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Phleum pratense is an allergenic grass that pollinates in spring in Pakistan. Databases Allergenonline.org and Allergen.org record ten P. pratense allergens and their isoforms. Phl P 1, Phlp 5, and Phl p 11 are major P. pratense-pollen allergens with demonstrated basophil activity and skin test reactivity. Little is known about P. pratense pollen adaptive variations in different climatic regions and pollen-associated microbial diversity. In this study, we collected P. pratense-pollen and soils in the spring season 2022. Samples were collected from three climatic regions in Pakistan (R1, R2 and R3) with differences in mean monthly air temperature, mean monthly precipitation and elevation. The morphology of pollen was observed by light microscopy, scanning electron microscopy (SEM), biochemical fingerprint analysis, and composition of pollen were investigated by fourier-transform infrared spectroscopy (FTIR). The pollen-associated bacterial populations were identified through a Biolog GEN III microplate system. The pollen water-soluble proteins were isolated and stabilized in phosphate buffer saline (PBS) and tested for allergenicity responses through dot blots and western blots analysis. The morphology study found difference in pollen biochemical composition. Biolog identified Brevibacterium epidermidis and Pantoea agglomerans from P. pratense pollen. Protein extract quantification and sodium dodecyl sulfate-poly acrylamide gel electrophoresis (SDS-PAGE) gel found decreased protein expression in R1 region pollen compared to R2 and R3 region pollen. Allergenicity studies found differential expression of beta-expansin and profilin allergens in pollen obtained from the three regions. Beta-expansin and profilin were suppressed in R1 pollen and expressed in compared to R2 and R3 pollen. This is the first study to identify B. epidermidis and P. agglomerans growth on P. pratense pollen. Variable allergen expression in P. pratense pollen has also been observed in different regions. Soil pH, an increase in mean monthly temperature and a decrease in mean monthly precipitation correlated with pollen biochemical composition, and reduced beta-expansin and profilin expression involved in pollen growth and development. The findings of this research are unique, which enhances basic knowledge and understanding of P. pratense-pollen associated microbiota and climate change impacts on the pollen allergen expression. [ABSTRACT FROM AUTHOR]

Education is a fundamental process that facilitates human learning, skill development, and knowledge transfer. It plays a pivotal role in fostering economic growth, improving quality of life, and shaping societies. This study focuses on the performance of secondary school students in Biology and Chemistry in the Nigerian states of Ondo and Ekiti from 2015 to 2018. The research examines the comparative performance of these subjects and explores factors that might contribute to variations. Using an ex-post facto research design, the study analyzed data from the West African Senior School Certificate Examination (WASSCE) to determine academic outcomes. The results indicate significant differences in performance between the two subjects and the two states. Students in Ondo state performed better in Biology, while those in Ekiti state excelled in Chemistry. Factors that caused the differences in their performances included access to learning tools, student attitudes, students' resource availability, students' interpersonal relationship, students' regularity to class, parental education, and the learning environment, were discussed. The study suggested that laboratory facilities be improved, teacher should be trained, and class sizes be optimized to enhance student achievement. [ABSTRACT FROM AUTHOR]

Turquoise blue dye is frequently used for industrial dyeing applications. But the release of untreated colored wastewater became an environmental and public health hazard. Microbial remediation of Azodye is environmentally safe and an alternative to a physicochemical approach. The aim of this research is to isolate and characterize turquoise blue dye degrading microbes from polluted environment. Microbial isolation and purification from soil and effluent sample was done on PDA and NA. Turquoise blue dye degrading test was investigated under optimized conditions using -the definitive screening design method. UV–Vis spectrophotometer used to measure the degradation percentage at 620 nm and 25 °C. The results revealed that 24 fungi and 6 bacterial species were identified from the contaminated site using Biolog Microstation and MALDI-TOF. Among all identified microbial species Pencilium citrinum Thom BCA & Penicillium heriquei show the highest percentage decolorization of turquoise blue dye up to 300 ppm with 90 % removal at pH4 and 87 % at pH 7 up to 400 ppm respectively. The azodye degradation ability of these fungi species used in the development of mycoremediation technologies provide an alternative option for Azodye removal after HPLC analysis, molecular characterization, and toxic analysis.

Bouslama, T., Laarif, A., Chattaoui, M., Vial, L., Lavire, C., and Doré, J., and Rhouma, A. 2023. Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera). Tunisian Journal of Plant Protection 18 (2): 71-91.

