Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation [PDF]
Water Research X, 2023 Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to ...
Jinha Kim +3 more
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HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. [PDF]
PLoS ONE, 2018 Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa.
Nicholas D Youngblut +2 more
doaj +9 more sources
Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing [PDF]
iScienceSummary: Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-
Simon Klaes +4 more
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Environment InternationalHigh-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches.
Jibing Li +5 more
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Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics [PDF]
mSystemsViruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood.
Gareth Trubl +10 more
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Heterotrophic inorganic carbon fixation varies with temperature and resource availability in marine and soil bacterial isolates [PDF]
Applied and Environmental MicrobiologyInorganic carbon use in cellular metabolism is ubiquitous in all living organisms. The assimilation of inorganic carbon into biomass via heterotrophic inorganic carbon fixation (HICF) is estimated to contribute significantly to global carbon fixation ...
Emma K. Brown +6 more
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A standardized quantitative analysis strategy for stable isotope probing metagenomics [PDF]
mSystems, 2023 Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids.
Dariia Vyshenska +16 more
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Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms [PDF]
ToxicsBisphenol A (BPA) is a persistent environmental contaminant requiring effective removal strategies. Biofilms offer advantages over conventional activated sludge for refractory compound degradation, yet the specific microorganisms and mechanisms driving ...
Di Wang +6 more
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De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution [PDF]
Environmental MicrobiomeBackground Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities.
Simon Klaes +4 more
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Restoration of deuterium marker for multi-isotope mapping of cellular metabolic activity [PDF]
Scientific ReportsInvestigation of cellular metabolic activity with stable-isotope probing (SIP) implies the admittance of an isotope tracer into the metabolic pathway.
Nadiia Yamborko +10 more
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