Culturable Microbial Community Research Articles

Deep Impact: Shifts of Native Cultivable Microbial Communities on Fresh Lettuce after Treatment with Plasma-Treated Water.

Foods consumed raw, such as lettuce, can host food-borne human-pathogenic bacteria. In the worst-case, these diseases cause to death. To limit illness and industrial losses, one innovative sanitation method is non-thermal plasma, which offers an extremely efficient reduction of living microbial biomass. Unfortunately, the total viable count (TVC), one of the most common methods for quantifying antimicrobial effects, provides no detailed insights into the composition of the surviving microbial community after treatment. To address this information gap, different special agars were used to investigate the reduction efficiency of plasma-treated water (PTW) on different native cultivable microorganisms. All tested cultivable microbial groups were reduced using PTW. Gram-negative bacteria showed a reduction of 3.81 log10, and Gram-positive bacteria showed a reduction of 3.49 log10. Fungi were reduced by 3.89 log10. These results were further validated using a live/dead assay. MALDI-ToF (matrix-assisted laser-desorption-ionization time-of-flight)-based determination was used for a diversified overview. The results demonstrated that Gram-negative bacteria were strongly reduced. Interestingly, Gram-positive bacteria and fungi were reduced by nearly equal amounts, but could still recover from PTW treatment. MALDI-ToF mainly identified Pseudomonas spp. and groups of Bacillus on the tested lettuce. These results indicate that the PTW treatment could efficiently achieve a ubiquitous, spectrum-wide reduction of microbial life.

Response of Microbial Recovery Rate to Straw Return after Calcium Cyanamide Soil Disinfection

At present, returning vegetable straw in situ is an effective measure to solve environmental pollution and improve soil properties. However, the direct return of straw to the field can reduce the release rate of soil organic matter and cause serious soilborne diseases. The combined application of calcium cyanamide (CaCN2) and straw can solve this problem. The objective of this study was to determine the effect of CaCN2 combined with pepper straw return on cucumber yield, soil physicochemical properties, and soil microbial communities during 2020 to 2021 in Shandong Province, China. The treatments were designed as follows: (1) calcium cyanamide soil disinfection, CC; (2) fresh pepper straw return, LJ; (3) fresh pepper straw return combined with calcium cyanamide disinfection, LJ+CC; and (4) natural soil without straw return treatment, CK. Compared with CK, the LJ+CC treatment significantly improved cucumber production by 20%. The cultivable microbial community in the soil was temporarily inhibited during soil fumigation treatment, and the cultivable bacterial and actinomycete communities in the soil return to their initial levels after the film was removed (harvest period). The numbers of culturable bacteria and actinomycetes in the soil in the LJ+CC treatment were 4.68 × 107 CFU/g and 5.17 × 107 CFU/g, respectively, higher than those in the soil in the CC treatment. The contents of TN and OM in the LJ+CC treatment increased by 13.1% and 13.5%, respectively, compared with that in LJ. Therefore, the LJ+CC treatment enhanced soil fertility and cucumber yields. CaCN2 can promote straw decomposition and straw can promote soil microbial recovery, and their combined application is considered a feasible and sustainable technique for utilizing vegetable residues in the greenhouse. The combination of returning pepper straw to the field and calcium cyanamide technology achieves a win-win situation of resource circulation and economic circulation by converting agricultural waste into fertilizer before being put into production. Based on this, it is recommended that the straw returning technology receives strong policy support, stimulates researchers to explore the feasibility of different vegetable straw returning to the field, promotes the implementation of this technology achievement, and leverages the environmental benefits of the application of straw returning technology.

Rhizosphere microbial ecological characteristics of strawberry root rot.

Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure. In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure. According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants. In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.

The Roman Houses of the Caelian Hill (Rome, Italy): Multitemporal Evaluation of Biodeterioration Patterns.