In the present study, different Pseudomonas strains were isolated from the rhizospheric soil of Curcuma longa (turmeric) and further identified and characterized based on morphological, biochemical, and molecular characteristics through the 16S rRNA gene sequencing analysis. The identified bacterial strains belong to the Pseudomonas genus viz. Pseudomonas sp. CL10, Pseudomonas sp. CL11, and P. fluorescence CLI4. However, the isolated strains tested positive for IAA production, siderophore production, and the solubilization of tricalcium phosphate during plant growth promoting traits analysis. Further phenotype microArray (PM) technology was used to evaluate the antibiotic and chemical sensitivity of the isolated bacterial strains. The antibiotics phleomycin, oxacillin, vancomycin, novobiocin, spiramycin, and rifampicin, as well as chemicals like, 5-7 dichloro-8-hydroxy quanaldine, 5-7 dichloro-8-hydroxyquinoline, domophenbrobide, and 3-5 dimethoxy benzyl alcohol, showed resistance in all the rhizobacterial strains. However, upon further detailed study, Pseudomonas sp. CL10 exhibited resistance to thirteen antibiotics, CL11 to fourteen, and CL14 showed resistance against seventeen antibiotics and chemical classes. The results of the study indicate that some of these strains can be used as bioinoculum to enhance the plant growth and health. [ABSTRACT FROM AUTHOR]

In the present study, different Pseudomonas strains were isolated from the rhizospheric soil of Curcuma longa (turmeric) and further identified and characterized based on morphological, biochemical, and molecular characteristics through the 16S rRNA gene sequencing analysis. The identified bacterial strains belong to the Pseudomonas genus viz. Pseudomonas sp. CL10, Pseudomonas sp. CL11, and P. fluorescence CLI4. However, the isolated strains tested positive for IAA production, siderophore production, and the solubilization of tricalcium phosphate during plant growth promoting traits analysis. Further phenotype microArray (PM) technology was used to evaluate the antibiotic and chemical sensitivity of the isolated bacterial strains. The antibiotics phleomycin, oxacillin, vancomycin, novobiocin, spiramycin, and rifampicin, as well as chemicals like, 5-7 dichloro-8-hydroxy quanaldine, 5-7 dichloro-8-hydroxyquinoline, domophenbrobide, and 3-5 dimethoxy benzyl alcohol, showed resistance in all the rhizobacterial strains. However, upon further detailed study, Pseudomonas sp. CL10 exhibited resistance to thirteen antibiotics, CL11 to fourteen, and CL14 showed resistance against seventeen antibiotics and chemical classes. The results of the study indicate that some of these strains can be used as bioinoculum to enhance the plant growth and health.

A long-term field experiment was conducted to investigate the effects of organic manure (commercial organic manure, CFM1; cow manure, CFM2; green manure, CFM3) and chemical fertiliser (CK) on the microbial diversity of a tobacco-planted soil using Biolog ECO and 16S rRNA sequencing technology. The results showed that organic manure treatments increased the available nutrient content in the soil, including nitrogen (AN, 2.1–13.3%), potassium (AK, 14.2–31.8%), labile organic carbon (19.9–37.4%), and microbial biomass carbon (11.9–21.0%), as well as the mean weight diameter and geometric mean diameter. The average well colour development value and McIntosh diversity index in CFM1 treatment increased by 23.6% and 18.9%, respectively, compared with CK. The 16S rRNA sequencing analysis suggested that CFM1 and CFM2 treatments improved the richness and diversity of soil bacteria and recruited more potentially beneficial bacteria. Redundancy analysis showed that soil physicochemical properties, excluding AN and Olsen–P were positively correlated with the abundance of bacteria dominant in the CFM1 treatment. This indicates that application of CFM1 is a sound fertilisation strategy to improve soil fertility and create a good ecological environment. [ABSTRACT FROM AUTHOR]

In order to investigate the effect of pruning on the soil environment in which tea trees grow and the growth of tea trees, this study used Wuyi Meizhan (Camellia sinensis) as a research object and measured its growth indexes, soil physicochemical indexes, soil enzyme activity and microbial functional diversity to analyze the effects of pruning treatments on the growth of tea trees, soil enzyme activity and soil microbial functional diversity and the correlation between them. The results of the analysis of tea tree growth indexes showed that the hundred-bud weight, leaf area and yield in the pruning treatment were significantly higher than those in the unpruned treatment. The results of soil physicochemical index analysis showed that pH, available phosphorus, available potassium and organic matter were significantly higher in the pruning treatment than in the unpruned treatment (p < 0.05), while available nitrogen and total phosphorus were significantly lower than in unpruned treatment (p < 0.05). The results of soil enzyme activities showed that only polyphenol oxidase and catalase activities were significantly higher in the pruning than in the unpruned treatment, while urease, protease, acid phosphatase, asparaginase and glutaminase activities were significantly lower than in the unpruned treatment (p < 0.05). Biolog analysis showed that the utilization of microbial carbon sources, especially amino acid and amine, increased in the rhizosphere soil of the pruned tea tree, while there was a significant decrease (p < 0.05) in microbial diversity. It is evident that pruning promoted tea tree growth and some enzyme activity, while inhibiting the activity of enzymes associated with the nitrogen cycle, and the utilization of microbial carbon sources increased, but their diversity decreased. This study provides a theoretical basis for the daily management of tea plantation after pruning. [ABSTRACT FROM AUTHOR]

