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Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide....
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Integrated Analysis of Soil Metagenome and Soil Metabolome Reveals the Differential Responses of Sorghum and Peanut Rhizosphere Microbes to Salt Stress
Soil salinization is a major constraint to crop cultivation. To improve the use-efficiency of salinized soil, sorghum and peanut are generally...
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Preparation of Soil Metagenome Libraries and Screening for Gene-Specific Amplicons
Cosmid libraries constructed from environmental metagenome samples are powerful tools for capturing the genomic diversity of complex microbial...
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How to Obtain and Compare Metagenome-Assembled Genomes
Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from...
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Metagenome-derived virus-microbe ratios across ecosystems
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of...
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Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining
AbstractEnzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes....
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High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an...
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Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome
Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to...
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CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine
Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a...
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Revealing the diversity of Jojoba-associated fungi using amplicon metagenome approach and assessing the in vitro biocontrol activity of its cultivable community
Jojoba shrubs are wild plants cultivated in arid and semiarid lands and characterized by tolerance to drought, salinity, and high temperatures. Fungi...
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Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome
BackgroundAdvances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex...
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using...
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Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from...
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Application of Paclobutrazol Altered the Soil Bacterial Diversity and Richness of Mango Orchards: A Metagenomic Study
The soil microbiome regulates plant and soil health by cycling nutrients, reconstructing soil, degrading xenobiotics, and regulating growth....
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Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation
The effect of Streptomyces spp. on organic matter degradation was investigated in the present study. Streptomyces spp. isolated from compost systems...
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Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil
The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural...
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Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures
Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes....
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A novel salt-tolerant GH42 β-galactosidase with transglycosylation activity from deep-sea metagenome
β-Galactosidase is a widely adopted enzyme in the food and pharmaceutical industries. Metagenome techniques have the advantage of discovering novel...
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Extreme summers impact cropland and grassland soil microbiomes
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here,...
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An in-depth evaluation of metagenomic classifiers for soil microbiomes
BackgroundRecent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the...
