Results 11 to 20 of about 1,347 (156)

Identification of protein-degraders in an anaerobic digester by protein stable isotope probing and metagenomics [PDF]

Applied Microbiology and Biotechnology
Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations.
Zhe Deng, Jan Struckmann Poulsen, Jeppe Lund Nielsen, David G. Weissbrodt, Henri Spanjers, Jules B. van Lier   +5 more
doaj   +2 more sources

High-Resolution Community Profiling of Active Bacteria and Eukaryotes in Replant-Diseased Blueberry Farm Soils From New Jersey, USA. [PDF]

Environ Microbiol
Long read bacterial and eukaryotic ribosomal operon sequencing combined with stable isotope probing (SIP) allowed the differentiation of microbiomes in low‐ and high‐yield blueberry farm soils. This report may ultimately be used to improve productivity and potentially detect the responsible pathogenic agent(s) or other deleterious microbes.
Mirzoyan S, Polashock JJ, Kerkhof LJ.
europepmc   +2 more sources

Marine Cold Seep ANME-2/SRB Consortia Produce Their Lipid Biomass From Inorganic Carbon. [PDF]

Environ Microbiol
Lipid‐stable isotope probing (SIP) experiments in Astoria Canyon sediments revealed that both ANME‐2 and SRB primarily assimilate dissolved inorganic carbon (DIC or HCO3‐), not methane, into biomass. SRB‐specific lipids showed eightfold higher DI13C‐assimilation than ANME lipids, suggesting SRB directly assimilate DIC, while ANME assimilate an ...
Stock L, Wegener G, Wang Y, Zander Y, Elvert M.   +4 more
europepmc   +2 more sources

A standardized quantitative analysis strategy for stable isotope probing metagenomics

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, Pranav Sampara, Kanwar Singh, Andy Tomatsu, W. Berkeley Kauffman, Erin E. Nuccio, Steven J. Blazewicz, Jennifer Pett-Ridge, Katherine B. Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe-Fadrosh, Ryan M. Ziels, Rex R. Malmstrom   +16 more
doaj   +1 more source

DNA Stable-Isotope Probing (DNA-SIP) [PDF]

Journal of Visualized Experiments, 2010
DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of ...
Eric A, Dunford, Josh D, Neufeld
openaire   +2 more sources

Bioelectrochemically enhanced degradation of bisphenol S: mechanistic insights from stable isotope-assisted investigations

iScience, 2021
Summary: Electroactive microbes is the driving force for the bioelectrochemical degradation of organic pollutants, but the underlying microbial interactions between electrogenesis and pollutant degradation have not been clearly identified.
Rui Hou, Lin Gan, Fengyi Guan, Yi Wang, Jibing Li, Shungui Zhou, Yong Yuan   +6 more
doaj   +1 more source

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Microbiome, 2023
Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial
Manuel Kleiner, Angela Kouris, Marlene Violette, Grace D’Angelo, Yihua Liu, Abigail Korenek, Nikola Tolić, Timo Sachsenberg, Janine McCalder, Mary S. Lipton, Marc Strous   +10 more
doaj   +1 more source

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities [PDF]

The ISME Journal, 2020
Abstract Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release
Maria Mooshammer, Katharina Kitzinger, Arno Schintlmeister, Soeren Ahmerkamp, Jeppe Lund Nielsen, Per Halkjær Nielsen, Michael Wagner   +6 more
openaire   +5 more sources

DNA ‐stable isotope probing (DNA‐SIP) identifies marine sponge‐associated bacteria actively utilizing dissolved organic matter (DOM) [PDF]

Environmental Microbiology, 2021
Summary Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge‐associated community structure with DOM utilization is essential to understand host–microbe interactions in the uptake ...
Campana, Sara, Busch, Kathrin, Hentschel, Ute, Muyzer, Gerard, de Goeij, Jasper M.   +4 more
openaire   +3 more sources

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

BMC Bioinformatics, 2020
Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific ...
Samuel E. Barnett, Daniel H. Buckley
doaj   +1 more source