Atrazine has been intensively applied to control weeds in agriculture and frequently detected in soil far from the point of application due to its special property, which causes serious soil environmental problems. Therefore, the aim of this study was to investigate the effects of environmental concentrations of atrazine (0, 0.1, 1.0, and 10 mg kg−1) on the soil microbial community during 42 days of culture using biochemical and molecular methods. The results showed that the number of culturable bacteria, fungi, and actinomycetes decreased significantly with the increase of atrazine concentration during the whole exposure process, showing a certain dose-effect relationship. Soil microbial biomass carbon also decreased significantly during atrazine exposure. Biolog ECO analysis showed that 10 mg kg−1 treatment had an inhibitory effect on the overall activity of microbial community (AWCD) at the later stage of the experiment (days 28 and 42). Additionally, 10.0 mg kg−1 atrazine treatment for 28 days decreased the richness of the soil microbial community (Shannon), the dominance of common species (Simpson), and the homogeneity of species (Mcintosh). PCR-T-RFLP analysis showed that atrazine exposure significantly affected the structure of bacterial dominant flora in the soil at days 0, 7, 14, and 21. Further PCR-DGGE analysis showed that the dominant bacteria flora mainly belonged to Proteobacteria, Firmicutes, Deinococcus-Thermus, Actinobacteria, and Acidobacteria. Overall, this study demonstrates that atrazine has a certain influence on soil microorganisms and provides an objective assessment of the ecological risk of atrazine to soil microorganisms. [ABSTRACT FROM AUTHOR]

Hexavalent chromium is resistant to degradation and harmful toxic substance to environment and community health. Physicochemical treatment methods are demanding high cost, used large quantities of chemicals & energy, release large amount of secondary toxic degradants. Mycoremediation is an eco-friendly alternative treatment method. The main objective of this research is to isolate and characterize chrome (VI) tolerant fungi from farm soil & industry effluent for mycoremedation purpose. The screening and isolation of yeast was carried out on potato dextrose agar media. PDA and broth assay test for fungi tolerance to hexavalent chromium at different concentration, temperature and pH was evaluated. Fungi species was identified biochemically using Biolog Microstation depending on carbon utilization and chemical sensitivity test. The result revealed that 10 yeast species was identified with full ID from effluent waste and farm soil based on their probability ≥ 75% and similarity index ≥ 0.5 as well as their Cr (VI) tolerance ability up to 2500 ppm. These are Yarrowia lipolytica (100%, 0.7), Cryptococcus luteolus(100%, 0.64), Rhodotorula aurantiaca A(100%, 0.62), Ustilago maydis(100%, 0.58) Trichosporon beigelii B (100%, 0.51), Cryptococcus terreus A (100%, 0.62), Zygosaccharomyces bailii (98%, 0.65), Nadsoniafulvenscens (90%, 0.62), Schizoblastosporonstarkeyihenricii (89%, 0.56), Endomycopsis vivi (84%, 0.62), Rhodotorula pustula (Sim, 0.59). Two yeast species Yarrowia lipolytica and Nadsoniafulvenscens show the highest growth mean Optical density (OD) measure 0.74 ± 0.2 & 0.60 ± 0.2 respectively at pH 7 & 25 °C. The highest tolerance index (mm) was recorded by Schizoblastosporon starkey henricii 0.3067 ± 0.152. Cr (VI)-tolerance ability of these yeast strains used in the development of chromium-bioremediation technologies provide an alternative option for chromium sequestration after HPLC analysis& molecular characterization. [ABSTRACT FROM AUTHOR]

To engage sustainable forest management, understanding the impact of disturbances on the stability of soil microorganisms is important. This study reported the immediate effects of two-level thinning intensities on the soil microbial population, community composition and functions of a plantation forest over two years. Results showed that the thinning of Cryptomeria japonica forest significantly increased viable counts of soil bacteria from 7.7 × 106 to 1.4 × 107 or 1.6 × 107 in the 3rd month and the effect subsided in the 6th month post-thinning. The counts of actinobacteria, cellulolytic, nitrogen-fixing and phosphate-solubilizing bacteria groups maintained stable populations in the forest soils. Denaturing gradient gel electrophoresis profiles indicated that soil bacterial communities significantly differed among 25% thinning, 50% thinning and control treatment from the 12th to 18th month post-thinning, with no significant differences after 22 months. The community level physiological profiles were significantly different between control and thinning treatments in the 12th month post-thinning, the impacts of thinning then subsided by the 22nd month post-thinning as well. Soil bacteria were sensitive to thinning disturbances, but with resilience, their community and function approached to the control status in 2 years. This study demonstrates that the soil microbes of Taiwanese C. japonica forests are very sensitive to thinning disturbances, but recover stability after a relatively short period of time. [ABSTRACT FROM AUTHOR]

