An emerging view of the diversity, ecology, and function of Archaea in alkaline hydrothermal environments

2020 ◽  
Author(s):  
Rebecca C Mueller ◽  
Jesse T Peach ◽  
Dana J Skorupa ◽  
Valerie Copié ◽  
Brian Bothner ◽  
...  
Keyword(s):  
High Temperatures ◽  
Metabolic Pathways ◽  
Hot Springs ◽  
Hydrothermal Systems ◽  
Environmental Pressures ◽  
High Ph ◽  
Sequencing Technologies ◽  
And Function ◽  
Hydrothermal Environments

Abstract The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi–omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.

scholarly journals Mineralogical and Geochemical Signatures of Metalliferous Sediments in Wocan-1 and Wocan-2 Hydrothermal Sites on the Carlsberg Ridge, Indian Ocean

Minerals ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 26 ◽  
Author(s):  
Samuel Olatunde Popoola ◽  
Xiqiu Han ◽  
Yejian Wang ◽  
Zhongyan Qiu ◽  
Ying Ye ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Volcanic Glass ◽  
Mineral Chemistry ◽  
Hydrothermal Systems ◽  
Bulk Sediment ◽  
Sediment Samples ◽  
Metalliferous Sediments ◽  
Metalliferous Sediment ◽  
Carlsberg Ridge ◽  
Hydrothermal Environments

In this paper, we conduct a comparative study on the mineralogy and geochemistry of metalliferous sediment collected near the active hydrothermal site (Wocan-1) and inactive hydrothermal site (Wocan-2) from Wocan Hydrothermal Field, on the Carlsberg Ridge (CR), northwest Indian Ocean. We aim to understand the spatial variations in the primary and post-depositional conditions and the intensity of hydrothermal circulations in the Wocan hydrothermal systems. Sediment samples were collected from six stations which includes TVG-07, TVG-08 (Wocan-1), TVG-05, TVG-10 (Wocan-2), TVG-12 and TVG-13 (ridge flanks). The mineralogical investigations show that sediment samples from Wocan-1 and Wocan-2 are composed of chalcopyrite, pyrite, sphalerite, barite, gypsum, amorphous silica, altered volcanic glass, Fe-oxides, and hydroxides. The ridge flank sediments are dominated by biogenic calcite and foraminifera assemblages. The bulk sediment samples of Wocan-1 have an elevated Fe/Mn ratio (up to ~1545), with lower U contents (<7.4 ppm) and U/Fe ratio (<~1.8 × 10−5). The sulfide separates (chalcopyrite, pyrite, and sphalerite) are enriched in Se, Co, As, Sb, and Pb. The calculated sphalerite precipitation temperature (Sph.PT) yields ~278 °C. The sulfur isotope (δ34S) analysis returned a light value of 3.0–3.6‰. The bulk sediment samples of Wocan-2 have a lower Fe/Mn ratio (<~523), with high U contents (up to 19.6 ppm) and U/Fe ratio (up to ~6.2 × 10−5). The sulfide separates are enriched in Zn, Cu, Tl, and Sn. The calculated Sph.PT is ~233 °C. The δ34S returned significant values of 4.1–4.3‰ and 6.4–8.7‰ in stations TVG-10 and TVG-05, respectively. The geochemical signatures (e.g., Fe/Mn and U/Fe ratio, mineral chemistry of sulfides separates, and S-isotopes and Sph.PT) suggest that sediment samples from Wocan-1 are located near intermediate–high temperature hydrothermal discharge environments. Additionally, relatively low δ34S values exhibit a lower proportion (less than 20%) of seawater-derived components. The geochemical signatures suggest that sediment samples from Wocan-2 has undergone moderate–extensive oxidation and secondary alterations by seawater in a low–intermediate temperature hydrothermal environments. Additionally, the significant δ34S values of station TVG-05 exhibit a higher estimated proportion (up to 41%) of seawater-derived components. Our results showed pervasive hydrothermal contributions into station TVG-08 relative to TVG-07, it further showed the increased process of seafloor weathering at TVG-05 relative to TVG-10.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

scholarly journals How Changes in the Nutritional Landscape Shape Gut Immunometabolism