Like other hypogeal environments, the Roman Houses of the Caelian Hill are prone to unwanted biological growth. Wide conservative interventions have been carried out at the beginning of this millenium to reduce biodeterioration and physical-chemical damages. Retracing the last monitoring work, we assessed the site's current state of conservation and biodeterioration intending to check the previous treatments' effectiveness and deepen the common knowledge of the subterranean biota and their possible biodeteriogenic effects. Starting from the past test areas and the previous identifications of the occurring biodeteriogens, we further isolated and identified the main eubacterial, fungal, and phototrophic settlers, focusing on some detrimental traits for wall paintings (i.e., acid production and carbonate precipitation). The achieved results proved the success of the performed interventions in reducing the wall's water content. Otherwise, the new conditions raise, in the long term, new concerns about lampenflora, carbonate precipitations, and salt efflorescence. Here, the Caelian Houses' new status is documented. The possible favouring conditions for the different groups of biodeteriogens, along with the taxonomical novelties, additional risks tied to the anthropization of the resident culturable microbial community, and the possible relation between the black fungus Cyphellophora olivacea and roots, are reported and discussed.

Nitrite-Oxidizing Bacterial Strains Isolated from Soils of Andean Ecosystems and Their Potential Use in Nitrogen Reduction

Nitrification is part of the nitrogen cycle that occurs naturally in ecosystems. It is related to the presence of microorganisms and their metabolism, especially bacteria, which are involved in oxidizing compounds such as NH4+ and NO2− to NO3−. In this study, we evaluated the nitrification potential in 12 bacteria strains that belong to the genera Aeromonas, Bacillus, Buttiauxella, Mycobacterium, Paenibacillus, Serratia, and Yersenia, which are part of the cultivable microbial community from soil in a native forest and pine forest in The Labrado area within the Machangara micro-watershed in the Andes located in the south of Ecuador. This investigation aims to identify heterotrophic and lithoautotrophic strains using specific culture media for ammonium oxidative (AOL-AOH) and nitrate oxidation bacteria (ONL-ONH). The formation of nitrifying halos in the culture media allowed the identification of 10 strains with nitrifying potential. Five strains were from the pine forest, four were isolated from the native forest, and one strain was shared between both forests. The Serratia and Yersinia genera have a high NO2− oxidation capacity. Their inoculation in synthetic water rich in nitrogenous products allowed us to determine 40% and 94% nitrite reduction percentages and cell retention times of 20 to 40 days. Our results are promising for their possible potential use in environmental bioremediation processes through inoculation in wastewater for the biological removal of nitrogenous compounds.

Diversity and Composition of Culturable Microorganisms and Their Biodeterioration Potentials in the Sandstone of Beishiku Temple, China.

Microbial colonization on stone monuments leads to subsequent biodeterioration; determining the microbe diversity, compositions, and metabolic capacities is essential for understanding biodeterioration mechanisms and undertaking heritage management. Here, samples of epilithic biofilm and naturally weathered and exfoliated sandstone particles from different locations at the Beishiku Temple were collected to investigate bacterial and fungal community diversity and structure using a culture-based method. The biodeterioration potential of isolated fungal strains was analyzed in terms of pigmentation, calcite dissolution, organic acids, biomineralization ability, and biocide susceptibility. The results showed that the diversities and communities of bacteria and fungi differed for the different sample types from different locations. The population of culturable microorganisms in biofilm samples was more abundant than that present in the samples exposed to natural weathering. The environmental temperature, relative humidity, and pH were closely related to the variation in and distribution of microbial communities. Fungal biodeterioration tests showed that isolated strains four and five were pigment producers and capable of dissolving carbonates, respectively. Their biomineralization through the precipitation of calcium oxalate and calcite carbonate could be potentially applied as a biotechnology for stone heritage consolidation and the mitigation of weathering for monuments. This study adds to our understanding of culturable microbial communities and the bioprotection potential of fungal biomineralization.

Characterizing Effects of Microbial Biostimulants and Whole-Soil Inoculums for Native Plant Revegetation

