Results 1 to 10 of about 1,347 (156)

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, Myung Hwangbo, Chih-Hsuan Shih, Kung-Hui Chu   +3 more
doaj   +6 more sources

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, Samuel E Barnett, Daniel H Buckley   +2 more
doaj   +7 more sources

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC)

Environment International
High-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, Chunling Luo, Xixi Cai, Yeliang Dai, Dayi Zhang, Gan Zhang   +5 more
doaj   +5 more sources

Unraveling uncultivable pesticide degraders via stable isotope probing (SIP) [PDF]

Critical Reviews in Biotechnology, 2018
Uncultivable microorganisms account for over 99% of all species on earth, playing essential roles in ecological processes such as carbon/nitrogen cycle and chemical mineralization. Their functions remain unclear in ecosystems and natural habitats, requiring cutting-edge biotechnologies for a deeper understanding.
Bo Jiang, Dayi Zhang, Naifu Jin
exaly   +4 more sources

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi [PDF]

Microbiome, 2022
Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists.
Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone, Jennifer Pett-Ridge   +13 more
doaj   +4 more sources

Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing [PDF]

iScience
Summary: 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, Shobhit Madan, Darja Deobald, Myriel Cooper, Lorenz Adrian   +4 more
doaj   +2 more sources

Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms [PDF]

Toxics
Bisphenol 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, Jiayue Sun, Yunian Zhang, Lingjue Yuan, Xia Xu, Yingang Xue, Haohao Sun   +6 more
doaj   +2 more sources

De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution [PDF]

Environmental Microbiome
Background 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, Christian White, Lisa Alvarez-Cohen, Lorenz Adrian, Chang Ding   +4 more
doaj   +2 more sources

Restoration of deuterium marker for multi-isotope mapping of cellular metabolic activity [PDF]

Scientific Reports
Investigation of cellular metabolic activity with stable-isotope probing (SIP) implies the admittance of an isotope tracer into the metabolic pathway.
Nadiia Yamborko, Laura Schwab, Lubos Polerecky, Yalda Davoudpour, Hugo Berthelot, Niculina Musat, Kim Milferstedt, Jérôme Hamelin, Hans-Hermann Richnow, Carsten Vogt, Hryhoriy Stryhanyuk   +10 more
doaj   +2 more sources

15N-amino sugar stable isotope probing (15N-SIP) to trace the assimilation of fertiliser-N by soil bacterial and fungal communities [PDF]

Soil Biology and Biochemistry, 2019
Abstract Although amino sugars represent a major component of soil organic nitrogen (ON), the assimilation of nitrate (NO3−) and ammonium (NH4+) into amino sugars (AS) by soil bacteria and fungi represents a neglected aspect of the global N cycle.
Davey Jones, Richard Evershed, Michaela K Reay   +2 more
exaly   +3 more sources