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 823
Author(s):  
Jian Tan ◽  
Duan Ni ◽  
Rosilene V. Ribeiro ◽  
Gabriela V. Pinget ◽  
Laurence Macia
Keyword(s):  
Immune Cells ◽  
Metabolic Pathways ◽  
Immune Cell ◽  
Food Additives ◽  
Cell Activity ◽  
Inflammatory Cells ◽  
Therapeutic Approaches ◽  
Food Antigens ◽  
And Function ◽  
Micro Organisms

Cell survival, proliferation and function are energy-demanding processes, fuelled by different metabolic pathways. Immune cells like any other cells will adapt their energy production to their function with specific metabolic pathways characteristic of resting, inflammatory or anti-inflammatory cells. This concept of immunometabolism is revolutionising the field of immunology, opening the gates for novel therapeutic approaches aimed at altering immune responses through immune metabolic manipulations. The first part of this review will give an extensive overview on the metabolic pathways used by immune cells. Diet is a major source of energy, providing substrates to fuel these different metabolic pathways. Protein, lipid and carbohydrate composition as well as food additives can thus shape the immune response particularly in the gut, the first immune point of contact with food antigens and gastrointestinal tract pathogens. How diet composition might affect gut immunometabolism and its impact on diseases will also be discussed. Finally, the food ingested by the host is also a source of energy for the micro-organisms inhabiting the gut lumen particularly in the colon. The by-products released through the processing of specific nutrients by gut bacteria also influence immune cell activity and differentiation. How bacterial metabolites influence gut immunometabolism will be covered in the third part of this review. This notion of immunometabolism and immune function is recent and a deeper understanding of how lifestyle might influence gut immunometabolism is key to prevent or treat diseases.

scholarly journals Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks

2020 ◽  
Author(s):  
Tom J. Clement ◽  
Erik B. Baalhuis ◽  
Bas Teusink ◽  
Frank J. Bruggeman ◽  
Robert Planqué ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Networks ◽  
Full Range ◽  
Biotechnological Potential ◽  
Metabolic Network Reconstruction ◽  
And Function ◽  
Multicellular Organisms ◽  
Genome Scale ◽  
Threat Levels ◽  
Experimental Characterisation

AbstractThe metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterisation is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be computed from an organism’s annotated genome using metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods aim to enumerate all metabolic pathways, while computation of all (elementally balanced) conversions between nutrients and products would suffice. Indeed, the elementary conversion modes (ECMs, defined by Urbanczik and Wagner) capture the full metabolic capabilities of a network, but the use of ECMs has not been accessible, until now. We extend and explain the theory of ECMs, implement their enumeration in ecmtool, and illustrate their applicability. This work contributes to the elucidation of the full metabolic footprint of any cell.

scholarly journals A Deep Dive into Genome Assemblies of Non-vertebrate Animals

2021 ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Ramón Rivera-Vicéns ◽  
Romain Koszul ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Current Knowledge ◽  
Genome Structure ◽  
Deep Dive ◽  
Sequencing Technologies ◽  
Current State ◽  
Animal Diversity ◽  
And Function ◽  
Genome Assemblies ◽  
Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

Pentose Phosphate Pathway in Disease and Therapy

2014 ◽  
Vol 995 ◽  
pp. 1-27 ◽  
Author(s):  
Mahbuba Rahman ◽  
M. Rubayet Hasan
Keyword(s):  
Metabolic Pathways ◽  
Cell Cycle Progression ◽  
Metabolic Diseases ◽  
Pentose Phosphate ◽  
Cycle Progression ◽  
Novel Drugs ◽  
Abnormal Cells ◽  
Living Organisms ◽  
And Function

