Bacterial Profiling and Dynamic Succession Analysis of Phlebopus portentosus Casing Soil Using MiSeq Sequencing

Yang, Runqiang; Bao, Dapeng; Guo, Ting; Li, Yan; Ji, Guang-Yan; Ji, Kai-Ping; Tan, Qian

doi:10.3389/fmicb.2019.01927

Cited by 25 publications

(27 citation statements)

References 60 publications

(69 reference statements)

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“…Generalists in the network could link with both members within their own module and those belonging to other modules [ 29 ]. The results in our study show that high percentage of super generalists (Acidobacteriales) and 50% generalists belongs to Acidobacteria, which appears mostly in magnetite and quartz as Yang et al recorded [ 62 ]. In addition, Acidobacteria could decompose litter as soil saprophytes, affecting nitrogen cycling and remineralization [ 63 ].…”

Section: Discussionsupporting

confidence: 70%

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China

et al. 2020

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Environments in both biotic and abiotic ecosystems have been affected by the colonization of non-native flora. In this study, we examined the effect of Bidens alba invasion on different land-use types along a coastline in southern China. Bacterial communities in each site were determined using 16S rDNA sequencing, and soil physicochemical properties were analyzed using standard methods. Although our results indicated that B . alba invasion did not have a significant effect on the alpha diversity of bacteria, it caused significant differences in soil bacterial community composition between invaded and uninvaded soil across different land-use types. Beta diversity and several physicochemical properties in forest, orchard and waterfront environments were recorded to be more susceptible to B . alba invasion. A high proportion of the variation of bacterial communities can be explained by a combination of environmental variables, indicating that environmental selection rather than plant invasion is a more effective process in coastal microbial assemblages. By comparing topological roles of shared OTUs among invaded and uninvaded soil, keystone taxa in invaded soil were identified. Acidobacteria was the major phyla involved in the invasive process which could be driven by environmental selection. How key phyla react in our experiment should be verified by further studies.

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Section: Discussionsupporting

confidence: 70%

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China

et al. 2020

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“…α-diversity was measured by microbial community richness (Chao, Ace) (Minamoto et al, 2015) and diversity (Shannon, Invsimpson) (Zheng et al, 2019b). Beta diversity were assessed using unweighted UniFrac algorithms and visualized by non-metric multidimensional scaling (NMDS) analysis (Yang et al, 2019). The key different OTUs responsible for discrimination among the three groups were identified using linear discriminant analysis (LDA) effect size (LEfSe) analysis (Riquelme et al, 2019).…”

Section: S Rrna Gene Sequence Analysismentioning

confidence: 99%

Differential Gut Microbiota and Fecal Metabolites Related With the Clinical Subtypes of Myasthenia Gravis

et al. 2020

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Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Previous studies have observed that disturbances of gut microbiome may attribute to the development of MG through fecal metabolomic signatures in humans. However, whether there were differential gut microbial and fecal metabolomic phenotypes in different subtypes of MG remains unclear. Here, our objective was to explore whether the microbial and metabolic signatures of ocular (OMG) and generalized myasthenia gravis (GMG) were different, and further identify the shared and distinct markers for patients with OMG and GMG. In this study, 16S ribosomal RNA (rRNA) gene sequencing and gas chromatographymass spectrometry (GC/MS) were performed to capture the microbial and metabolic signatures of OMG and GMG, respectively. Random forest (RF) classifiers was used to identify the discriminative markers for OMG and GMG. Compared with healthy control (HC) group, GMG group, but not OMG group, showed a significant decrease in α-phylogenetic diversity. Both OMG and GMG groups, however, displayed significant gut microbial and metabolic disorders. Totally, we identified 20 OTUs and 9 metabolites specific to OMG group, and 23 OTUs and 7 metabolites specific to GMG group. Moreover, combinatorial biomarkers containing 15 discriminative OTUs and 2 differential metabolites were capable of discriminating OMG and GMG from each other, as well as from HCs, with AUC values ranging from 0.934 to 0.990. In conclusion, different subtypes of MG harbored differential gut microbiota, which generated discriminative fecal metabolism.

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“…Metataxonomic analysis conducted through NGS does not rely on enrichment or isolation, and so it is possible to work with crude environmental samples, offering a new spectrum of possibilities to characterize the microbe-rich environmental niche in which A. bisporus grows and develops. Recent publications have reported the role of bacterial strains during the aerobic solid fermentation process required to produce the selective substrate employed in champignon cultivation (Kertesz and Thai, 2018;Vieira and Pecchia, 2018), the structure and dynamics of the bacterial and fungal community associated with the mycelium of the crop during cultivation (Kertesz and Thai, 2018;McGee et al, 2017aMcGee et al, , 2017b, and the bacterial and fungal profiling and dynamic succession of the microbiota that cohabits with the crop in the casing material (Carrasco et al, 2019;Yang et al, 2019). In order to deepen our knowledge of the interactions of champignon and the surrounding microbiota, the objective of this study was to evaluate the composition and progression of the fungal and bacterial microbiome living in different commercial substrates employed in commercial champignon cultivation.…”

Section: Introductionmentioning

confidence: 99%

Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation

Carrasco

García‐Delgado

Lavega

et al. 2020

Microbial Biotechnology

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Microorganisms strongly influence and are required to generate the selective substrate that provides nutrients and support for fungal growth, and ultimately to induce mushroom fructification under controlled environmental conditions. In this work, the fungal and bacterial microbiota living in the different substrates employed in a commercial crop (compost phase I, II and III, flush 1 and 2, and casing material on day 1, 6 and 8 after compost casing and during flush 1 and 2) have been characterized along the different stages of cultivation by metataxonomic analysis (16S rRNA and ITS2), analysis of phospholipid fatty acid content (PLFAs) and RT-qPCR. Additionally, laccase activity and the content of lignin and complex carbohydrates in compost and casing have been quantified. The bacterial diversity in compost and casing increased throughout the crop cycle boosted by the connection of both substrates. As reflected by the PLFAs, the total living bacterial biomass appears to be negatively correlated with the mycelium of the crop. Agaricus bisporus was the dominant fungal species in colonized substrates, displacing the pre-eminent Ascomycota, accompanied by a sustained increase in laccase activity, which is considered to be a major product of protein synthesis during the mycelial growth of champignon. From phase II onwards, the metabolic machinery of the fungal crop degrades lignin and carbohydrates in compost, while these components are hardly degraded in casing, which reflects the minor role of the casing for nourishing the crop. The techniques employed in this study provide a holistic and detailed characterization of the changing microbial composition in commercial champignon substrates. The knowledge generated will contribute to improve compost formulations (selection of base materials) and accelerate compost production, for instance, through biotechnological interventions in the form of tailored biostimulants and to design environmentally sustainable bio-based casing materials.

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Bacterial Profiling and Dynamic Succession Analysis of Phlebopus portentosus Casing Soil Using MiSeq Sequencing

Cited by 25 publications

References 60 publications

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China

Differential Gut Microbiota and Fecal Metabolites Related With the Clinical Subtypes of Myasthenia Gravis

Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation

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