Soil microbes play important roles in plant health and ecosystem functioning, however, they can often be disturbed or depleted in degraded lands. During seed-based revegetation of such sites there is often very low germination and seedling establishment success, with recruitment of beneficial microbes to the rhizosphere one potential contributor to this problem. Here we investigated whether Australian native plant species may benefit from planting seed encapsulated within extruded seed pellets amended with one of two microbe-rich products: a commercial vermicast extract biostimulant or a whole-soil inoculum from a healthy reference site of native vegetation. Two manipulative glasshouse trials assessing the performance of two Australian native plant species (Acacia parramattensis and Indigofera australis) were carried out in both unmodified field-collected soil (trial 1) and in the same soil reduced in nutrients and microbes (trial 2). Seedling emergence and growth were compared between pelleted and bare-seeded controls and analyzed alongside soil nutrient concentrations and culturable microbial community assessments. The addition of microbial amendments maintained, but did not improve upon, high levels of emergence in both plant species relative to unamended pellets. In trial 1, mean time to emergence of Acacia parramattensis seedlings was slightly shorter in both amended pellet types relative to the standard pellets, and in trial 2, whole-soil inoculum pellets showed significantly improved growth metrics. This work shows that there is potential for microbial amendments to positively affect native plant emergence and growth, however exact effects are dependent on the type of amendment, the plant species, and the characteristics of the planting site soil.

Distinct Changes in Abundance of Culturable Microbial Community and Respiration Activities in Response to Mineral–Organic Mixture Application in Contaminated Soil

The availability and affordability of fertilizers are the main risks currently faced by the fertilizer market. Therefore, there is a need to look for other sources of nutrient supply for plants, while taking care of soil properties. The application of fertilizers with the addition of functionalized materials could help in the efficient use of nutrients. The aim of the study was to assess the impact of the application of mixtures with the addition of zeolite–vermiculite composites (NaX–Ver) on the culturable microorganisms and selected soil properties. A two-year pot experiment was conducted on soil with elevated contents of cadmium, zinc, and lead. The test treatments included soil mixed with NPK and additives in two doses of NaX–Ver combined with leonardite (Leo) or lignite (L). The test plant used in the experiment was maize. The soil material was analyzed for the number of bacteria, mold fungi, actinomycetes, and ammonifiers. Furthermore, soil pH, EC, N total, and SOC contents, as well as soil respiration activity, were tested. The applied fertilizer mixtures had a great effect on changes in the N total and SOC contents. The N total increase was 45.5% in NaX–Ver3%L3% and 51% in NaX–Ver9%Leo6%, and the largest SOC increase (24.3%) was recorded in the NaX–Ver3%Leo3% treatment. The highest respiration activity was determined in NaX–Ver3%Leo3% and NaX–Ver9%Leo6%: 2.12 µg C-CO2 g−1 DM h−1 and 2.14 µg C-CO2 g−1 DM h−1, respectively. A significant correlation between pH values and the number of culturable microorganisms was found. The number of soil microorganisms depended on the type of fertilization used. The best stimulation of the number of culturable soil microorganisms was found in treatments with the addition of 3% of L or Leo in combination with NaX–Ver. The percentage increases in the number of the analyzed culturable microorganisms after the application of leonardite-based fertilization in combination with the zeolite–vermiculite composite were, on average: bacteria, 1096%; mold fungi, 1529%; actinomycetes, 1477%; ammonifiers, 910%.

Compositional, genetic and functional characterization of soil culturable microbial communities in polychlorinated dibenzo-p-dioxins/furans contaminated soil

Dioxins (PCDD/Fs) are one of the most toxic environmental pollutants known to date. Due to their structural stability and extreme hydrophobicity dioxins persist in the ecosystems and can be bioaccumulated to critical levels in both human and animal food chains. Soils are the most important reservoirs of dioxins, thus soil microbes are highly exposed to dioxins, impacting their diversity, genetics and functional characteristics. To experimentally evaluate these effects, the diversity and functionality of soil microbes were assessed in seven local sites potentially exposed to PCDD/Fs.Concentration of dioxins in soils samples was firstly determined and the soils cultivable microbes were identified and molecularly characterized as a function of their in vitro ability to degrade the TCDD. Our results revealed that the diversity of microbial communities largely varied among the sites and was likely inversely proportional to their level of contamination with PCDD/Fs. Furthermore, the genetics profiling of dioxin-degrading bacteria revealed that the Cytochrome P450 CYPBM3-positive species largely belong to the genus Bacillus and were randomly distributed among the soils samples, while the angular dioxygenase (AD)-positive species were mainly found in highly polluted soils with a major presence of the genus Pseudomonas. Finally, the functionality of dioxin-biodegrading genes (AD or CYPBM3), was confirmed by the ability of bacteria to consume 2,3,7,8-TCDD, and this was synchronized with an induced level of both pathways. Our results suggest that different dioxin-metabolizing pathways exist under the same environmental conditions and work differentially for an effective removal of PCDD/Fs.

