BackgroundNumerous chemical pesticides have been used in agricultural production to combat crop diseases and pests. Despite ensuring certain economic advantages, they have also resulted in issues like environmental contamination, declining soil quality, and pesticide residues. Because biological control is environmentally friendly and difficult to acquire resistance to, it has been used in practice recently.MethodsIn this study, we isolated the endophytic fungus Purpureocillium lilacinum from Portulaca oleracea L., which was previously found to have inhibitory effects on soil pathogens in tobacco fields. To find out how the biocontrol agent P. lilacinum affects soil microorganisms and plant metabolism in tobacco cultivation, we used amplicon sequencing technology and gas chromatography-mass spectrometry to look at the structure of soil microbial communities and the networks of interactions between microorganisms and metabolites in the inter-rhizosphere soil of tobacco fields treated with different amounts of P. lilacinum.ResultsThe findings showed that there was a trend toward less microbial diversity among inter-root microorganisms as solid-state fermentation (SSF) products of P. lilacinum increased; however, submerged fermentation (SmF) had no discernible impact on microbial diversity when compared to the direct use of SSF. Additionally, the relationship between inter-root fungi and volatile compounds in tobacco leaves was dominated by a negative correlation.ConclusionsThe result demonstrated that P. lilacinum’s antagonistic interaction in the inter-rhizosphere microbial community was dominant and valuable for biopesticide application. P. lilacinum can work more effectively on tobacco roots by using SSF products. P. lilacinum’s opposition to fungal colonies may enhance the volatile chemicals in tobacco leaves. These provide some implications for the biocontrol application of P. lilacinum.

PurposeCoral degradation is a worldwide ecological problem. Bacterial diseases are a great danger to coral health. The pathogenic bacterium Vibrio alginolyticus XSBZ14 isolated from diseased coral had been identified as the pathogenic bacterium of Porites andrewsi White syndrome (PAWS) in Xisha Archipelago on transmission experiment. To date, the molecular mechanism by which this pathogen causes disease is unknown, and molecular diagnostics for diseases caused by this bacterium have not been developed. In an effort to restore damaged coral ecosystems in the South China Sea, efforts are underway to transplant flat-branch shore corals. There is therefore an urgent need to further develop specific and rapid detection methods for V. alginolyticus XSBZ14 in order to prevent this epidemic and ensure the successful implementation of compilation transplants.MethodsAt first, a low sequence identity single-copy sequence S2 was selected from the genome by in-house Perl script. Using the designed specific primers, four different types of standard curves were subsequently plotted for the accurate quantification of the strain XSBZ14 in four different samples (DNA, bacterial suspension, coral tissue, seawater). Then, use the strain to infect the Galaxea fascicularis and test the strain in the coral culture water during the week.ResultsThe rapid detection method of pathogenic bacteria by RT-PCR was established. The limit of detection (LOD) of the RT-PCR was 0.88 pg/reaction (0.44 pg/μL) in DNA, 2 CFU/reaction (1000 CFU/mL) in bacterial suspension, 2 CFU/reaction in coral tissue, and 20 CFU/reaction in seawater for the strain XSBZ14, respectively. In addition, according to the detection results of the RT-PCR, the strain XSBZ14 could survive in Galaxea fascicularis for a week, and the strain could also be detected from its reared seawater.ConclusionThese results indicated that the RT-PCR detection method of a coral pathogenic strain XSBZ14 was established. The method is a robust tool for the rapid detection and quantification of the coral pathogen, XSBZ14, and is very useful for PAWS epidemiological survey and specific pathogen-free coral transplantation in the South China Sea. And other coral species and their habitats might act as an important reservoir for the strain XSBZ14 and mediated its horizontal transmission in coral reefs.

