Dataset Information

Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry.

ABSTRACT: In this study, the aerobic activated sludge for skatole removal was enriched from pig slurry in three parallel sequencing batch reactors. The sludge system exhibited a satisfactory performance for skatole removal during the 40 days operation. High-throughput sequencing results showed that the α-diversity remained unchanged before and after the operation process. However, the structures of bacterial and fungal communities notably shifted. Particularly, Arthrobacter increased to be the major bacterial genus from 2.15 ± 0.76% (day 0) to 23.80 ± 24.36% (day 40), and Fusicolla became the major fungal genus from 1.20 ± 0.48% (day 0) to 37.17 ± 7.47% (day 40). These results indicated that Arthrobacter and Fusicolla might participate in skatole removal in sludge systems, though both genera were not reported to be able to degrade skatole. This is the first study describing skatole-degrading bacterial and fungal communities in the enrichment from pig slurry to the best of our knowledge, providing important guidance for skatole control and bioremediation.

SUBMITTER: Qu H

PROVIDER: S-EPMC7550505 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry.

Qu Hui H Meng Nan N Liu Shengwei S Wang Jingwei J Sun Yeqing Y Ma Qiao Q

3 Biotech 20201012 11

In this study, the aerobic activated sludge for skatole removal was enriched from pig slurry in three parallel sequencing batch reactors. The sludge system exhibited a satisfactory performance for skatole removal during the 40 days operation. High-throughput sequencing results showed that the α-diversity remained unchanged before and after the operation process. However, the structures of bacterial and fungal communities notably shifted. Particularly, <i>Arthrobacter</i> increased to be the majo ...[more]

PMID: 33088667

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Project description:(1) Objective: The objective of this study was to screen amoxicillin (AMX)-degrading bacterial strains in pig manure and optimize the fermentation conditions for these strains to achieve high fermentation rate, which can provide an effective way for the practical application of bacterial strains as antibiotic-degrading bacterial in treating livestock waste for antibiotic residues. (2) Methods: Antibiotic susceptibility tests and high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) were employed to screen AMX-degrading bacterial strains in pig manure. The culture conditions were optimized for AMX-degrading bacterial strains using Plackeet-Burman design (PBD), the steepest ascent design, and the response surface methods, coupled with the Box-Behnken design (BBD). The effects of culture time, temperature, rotator (mixing) speed, inoculum level, and initial pH value on the growth of AMX-degrading strains were investigated. Experimental data obtained from BBD were utilized to generate a second-order polynomial regression model for evaluating the effects of the tested variables on the optical density at 600 nm (OD600) of culture solutions as the growth indicator for the screened AMX-degrading strains. (3) Results: The initial pH, culture time, and the inoculum level had significant effects on the OD600 value (growth) of the screened AMX-degrading strains. The initial pH value was found to be the most critical factor influencing the growth of bacteria. The optimized culture condition for the bacterial growth determined by the response surface methodology was: the initial pH of 6.9, culture time of 52 h, and inoculum level of 2%. The average OD value of 12 different fermentation conditions in the initial fermentation tests in this study was 1.72 and the optimization resulted in an OD value of 3.00. The verification experiment resulted in an OD value of 2.94, which confirmed the adequacy of the optimization model for the determining the optimal culture condition. (4) Conclusions: The growth of the screened strain of AMX-degrading bacteria could be optimized by changing the fermentation conditions. The optimization could be achieved by using the Box-Behnken response surface method and Plackett-Burman experimental design.

Project description:Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi'an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (CODMn) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively (p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., CODMn and total nitrogen, TN). Several microbes (Legionella sp. and Streptococcus sp.) related to human diseases, such as infectious diseases, were also found. The results from this study provides useful information related to the water quality and microbial community compositions harbored in the aquatic ecosystems of urban lakes.

Project description:BackgroundPrevious studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7-80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons. In order to identify the causal mutation(s) for the QTL and/or identify genetic markers for selection purposes we performed a fine mapping of the SSC7 skatole QTL region.ResultsA dense set of markers on SSC7 was obtained by whole genome re-sequencing of 24 Norwegian Landrace and 23 Duroc boars. Subsets of 126 and 157 SNPs were used for association analyses in Landrace and Duroc, respectively. Significant single markers associated with skatole spanned a large 4.4 Mb region from 75.9-80.3 Mb in Landrace, with the highest test scores found in a region between the genes NOVA1 and TGM1 (p < 0.001). The same QTL was obtained in Duroc and, although less significant, with associated SNPs spanning a 1.2 Mb region from 78.9-80.1 Mb (p < 0.01). The highest test scores in Duroc were found in genes of the granzyme family (GZMB and GZMH-like) and STXBP6. Haplotypes associated with levels of skatole were identified in Landrace but not in Duroc, and a haplotype block was found to explain 2.3% of the phenotypic variation for skatole. The SNPs in this region were not associated with levels of sex steroids.ConclusionsFine mapping of a QTL for skatole on SSC7 confirmed associations of this region with skatole levels in pigs. The QTL region was narrowed down to 4.4 Mb in Landrace and haplotypes explaining 2.3% of the phenotypic variance for skatole levels were identified. Results confirmed that sex steroids are not affected by this QTL region, making these markers attractive for selection against boar taint.

Project description:Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using (13)C-labeled bacterial biomass probing. After 3 days of forced aeration, (13)C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained (13)C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant (13)C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence of Acholeplasma spp. in pig manure slurry.

Dataset Information

Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry.

Publications

Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry.

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