A novel belowground in-situ gas labeling approach: CH4 oxidation in deep peat using passive diffusion chambers and 13C excess

ABSTRACT To evaluate the persistence of PCR-detectable Bacteroides distasonis in surface water, whole human feces were dispersed into water from the Ohio River and incubated in flasks in the laboratory or in diffusion chambers in situ. Duplicate samples were taken daily, and material that pelleted at 16,000 × gwas assayed by PCR. Persistence of PCR-detectable DNA from this anaerobe depended upon temperature and predation, two of the factors shown by others to influence the survival of aerobic bacteria detected by culture. B. distasonis was detected by PCR for at least 2 weeks at 4°C but for only 4 to 5 days at 14°C, 1 to 2 days at 24°C, and 1 day at 30°C. In filtered water or in the presence of cycloheximide, a eukaryotic inhibitor, persistence at 24°C was extended by at least a week.

Download Full-text

Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems?

Biogeosciences Discussions ◽

10.5194/bgd-7-7945-2010 ◽

2010 ◽

Vol 7 (5) ◽

pp. 7945-7983 ◽

Cited By ~ 4

Author(s):

K. A. Smemo ◽

J. B. Yavitt

Keyword(s):

Large Body ◽

Conclusive Evidence ◽

Future Research ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Ch4 Oxidation ◽

Oxidation Of Methane ◽

Ch4 Production

Abstract. Despite a large body of literature on microbial anaerobic oxidation of methane (AOM) in marine sediments and saline waters and its importance to the global methane (CH4) cycle, until recently little work has addressed the potential occurrence and importance of AOM in non-marine systems. This is particularly true for peatlands, which represent both a massive sink for atmospheric CO2 and a significant source of atmospheric CH4. Our knowledge of this process in peatlands is inherently limited by the methods used to study CH4 dynamics in soil and sediment and the assumption that there are no anaerobic sinks for CH4 in these systems. Studies suggest that AOM is CH4-limited and difficult to detect in potential CH4 production assays against a background of CH4 production. In situ rates also might be elusive due to background rates of aerobic CH4 oxidation and the difficulty in separating net and gross process rates. Conclusive evidence for the electron acceptor in this process has not been presented. Nitrate and sulfate are both plausible and favorable electron acceptors, as seen in other systems, but there exist theoretical issues related to the availability of these ions in peatlands and only circumstantial evidence suggests that these pathways are important. Iron cycling is important in many wetland systems, but recent evidence does not support the notion of CH4 oxidation via dissimilatory Fe(III) reduction or a CH4 oxidizing archaea in consortium with an Fe(III) reducer. Calculations based on published rates demonstrate that AOM might be a significant and underappreciated constraint on the global CH4 cycle, although much about the process in unknown, in vitro rates may not relate well to in situ rates, and projections based on those rates are fraught with uncertainty. We suggest electron transfer mechanisms, C flow and pathways, and quantifying in situ peatland AOM rates as the highest priority topics for future research.

Download Full-text

Sources and sinks of methane in sea ice

Elem Sci Anth ◽

10.1525/elementa.2020.00167 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Caroline Jacques ◽

Célia J. Sapart ◽

François Fripiat ◽

Gauthier Carnat ◽

Jiayun Zhou ◽

...

Keyword(s):