Petroleum oil contaminants have become severe ecological problems and negatively impact human health. It is, therefore, imperative to identify environmentally friendly approaches to remediate oil-polluted environments. Therefore, bacterial oil degradation stimulated with a nitrogen source under optimum conditions was assessed in this study. Based on the 16S rRNA analysis, strain ODB H32 recovered from oil-based mud of some petroleum drilling sites in the western desert, Egypt, was identified as Enterobacter hormaechei. The metabolic fingerprint of E. hormaechei, achieved using BIOLOG GEN III, revealed that the strain could utilize diverse carbon and chemical sources. Also, E. hormaechei could biodegrade 0.6% of oil under optimized pH (7.0) and temperature (30 °C) conditions. Analyzing different nitrogen stimulants revealed that peptone ˃ yeast extract ˃ ammonium nitrate ˃ urea enhanced the growth of E. hormaechei on mineral salts medium (MSM). Analysis by capillary gas chromatography revealed maximum (70.7%) degradation of peptone by E. hormaechei, indicating that peptone was a good biostimulant for oil degradation. These findings recommend using biostimulated E. hormaechei as an eco-friendly approach for remediating oil-polluted environments, under optimized conditions, especially in arid regions like the western desert of Egypt. [ABSTRACT FROM AUTHOR]

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methylD-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future. [ABSTRACT FROM AUTHOR]

Chinese fir (Cunninghamia lanceolata) plantation is a dominant forest type and carbon sink in the subtropical region in China. An experiment with simulated nitrogen deposition (addition of 40 kg N ⋅ hm-2 ⋅ a-1) and drought (50% of precipitation exclusion, PE) was established in Chinese fir plantation in 2018. Soil samples (0-15 cm) were collected in summer (July 2020) and winter (January 2021). Soil microbial biomass, colony forming units (CFUs) and carbon source utilization were determined through phospholipid fatty acids (PLFAs), plate count, and Biolog methods, respectively. The results showed significant seasonal variations of PLFAs-related microbial biomass and composition. Soil bacterial and fungal CFUs tended to be decreased by nitrogen addition or precipitation exclusion treatment, and bacterial CFUs were more sensitive to the two treatments than fungal CFUs. Soil microbial function (i. e. carbon source utilization) was not affected by nitrogen addition, but significantly decreased by precipitation exclusion. There was a significant positive correlation between bacterial CFUs and microbial function, indicating the crucial roles of culturable bacteria in microbial carbon transformation. Our results highlight the critical effects of nitrogen deposition and 50% reduced precipitation on microbes in topsoil of fir plantation, with implications for unraveling soil microbial ecological function of subtropical forest ecosystem under global changes in future. [ABSTRACT FROM AUTHOR]

The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r2 = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r2 = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity. [ABSTRACT FROM AUTHOR]

In order to investigate the effect of pruning on the soil environment in which tea trees grow and the growth of tea trees, this study used Wuyi Meizhan (Camellia sinensis) as a research object and measured its growth indexes, soil physicochemical indexes, soil enzyme activity and microbial functional diversity to analyze the effects of pruning treatments on the growth of tea trees, soil enzyme activity and soil microbial functional diversity and the correlation between them. The results of the analysis of tea tree growth indexes showed that the hundred-bud weight, leaf area and yield in the pruning treatment were significantly higher than those in the unpruned treatment. The results of soil physicochemical index analysis showed that pH, available phosphorus, available potassium and organic matter were significantly higher in the pruning treatment than in the unpruned treatment (p < 0.05), while available nitrogen and total phosphorus were significantly lower than in unpruned treatment (p < 0.05). The results of soil enzyme activities showed that only polyphenol oxidase and catalase activities were significantly higher in the pruning than in the unpruned treatment, while urease, protease, acid phosphatase, asparaginase and glutaminase activities were significantly lower than in the unpruned treatment (p < 0.05). Biolog analysis showed that the utilization of microbial carbon sources, especially amino acid and amine, increased in the rhizosphere soil of the pruned tea tree, while there was a significant decrease (p < 0.05) in microbial diversity. It is evident that pruning promoted tea tree growth and some enzyme activity, while inhibiting the activity of enzymes associated with the nitrogen cycle, and the utilization of microbial carbon sources increased, but their diversity decreased. This study provides a theoretical basis for the daily management of tea plantation after pruning.

