In Situ Non-Destructive Temporal Measurements of the Rhizosphere Microbiome ‘Hot-Spots’ Using Metaproteomics

Rhizosphere arguably embodies the most diverse microbial ecosystem on the planet, yet it is largely a functional ‘black box’ of belowground plant-microbiome interactions. The rhizosphere is the primary site of entry for subsurface injection of fixed carbon (C) into soil with impacts on local to global scale C biogeochemistry and ultimately Earth’s climate. While spatial organization of rhizosphere is central to its function, small scale and steep microbial and geochemical gradients within this dynamic region make it easily disrupted by sampling. The significant challenge presented by sampling blocks elucidation of discreet functions, drivers, and interactions within rhizosphere ecosystems. Here, we describe a non-destructive sampling method linked to metaproteomic analysis in order to measure temporal shifts in the microbial composition and function of rhizosphere. A robust, non-destructive method of sampling microbial hotspots within rhizosphere provides an unperturbed window into the elusive functional interactome of this system over time and space.

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Weathering conditions of Buddhist caves dug in soft rocks and conservation attempting from the deterioration

10.5194/egusphere-egu21-13752 ◽

2021 ◽

Author(s):

Chiaki Oguchi ◽

Momoko Ogawa ◽

Kaisei Sakane ◽

Yasuhiko Tamura

Keyword(s):

Environmental Monitoring ◽

Layer Structure ◽

Physical And Mechanical Properties ◽

Small Scale ◽

Central Japan ◽

Soft Rocks ◽

Geologic Materials ◽

Temperature And Humidity ◽

Non Destructive

<p>The Taya Cave, a sacred Buddhist cave, locates in the precincts of Josenji Temple in Yokohama City, central Japan. The geologic materials of the hills surrounding the cave are soft rocks composed of early Quaternary sedimentary rocks. The cave has a complex three-layer structure with a total length of 570 m. The excavation of the cave is estimated to start in the Kamakura era around A.D. 1200. Since then, the cave became a training place for Buddhists until around 19 C. There are many Buddhist reliefs on the walls and ceiling inside the cave. Because the bedrock is extremely weak, the rocks easily break when they get wet again after drying, namely prone to slaking. Thus, weathering and deterioration have progressed in various parts of the cave. Many valuable Buddhist reliefs have damaged by exfoliation. The walls at several points in the cave have also collapsed on a small scale. Therefore, it is necessary to investigate such deteriorated parts in the cave by simple non-destructive tests of physical and mechanical properties by using Silver Schmidt hammer and ultrasonic velocity test. These measurements clarified the vulnerable points even in the main worship route of the cave. In October 2018, a stainless-steel door installed at the cave entrance to save from deterioration due to slaking. The effect of the door was verified as well by monitoring the environmental conditions inside the cave. Environmental monitoring results revealed that the temperature and humidity near the entrance changed most drastically in this cave. Although the door was closed only at night, the range of maximum and minimum values &#8203;&#8203;of temperature and humidity near the entrance became smaller after installation than before. Non-destructive measurements and in situ environmental monitoring are a useful way to assess weathering without damaging geoarchaeological sites.&#160;</p>

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Reassessing the ratio of glyoxal to formaldehyde as an indicator of hydrocarbon precursor speciation

Atmospheric Chemistry and Physics ◽

10.5194/acp-15-7571-2015 ◽

2015 ◽

Vol 15 (13) ◽

pp. 7571-7583 ◽

Cited By ~ 27

Author(s):

J. Kaiser ◽

G. M. Wolfe ◽

K. E. Min ◽

S. S. Brown ◽

C. C. Miller ◽

...

Keyword(s):

Oil And Gas ◽

Global Scale ◽

Gas Production ◽

Retrieval Algorithm ◽

Small Scale ◽

High Time Resolution ◽

Ozone Monitoring Instrument ◽

Oil And Gas Production ◽

Isoprene Oxidation

Abstract. The yield of formaldehyde (HCHO) and glyoxal (CHOCHO) from oxidation of volatile organic compounds (VOCs) depends on precursor VOC structure and the concentration of NOx (NOx = NO + NO2). Previous work has proposed that the ratio of CHOCHO to HCHO (RGF) can be used as an indicator of precursor VOC speciation, and absolute concentrations of the CHOCHO and HCHO as indicators of NOx. Because this metric is measurable by satellite, it is potentially useful on a global scale; however, absolute values and trends in RGF have differed between satellite and ground-based observations. To investigate potential causes of previous discrepancies and the usefulness of this ratio, we present measurements of CHOCHO and HCHO over the southeastern United States (SE US) from the 2013 SENEX (Southeast Nexus) flight campaign, and compare these measurements with OMI (Ozone Monitoring Instrument) satellite retrievals. High time-resolution flight measurements show that high RGF is associated with monoterpene emissions, low RGF is associated with isoprene oxidation, and emissions associated with oil and gas production can lead to small-scale variation in regional RGF. During the summertime in the SE US, RGF is not a reliable diagnostic of anthropogenic VOC emissions, as HCHO and CHOCHO production are dominated by isoprene oxidation. Our results show that the new CHOCHO retrieval algorithm reduces the previous disagreement between satellite and in situ RGF observations. As the absolute values and trends in RGF observed during SENEX are largely reproduced by OMI observations, we conclude that satellite-based observations of RGF can be used alongside knowledge of land use as a global diagnostic of dominant hydrocarbon speciation.

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Cloud-scale ice supersaturated regions spatially correlate with high water vapor heterogeneities

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-13-22249-2013 ◽

2013 ◽

Vol 13 (8) ◽

pp. 22249-22296

Author(s):

M. Diao ◽

M. A. Zondlo ◽

A. J. Heymsfield ◽

L. M. Avallone ◽

M. E. Paige ◽

...

Keyword(s):

Water Vapor ◽

High Water ◽

Ice Nucleation ◽

Cloud Formation ◽

Small Scale ◽

Cirrus Cloud ◽

Median Length ◽

Upper Troposphere ◽

Earth’S Climate

Abstract. Cirrus clouds have large yet uncertain impacts on the Earth's climate. Ice supersaturation (ISS) – where the relative humidity with respect to ice (RHi) is greater than 100% – is the prerequisite condition of ice nucleation. Here we use 1 Hz (~230 m) in situ aircraft-based observations from 87° N–67° S to analyze the spatial characteristics of ice supersaturated regions (ISSRs). The median length of 1-D horizontal ISSR segments is found to be very small (~1 km), which is two orders of magnitude smaller than previously reported. To understand the conditions of these small scale ISSRs, we compare individual ISSRs with their horizontally adjacent subsaturated surroundings and show that 99% and 73% of the ISSRs are moister and colder, respectively. When quantifying the contributions of water vapor (H2O) and temperature (T) individually, the magnitudes of the differences between the maximum RHi values inside ISSRs (RHimax) and the RHi in subsaturated surroundings are largely derived from the H2O spatial variabilities (by 88%) than from those of T (by 9%). These features hold for both ISSRs with and without ice crystals present. Similar analyses for all RHi horizontal variabilities (including ISS and non-ISS) show strong contributions from H2O variabilities at various T, H2O, pressure (P) and various horizontal scales (~1–100 km). Our results provide a new observational constraint on ISSRs on the microscale (~100 m) and point to the importance of understanding how these fine scale features originate and impact cirrus cloud formation and the RHi field in the upper troposphere (UT).

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Cloud-scale ice-supersaturated regions spatially correlate with high water vapor heterogeneities

Atmospheric Chemistry and Physics ◽

10.5194/acp-14-2639-2014 ◽

2014 ◽

Vol 14 (5) ◽

pp. 2639-2656 ◽

Cited By ~ 12

Author(s):

M. Diao ◽

M. A. Zondlo ◽

A. J. Heymsfield ◽

L. M. Avallone ◽

M. E. Paige ◽

...

Keyword(s):

Water Vapor ◽

High Water ◽

Ice Nucleation ◽

Cloud Formation ◽

Small Scale ◽

Cirrus Cloud ◽

Median Length ◽

Upper Troposphere ◽

Earth’S Climate

Abstract. Cirrus clouds have large yet uncertain impacts on Earth's climate. Ice supersaturation (ISS) – where the relative humidity with respect to ice (RHi) is greater than 100% – is the prerequisite condition of ice nucleation. Here we use 1 Hz (~230 m) in situ, aircraft-based observations from 87° N to 67° S to analyze the spatial characteristics of ice-supersaturated regions (ISSRs). The median length of 1-D horizontal ISSR segments is found to be very small (~1 km), which is 2 orders of magnitude smaller than previously reported. To understand the conditions of these small-scale ISSRs, we compare individual ISSRs with their horizontally adjacent subsaturated surroundings and show that 99% and 73% of the ISSRs are moister and colder, respectively. When quantifying the contributions of water vapor (H2O) and temperature (T) individually, the magnitudes of the differences between the maximum RHi values inside ISSRs (RHimax) and the RHi in subsaturated surroundings are largely derived from the H2O spatial variabilities (by 88%) than from those of T (by 9%). These features hold for both ISSRs with and without ice crystals present. Similar analyses for all RHi horizontal variabilities (including ISS and non-ISS) show strong contributions from H2O variabilities at various T, H2O, pressure (P) and various horizontal scales (~1–100 km). Our results provide a new observational constraint on ISSRs on the microscale (~100 m) and point to the importance of understanding how these fine-scale features originate and impact cirrus cloud formation and the RHi field in the upper troposphere (UT).

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Neurocartography: Geometry and Biology of the Central Nervous System

Microscopy and Microanalysis ◽

10.1017/s1431927600008369 ◽

1997 ◽

Vol 3 (S2) ◽

pp. 295-296

Author(s):

O. J. Tretiak ◽

J. Nissanov

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Brain Function ◽

Spatial Organization ◽

Mrna In Situ Hybridization ◽

Functional Images ◽

Recent Developments ◽

The Central Nervous System ◽

And Function

The central nervous system of a vertebrate organism exhibits a very complex spatial organization structure and function. These relationships are the subject of intense study for over a century, and recent developments in imaging have attracted ever increasing effort devoted to the understanding of brain function. One can produce any number of quantitative images that provide maps of the anatomy and function of nerve tissues. For example, autoradiography can yield functional images (2-deoxy glucose), maps of neurotransmitters receptors (over 100 know types), and gene expression labeled with complementary mRNA (in-situ hybridization). Immunohistochemistry produces maps of a large variety of neuroactive components, such as transmitters.To illustrate a typical procedure, we describe the mapping of brain function with 2-deoxy glucose (2DG). A rat performing some task is injected with a solution of 2DG radiolabeled with 14C¨ Subsequently, the animal is sacrificed, the brain is cryosectioned (ca. 20 μm), and contact autoradio-grams of these sections are made on X-ray film.

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Air Pollution and Sea Pollution Seen from Space

Surveys in Geophysics ◽

10.1007/s10712-020-09599-0 ◽

2020 ◽

Vol 41 (6) ◽

pp. 1583-1609 ◽

Cited By ~ 2

Author(s):

Camille Viatte ◽

Cathy Clerbaux ◽

Christophe Maes ◽

Pierre Daniel ◽

René Garello ◽

...

Keyword(s):

Air Pollution ◽

Marine Pollution ◽

Global Scale ◽

Small Scale ◽

Natural Environments ◽

Environmental Threats ◽

Remote Sensors ◽

Sea Pollution ◽

Complex Interactions

Abstract Air pollution and sea pollution are both impacting human health and all the natural environments on Earth. These complex interactions in the biosphere are becoming better known and understood. Major progress has been made in recent past years for understanding their societal and environmental impacts, thanks to remote sensors placed aboard satellites. This paper describes the state of the art of what is known about air pollution and focuses on specific aspects of marine pollution, which all benefit from the improved knowledge of the small-scale eddy field in the oceans. Examples of recent findings are shown, based on the global observing system (both remote and in situ) with standardized protocols for monitoring emerging environmental threats at the global scale.

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Friends with Benefits: An Inside Look of Periodontal Microbes’ Interactions Using Fluorescence In Situ Hybridization—Scoping Review

Microorganisms ◽

10.3390/microorganisms9071504 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1504

Author(s):

Guilherme Melo Esteves ◽

José António Pereira ◽

Nuno Filipe Azevedo ◽

Andreia Sofia Azevedo ◽

Luzia Mendes

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Scoping Review ◽

Large Scale ◽

Spatial Organization ◽

Ex Vivo ◽

Microbial Composition ◽

Friends With Benefits ◽

Anaerobic Microorganisms

Fluorescence in situ hybridization (FISH) has proven to be particularly useful to describe the microbial composition and spatial organization of mixed microbial infections, as it happens in periodontitis. This scoping review aims to identify and map all the documented interactions between microbes in periodontal pockets by the FISH technique. Three electronic sources of evidence were consulted in search of suitable articles up to 7 November 2020: MEDLINE (via PubMed), Scopus (Elsevier: Amsterdam, The Netherlands), and Web of Science (Clarivate Analytics: Philadelphia, PA, USA) online databases. Studies that showed ex vivo and in situ interactions between, at least, two microorganisms were found eligible. Ten papers were included. Layered or radially ordered multiple-taxon structures are the most common form of consortium. Strict or facultative anaerobic microorganisms are mostly found in the interior and the deepest portions of the structures, while aerobic microorganisms are mostly found on the periphery. We present a model of the microbial spatial organization in sub- and supragingival biofilms, as well as how the documented interactions can shape the biofilm formation. Despite the already acquired knowledge, available evidence regarding the structural composition and interactions of microorganisms within dental biofilms is incomplete and large-scale studies are needed.

