Snowball Earth, population bottleneck and
            Prochlorococcus
            evolution

Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that this Prochlorococcus genome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibited Prochlorococcus growth and proliferation, and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations accumulated across genomic regions and inherited by descendant lineages. Prochlorococcus adaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. Key metabolic innovation includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event may have altered the physiological characters of Prochlorococcus , shaping their ecologically vital role as the most abundant primary producers in the modern oceans.

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Snowball Earths, population bottlenecks, and the evolution of marine photosynthetic bacteria

10.1101/2020.11.24.395392 ◽

2020 ◽

Author(s):

Hao Zhang ◽

Ying Sun ◽

Qinglu Zeng ◽

Sean A. Crowe ◽

Haiwei Luo

Keyword(s):

Vital Role ◽

Genome Reduction ◽

Snowball Earth ◽

Population Bottlenecks ◽

Metabolic Potential ◽

Nitrogen Acquisition ◽

Peptidoglycan Biosynthesis ◽

Photosynthetic Organisms ◽

Dim Light ◽

Genomic Imprints

AbstractProchlorococcus are the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that this Prochlorococcus genome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibited Prochlorococcus growth and proliferation and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations that accumulated across genomic regions in the descendant lineages. Prochlorococcus adaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. This metabolic potential includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption, and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event altered the physiological characters of Prochlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.Significance StatementProchlorococcus are the most abundant photosynthetic organisms in the modern ocean, where they support much of the marine and global biological productivity. In this study, we reconstructed a precise timeline of Prochlorococcus evolution and discovered that a major Prochlorococcus genome reduction took place during the Neoproterozoic Snowball Earth events. Since Prochlorococcus are generally adapted to warm waters, the extremely cold conditions during the Snowball Earth drove population bottlenecks, which left strong signatures in genomic DNA through the accumulation of detrimental mutations. The reconstruction of ancestral genome content further unveiled the metabolic strategies that Prochlorococcus evolved to overcome the extreme conditions during the climate catastrophe. These findings show how large changes in Earth’s past climate have left genomic imprints on extant microorganisms, likely shaping their metabolic potential and ecological role in the oceans today.

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Genomic insights into the ecological role and evolution of a novel Thermoplasmata order, “ Candidatus Sysuiplasmatales”

Applied and Environmental Microbiology ◽

10.1128/aem.01065-21 ◽

2021 ◽

Author(s):

Yang Yuan ◽

Jun Liu ◽

Tao-Tao Yang ◽

Shao-Ming Gao ◽

Bin Liao ◽

...

Keyword(s):

Carbon Fixation ◽

Extreme Environments ◽

Metabolic Reconstruction ◽

Rrna Gene ◽

Ancestral State ◽

Metabolic Potential ◽

Facultatively Anaerobic ◽

Acid Generation ◽

A Genome ◽

Evolutionary Paths

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation and evolution of novel archaeal lineages from a variety of extreme environments. We have utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (“ Candidatus Sysuiplasmatales”) within Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene based analyses revealed a narrow habitat range for these uncultured archaea limiting to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea which typically show obligately anaerobic metabolisms. Notably, “ Ca. Sysuiplasmatales” could conserve energy through degradation of fatty acids, amino acid metabolism and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike its closely related Methanomassiliicoccales and “ Ca. Gimiplasmatales”, “ Ca. Sysuiplasmatales” lack the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that “ Ca. Sysuiplasmatales” and its closely related Methanomassiliicoccales, “ Ca. Gimiplasmatales”, and the SG8-5 and the RBG-16-68-12 orders originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H 4 F Wood–Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. Importance A wide array of archaea populate Earth’s extreme environments thereby they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited considering the uncultured majority of archaeal diversity. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, namely “ Ca . Sysuiplasmatales”, within Thermoplasmata in the extremely acidic mine environments. “ Ca . Sysuiplasmatales” are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between “ Ca . Sysuiplasmatales” and its closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.