A phagemid-cured strain, NC7401-∆Pf, was constructed to survey the biological function of the plasmidal prophage PfNC7401 in cereulide-producing Bacillus cereus NC7401. The transcriptome analysis between the mutant and the wild strains revealed a series of differentially expressed genes mainly involved in different function classifications, including the two-component signal transduction system, bacterial structure, transporters, related antibiotic response, purine biosynthesis, non-ribosomal peptide synthetases (NRPS) and related secondary metabolites, and aromatic or other amino acid synthesis. BIOLOG and phenotypic experiment analyses confirmed that PfNC7401 may affect phage immunity and the metabolism of several amino acids, including L-Alanine, which was suggested to be related to one precursor (D-Alanine) of cereulide synthesis. However, neither the transcription levels of the cereulide production-related genes (e.g., ilvB, cesA, cesB, and cesH) nor the cereulide production nor cell cytotoxicity were affected by the presence or absence of PfNC7401, corresponding with the transcriptome data, in which only four genes unrelated to cereulide synthesis on the plasmid-carrying ces gene cluster were affected by the curing of PfNC7401. [ABSTRACT FROM AUTHOR]

In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum , Fusarium moniliforme , Fusarium proliferatum , and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent. [ABSTRACT FROM AUTHOR]

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S-1 MitoPlates™ from Biolog enable the characterization of mitochondria's function in live cells by measuring the rates of electron flow into and through the electron transport chain from different NADH or FADH 2 producing metabolic substrates. This technology uses 96-well microplates pre-coated with triplicate repeats of a set of 31 substrates. Those 31 metabolic substrates have different routes of entry into the mitochondria, use different transporters, and are also oxidated by different dehydrogenases, producing reducing equivalents in the form of NADH or FADH 2 . The electrons produced upon oxidation of NADH or FADH 2 at complex I or II, respectively, then travel to cytochrome c, where a tetrazolium redox dye (MC) can act as terminal acceptor, turning purple and absorbing at 590 nm. This mechanism allows the evaluation of cellular substrate preference by following the kinetics of MC reduction in the presence of selected substrates.In this chapter, we describe the step-by-step protocol to prepare an experiment using MitoPlate S-1 array and the OmniLog instrument to assess the metabolism of human dermal fibroblasts. We also give detailed information on how to analyze the raw data generated by the Biolog Data Analysis software to extract meaningful information and produce useful data visualizations, using reproducible methods based on a single structured dataset., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent.

Crops yield and quality are difficult to predict using soil physico-chemical parameters. Because of their key roles in nutrient cycles, we hypothesized that there is an untapped predictive potential in the soil microbial communities. To test our hypothesis, we sampled soils across 80 wheat fields of the province of Quebec at the beginning of the growing season in May–June. We used a wide array of methods to characterize the microbial communities, their functions and activities, including: (1) amplicon sequencing, (2) real-time PCR quantification and (3) community-level substrate utilization. We also measured grain yield and quality at the end of the growing season, and key soil parameters at sampling. The diversity of fungi, the abundance of nitrification genes and the use of specific organic carbon sources were often the best predictors for wheat yield and grain quality. Using 11 or less parameters, we were able to explain 64–90% of the variation in wheat yield and grain and flour quality across the province of Quebec. Microbial-based regression models outperformed basic soil-based models for predicting wheat quality indicators. Our results suggest that the measurement of microbial parameters early in the season could help predict accurately grain quality and quantity. [ABSTRACT FROM AUTHOR]

This study investigated the variances in soil microbial community (SMC) structure and metabolic potentials in subtropical mountain forest ecosystem. Soil samples (0–10, 10–30 and 30–60 cm) were collected within 27 plots (20×20 m2) that were randomly assigned. Changes in SMC structure were mainly regulated by soil physicochemical property and tree diversity in 0–10 cm depth, by total nitrogen (TN) and clay in 10–30 cm depth, and by soil organic carbon (SOC) and pH in 30–60 cm depth. Metabolic potential variance was mainly driven by soil chemical property in 0–10 cm depth, by SOC and TN in 10–30 cm depth, and by TN in 30–60 cm depth. Collectively, soil physicochemical properties were the primary factors influencing SMC structure and its metabolic potentials along the soil profile, but the expected effects of tree diversity and topography were not evident.

Agar is a polysaccharide that primarily constitutes the cell wall of red algae. It is a good source of carbon and energy for many microbes. In the present study, an agarolytic bacterium, UQAD-3, was obtained from the waters of Al-Uqair, the Arabian Gulf, Al-Ahsaa, Saudi Arabia. UQAD-3 exhibited agarolytic activity when grown on agar as the sole source of carbon and energy. The strain was identified as Pseudoalteromonas ruthenica based on comparative analysis of the 16S rRNA, with 99.6% similarity. This finding was further confirmed by phylogenetic analyses based on 16S rRNA gene sequences, which highlighted that UQAD-3 was assembled within the Pseudoalteromonas clade and constituted a monophyletic subcluster with P. ruthenica, KMM 300T. The strain was further characterised biochemically using the Biolog Gen III microtest system. UQAD-3 showed positive reactions to 16 (17%) of the 94 diverse traits assessed. Good growth was reported in 10% NaCl indicating its moderate halophilic nature. These observations indicate the agarolytic potential of the strain and opens new horizons for industrial applications in the future.