Sea Ice ◽

Ch4 Oxidation ◽

Data Set ◽

Sources And Sinks ◽

Ch4 Production ◽

Antarctic Sea Ice ◽

Production And Consumption ◽

Mount Erebus ◽

Landfast Sea Ice

We report on methane (CH4) stable isotope (δ13C and δ2H) measurements from landfast sea ice collected near Barrow (Utqiagvik, Alaska) and Cape Evans (Antarctica) over the winter-to-spring transition. These measurements provide novel insights into pathways of CH4 production and consumption in sea ice. We found substantial differences between the two sites. Sea ice overlying the shallow shelf of Barrow was supersaturated in CH4 with a clear microbial origin, most likely from methanogenesis in the sediments. We estimated that in situ CH4 oxidation consumed a substantial fraction of the CH4 being supplied to the sea ice, partly explaining the large range of isotopic values observed (δ13C between –68.5 and –48.5 ‰ and δ2H between –246 and –104 ‰). Sea ice at Cape Evans was also supersaturated in CH4 but with surprisingly high δ13C values (between –46.9 and –13.0 ‰), whereas δ2H values (between –313 and –113 ‰) were in the range of those observed at Barrow. These are the first measurements of CH4 isotopic composition in Antarctic sea ice. Our data set suggests a potential combination of a hydrothermal source, in the vicinity of the Mount Erebus, with aerobic CH4 formation in sea ice, although the metabolic pathway for the latter still needs to be elucidated. Our observations show that sea ice needs to be considered as an active biogeochemical interface, contributing to CH4 production and consumption, which disputes the standing paradigm that sea ice is an inert barrier passively accumulating CH4 at the ocean-atmosphere boundary.

Download Full-text

In situ Infrared Spectroscopic Study of CH4 Oxidation Over Co–ZSM-5

Topics in Catalysis ◽

10.1007/s11244-012-9774-6 ◽

2012 ◽

Vol 55 (1-2) ◽

pp. 108-115 ◽

Cited By ~ 22

Author(s):

Mayfair C. Kung ◽

Sean S. -Y. Lin ◽

Harold H. Kung

Keyword(s):

Spectroscopic Study ◽

Infrared Spectroscopic Study ◽

Ch4 Oxidation ◽

Infrared Spectroscopic

Download Full-text

An in situ ascorbate peroxidase labeling in secreted exosomes identifies a stress-induced exosome proteome alteration

10.21203/rs.3.rs-428162/v1 ◽

2021 ◽

Author(s):

Byung Rho Lee ◽

Tae Jin Lee ◽

Sekyung Oh ◽

Chenglong Li ◽

Jin-Hyuk Song ◽

...

Keyword(s):

Ribosomal Proteins ◽

Extracellular Vesicle ◽

Mass Spectrometry Analysis ◽

Biological Processes ◽

Ribonucleic Acids ◽

Spectrometry Analysis ◽

Exosome Biogenesis ◽

Cargo Protein ◽

Labeling Approach

Abstract The extracellular vesicle exosome mediates intercellular communication by transporting macromolecules such as proteins and ribonucleic acids. Determining cargo content with high accuracy will help decipher the biological processes that exosomes mediate in various contexts. Existing methods for probing exosome cargo molecules rely on a prior exosome isolation procedure. Here we report an in situ labeling approach for exosome proteome profiling, termed Exosome-Proxy APEX Labeling (EPAL), which bypasses the exosome isolation steps. In EPAL, proteins either in the exosome biogenesis vesicles in cells or in secreted exosomes in the conditioned medium can specifically be biotinylated with expressing a variant of the engineered ascorbic peroxidase APEX that is fused to an exosome cargo protein such as CD63. Mass spectrometry analysis of the proteins biotinylated in exosomes secreted from kidney proximal tubule-derived cells reveals that oxidative stress can induce an alteration in exosome protein contents, including accumulation of ribosomal proteins in exosomes.

Download Full-text

Multiplexed imaging of high density libraries of RNAs with MERFISH and expansion microscopy

10.1101/238899 ◽

2017 ◽

Cited By ~ 1

Author(s):

Guiping Wang ◽

Jeffrey R. Moffitt ◽

Xiaowei Zhuang

Keyword(s):

Single Molecule ◽

Detection Efficiency ◽

High Abundance ◽

Total Density ◽

Accurate Identification ◽

Rna Molecules ◽

Wide Range ◽

Multiplexed Imaging ◽

Labeling Approach

AbstractAs an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging. Here we report an approach that combines MERFISH and expansion microscopy to substantially increase the total density of RNAs that can be measured. Using this approach, we demonstrate accurate identification and counting of RNAs, with a near 100% detection efficiency, in a ~130-RNA library composed of many high-abundance RNAs, the total density of which is more than 10 fold higher than previously reported. In parallel, we demonstrate the combination of MERFISH with immunofluorescence. These advances increase the versatility of MERFISH and will facilitate its application of a wide range of biological problems.

Download Full-text