PurposeThe biodegradation of skatole was used as a starting point in this study, and existing strains of degrading NH3 and H2S in the laboratory were combined to create a composite deodorant. The deodorization effect of the composite deodorant on human feces was investigated in order to provide a foundation for fecal odor gas treatment.MethodsSkatole-degrading bacteria were identified, degradation conditions were optimized, and skatole metabolites were identified using liquid chromatography-mass spectrometry (LC-MS). The skatole-degrading bacteria were combined with the existing strains of degrading NH3 and H2S in the laboratory to make a compound deodorizer, and the deodorizing effect of the compound deodorizer on fresh human feces and old human feces was compared. Liquid chromatography, specific sensors, and gas chromatography were used to determine the contents of skatole, NH3, H2S, and volatile organic compounds, and the microbial diversity was examined.ResultsMicrobial agents H and Y capable of utilizing skatole were screened out under aerobic and facultative anaerobic conditions, respectively. Within 48 h, the degradation rate of skatole by microbial agent Y was 88.52%. Following condition optimization, the optimum temperature for skatole degradation by microbial agent Y was 33 °C, and the optimum pH was 7. The main functional bacteria were Acinetobacter xiamenensis. The metabolites of skatole were determined by liquid chromatography-mass spectrometry (LC–MS), and six possible metabolites were found, including 3-aldehyde indole, 3-carboxyl indole, 1H-indole-2,3-dione, and 3-methyl indole pyruvate. The skatole-degrading bacteria Lactobacillus rhamnosus and Saccharomyces cerevisiae were then combined in proportion to form a composite deodorant. The 5-day degradation rate of skatole in the old manure group was 88.11%, while the 5-day degradation rate in the fresh manure group was 47.56%.ConclusionsThe compound microbial agent developed in this study has a solid deodorizing effect, particularly in the control of the odor of obsolete feces. The use of composite microbial agents can efficiently degrade skatole in human feces, providing a theoretical foundation for the use of microbial remediation in the actual world.Graphical

PurposeThe microorganisms that possess diverse and improved traits for biotechnological applications provide an opportunity to address some of the current industrial challenges such as the sustainability of fuel energy and food. The aim of this study was to isolate and select the potential yeast isolates from sugarcane bagasse for single oil production.MethodsThe oleaginocity of the yeasts was confirmed through a gravimetric analysis of lipids, Nile red, sulfo-phosphovanillin (SPV) and a gas chromatography method for fatty acid methyl esters (FAME). The identification of the selected yeasts was carried out through a 5.8S of the ribosomal internal transcribed spacer (ITS) and 26S ribosomal DNA (rDNA) sequences. The carbohydrate and protein contents were estimated using phenol-sulfuric acid and hot trichloroacetic acid method, respectively.ResultsThe yeast isolates accumulated lipids of between 28% and 67% of the dry cell weight, and 22–33% based on the SPV assay, qualifying them as oleaginous yeasts. The selected yeasts were identified as Candida ethanolica and Pichia manshuriica. The lipids contained high levels of fatty acids in the following order: oleic acid, palmitic acid, stearic acid, and linoleic acid, which made up 82% of the total lipids.ConclusionAll the six selected yeast strains have the potential to produce single cell oils and other metabolites. The fatty acids composition of the selected yeast species was found to be suitable for the applications in biofuel, nutraceutical, and food industry. The yeast strains require evaluation in lignocellulosic hydrolysate for the production of single cell oils to be cost effective.

BackgroundIt has become commonplace to explore the spatial distribution patterns of microbial communities in natural ecosystems. However, few have looked at the responses of community diversity, structure, and assembly processes from different microbial groups to changes in environmental stress caused by altitude.PurposeWe investigated the spatial and biogeographical patterns of different microbial groups, including bacteria, fungi, and protists, from tobacco soil along an altitudinal gradient to evaluate the influence of geographic distance and environmental stress on microbial distribution pattern.MethodsDDR (distance decay relationship) model was calculated to evaluate the spatial distribution pattern. Then, NCM (neutral community model) and two null-modelling-based approaches, NST (normalized stochasticity ratio) and iCAMP (the infer community assembly mechanism by phylogenetic-bin-based null model analysis), were used to reveal the importance of stochastic and deterministic processes to microbial community assembly by utilizing high-throughput sequencing data.ResultBacterial community α-diversity decreased significantly (P < 0.05) with increasing environmental stress. Moreover, all communities exhibited a significant DDR pattern (P < 0.001), with the slope of bacteria (0.146) being significantly higher (P < 0.05) than that of fungi (0.059) and protists (0.060). The results of NCM and the two null-modelling-based approaches revealed the importance of stochastic processes to bacterial (83.4%) and protist (69.9%) communities, which were primarily shaped by drift and dispersal limitation, respectively; meanwhile, deterministic processes were important to the fungal community (53.7%). Additionally, we found a significant correlation between the assembly process and geographic distance (P < 0.05).ConclusionOur study provides a complementary perspective to the study of multiple hierarchical groups across different spatial scales (i.e., horizontal and vertical scales).Graphical