Turquoise blue dye is frequently used for industrial dyeing applications. But the release of untreated colored wastewater became an environmental and public health hazard. Microbial remediation of Azodye is environmentally safe and an alternative to a physicochemical approach. The aim of this research is to isolate and characterize turquoise blue dye degrading microbes from polluted environment. Microbial isolation and purification from soil and effluent sample was done on PDA and NA. Turquoise blue dye degrading test was investigated under optimized conditions using -the definitive screening design method. UV-Vis spectrophotometer used to measure the degradation percentage at 620 nm and 25 °C. The results revealed that 24 fungi and 6 bacterial species were identified from the contaminated site using Biolog Microstation and MALDI-TOF. Among all identified microbial species Pencilium citrinum Thom BCA & Penicillium heriquei show the highest percentage decolorization of turquoise blue dye up to 300 ppm with 90 % removal at pH4 and 87 % at pH 7 up to 400 ppm respectively. The azodye degradation ability of these fungi species used in the development of mycoremediation technologies provide an alternative option for Azodye removal after HPLC analysis, molecular characterization, and toxic analysis., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Birhanu Gizaw reports equipment, drugs, or supplies was provided by Addisababa University and Ethiopian Biodiversity Institute Microbial Biodiversity Directrate. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere. [ABSTRACT FROM AUTHOR]

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According to the European Food Safety Agency (EFSA) campylobacteriosis, salmonellosis and escherichiosis are major foodborne pathogens and, as a consequence, a serious public health problem. Due to the uncontrolled use of antibiotics as food additives, the poultry industry was one of the first faced the problem of spreading antibiotic resistance among bacterial pathogens. The emergence of multidrug-resistant infections and the ineffectiveness of antibiotics is one of the main problems of modern veterinary medicine. The gradual increase in the number of multidrug-resistant bacteria has led to an increase in research on the use of bacteriophages to combat bacterial infections. Phage therapy is a very promising alternative approach, due to the high specificity of bacteriophages, their harmlessness and the ability to reproduce directly on the pathogen. In addition, bacteriophages are the most abundant organisms and their approximate number on Earth can reach 1031, and are an almost inexhaustible source for isolating new, more effective strains. In this study, the distribution of E. coli strains on poultry farms in the Almaty region were analyzed, as well as studied the morphology of the CEC&lowbar;KAZ&lowbar;2018 bacteriophage and its lytic properties in relation to newly isolated E. coli strains. From samples of internal organs of chickens with signs of colibacillosis, 15 cultures of Escherichia coli were isolated and identified. Analysis of the phylogenetic groups of isolates showed that the majority (73.4%) belonged to phylogroup D. It was revealed that up to 50% of the isolates showed resistance to antibiotics of the third generation: ceftazidime, aztreonam, and ceftazidime / clavulanate. Findings of the current study on the spectrum of lytic activity showed that the bacteriophage CEC&lowbar; KAZ&lowbar;2018 is able to lyse 10 out of 15 isolated cultures. Thus, this bacteriophage is a very promising candidate for the creation of antibacterial agents to combat colibacillosis in chickens. [ABSTRACT FROM AUTHOR]

A phagemid-cured strain, NC7401-∆Pf, was constructed to survey the biological function of the plasmidal prophage PfNC7401 in cereulide-producing Bacillus cereus NC7401. The transcriptome analysis between the mutant and the wild strains revealed a series of differentially expressed genes mainly involved in different function classifications, including the two-component signal transduction system, bacterial structure, transporters, related antibiotic response, purine biosynthesis, non-ribosomal peptide synthetases (NRPS) and related secondary metabolites, and aromatic or other amino acid synthesis. BIOLOG and phenotypic experiment analyses confirmed that PfNC7401 may affect phage immunity and the metabolism of several amino acids, including L-Alanine, which was suggested to be related to one precursor (D-Alanine) of cereulide synthesis. However, neither the transcription levels of the cereulide production-related genes (e.g., ilvB, cesA, cesB, and cesH) nor the cereulide production nor cell cytotoxicity were affected by the presence or absence of PfNC7401, corresponding with the transcriptome data, in which only four genes unrelated to cereulide synthesis on the plasmid-carrying ces gene cluster were affected by the curing of PfNC7401.