Insights into the effects of drying treatments on cultivable microbial diversity of marine sediments

Microbes are widespread in the sea that covers more than two-thirds of the earth’s surface and most microorganisms living in the marine environment have yet to be cultured. Previous studies showed that drying treatment, a strategy of sample pre-treatment widely applied in microbial isolation and incubation, may alter the cultivable microbial diversity, such as Actinomycetota, essential for exploring novel secondary metabolites from the marine environment, isolated from drying-treated samples. However, whether drying treatments actually can change microbial community diversity and how the drying treatments of samples influence the cultivable microbial diversity of marine samples have not yet adequately been evaluated. Here, three marine sediment samples were dried and incubated at 28 ºC, 37 ºC, and 45 ºC, and the microbial diversity was assessed with high-throughput sequencing. Our results suggested that drying treatments had different effects on different genera and some potential novel species could be cultured only from drying-treated samples, including the novel members from the families Paenibacillaceae and Thermoactinomycetaceae. Non-metric multidimensional scaling analysis showed that the treated samples were clustered according to the cultivation temperatures rather than the drying conditions at high cultivation temperatures. However, at the cultivation temperatures of 28 ºC, drying treatments were the larger separation between cultivable microbial communities in the process of microbial isolation. These results showed that the drying treatments influenced the cultivated microbes in a taxon-specific pattern and extended potential novel taxa. Combining high-throughput sequencing to various drying conditions and incubation temperatures, this study provides new insight into the effects of drying treatment on the cultivable microbial diversity of marine sediments.

Effects of Three Feed Additives on the Culturable Microbiota Composition and Histology of the Anterior and Posterior Intestines of Zebrafish (Danio rerio).

Simple SummaryThis work is dedicated to the study of the effects of three feed additives that are promising for use in aquaculture on the culturable microbial community and the tissue structure (histology) of the intestines of laboratory zebrafish. The feed additives used in this research have different functional properties: (i) micronutrient chelated compounds, which eliminate mineral nutrition deficiencies; (ii) butyric acid, a postbiotic drug aimed at stimulating intestinal bacteria growth and improving immunity; and (iii) lycopene, a carotenoid and wide-spectrum antioxidant. All of the tested supplements resulted in changes in the intestinal microbial community in both the anterior and posterior intestines. The change in gut microbiota correlated with histological changes in the intestines. The results of the study showed that in most concentrations, the feed additives had a positive effect on certain groups of microorganisms. The method of microbiota research based on microorganism cultivation used in this work makes it possible to evaluate the effect of feed additives on the relative abundance of key representatives of the microbial community.In this study, the effect of three promising feed additives (chelated compounds of trace elements, butyric acid, lycopene) on changes in the culturable microbiota and histological parameters of two sections of the intestines of Danio rerio (zebrafish) was studied. The use of these feed additives can help to eliminate the deficiency of trace elements, modulate the composition of the microbiota due to the postbiotic properties of butyric acid, and reduce oxidative stress when using lycopene. Incorporation of the investigated supplements in the feed resulted in a significant change in the relative abundance of certain groups of microorganisms. The taxonomic diversity of cultured microorganisms did not differ in the anterior and posterior intestines, while there were differences in the relative abundance of these microorganisms. The most sensitive groups of microorganisms were the genera Bacillus and Serratia. A significant effect on the composition of the cultured microbiota was caused by lycopene (in all studied concentrations), leading to a significant increase in the relative abundance of Firmicutes in the anterior gut. Studies of the histological structure of the anterior and posterior guts have shown the relationship between the barrier and secretory functions of the gut and the composition of the microbiota while using butyric acid (1 and 2 g kg−1) and trace element chelated compounds (2 mg kg−1). This culture-dependent method of studying the microbiome makes it possible to assess changes in some representatives of the main groups of microorganisms (Firmicutes and Proteobacteria). Despite the incompleteness of the data obtained by the culture-dependent method, its application makes it possible to assess the bioactive properties of feed and feed additives and their impact on the microbiota involved in digestive processes.