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Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulation in Rice

10.21203/rs.3.rs-132374/v1 ◽

2020 ◽

Author(s):

Shoudong Wang ◽

Shuo Sun ◽

Runze Guo ◽

Wenying Liao ◽

Huixia Shou

Keyword(s):

Regulatory Networks ◽

Rice Genome ◽

Vital Role ◽

Fe Deficiency ◽

Transcriptional Level ◽

Systematic Screening ◽

Cellular Processes ◽

Yield And Quality ◽

Fe Homeostasis ◽

Genomic Regions

Abstract Background Iron (Fe) plays a vital role in various cellular processes in plants, including biosynthesis of chlorophyll, photosynthesis and respiration. Fe deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Long non-coding RNAs (lncRNAs) have recently been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency in plants has not been reported. Results In this work, lncRNAs responsive to Fe deficiency were identified across the rice genome by strand-specific RNA sequencing. In total, 6,477 lncRNAs were identified. In Fe-deficient conditions, 47 lncRNAs were up-regulated and 33 lncRNAs were down-regulated in shoots, while 89 lncRNAs were up-regulated and 32 lncRNAs were down-regulated in roots, compared to normal conditions. Two lncRNAs (XLOC_010112 and XLOC_053944) were identified as potential miRNA precursors and another two (XLOC_012715 and XLOC_054182) as miRNA target mimics that may participate in Fe regulation. A number of differentially expressed lncRNAs (DE-lncRNAs) are likely to modulate the expression of Fe-related genes via a cis- or trans-regulation mode, including 3 DE-lncRNAs (XLOC_034336, XLOC_037283 and XLOC_043545) located nearby OsbHLH156 and OsHRZ2 genomic regions. Seventy-six DE-lncRNAs were found to be regulated by bHLH156 at the transcriptional level. Conclusions This study provides a first profile of lncRNA expression as well as identifies the lncRNAs likely to play important roles in the regulation of Fe homeostasis. This identification and characterization form an important basis for understanding Fe regulatory networks in rice.

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Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach

Scientific Reports ◽

10.1038/s41598-020-64074-5 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Viktor Vernyik ◽

Ildikó Karcagi ◽

Edit Tímár ◽

István Nagy ◽

Ádám Györkei ◽

...

Keyword(s):

Growth Parameters ◽

Genetic Material ◽

Genome Reduction ◽

Wild Type ◽

Bacterial Genomes ◽

E Coli ◽

Full Knowledge ◽

Fitness Benefits ◽

Genomic Regions ◽

Selection Of

AbstractArtificial simplification of bacterial genomes is thought to have the potential to yield cells with reduced complexity, enhanced genetic stability, and improved cellular economy. Of these goals, economical gains, supposedly due to the elimination of superfluous genetic material, and manifested in elevated growth parameters in selected niches, have not yet been convincingly achieved. This failure might stem from limitations of the targeted genome reduction approach that assumes full knowledge of gene functions and interactions, and allows only a limited number of reduction trajectories to interrogate. To explore the potential fitness benefits of genome reduction, we generated successive random deletions in E. coli by a novel, selection-driven, iterative streamlining process. The approach allows the exploration of multiple streamlining trajectories, and growth periods inherent in the procedure ensure selection of the fittest variants of the population. By generating single- and multiple-deletion strains and reconstructing the deletions in the parental genetic background, we showed that favourable deletions can be obtained and accumulated by the procedure. The most reduced multiple-deletion strain, obtained in five deletion cycles (2.5% genome reduction), outcompeted the wild-type, and showed elevated biomass yield. The spectrum of advantageous deletions, however, affecting only a few genomic regions, appears to be limited.

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Ultrastructure of Lymphatic Capillaries in the Transport of Colloidal Particles

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100060945 ◽

1967 ◽

Vol 25 ◽

pp. 186-187

Author(s):

L. V. Leak ◽

J. F. Burke

Keyword(s):

Connective Tissue ◽

Colloidal Particles ◽

Ultrastructural Level ◽

Vital Role ◽

Time Intervals ◽

Thorium Dioxide ◽

Lymphatic Capillary ◽

Tissue Area ◽

Rapid Removal ◽

Tissue Fluids

The vital role played by the lymphatic capillaries in the transfer of tissue fluids and particulate materials from the connective tissue area can be demonstrated by the rapid removal of injected vital dyes into the tissue areas. In order to ascertain the mechanisms involved in the transfer of substances from the connective tissue area at the ultrastructural level, we have injected colloidal particles of varying sizes which range from 80 A up to 900-mμ. These colloidal particles (colloidal ferritin 80-100A, thorium dioxide 100-200 A, biological carbon 200-300 and latex spheres 900-mμ) are injected directly into the interstitial spaces of the connective tissue with glass micro-needles mounted in a modified Chambers micromanipulator. The progress of the particles from the interstitial space into the lymphatic capillary lumen is followed by observing tissues from animals (skin of the guinea pig ear) that were injected at various time intervals ranging from 5 minutes up to 6 months.