A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

Biochar has the potential to mitigate the impacts of climate change and soil degradation by simultaneously sequestering C in soil and improving soil quality. However, the mechanism of biochar's effect on soil microbial communities remains unclear. Therefore, we conducted a global meta‐analysis, where we collected 2,110 paired observations from 107 published papers and used structural equation modeling (SEM) to analyze the effects of biochar on microbial community structure and function. Our result indicated that arbuscular mycorrhizal fungal abundance, microbial biomass C, and functional richness increased with biochar addition regardless of loads, time since application, and experiment types. Results from mixed linear model analysis suggested that soil respiration and actinomycetes (ACT) abundance decreased with biochar application. With the increase of soil pH, the effect of biochar on fungal abundance and C metabolic ability was lessened. Higher biochar pH associated with higher pyrolysis temperatures reduced the abundance of bacteria, fungi, ACT, and soil microbes feeding on miscellaneous C from Biolog Eco‐plate experiments. SEM that examined the effect of biochar properties, load, and soil properties on microbial community indicated that fungal abundance was the dominant factor affecting the response of the bacterial abundance to biochar. The response of bacterial abundance to biochar addition was soil dependent, whereas fungi abundance was mostly related to biochar load and pyrolysis temperature. Based on soil conditions, controlling biochar load and production conditions would be a direct way to regulate the effect of biochar application on soil microbial function and increase the capacity to sequester C. [ABSTRACT FROM AUTHOR]

Microbes that can be cultured and degrade petroleum are of particular interest for biotechnology such as bioremediation. This study aims to isolate and identify culturable petroleum-degrading bacteria and fungi from Brunei Darussalam, which has not previously been explored. A total of eight bacterial and nine fungal isolates that could degrade petroleum were obtained from petroleum-contaminated water or soil samples. DNA barcoding using 16S rRNA gene sequence identified five different bacterial genera which were Bacillus, Enterobacter, Micrococcus, Pseudoaltermonas and Pseudomonas. DNA barcoding using rRNA-ITS gene sequence identified nine different fungal taxa which were Aspergillus, Cladosporium, Exophiala, Flavodon, Hypocreales, Nectriaceae, Penicillium, Peniophora and Trichoderma. Biolog provided additional support to the identification of some isolates. This study is the first to report these unique microbes from Brunei Darussalam, which are of ecological and biotechnological value. [ABSTRACT FROM AUTHOR]

This study investigated the variances in soil microbial community (SMC) structure and metabolic potentials in subtropical mountain forest ecosystem. Soil samples (0–10, 10–30 and 30–60 cm) were collected within 27 plots (20×20 m2) that were randomly assigned. Changes in SMC structure were mainly regulated by soil physicochemical property and tree diversity in 0–10 cm depth, by total nitrogen (TN) and clay in 10–30 cm depth, and by soil organic carbon (SOC) and pH in 30–60 cm depth. Metabolic potential variance was mainly driven by soil chemical property in 0–10 cm depth, by SOC and TN in 10–30 cm depth, and by TN in 30–60 cm depth. Collectively, soil physicochemical properties were the primary factors influencing SMC structure and its metabolic potentials along the soil profile, but the expected effects of tree diversity and topography were not evident. [ABSTRACT FROM AUTHOR]

Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean.

Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep’s milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep’s milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.

Abstract Background Coagulase-negative staphylococci (CoNS) are among the leading bacterial causes of bovine mastitis in many dairy-producing countries. Among the challenges associated with the specific diagnosis of CoNS infections is the biochemical heterogeneity of the species in the genus and the unavailability of accurate, cost-effective and up-to-date diagnostic tests. A previous study investigating the diversity of CoNS associated with cases of bovine mastitis in South Africa, resulted in six CoNS isolates which could not be identified despite the use of a combination of different molecular assays. The identification and characterisation of the isolates was pursued further in this study. Results The six CoNS isolates in question were identified by sequencing multiple housekeeping genes (dnaJ, hsp60, rpoB, 16S rRNA) and characterized through the use of matrix-assisted laser/desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and the Biolog GEN III Microplate™ bacterial identification system. Sequencing of housekeeping genes identified the isolates as S. devriesei. This Staphylococcus species was only described in 2010 and this is the first report documenting the isolation of S. devriesei from cases of bovine IMIs in South Africa. Analysis of mass spectra generated by the six isolates showed intra-species variation which was also observed when evaluating the metabolic profiles of the isolates using the Biolog GEN III system. Neither the MALDI-TOF MS nor the Biolog database are currently populated with data relating to S. devriesei, resulting in the isolates not being identified, in the case of MALDI-TOF MS analysis, or mis-identified as was observed with the Biolog GEN III system. Conclusions The phenotyping data collected during this investigation provides useful information concerning Staphylococcus devriesei which could be used to populate user system databases thereby ensuring the accurate identification of isolates in future. The availability of improved diagnostics will in turn facilitate studies to elucidate the epidemiology, pathogenicity and true prevalence of this species in dairy herds.