Effect of Feedstock Type on Biostimulation Efficiency and Microbial Community Structure during Biochar-Facilitated Remediation of Petroleum Contaminated Soil

This study investigated the effect of plant feedstock– and animal feedstock–derived biochar at 10%w/w and 15%w/w amendment levels on the biostimulation efficiency and the cultivable microbial community in the soil during biochar-facilitated remediation of petroleum contaminated soil using standard techniques. Biostimulation was most effective with the animal-based biochar (ABB) treatment while total petroleum hydrocarbon (TPH) removal was greatest in the plant-based biochar (PBB) amended soil. Observed mean TPH levels on Day 60 ranged from about 7000 mg/kg – 7800 mg/kg for the PBB and 11000 mg/kg – 14000 mg/kg for ABB representing removal levels of roughly 51.0%, 57.7%, 72.4% and 73.7% in 10% ABB, 15% ABB, 10% PBB and 15% PBB amended contaminated soils respectively. The cultivable bacterial diversity for both feedstock types shifted from the combination of Firmicutes, Actinobacteria and Proteobacteria phyla at the onset of the study to predominantly Proteobacteria by the end of the study with a distinct reduction in diversity observed with increasing contact time. The dominant cultivable heterotrophic bacterial isolates were Bacillus spp., Pseudomonas spp. and Staphylococcus aureus for ABB and Pseudomonas spp., Klebsiella pneumoniae and Bacillus spp. for PBB. Amongst the cultivable hydrocarbon utilising bacteria obtained, Klebsiella pneumoniae, Pseudomonas spp. and Enterobacter spp. dominated. There were significant differences in TCHB and CHUB abundance and TPH removal efficiency between PBB and ABB amendments at 95% confidence interval. The study established that application of biochar effectively manages petroleum pollutants in soil by stimulating the proliferation and activities of relevant degradative species.

Cultivable microbial diversity in speleothems using MALDI-TOF spectrometry and DNA sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

The microbial diversity in the Indian caves is inadequately characterized. This study reports on the culturable microbial communities in caves from the Indian sub-continent. This study aims to expand the current understanding of bacterial diversity in the speleothems and wall deposits from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. A culture-dependent approach was employed for elucidating the community structure in the caves using MALDI-TOF spectrometry and 16S rRNA gene sequencing. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. A total 91% of the bacterial diversity was dominated by Proteobacteria (61%) and Actinobacteria (30%). In addition, bacterial phyla include Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%) were found in the samples. At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

Functional characterization of culturable fungi from microbiomes of the "conical cobs" Mexican maize (Zea mays L.) landrace.

Mexican maize landraces, produced for local consumption, are adapted to different environmental conditions, and their yield is affected by abiotic and biotic factors, including the use of agrochemicals. The search for sustainable alternatives to agrochemicals includes the study of the culturable microbial communities. In this study, the fungal communities associated with 2 Mexican maize landraces reddish and bluish "conical cobs" were found to be comprised of Ascomycota fungi, represented by 89 strains within 6 orders (Pleosporales, Hypocreales, Onygenales, Capnodiales, Helotiales, and Eurotiales) and 16 genera. Cellulases and metallophores production were the primary enzymatic products and plant growth-promoting activities were detectedamong the isolates. Penicillium, Didymella, and Fusarium strains had the most active enzymatic and plant growth promoting activities, however, Aspergillus sp. HES2-2.2, Talaromyces sp. RS1-7, and Penicillium sp. HFS3-3 showed antagonistic activity against the four phytopathogenic Fusarium strains Fusarium oxysporum, Fusarium sambucinum, Fusarium fujikuroi and Fusarium incarnatum-equiseti and also a high and diverse production of enzymatic and plant growth promoting activities; here we identified fungal strains as candidates to promote maize growth.

Characteristics of Culturable Microbial Community in Rhizosphere/Non-rhizosphere Soil of Potentilla Fruticosa Population in Alpine Meadow Elevation Gradient

