Acetate-utilizing microbial communities revealed by stable-isotope probing in sediment underlying the upwelling system of the Ulleung Basin, East Sea

2020 ◽  
Vol 634 ◽  
pp. 45-61
Author(s):  
H Cho ◽  
B Kim ◽  
JS Mok ◽  
A Choi ◽  
B Thamdrup ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
East Sea ◽  
Ulleung Basin ◽  
Upwelling System

scholarly journals Generation of 13C-Labeled MUC5AC Mucin Oligosaccharides for Stable Isotope Probing of Host-Associated Microbial Communities

2019 ◽  
Vol 5 (3) ◽  
pp. 385-393 ◽  
Author(s):  
Clayton Evert ◽  
Tina Loesekann ◽  
Ganapati Bhat ◽  
Asif Shajahan ◽  
Roberto Sonon ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing

scholarly journals Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

2016 ◽  
Vol 7 ◽  
Author(s):  
Jeffrey J. Marlow ◽  
Connor T. Skennerton ◽  
Zhou Li ◽  
Karuna Chourey ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
Slow Growing

Application of 13C and 15N stable isotope probing to characterize RDX degrading microbial communities under different electron-accepting conditions

2015 ◽  
Vol 297 ◽  
pp. 42-51 ◽  
Author(s):  
Kun-Ching Cho ◽  
Do Gyun Lee ◽  
Mark E. Fuller ◽  
Paul B. Hatzinger ◽  
Charles W. Condee ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
15N Stable Isotope

scholarly journals Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities

2021 ◽  
Author(s):  
Caroline S. Fortunato ◽  
David A. Butterfield ◽  
Benjamin Larson ◽  
Noah Lawrence-Slavas ◽  
Christopher K. Algar ◽  
...  
Keyword(s):  
Thermal Stress ◽  
Stable Isotope ◽  
Microbial Communities ◽  
Deep Sea ◽  
Stress Proteins ◽  
Natural Habitat ◽  
Deep Ocean ◽  
Stable Isotope Probing ◽  
Sample Processing

Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed an ROV-powered incubator instrument to carry out and compare results from in situ and shipboard RNA Stable Isotope Probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under near-native conditions in the ocean. Importance: Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delay, with shipboard microbial communities more stressed compared to seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.

scholarly journals Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

2020 ◽  
Vol 15 (1) ◽  
pp. 348-353
Author(s):  
Maria Mooshammer ◽  
Katharina Kitzinger ◽  
Arno Schintlmeister ◽  
Soeren Ahmerkamp ◽  
Jeppe Lund Nielsen ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Degradation Products ◽  
Membrane Filter ◽  
Stable Isotope Probing ◽  
Biogeochemical Processes ◽  
Proof Of Concept ◽  
Microbial Food Webs ◽  
Flow Through ◽  
Primary Consumers

AbstractStable 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 isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.

Sign in / Sign up

Export Citation Format

Share Document