Pentose phosphate (PP) pathway, which is ubiquitously present in all living organisms, is one of the major metabolic pathways associated with glucose metabolism. The most important functions of this pathway includes the generation of reducing equivalents in the form of NADPH for reductive biosynthesis, and production of ribose sugars for the biosynthesis of nucleotides, amino acids, and other macromolecules required by all living cells. Under normal conditions of growth, PP pathway is important for cell cycle progression, myelin formation, and the maintenance of the structure and function of brain, liver, cortex and other organs. Under diseased conditions, such as in cases of many metabolic, neurological or malignant diseases, pathological mechanisms augment due to defects in the PP pathway genes. Adoption of alternative metabolic pathways by cells that are metabolically abnormal, or malignant cells that are resistant to chemotherapeutic drugs often plays important roles in disease progression and severity. Accordingly, the PP pathway has been suggested to play critical roles in protecting cancer or abnormal cells by providing reduced environment, to protect cells from oxidative damage and generating structural components for nucleic acids biosynthesis. Novel drugs that targets one or more components of the PP pathway could potentially serve to overcome challenges associated with currently available therapeutic options for many metabolic and non-metabolic diseases. However, careful designing of drugs is critical that takes into the accounts of cell’s broader genomic, proteomic and metabolic contexts under consideration, in order to avoid undesirable side-effects. In this review, we discuss the role of PP pathway under normal and abnormal physiological conditions and the potential of the PP pathway as a target for new drug development to treat metabolic and non-metabolic diseases.

INTERACTION: INTeraction between lifE, Rifting And Caldera Tectonics In OkataiNa

2021 ◽  
Author(s):  
Cécile Massiot ◽  
Craig Miller ◽  
Matthew Stott ◽  
Pilar Villamor ◽  
Hiroshi Asanuma ◽  
...  
Keyword(s):  
Hot Springs ◽  
Microbial Community Composition ◽  
Volcanic Eruptions ◽  
Economic Benefits ◽  
Hydrothermal Systems ◽  
Seismic Hazards ◽  
Geothermal Resources ◽  
Ongoing Research ◽  
Scientific Drilling ◽  
Drill Cores

&lt;p&gt;Calderas are major volcanic features with large volcanic and seismic hazards. They also host diverse microbiota, provide heat, energy, mineral and economic benefits. Despite their scientific and socio-economic importance, we still do not completely understand calderas and the interactions between volcanism, tectonism, fluid circulation and the deep biosphere because in-situ and subsurface observations are sparse.&lt;/p&gt;&lt;p&gt;The Okataina Volcanic Centre (OVC) in Aotearoa New Zealand, is one of two active giant calderas of the Taup&amp;#333; Volcanic Zone within the rapidly extending continental intra-arc Taup&amp;#333; Rift. This superb natural laboratory has: 1) numerous past eruptions of varied size and style, 2) documented co-eruptive earthquakes, 3) vigorous hydrothermal manifestations, 4) diverse microbial communities in hot springs but unknown in the subsurface.&lt;/p&gt;&lt;p&gt;We propose to establish a scientific drilling programme at the OVC to address:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;What are the conditions leading to volcanic eruptions; and volcano-tectonic feedbacks in intra-rift calderas?&lt;/li&gt; &lt;li&gt;What controls fluid circulations in active calderas/rift regions?&lt;/li&gt; &lt;li&gt;Does subsurface microbial community composition vary with tectonic and/or volcanic activity?&lt;/li&gt; &lt;/ul&gt;&lt;p&gt;High temperatures complicate drillhole design, restrict data collection and prevent exploration of the biosphere. By targeting the cooler parts of the caldera, this project will use conventional engineering to maximise sampling (drill cores and fluids), downhole logging and establish long-term observatories.&lt;/p&gt;&lt;p&gt;Two preliminary drill targets are suggested: (1) in the centre of the caldera; (2) through the caldera margin. Drill data will provide a comprehensive record of past activity, establishing eruption frequency-magnitude relationships and precursors. Combined with well-known fault rupture history, the relative timing of tectonic and magmatic activity will be untangled. Drill data will unravel the relationships between the groundwater and hydrothermal systems, magma, faults and stress, informing thermo-hydro-mechanical regional caldera models with findings applicable worldwide. Drill cores and a dedicated fluid sampler triggered by nearby earthquakes will reveal the composition, function and potential change of microbial activity in response to rock and fluid variations.&lt;/p&gt;&lt;p&gt;The programme is informed by indigenous M&amp;#257;ori, regulatory authorities and emergency managers to ensure scientific, cultural, regulatory and resilience outcomes. The programme will underpin 1) community resilience to volcanic and seismic hazards; 2) sustainable management of groundwater and geothermal resources, and 3) understanding of subsurface microbial diversity, function and geobiological interactions. At these early stages of planning, we invite the scientific community to contribute to the concept of this project in the exceptional OVC settings and strengthen linkages with other ongoing research and scientific drilling programmes.&lt;/p&gt;

scholarly journals Ideas and perspectives: Development of nascent autotrophic carbon fixation systems in various redox conditions of the fluid degassing on early Earth

2019 ◽  
Vol 16 (8) ◽  
pp. 1817-1828 ◽  
Author(s):  
Sergey A. Marakushev ◽  
Ol'ga V. Belonogova
Keyword(s):  
Carbon Fixation ◽  
Hydrothermal Systems ◽  
System Model ◽  
Early Earth ◽  
Hydrothermal Conditions ◽  
Oxidation Of Methane ◽  
The Earth ◽  
Autotrophic Metabolism ◽  
Metabolic Systems ◽  
Hydrothermal Environments

Abstract. The origin and development of the primary autotrophic metabolism on early Earth were influenced by the two main regimes of degassing of the Earth – reducing (predominance CH4) and oxidative (CO2). Among the existing theories of the autotrophic origin of life in hydrothermal environments, CO2 is usually considered to be the carbon source for nascent autotrophic metabolism. However, the ancestral carbon used in metabolism may have been derived from CH4 if the outflow of magma fluid to the surface of the Earth consisted mainly of methane. In such an environment, the primary autotrophic metabolic systems had to be methanotrophic. Due to the absence of molecular oxygen in the Archean conditions, this metabolism would have been anaerobic; i.e., oxidation of methane must be realized by inorganic high-potential electron acceptors. In light of the primacy and prevalence of CH4-dependent metabolism in hydrothermal systems of the ancient Earth, we propose a model of carbon fixation where the methane is fixed or transformed in a sequence of reactions in an autocatalytic methane–fumarate cycle. Nitrogen oxides are thermodynamically the most favorable among possible oxidants of methane; however, even the activity of oxygen created by mineral buffers of iron in hydrothermal conditions is sufficient for methanotrophic acetogenesis. The hydrothermal system model is considered in the form of a phase diagram, which demonstrates the area of redox and P and T conditions favorable for the development of the primary methanotrophic metabolism.

scholarly journals Energy metabolism manipulates the fate and function of tumour myeloid-derived suppressor cells

2019 ◽  
Vol 122 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Cong Hu ◽  
Bo Pang ◽  
Guangzhu Lin ◽  
Yu Zhen ◽  
Huanfa Yi
Keyword(s):  
Metabolic Pathways ◽  
Immune Surveillance ◽  
Suppressor Cells ◽  
Tumour Microenvironment ◽  
Metabolic Energy ◽  
Myeloid Derived Suppressor Cells ◽  
Cell Responses ◽  
And Function ◽  
Promote Tumour Development

AbstractIn recent years, a large number of studies have been carried out in the field of immune metabolism, highlighting the role of metabolic energy reprogramming in altering the function of immune cells. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells generated during a large array of pathological conditions, such as cancer, inflammation, and infection, and show remarkable ability to suppress T-cell responses. These cells can also change their metabolic pathways in response to various pathogen-derived or inflammatory signals. In this review, we focus on the roles of glucose, fatty acid (FA), and amino acid (AA) metabolism in the differentiation and function of MDSCs in the tumour microenvironment, highlighting their potential as targets to inhibit tumour growth and enhance tumour immune surveillance by the host. We further highlight the remaining gaps in knowledge concerning the mechanisms determining the plasticity of MDSCs in different environments and their specific responses in the tumour environment. Therefore, this review should motivate further research in the field of metabolomics to identify the metabolic pathways driving the enhancement of MDSCs in order to effectively target their ability to promote tumour development and progression.

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