Potentilla fruticosa is a typical shrub of alpine meadows with canopy effects that can greatly influence soil fertility and microbiological parameters. Changes in rhizosphere microorganisms can reflect the response of these plants to environmental changes. This study aimed to examine the rhizosphere and non-rhizosphere of P. fruticosa on the amount of selected microorganisms and main environmental factors at different elevation gradients (3,000, 3,250, 3,500, 3,750, and 4,000 m). The results suggested that bacteria were predominant of the microbial soil community in the rhizosphere and non-rhizosphere, while fungi and actinomycetes represented the minority. With the increase of altitude, the total amount of microbial, bacteria, and actinomycetes in the rhizosphere and non-rhizosphere of P. fruticosa showed a downward trend, and microbial functional groups showed that the “hump shape” changed, but the fungi showed the opposite. Variance inflation factor (VIF) screening environmental factors and path analysis were obtained. In the rhizosphere soil, bacteria were affected by Soil organic carbon (SOC), and soil bulk density (SBD) became the main environmental limiting factor with the increase of altitude. The main environmental limiting factor of actinomycetes changed from SBD to Soil total (ST). In the non-rhizosphere soil, the bacteria and actinomycetes changed from ST to SOC and SBD, respectively. The main environmental limiting factor of the fungi was SOC in the rhizosphere and non-rhizosphere. Soil water content (SWC) was the main environmental determinant factor for all microbial groups, microbial functional groups were related to Soil total nitrogen (STN). Our results help to understand the relationship between nutrient cycling and the ecosystem function of alpine meadow plant soil microorganisms and provide theoretical support for alpine meadow ecosystem restoration, biodiversity protection, and the use of microbial resources.

Influence of the biocontrol agents Trichoderma spp. on the structure and functionality of the edaphic microbial community in common bean cultivars (Phaseolus vulgaris L.) inoculated with Sclerotinia sclerotiorum (Lib.) de Bary

Control of agricultural pathogens can be achieved by biological control agents, but information about their impacts on the native microbiota is scarce. In this work, the commercial biocontrol agent Trichoderma harzianum ESALQ-1306 and the experimental strain Trichoderma asperellum BRM-29104 were selected to determine the effects of their application on the edaphic microbial community and on their functional traits in common bean cultivation (Phaseolus vulgaris L.) infected with Sclerotinia sclerotiorum (Lib.) de Bary in the Brazilian savannah. Soil samples were collected before planting and after 90 days of cultivation. The bean yield and disease severity were estimated. Spores of arbuscular mycorrhizal fungi (AMF) were quantified and identified, and the rate of root colonisation was measured. The total colony-forming units (CFU), species richness and alpha diversity, production of hydrolytic enzymes, microbial carbon biomass, microbial soil respiration, metabolic diversity and glomalin mass were quantified. After 90 days of cultivation, the microbial richness, diversity and abundance increased significantly, stimulated by bean plant development. The biocontrol strains did not significantly change the abundance of CFU with enzymatic activity, as well as microbial soil respiration, the microbial carbon biomass, metabolic diversity, the glomalin mass and the root colonisation rates; however, they changed the composition of cultivable microbial communities. S. sclerotiorum was controlled, and bean productivity was maintained. Therefore, the cultivation time is the variable with the major influence over the structure and functionality of cultivable microbial communities and AMF. We identified microbial species not previously reported in this biome and determined that T. asperellum BRM-29104 has the potential to be used as a new eco-friendly commercial product against white mold.

Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS.

Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.

Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India.

Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.

Physico-Chemical Characteristics and Culturable Microbial Communities of Grape Berries Change Strongly during Noble Rot Development.

Botrytis cinerea is a well-known pathogen of grapevine. However, under certain microclimatic conditions, Botrytis infection results in noble rot, an essential process in the production of the world-known Tokaji aszú wines in Hungary. We investigated the physico-chemical characteristics and culturable microorganisms associated with grape berries through several noble rot phases in the two main cultivars grown in Tokaj: Vitis vinifera cv. “Furmint” and “Hárslevelű”. We measured physical and analytical parameters routinely tested in viticulture and analyzed the ITS rDNA sequence data of fungi isolated from the sampled berries. We observed significant differences in the physico-chemical parameters among the noble rot phases as well as sampling dates. The greatest variation in berry texture and microbial structure was observed in the initial phases, with variables converging as the noble rot progressed. By finding a bijection between the examined chemical properties and the factorial parameters (e.g., noble rot phase, collection time, cultivar), an appropriate sweet winemaking material can be designed. Fungal community differed significantly among cultivars, with higher number of species observed in Hárslevelű. Our results reveal that there is more to noble rot than only Botrytis cinerea and other microorganisms may play important roles in the aszú process.

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome.

Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose’ gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics.