scholarly journals Phyllosphere Microbiome in Response to Citrus Melanose

2020 ◽  
Author(s):  
Pudong Li ◽  
Jianping Xu ◽  
Zhengyi Wang ◽  
Hongye Li
Keyword(s):  
Microbial Community ◽  
Community Response ◽  
Microbial Interactions ◽  
Metagenomic Sequencing ◽  
Fungal Cell ◽  
Pathogen Invasion ◽  
Shotgun Metagenomic Sequencing ◽  
Dna Metabarcoding ◽  
Functional Features ◽  
Microbial Community Assembly

Abstract Background: Like microbiomes in the rhizosphere, phyllosphere microbiomes can have an important role in plant growth and health. However, whether and how the phyllosphere microbiomes respond to the invasion of pathogens is not well understood. In this study, we address this question using the citrus phyllosphere-associated microbiome as a model.Results: Through DNA metabarcoding (16S for bacteria and ITS for fungi) and shotgun metagenomic sequencing, we found that phyllosphere microbiomes in different ecological habitats (epiphytes and endophytes) responded differently to melanose disease caused by the fungal pathogen Diaporthe citri on citrus (Citrus unshiu) leaves. We observed that citrus phyllosphere-associated microbiome responded to the melanose disease in five ways: (1) increasing microbial richness; (2) reducing community evenness; (3) enriching selected microbes; (4) enhancing microbial interactions; and (5) enriching functional features involved in metabolism and fungal cell wall degrading.Conclusions: Our study revealed how phyllosphere microbiomes in the epiphytic and endophytic habitats differ between diseased and healthy leaves. Based on the differences at both the taxonomic and functional levels, we propose a general conceptual paradigm to describe the different microbial community assembly processes for the phyllosphere microbiome in response to leaf disease and how such processes impact plant health. Our results provide novel insights for understanding the contributions of the phyllosphere microbial community response during pathogen invasion.

scholarly journals Microbial adaptation in vertical soil profiles contaminated by antimony smelting plant

2020 ◽  
Author(s):  
Rui Xu ◽  
Xiaoxu Sun ◽  
Feng Han ◽  
Enzong Xiao ◽  
Baoqin Li ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Soil Depth ◽  
Microbial Interactions ◽  
Individual Species ◽  
Soil Profiles ◽  
Metagenomic Sequencing ◽  
Deep Soil ◽  
Metabolic Potential ◽  
Microbial Adaptation ◽  
Shotgun Metagenomic Sequencing

Abstract BackgroundSoil microbes play critical roles in the biogeochemical cycling of antimony (Sb) and arsenic (As), and the effects of Sb and As contamination on soil microbiota have been well documented in surface soils (< 0.2 m). However, their effects in deep soils remain poorly understood. This study determined the depth-resolved effects of Sb and As contamination on the microbial adaptation throughout soil profiles (0–2 m) and compared contaminated soil samples to uncontaminated samples.Methods16S rRNA amplicon sequencing and shotgun metagenomic sequencing were employed to investigate the microbial community and their metabolism traits in soil profiles. Co-occurrence network analysis was used to present the pairwise interactions of microbes.ResultsAs soil depth increased, Acidobacteria (18.8%–44.7% from top to bottom, hereafter), Chloroflexi (8.7%–42.4%), Proteobacteria (11.4%–27.1%), and Thaumarchaeota (0.49%–20.17%) were the most variable phyla from surface to deep soil. A set of co-occurrence networks revealed an obvious changing pattern of microbial interactions as soil depth increased. The networks were loosely connected in the heavily contaminated surface soil but gradually recovered and were well connected in the less contaminated deep soil. Results suggested that individual species became more connected with other patterns to perform syntrophic functions in the less contaminated soil depth. Shotgun metagenomic sequencing results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with Sb and As concentrations. A set of arsenic-related genes was enriched by the high Sb and As contamination but reduced with soil depth. ConclusionsSoil depth-resolved characteristics are often many meters deep and their microbial diversity and community structures obviously change along their vertical soil profiles due to different nutrient contents and biomasses. The significance of this study is that it further reveals how the microbial communities and microbial physiological traits respond to different soil profiles contaminated by high concentrations of Sb and As.

scholarly journals Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa

Data in Brief ◽  
2020 ◽  
Vol 31 ◽  
pp. 105831
Author(s):  
Olubukola Oluranti Babalola ◽  
Temitayo Tosin Alawiye ◽  
Carlos Rodriguez Lopez ◽  
Ayansina Segun Ayangbenro
Keyword(s):  
South Africa ◽  
Microbial Community ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing ◽  
Rhizosphere Microbial Community

scholarly journals Genome-Centered Metagenomics Analysis Reveals the Microbial Interactions of a Syntrophic Consortium during Methane Generation in a Decentralized Wastewater Treatment System

2019 ◽  
Vol 10 (1) ◽  
pp. 135 ◽  
Author(s):  
Kun Zhang ◽  
Yan-Ling Zhang ◽  
Xin Ouyang ◽  
Jun-Peng Li ◽  
Jun-Jie Liao ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Microbial Community ◽  
Anaerobic Digestion ◽  
Microbial Community Structure ◽  
High Efficiency ◽  
Microbial Interactions ◽  
Clear Understanding ◽  
Metagenomic Sequencing ◽  
Decentralized Wastewater Treatment

The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.

scholarly journals Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander G. Shaw ◽  
Kathleen Sim ◽  
Graham Rose ◽  
David J. Wooldridge ◽  
Ming-Shi Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bayesian Regression ◽  
Validation Dataset ◽  
Metagenomic Sequencing ◽  
Faecal Microbiota ◽  
Community Patterns ◽  
Cpg Dna ◽  
Shotgun Metagenomic Sequencing ◽  
Low Levels ◽  
Stimulation Of

Abstract Background Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data. Results We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation. Conclusions The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

scholarly journals Metagenome-Assembled Genomes Isolated from a Human Fecal Diarrhea Sample

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Tshepiso Pleasure Ateba ◽  
Kazeem Adekunle Alayande ◽  
Ngoma Lubanza ◽  
Mulunda Mwanza
Keyword(s):  
Infectious Disease ◽  
Microbial Community ◽  
Fecal Sample ◽  
Metagenomic Sequencing ◽  
Affected Child ◽  
Shotgun Metagenomic Sequencing

ABSTRACT Diarrheal infection is the second leading infectious disease that is killing children under the age of 5 years. This study investigates the microbial community within a fecal sample from a diarrhea-affected child through shotgun metagenomic sequencing.

scholarly journals Metagenome Analysis of Surface Waters of the Shardara Reservoir, the Largest Artificial Reservoir in Southern Kazakhstan

2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Madina S. Alexyuk ◽  
Andrey P. Bogoyavlenskiy ◽  
Pavel G. Alexyuk ◽  
Yergali S. Moldakhanov ◽  
Vladimir E. Berezin
Keyword(s):  
Microbial Community ◽  
Surface Waters ◽  
Metagenomic Analysis ◽  
Metagenomic Sequencing ◽  
Metagenome Analysis ◽  
Artificial Reservoir ◽  
Shotgun Metagenomic Sequencing ◽  
Hydropower Engineering

Here, we present a metagenomic analysis of the microflora of the surface waters of the Shardara reservoir, the largest artificial reservoir in Southern Kazakhstan, created to meet irrigation and hydropower engineering needs. In this case, shotgun metagenomic sequencing of the microbial community DNA was used.

scholarly journals Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

2017 ◽  
Vol 83 (8) ◽  
Author(s):  
Yuanqi Wang ◽  
Janet K. Hatt ◽  
Despina Tsementzi ◽  
Luis M. Rodriguez-R ◽  
Carlos A. Ruiz-Pérez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Pollutants ◽  
Environmental Conditions ◽  
Rare Species ◽  
Community Response ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Rare Taxa ◽  
Rare Biosphere ◽  
Archaeal Species

ABSTRACTA single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called “rare biosphere.” How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCEA single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.

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