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A Single Cell Atlas of Lung Development

10.1101/2021.01.21.427641 ◽

2021 ◽

Author(s):

Nicholas M. Negretti ◽

Erin J. Plosa ◽

John T. Benjamin ◽

Bryce A. Schuler ◽

A. Christian Habermann ◽

...

Keyword(s):

Single Cell ◽

Lung Development ◽

Spatial Organization ◽

Single Cell Rna Sequencing ◽

And Function ◽

Parenchymal Cells ◽

Computational Analyses ◽

Spatiotemporal Localization

SummaryLung organogenesis requires precisely timed shifts in the spatial organization and function of parenchymal cells, especially during the later stages of lung development. To investigate the mechanisms governing lung parenchymal dynamics during development, we performed a single cell RNA sequencing (scRNA-seq) time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14) in mice. We combined new computational analyses with RNA in situ hybridization to explore transcriptional velocity, fate likelihood prediction, and spatiotemporal localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of type 1 pneumocyte function during the saccular and alveolar stages, and we demonstrate an integrated view of the cellular dynamics during lung development.

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A single-cell atlas of mouse lung development

Development ◽

10.1242/dev.199512 ◽

2021 ◽

Vol 148 (24) ◽

Author(s):

Nicholas M. Negretti ◽

Erin J. Plosa ◽

John T. Benjamin ◽

Bryce A. Schuler ◽

A. Christian Habermann ◽

...

Keyword(s):

Single Cell ◽

Spatial Organization ◽

Expression Patterns ◽

Mesenchymal Cell ◽

Mouse Lung ◽

Rna In Situ Hybridization ◽

And Function ◽

Parenchymal Cells

ABSTRACT Lung organogenesis requires precise timing and coordination to effect spatial organization and function of the parenchymal cells. To provide a systematic broad-based view of the mechanisms governing the dynamic alterations in parenchymal cells over crucial periods of development, we performed a single-cell RNA-sequencing time-series yielding 102,571 epithelial, endothelial and mesenchymal cells across nine time points from embryonic day 12 to postnatal day 14 in mice. Combining computational fate-likelihood prediction with RNA in situ hybridization and immunofluorescence, we explore lineage relationships during the saccular to alveolar stage transition. The utility of this publicly searchable atlas resource (www.sucrelab.org/lungcells) is exemplified by discoveries of the complexity of type 1 pneumocyte function and characterization of mesenchymal Wnt expression patterns during the saccular and alveolar stages – wherein major expansion of the gas-exchange surface occurs. We provide an integrated view of cellular dynamics in epithelial, endothelial and mesenchymal cell populations during lung organogenesis.

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Laboratory Measurements to Image Endobenthos and Bioturbation with a High-Frequency 3D Seismic Lander

Geosciences ◽

10.3390/geosciences11120508 ◽

2021 ◽

Vol 11 (12) ◽

pp. 508

Author(s):

Inken Schulze ◽

Dennis Wilken ◽

Michael L. Zettler ◽

Mayya Gogina ◽

Mischa Schönke ◽

...

Keyword(s):

Spatial Orientation ◽

High Frequency ◽

Laboratory Experiments ◽

Small Scale ◽

3D Seismic ◽

Laboratory Measurements ◽

Practical Application ◽

Non Destructive ◽

Seismic System

The presented 3D seismic system operates three transducers (130 kHz) from a stationary lander and allows non-destructive imaging of small-scale objects within the top decimeters of silty sediments, covering a surface area of 0.2 m2. In laboratory experiments, samples such as shells, stones, and gummy worms of varied sizes (down to approx. 1 cm diameter) could be located in the 3D seismic cube to a depth of more than 20 cm and differentiated by a reflected amplitude intensity and spatial orientation. In addition, simulated bioturbation structures could be imaged. In a practical application, the system allows to determine the abundance of endobenthos and its dynamic in muddy deposits in-situ and thus identify the intensity of local bioturbation.

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