An ecophysiological explanation for manganese enrichment in rock varnish

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese—over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant—a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

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Merging Preclinical EPR Tomography with other Imaging Techniques

Cell Biochemistry and Biophysics ◽

10.1007/s12013-019-00880-7 ◽

2019 ◽

Vol 77 (3) ◽

pp. 187-196 ◽

Cited By ~ 2

Author(s):

Michal Gonet ◽

Boris Epel ◽

Howard J. Halpern ◽

Martyna Elas

Keyword(s):

Image Processing ◽

Electron Paramagnetic Resonance ◽

Image Registration ◽

Research Study ◽

Imaging Techniques ◽

Current Status ◽

Review Of The Literature ◽

Paramagnetic Resonance ◽

Preclinical Imaging ◽

Electron Paramagnetic

Abstract This paper presents a survey of electron paramagnetic resonance (EPR) image registration. Image registration is the process of overlaying images (two or more) of the same scene taken at different times, from different viewpoints and/or different techniques. EPR-imaging (EPRI) techniques belong to the functional-imaging modalities and therefore suffer from a lack of anatomical reference which is mandatory in preclinical imaging. For this reason, it is necessary to merging EPR images with other modalities which allow for obtaining anatomy images. Methodological analysis and review of the literature were done, providing a summary for developing a good foundation for research study in this field which is crucial in understanding the existing levels of knowledge. Out of these considerations, the aim of this paper is to enhance the scientific community’s understanding of the current status of research in EPR preclinical image registration and also communicate to them the contribution of this research in the field of image processing.

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Energy Filtering and Spectrum Imaging of Polymers

Microscopy and Microanalysis ◽

10.1017/s1431927600038071 ◽

2000 ◽

Vol 6 (S2) ◽

pp. 1116-1117

Author(s):

A. Aitouchen ◽

J. Taylor ◽

P. Crozier ◽

M. Libera

Keyword(s):

Imaging Techniques ◽

Polymeric Materials ◽

Chemical Imaging ◽

Polymer Particle ◽

Initial Image ◽

Image Region ◽

Energy Filtering ◽

Spectrum Imaging ◽

Field Imaging ◽

Tem Grid

Chemical imaging of polymeric materials is attractive, because of the inherently poor contrast typically afforded by multiphase amorphous polymers in bright-field imaging techniques. Spectrum imaging and energy-filtering approaches are being increasing applied to polymeric materials (1,2, 3).One recent example from the Stevens group using a Philips CM20 FEG TEM/STEM interfaced to an EmiSpec Vision data acquisition/control system and a Gatan 666 PEELS spectrometer is presented in figure 1. The specimen is a PVP sphere on a holey-carbon TEM grid. The specimen was cooled to approximately -125 °C in a single-tilt cryo stage. Drift correction was implemented by collecting HAADF STEM images from the sub-image region indicated by the dashed white box at periodic intervals. Based on an autocorrelation with the initial image, electronic shifts where imposed to correct for drift. A 3-D spectrum dataset was generated from the 70 x 70 pixel box around the polymer particle at an interpixel spacing of 5 nm and a pixel dwell time of 1.5 sec.

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Deterioration-Associated Microbiome of Stone Monuments: Structure, Variation, and Assembly

Applied and Environmental Microbiology ◽

10.1128/aem.02680-17 ◽

2018 ◽

Vol 84 (7) ◽

Cited By ~ 14

Author(s):

Qiang Li ◽

Bingjian Zhang ◽

Xiaoru Yang ◽

Qinya Ge

Keyword(s):

Microbial Communities ◽

Large Scale ◽

Imaging Techniques ◽

Bacterial Species ◽

Species Abundance ◽

Population Variation ◽

Structure Variation ◽

Content Type ◽

Stone Monuments ◽

Stone Deterioration

ABSTRACTResearch on the microbial communities that colonize stone monuments may provide a new understanding of stone biodeterioration and microbe-induced carbonate precipitation. This work investigated the seasonal variation of microbial communities in 2016 and 2017, as well as its effects on stone monuments. We determined the bacterial and fungal compositions of 12 samples from four well-separated geographic locations by using 16S rRNA and internal transcribed spacer gene amplicon sequencing.Cyanobacteriaand Ascomycota were the predominant bacterial and fungal phyla, respectively, and differences in species abundance among our 12 samples and 2 years showed no consistent temporal or spatial trends. Alpha diversity, estimated by Shannon and Simpson indices, revealed that an increase or decrease in bacterial diversity corresponded to a decrease or increase in the fungal community from 2016 to 2017. Large-scale association analysis identified potential bacteria and fungi correlated with stone deterioration. Functional prediction revealed specific pathways and microbiota associated with stone deterioration. Moreover, a culture-dependent technique was used to identify microbial isolates involved in biodeterioration and carbonatogenesis; 64% of 85 bacterial isolates caused precipitation of carbonates in biomineralization assays. Imaging techniques including scanning electron microscopy with energy-dispersive spectroscopy, X-ray diffraction, and fluorescence imaging identified CaCO3crystals as calcite and vaterite. Although CaCO3precipitation induced by bacteria often has esthetically deleterious impacts on stone monuments, this process may potentially serve as a novel, environmentally friendly bacterial self-inoculation approach to the conservation of stone.IMPORTANCEComprehensive analyses of the microbiomes associated with the deterioration of stone monuments may contribute to the understanding of mechanisms of deterioration, as well as to the identification of potentially beneficial or undesirable microbial communities and their genomic pathways. In our study, we demonstrated thatCyanobacteriawas the predominant bacterial phylum and exhibited an increase from 2016 to 2017, whileProteobacteriashowed a decreasing trend. Apart from esthetic deterioration caused by cyanobacteria and fungi, white plaque, which is composed mainly of CaCO3and is probably induced byCrossiellaandCyanobacteria, was also considered to be another threat to stone monuments. We showed that there was no significant correlation between microbial population variation and geographic location. Specific functional genes and pathways were also enriched in particular bacterial species. The CaCO3precipitation induced by an indigenous community of carbonatogenic bacteria also provides a self-inoculation approach for the conservation of stone.

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Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

Frontiers in Microbiology ◽

10.3389/fmicb.2021.618742 ◽

2021 ◽

Vol 12 ◽

Author(s):

Salma Mukhtar ◽

Samina Mehnaz ◽

Kauser Abdulla Malik

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Arid Regions ◽

Soil Moisture Content ◽

Abiotic Factors ◽

Arid Environments ◽

Desert Plants ◽

Limited Information ◽

Cholistan Desert ◽

Capparis Decidua

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.

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Applications of chemical imaging techniques in paleontology

National Science Review ◽

10.1093/nsr/nwy107 ◽

2018 ◽

Vol 6 (5) ◽

pp. 1040-1053 ◽

Cited By ~ 4

Author(s):

Yanhong Pan ◽

Liang Hu ◽

Tao Zhao

Keyword(s):

Trace Elements ◽

Spatial Distribution ◽

Imaging Techniques ◽

Chemical Imaging ◽

Specific Technique ◽

Heterogeneous Chemical ◽

Pros And Cons ◽

Organic Biomarkers ◽

Available Technology ◽

Near Future

AbstractChemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.