PurposeSome Bacillus licheniformis strain isolated from the environment has been reported to form aggregates during the suspension culture under carbon limitation. The aim of this study is to characterize the aggregation process of B. licheniformis RK14 strain isolated from the soil.MethodsB. licheniformis RK14 was cultured in a glucose-free lysogeny broth (LB) to confirm the aggregate formation under glucose limitation conditions and compared to model B. licheniformis strains. To characterize the aggregation process of RK14, microscopic analyses and time-lapse observations were conducted. Thioflavin T (ThT) was used to assess the involvement of transient cell elongation in aggregate formation.ResultsAlthough RK14 did not form aggregate when cultured in a glucose-rich γ-PGA production medium, it was found to self-aggregate when grown in a glucose-free LB. The optimal temperature for aggregation was approximately 40℃. Microscopic analysis showed that the aggregates were composed of viable cells with cell–cell cluster-like structures. Time-lapse observations clarified elongation of individual cells after 1 h of culture, followed by a return to rod-shape while maintaining the aggregation state. Addition of ThT at micromolar concentration inhibits aggregate formation, probably due to the suppression of cell elongation.ConclusionsThe aggregation process of RK14 was similar to the pellicle and submerged biofilm formation process of B. subtilis in terms of morphological changes. It was concluded that transient cell elongation is critical for aggregate formation of RK14 strain.

PurposeThousands of aquifers worldwide have been polluted by leachate from landfills and many more remained threatened. Microbial communities from these environments play a crucial role in mediating biodegradation and maintaining the biogeochemical cycles, but their co-occurrence and assembly mechanism have not been investigated.MethodHere, we coupled network analysis with multivariate statistics to assess the relative importance of deterministic versus stochastic microbial assembly in an aquifer undergoing intrinsic remediation, using 16S metabarcoding data generated through Illumina MiSeq sequencing of the archaeal/bacterial V3–V4 hypervariable region.ResultsResults show that both the aquifer-wide and localised community co-occurrences deviate from expectations under null models, indicating the predominance of deterministic processes in shaping the microbial communities. Further, the amount of variation in the microbial community explained by the measured environmental variables was 55.3%, which illustrates the importance of causal factors in forming the structure of microbial communities in the aquifer. Based on the network topology, several putative keystone taxa were identified which varied remarkably among the wells in terms of their number and composition. They included Nitrospira, Nitrosomonadaceae, Patulibacter, Legionella, uncharacterised Chloroflexi, Vicinamibacteriales, Neisseriaceae, Gemmatimonadaceae, and Steroidobacteraceae. The putative keystone taxa may be providing crucial functions in the aquifer ranging from nitrogen cycling by Nitrospira, Nitrosomonadaceae, and Steroidobacteraceae, to phosphorous bioaccumulation by Gemmatimonadaceae.ConclusionCollectively, the findings provide answers to fundamental ecological questions which improve our understanding of the microbial ecology of landfill leachate plumes, an ecosystem that remains understudied.