Abstract Background Salmonella enterica is a recognised cause of diarrhoea in dogs and humans, yet the potential for transfer of salmonellosis between dogs and their owners is unclear, with reported evidence both for and against Salmonella as a zoonotic pathogen. A collection of 174 S. enterica isolates from clinical infections in humans and dogs were analysed for serotype distribution, carbon source utilisation, chemical and antimicrobial sensitivity profiles. The aim of the study was to understand the degree of conservation in phenotypic characteristics of isolates across host species. Results Serovar distribution across human and canine isolates demonstrated nine serovars common to both host species, 24 serovars present in only the canine collection and 39 solely represented within the human collection. Significant differences in carbon source utilisation profiles and ampicillin, amoxicillin and chloramphenicol sensitivity profiles were detected in isolates of human and canine origin. Differences between the human and canine Salmonella collections were suggestive of evolutionary separation, with canine isolates better able to utilise several simple sugars than their human counterparts. Generally higher minimum inhibitory concentrations of three broad-spectrum antimicrobials, commonly used in veterinary medicine, were also observed in canine S. enterica isolates. Conclusions Differential carbon source utilisation and antimicrobial sensitivity profiles in pathogenic Salmonella isolated from humans and dogs are suggestive of distinct reservoirs of infection for these hosts. Although these findings do not preclude zoonotic or anthroponotic potential in salmonellae, the separation of carbon utilisation and antibiotic profiles with isolate source is indicative that infectious isolates are not part of a common reservoir shared frequently between these host species.

Pollution due to heavy metals is a serious global environmental problem, particularly in China. It is thus important to study the effects of heavy metal pollution, especially in mining areas. Cadmium(Cd) and lead(Pb) severely damage the microbial life in soil. The concentration of heavy metals and their toxic effects on microbes and enzymes in soil were examined in this study using contaminated soil samples. The Biolog method was used to analyze the characteristics of the microbial community. The results showed that the addition of Cd2+ and Pb2+ in different concentrations has a significant impact on microbial and enzyme activity in soil. With an increase in their concentrations, activities of the microbial community and enzymes decreased gradually. Each index related to the structure of the microbial community in soil decreased, indicating that pollution due to Cd and Pb reduced its size and functional activity. This study provides a reference for future research on the functional diversity of the microbial community in soil and plays its role in their environmental management. [ABSTRACT FROM AUTHOR]

Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean. [ABSTRACT FROM AUTHOR]

Di-(2-ethylhcxyl) phthalate (DEHP) is applied as plasticizer, which results in the pollution of environment. In this study, the effects of DEHP on soil microbial functions, structure and genetic diversity were investigated. The concentration of DEHP in the soil were 0, 0.1, 1, 10 and 50 mg/kg, and the experimental period were 28 days. DEHP reduced the quantity, abundance, species dominance and homogeneity of soil microbes during the first 14 days. In addition, microbial utilization efficiency of carbon (carbohydrates, aliphatics, amino acids, metabolites) was impacted after 28 days, though the effects gradually weakened. Based on denaturing gradient gel electrophoresis and clone library analysis, in the presence of DEHP, the dominant microbes in the DEHP-contaminated soil were Sphingomonas and Bacillus, which belonged to the Acidobacteria and Proteobacteriav, respectively. With 0.1 or 1 mg/kg of DEHP, the relative abundances of Acidobacteria were higher, and with 10 or 50 mg/kg of DEHP, the relative abundances of Proteobacteria were higher. [ABSTRACT FROM AUTHOR]

Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species. [ABSTRACT FROM AUTHOR]

Microbial metabolism and growth in the intestinal tract depend on the composition of substrates present in the digesta and their ability to be metabolised by the microorganisms. The aim of this pilot study was to characterise potential hindgut microbial activity during perinatal period in sows and their offspring. Rectal samples from three sows (1–3 weeks before and after birth) and three of their piglets (1–5 weeks after birth), were subjected to assays using BIOLOG GEN III microplates to produce metabolic fingerprints for each animal. The number of metabolised substrates of the sow hindgut microbiota was stable during the pregnancy and lactation periods, as assessed by the richness index. In piglets, the richness was stable during the suckling period and at beginning of weaning, however, it decreased when the piglets were 5 weeks old (P ≤ 0.05). Analysis of associations between the sows and the piglets and the microbial metabolic potential showed that microbial metabolism was strongly associated with the catabolism of carbohydrates especially in sows. Only 5-week-old weaned piglets clustered together with the sows regarding the microbial catabolism of substrates, but not suckling piglets. The association analyses clustered all the piglets in two groups distinctive for litter. The analysis of metabolic fingerprints via microbial growth with different substrates can be useful to positively influence microbial community function such as selectively enhancing desirable active microbial populations to benefit health of the gut and the animal. [ABSTRACT FROM AUTHOR]