fagus sylvatica subsp. sylvatica. Overall, an increase in plant species and family richness was found in the burned plots, mainly in the herbaceous and bryophyte layers, compared to the unburned plots. Burned plots showed an increase in therophytes, chamaephytes, cosmopolites, steno-Mediterranean and Atlantic species, and a decrease in geophytes and Eurasiatic plants. Significant differences were found in burned vs. control soils for 10 phyla, 40 classes, 79 orders, 145 families, 342 genera, and 499 species of bacteria, with about 50% of each taxon over-represented and 50% under-represented in burned than in control. Changes in bacterial richness within several families (reduction in Acidobacteriaceae, Solibacteraceae, Rhodospirillaceae, and Sinobacteraceae; increase in Micrococcaceae, Comamonadaceae, Oxalobacteraceae, Pseudomonadaceae, Hymenobacteraceae, Sphingomonadaceae, Cytophagaceae, Nocardioidaceae, Opitutaceae, Solirubrobacteraceae, and Bacillaceae) in burned soil were related to fire-induced chemical changes of soil (pH, electrical conductivity, and cation exchange capacity). No evident effect of the wildfire was found on organic C content, microbial biomass (total microbial carbon and fungal mycelium) and activity, and microbial indexes (fungal percentage of microbial C, metabolic quotient, and quotient of mineralization), suggesting that soil functions remained unchanged in the burned area. Therefore, we hypothesize that, without an additional disturbance event, a re-establishment of beech forest can be expected but with an unpredictable time of post-fire succession. Full article

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach. Full article

Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture. Full article