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Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

10.21203/rs.3.rs-15477/v1 ◽

2020 ◽

Author(s):

Ashraf Al-Ashhab ◽

Shiri Meshner ◽

Rivka Alexander-Shani ◽

Hana Dimerets ◽

Michael Brandwein ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Diversity ◽

16S Rdna ◽

Air Temperature ◽

Bacterial Communities ◽

Abiotic Factors ◽

Keystone Species ◽

Arid Environments ◽

Acacia Tortilis ◽

Biotic Factor

Abstract Background: The evolutionary relationships between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees ( Acacia raddiana and Acacia tortilis ) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results: our results showed amplifying V4 region of the 16S rDNA better presented the bacterial communities of both end and epiphytes of Acacia trees than V2, V3 and V5 regions of the 16S r DNA. When comparing the bacterial diversity of endo and epiphytes of the two acacia trees (shannon, choa1, PD and observed number of OTU’s), the epiphytes diversity indices showed about twice higher diversity compared to endophytes. The bacterial community compositions comparing both end and epiphytes were also significantly different. Interestingly, Acacia tortilis (umbral canopy shape) had a higher epiphytes bacterial diversity compared to Acacia raddiana, but were not statistically different. However the endophyte bacterial communities were significantly different compared to the two Acacia species (Firmicutes dominated Acacia raddiana and Proteobacteria dominated the Acacia tortilis ) . Alongside the biotic factor, Abiotic factors such as air temperature and precipitation also showed to significantly effect endo and epiphytes bacterial communities, while air humidity only affected the epiphytes bacterial communities.Conclusions: These results shed light on the unique desert phyllosphere microbiome in mitigating stress conditions highlighting the importance of epiphytic and endophytic microbial communities which are driven by different genotypic and abiotic factors. This paper also shows only a few bacteria species (OTUS’s) to dominate both epi and endophytes highlighting the importance of climate change (precipitation, Air temperature) in affecting arid land ecosystems where acacia trees are considered keystone species in many arid regions.

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Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

10.21203/rs.3.rs-15477/v2 ◽

2021 ◽

Author(s):

Ashraf Al-Ashhab ◽

Shiri Meshner ◽

Rivka Alexander-Shani ◽

Hana Dimerets ◽

Michael Brandwein ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Diversity ◽

Air Temperature ◽

Bacterial Communities ◽

Abiotic Factors ◽

Keystone Species ◽

Tree Canopy ◽

Arid Environments ◽

Acacia Tortilis ◽

Acacia Species

Abstract Background: The evolutionary relationships and interactions between plants and their microbiomes are of high importance to the survival of plants in extreme conditions. Changes in the plant’s microbiome can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopy) and seasonality on the epiphytic and endophytic microbiomes associated with these two tree species. One hundred and thirty nine leaf samples were collected throughout the year and their microbial communities were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity estimates (Shannon-Wiener, Chao1, Simpson and observed number of OTUs), were found to be nearly double compared to endophyte counterparts, in addition epi- and endophyte communities were significantly different from each other. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species but the canopy sides and sample months exhibited different diversity, while the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epi- and endophytes communities. Bacterial community compositions showed that Firmicutes dominate Acacia raddiana and Proteobacteria dominate Acacia tortilis; these bacterial communities only consisted of a small number of bacterial families mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities. Interestingly, about 60% of the obtained bacterial classification were unclassified below family level. Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epi- and endophytes, highlighting the importance of climate change (precipitation, air temperature and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

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Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00301 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 22

Author(s):

Alexander Crits-Christoph ◽

Courtney K. Robinson ◽

Bing Ma ◽

Jacques Ravel ◽

Jacek Wierzchos ◽

...

Keyword(s):

Substrate Specificity ◽

Microbial Communities ◽

Arid Environments

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Metagenomic Analyses: Past and Future Trends

Applied and Environmental Microbiology ◽

10.1128/aem.02345-10 ◽

2010 ◽

Vol 77 (4) ◽

pp. 1153-1161 ◽

Cited By ~ 386

Author(s):

Carola Simon ◽

Rolf Daniel

Keyword(s):

Microbial Communities ◽

Sequence Data ◽

Extreme Environments ◽

Data Sets ◽

Metagenomic Dna ◽

Functional Dynamics ◽

Dna Libraries ◽

Water Analyses ◽

Independent Assessment ◽

Generation Sequencing

ABSTRACTMetagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.

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