PurposeYeasts are widely used for the production of bioethanol from biomasses rich in sugar. The present study was aimed at isolating, screening, and characterizing fermentative wild yeast recovered from bio-waste and co-products of Ethiopian sugar factories for bioethanol production using sugarcane molasses as a substrate.MethodThe wild yeasts were identified according to their cellular morphology and D1/D2 and ITS1-5.8S-ITS2 rDNA sequencing. Analysis of ethanol and by-product concentration was done by HPLC equipped with a UV detector. Higher alcohols, acetaldehyde, and methanol were analyzed using GC-MS equipped with a flame ionization detector (FID).ResultSeven strains (Meyerozyma caribbica MJTm3, Meyerozyma caribbica MJTPm4, Meyerozyma caribbica SHJF, Saccharomyces cerevisiae TA2, Wickerhamomyces anomalus MJTPm2, Wickerhamomyces anomalus 4m10, and Wickerhamomyces anomalus HCJ2F) were found tolerant to 18% (v/v) ethanol, whereas one strain Meyerozyma caribbica MJTm3 tolerated 20%. These strains also showed tolerance to 45°C, 50% of sugar, and pH 2–10. Meyerozyma caribbica MJTm3 produced 12.7% (v/v) of alcohol with an actual ethanol concentration of 26 g L−1, an ethanol yield of 47%, 78% of theoretical yield, and a productivity of 0.54 g L−1 h−1 from 30 °Brix of molasses at 48 h incubation under laboratory scale. Based on the one variable at a time optimization (OVAT), the optimal parameters for maximum bioethanol production were at initial pH 5.5, 35 °Brix, 30°C, 15% inoculum size, 150 rpm, 4 g L−1 di-ammonium phosphate supplement, and 48 h incubation. Under these optimum conditions, 14% (v/v) alcohol, 42 g L−1 actual ethanol concentration, 69% ethanol yield, 89% of theoretical yield, and productivity of 0.88 g L−1 h−1 were obtained.ConclusionThese results indicated that M. caribbica MJTm3 should further be evaluated, optimized, and improved for industrial bioethanol production due to its fermentation potential.

PurposeWe determined the microbial community diversity and structure in soil samples under different amounts of biochar added. Meanwhile, we also researched the relationships between soil microbial and soil physicochemical properties.MethodIn this study, a field experiment was set up, with a total of three experimental treatments: no biochar application, 10 t/m3 biochar application, and 20 t/m3 application. High-throughput sequencing technologies were used for soil samples of different treatment groups to understand soil microbial diversity and community structure.ResultsWe found that the soil physicochemical properties after biochar addition were better than those without biochar addition, and the alpha diversity was higher in biochar addition level of 20 t/m3 than other processing groups. Proteobacteria, Cyanobacteria, and Actinobacteria were the dominant phyla of this study. The dominant genera were Skermanella, Nostoc, Frankia, and Unclassified-p-protecbacteria. At the gate level, Actinobacteria had significant differences among the three groups with different addition amounts. The microbial community structure was mainly influenced by soil porosity, soil moisture content, nitrogen fertilizer, and potassium fertilizer other than soil phosphate fertilizer and organic matter.ConclusionsThe results suggested that changes under different amounts of biochar added generate changes in soil physicochemical properties and control the soil composition of microbial communities. This provides a new basis for soil improvement.

PurposeIncorporating crop residues into the soil is considered a sustainable and valuable method to alleviate soil deterioration caused by continuous monoculture in greenhouse production. However, the effect of vegetable residues retention on soil amendments is poorly understood. In the present study, we investigated the impacts of sweet pepper, tomato, and cucumber plant residues on soil microbial communities and plant growth of continuously cropped cucumber in a solar greenhouse.MethodsThe 16S rRNA and ITS1 rRNA genes were amplified, and high-throughput sequencing was performed to explore the impacts of vegetable residues incorporation on soil microbial communities. Additionally, soil chemical properties, cucumber root vigor, and fruit yield were measured to assess the impacts of vegetable residues incorporation on continuously cropped soil and cucumber growth.ResultsThe results showed that incorporating vegetable residues could improve soil buffering capacity, increase the content of soil organic matter and available nutrients, and increased the diversity of soil microorganisms and improved community structure; vegetable residues increased the abundance of beneficial bacteria such as Actinobacteria, Firmicutes, Proteobacteria, and Chloroflexi, while reducing the quantity of soil-borne pathogens such as Bacillariophyta and Acidobacteria. Similar results were observed for the fungal communities: the relative abundance of Ascomycota was decreased to varying degrees, while the relative abundance of Rozellomycota and Basidiomycota was raised. The results demonstrated that vegetable residues incorporation significantly increased cucumber root vigor and enhanced fruit yield. The effects of different types of residues on improving soil properties were ordered sweet pepper plant residues > cucumber plant residues > tomato plant residues, and 20% of sweet pepper plant residues incorporation had the most significant effect on crop yield.ConclusionIn summary, returning vegetable residues alleviated soil continuous cropping obstacles by improving the soil fertility and the diversity and community structure of soil microorganisms, and consequently promoting the growth and yield of greenhouse-grown cucumbers. The findings demonstrated that returning vegetable residues was an effective and sustainable measure for soil amendment during continuous cropping in greenhouse production.