scholarly journals Comparative Metagenomic and Metabolomic Profiling of Rhizospheres of Panax notoginseng Grown under Forest and Field Conditions

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2488
Author(s):  
Rui Shi ◽  
Haiyan Gu ◽  
Shu He ◽  
Binjie Xiong ◽  
Youguo Huang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Microbial Population ◽  
Panax Notoginseng ◽  
Field Conditions ◽  
Root Weight ◽  
Metagenomic Sequencing ◽  
Forest Plantation ◽  
Metabolomic Profiling ◽  
Functional Profiles ◽  
Forest Conditions

The present study investigated the potential changes in the structure of bacterial communities and their functional profiles in the rhizospheres of Panax notoginseng cultivated under field (CK) and pine forest conditions (T). The rhizospheres of two-year-old P. notoginseng plants were used to extract DNA for metagenomic sequencing and metabolites for metabolomic profiling. The results revealed a higher root weight (p < 0.05) in plants grown under the forest than CK. The rhizospheric bacterial community comprised mainly three dominant phyla including Acidobacteria, Proteobacteria, and Candidatus rokubacteria which accounted for 75% of the total microbial population. Among them, Acidobacteria was the most abundant bacterial taxa, accounting for 42.4% and 40.4% of the total populations in CK and T, respectively. Relative abundances of bacterial genera revealed that Bradyrhizobium, Candidatus koribacter and Edaphobacter, were the dominant genera in both groups. Comparatively, a higher Proteobacteria to Acidobacteria ratio was observed in forest rhizospheres than in field conditions. Candidatus Rokubacteria and Candidatus nitrostelea were identified as biomarker taxa in forest rhizospheres, while the same could be said for taxa belonging to betaproteobacteria and gammaproteobacteria, Burkholderiales and Verrucomicrobia for field rhizospheres. No differential metabolite contents were observed between the two rhizosphere groups, indicating no adverse effects of P. notoginseng cultivation on the soil quality under forest plantation.

scholarly journals Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Ganesh Babu Malli Mohan ◽  
Ceth W. Parker ◽  
Camilla Urbaniak ◽  
Nitin K. Singh ◽  
Anthony Hood ◽  
...  
Keyword(s):  
16S Rrna ◽  
Metal Surfaces ◽  
Microbial Population ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Particle Board ◽  
Shotgun Metagenomics ◽  
Glass Surfaces ◽  
Glass Metal

ABSTRACT Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.

scholarly journals A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Lu Wu ◽  
Tiansheng Zeng ◽  
Angelo Zinellu ◽  
Salvatore Rubino ◽  
David J. Kelvin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Healthy Aging ◽  
High Capacity ◽  
Functional Independence ◽  
Metagenomic Sequencing ◽  
Bifidobacterium Adolescentis ◽  
Content Type ◽  
Age Related ◽  
Genes Encoding ◽  
Functional Profiles

ABSTRACT Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis. Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose. IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.

scholarly journals Field Validation of the Effect of Soil Fumigation of Ethanedinitrile (EDN) on the Mortality of Meloidogyne hapla and Carrot Yield Parameters

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 208
Author(s):  
Ondřej Douda ◽  
Marie Manasova ◽  
Miloslav Zouhar ◽  
Jonas Hnatek ◽  
Vaclav Stejskal
Keyword(s):  
Field Conditions ◽  
Root Weight ◽  
Meloidogyne Hapla ◽  
Field Validation ◽  
Available Nitrogen ◽  
Positive Effects ◽  
Yield And Quality ◽  
Plant Pest ◽  
Recent Phase ◽  
Phase Out

With the increasing importance of soilborne plant pest nematodes and the relatively recent phase-out of methyl bromide as a key soil fumigant, there is an urgent need for new fumigants with good nematicidal properties. Ethanedinitrile (EDN) is a promising fumigant and preparation because of its physical, agrochemical, and nematicidal properties. However, its efficacy against nematode pests of different crops under field conditions has not been fully validated and understood. Therefore, the aim of our study was to evaluate the effect of two concentrations of EDN on the survival of northern root-knot nematodes (Meloidogynehapla) and on carrot yield and quality under field conditions. The evaluation was performed using naturally infested carrot plots, and EDN application to the soil was followed by covering the treated area with film. A high biological effect was observed for both EDN concentrations tested, with even the lower dose (30 g·m−2) being sufficient for M. hapla suppression. Positive effects of EDN application—likely due to EDN partial conversion into biologically available nitrogen in soil—on carrot root weight, in comparison with the untreated control, were also observed.

scholarly journals Selective Extraction of Bacterial DNA from the Surfaces of Macroalgae

2008 ◽  
Vol 75 (1) ◽  
pp. 252-256 ◽  
Author(s):  
Catherine Burke ◽  
Staffan Kjelleberg ◽  
Torsten Thomas
Keyword(s):  
Bacterial Communities ◽  
Benthic Algae ◽  
Selective Extraction ◽  
High Yield ◽  
Metagenomic Sequencing ◽  
Bacterial Dna ◽  
Yield And Quality ◽  
Ulva Australis ◽  
Delisea Pulchra ◽  
Novel Method

ABSTRACT A novel method has been developed for the selective extraction of DNA from surface-associated bacterial communities from the two model marine benthic algae Ulva australis and Delisea pulchra. The extracted DNA had no detectable contamination with host DNA, was recovered in high yield and quality, and was representative of the bacterial community on the algal surfaces. The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing.

scholarly journals Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses

2021 ◽  
Author(s):  
Yingnan Gao ◽  
Martin Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Copy Number ◽  
Rrna Gene ◽  
Prediction Uncertainty ◽  
Functional Profiles ◽  
Diversity Studies