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Cytochemical Studies of Cell Wall Biosynthesis in Staphylococcus Aureus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100094905 ◽

1972 ◽

Vol 30 ◽

pp. 328-329

Author(s):

Masaatsu Koike ◽

Koichi Nakashima ◽

Kyoko Iida

Keyword(s):

Staphylococcus Aureus ◽

Periodate Oxidation ◽

Early Time ◽

The Other ◽

Penicillin G ◽

Cell Wall Biosynthesis ◽

Septal Wall ◽

Peptidoglycan Biosynthesis ◽

Gram Positive Bacteria ◽

Cross Linkage

Penicillin exerts the activity to inhibit the peptide cross linkage between each polysaccharide backbone at the final stage of wall-peptidoglycan biosynthesis of bacteria. Morphologically, alterations of the septal wall and mesosome in gram-positive bacteria, which were occurred in early time after treatment with penicillin, have been observed. In this experiment, these alterations were cytochemically investigated by means of silver-methenamine staining after periodate oxidation, which is applied for detection of localization of wall mucopolysaccharide.Staphylococcus aureus strain 209P treated with 100 u/ml of penicillin G was divided into two aliquotes. One was fixed by Kellenberger-Ryter's OSO4 fixative at 30, 60 and 120 min after addition of the antibiotic, dehydrated through alcohol series, and embedded in Epon 812 (Specimen A). The other was fixed by 21 glutaraldehyde, dehydrated through glycolmethacrylate series and embedded in glycolmethacrylate mixture, according to Bernhard's method (Specimen B).

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Three-Dimensional reconstruction of isolated centrosomes by automated electron tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100169286 ◽

1994 ◽

Vol 52 ◽

pp. 310-311

Author(s):

M.B. Braunfeld ◽

M. Moritz ◽

B.M. Alberts ◽

J.W. Sedat ◽

D.A. Agard

Keyword(s):

Electron Tomography ◽

Three Dimensional ◽

Vital Role ◽

Complex Nature ◽

Animal Cells ◽

Microtubule Organizing Center ◽

Nucleation Sites ◽

Dimensional Reconstruction ◽

Organizing Center ◽

Resolution Model

In animal cells, the centrosome functions as the primary microtubule organizing center (MTOC). As such the centrosome plays a vital role in determining a cell's shape, migration, and perhaps most importantly, its division. Despite the obvious importance of this organelle little is known about centrosomal regulation, duplication, or how it nucleates microtubules. Furthermore, no high resolution model for centrosomal structure exists.We have used automated electron tomography, and reconstruction techniques in an attempt to better understand the complex nature of the centrosome. Additionally we hope to identify nucleation sites for microtubule growth.Centrosomes were isolated from early Drosophila embryos. Briefly, after large organelles and debris from homogenized embryos were pelleted, the resulting supernatant was separated on a sucrose velocity gradient. Fractions were collected and assayed for centrosome-mediated microtubule -nucleating activity by incubating with fluorescently-labeled tubulin subunits. The resulting microtubule asters were then spun onto coverslips and viewed by fluorescence microscopy.

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Asiana Airlines Flight 214

Aviation Psychology and Applied Human Factors ◽

10.1027/2192-0923/a000066 ◽

2014 ◽

Vol 4 (2) ◽

pp. 113-121 ◽

Cited By ~ 5

Author(s):

Stephanie Chow ◽

Stephen Yortsos ◽

Najmedin Meshkati

Keyword(s):

Human Factors ◽

Aviation Safety ◽

Cultural Factors ◽

Vital Role ◽

Cultural Issues ◽

Flight Crew ◽

Pilot Performance ◽

Engineering Designs ◽

Flight Deck

This article focuses on a major human factors–related issue that includes the undeniable role of cultural factors and cockpit automation and their serious impact on flight crew performance, communication, and aviation safety. The report concentrates on the flight crew performance of the Boeing 777–Asiana Airlines Flight 214 accident, by exploring issues concerning mode confusion and autothrottle systems. It also further reviews the vital role of cultural factors in aviation safety and provides a brief overview of past, related accidents. Automation progressions have been created in an attempt to design an error-free flight deck. However, to do that, the pilot must still thoroughly understand every component of the flight deck – most importantly, the automation. Otherwise, if pilots are not completely competent in terms of their automation, the slightest errors can lead to fatal accidents. As seen in the case of Asiana Flight 214, even though engineering designs and pilot training have greatly evolved over the years, there are many cultural, design, and communication factors that affect pilot performance. It is concluded that aviation systems designers, in cooperation with pilots and regulatory bodies, should lead the strategic effort of systematically addressing the serious issues of cockpit automation, human factors, and cultural issues, including their interactions, which will certainly lead to better solutions for safer flights.

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