Background: 16S rRNA gene has been widely used in microbial diversity studies to determine the community composition and structure. 16S rRNA gene copy number (16S GCN) varies among microbial species and this variation introduces biases to the relative cell abundance estimated using 16S rRNA read counts. To correct the biases, methods (e.g., PICRUST2) have been developed to predict 16S GCN. 16S GCN predictions come with inherent uncertainty, which is often ignored in the downstream analyses. However, a recent study suggests that the uncertainty can be so great that copy number correction is not justified in practice. Despite the significant implications in 16S rRNA based microbial diversity studies, the uncertainty associated with 16S GCN predictions has not been well characterized and its impact on microbial diversity studies needs to be investigated. Results: Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S rRNA GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms PICRUST2 in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, PERMANOVA and random forest test. Conclusion: We have developed a method to accurately account for uncertainty in 16S rRNA GCN predictions and the downstream analyses. For almost all 16S rRNA surveyed bacterial communities, correction of 16S GCN should improve the results when estimating their compositional and functional profiles. However, such correction is not necessary for beta-diversity analyses.

scholarly journals Mechanism of Intermittent Deep Tillage and Different Depths Improving Crop Growth From the Perspective of Rhizosphere Soil Nutrients, Root System Architectures, Bacterial Communities, and Functional Profiles

2022 ◽  
Vol 12 ◽  
Author(s):  
Yabing Gu ◽  
Yongjun Liu ◽  
Jiaying Li ◽  
Mingfeng Cao ◽  
Zhenhua Wang ◽  
...  
Keyword(s):  
Root System ◽  
Soil Nutrients ◽  
Crop Yield ◽  
System Architecture ◽  
Bacterial Communities ◽  
Root System Architecture ◽  
Crop Growth ◽  
Deep Tillage ◽  
Tillage Practices ◽  
Functional Profiles

Long-term conventional shallow tillage reduced soil quality and limited the agriculture development. Intermittent deep tillage could effectively promote agricultural production, through optimizing soil structure, underground ecology system, and soil fertility. However, the microecological mechanism of intermittent deep tillage promoting agriculture production has never been reported, and the effect of tillage depth on crop growth has not been explored in detail. In this study, three levels of intermittent deep tillage (30, 40, and 50 cm) treatments were conducted in an experimental field site with over 10 years of conventional shallow tillage (20 cm). Our results indicated that intermittent deep tillage practices helped to improve plant physiological growth status, chlorophyll a, and resistance to diseases, and the crop yield and value of output were increased with the deeper tillage practices. Crop yield (18.59%) and value of output (37.03%) were highest in IDT-50. There were three mechanisms of intermittent deep tillage practices that improved crop growth: (1) Intermittent deep tillage practices increased soil nutrients and root system architecture traits, which improved the fertility and nutrient uptake of crop through root system. (2) Changing rhizosphere environments, especially for root length, root tips, pH, and available potassium contributed to dissimilarity of bacterial communities and enriched plant growth-promoting species. (3) Functions associated with stress tolerance, including signal transduction and biosynthesis of other secondary metabolites were increased significantly in intermittent deep tillage treatments. Moreover, IDT-30 only increased soil characters and root system architecture traits compared with CK, but deeper tillage could also change rhizosphere bacterial communities and functional profiles. Plant height and stem girth in IDT-40 and IDT-50 were higher compared with IDT-30, and infection rates of black shank and black root rot in IDT-50 were even lower in IDT-40. The study provided a comprehensive explanation into the effects of intermittent deep tillage in plant production and suggested an optimal depth.

scholarly journals Psyllium Supplementation is Associated with Changes in the Fecal Microbiota of Horses

2020 ◽  
Author(s):  
Michael J. Mienaltowski ◽  
Ashley Belt ◽  
John D. Henderson ◽  
Tannah N. Boyd ◽  
Nicole Marter ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Diversity ◽  
Microbial Population ◽  
Fecal Microbiota ◽  
Acid Detergent Fiber ◽  
Bacterial Populations ◽  
Psyllium Husk ◽  
Silica Concentration ◽  
Functional Profiles ◽  
Microbial Dna

Abstract Objective: Prophylactic supplementation of psyllium husk is recommended to enhance passage of ingested sand from the gastrointestinal tracts of horses. We hypothesized that psyllium supplementation would increase fecal sand passage and favorably alter bacterial populations in the hindgut. Six yearlings and six mature mares were fed a psyllium supplement in the diet daily for seven days. Voluntarily-voided feces were collected over the course of 29 days, prior, during, and after treatment. Feces were analyzed for acid detergent fiber (ADF) and acid detergent insoluble ash analyses. Microbial DNA was also isolated, and the V4 region of the 16S ribosomal RNA gene was PCR-amplified and sequenced using MiSeq technology.Results: Fecal ADF concentration was greater in adults while silica concentration was greater in yearlings. Mature mare fecal ADF decreased during and just after supplementation but thereafter increased. No changes in silica levels were noted in either group over time. Fecal microbial population phylogenetic diversity was greatest mid-supplementation and lowest at 11 days post-supplementation. Functional profiles of the microbial communities presented some benefits for psyllium supplementation. These findings provide compelling evidence for further detailed studies of prophylactic psyllium supplementation.

scholarly journals Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants

2018 ◽  
Author(s):  
Lily Khadempour ◽  
Huan Fan ◽  
Ken Keefover-Ring ◽  
Camila Carlos ◽  
Nilson S. Nagamoto ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Potential Role ◽  
Sequence Data ◽  
Bacterial Community Composition ◽  
Fungus Garden ◽  
Functional Profiles ◽  
Ant Fungus

AbstractLeaf-cutter ants in the genusAttaare dominant herbivores in the Neotropics. While most species ofAttacut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12Attafungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

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