scholarly journals Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

2021 ◽  
Author(s):  
Rulong Liu ◽  
Xing Wei ◽  
Li Wang ◽  
Junwei Cao ◽  
Weizhi Song ◽  
...  
Keyword(s):  
Deep Sea ◽  
Polyaromatic Hydrocarbons ◽  
Oxidative Degradation ◽  
Deep Ocean ◽  
Metabolic Reconstruction ◽  
Regulatory Modules ◽  
Metabolic Plasticity ◽  
Wide Range ◽  
Metabolic Strategies ◽  
First Time

Abstract Background: The deep-sea harbors the majority of the microbial biomass on Earth, and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolisms in the deep ocean are greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches - the deepest part of the ocean. Results: In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. Sixty-two metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family and one novel order within the classes Anaerolinea and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in-situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly have a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur and halogenated compounds. Our results reveal for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g. benzoate), polyaromatic hydrocarbons (e.g. fluorene), polychlorobiphenyl (e.g. 4-chlorobiphenyl) and organochlorine compounds (e.g. chloroalkanes, chlorocyclohexane). Moreover, these organisms show the potential to synthesize energy storage compounds (e.g. trehalose), and have regulatory modules to respond to changes in nutrient conditions. These metabolic traits lead us to postulate that the Chloroflexi may follow a “feast and famine” metabolic strategy, which allows them to efficiently consume labile OM and store the energy under rich OM conditions, and to survive under OM limitations by utilizing stored energy and degrading recalcitrant OM. Conclusion: This study expands the knowledge on metabolic processes in deep-ocean Chlorolfexi, and highlights their significance in deep-sea carbon, sulfur and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for the survival under variable and heterogenic OM inputs in the deep ocean.

scholarly journals Novel Chloroflexi Genomes From The Deepest Ocean Reveal Metabolic Strategies For The Adaptation To Deep-Sea Habitats

2021 ◽  
Author(s):  
Rulong Liu ◽  
Xing Wei ◽  
Li Wang ◽  
Junwei Cao ◽  
Weizhi Song ◽  
...  
Keyword(s):  
Deep Sea ◽  
Current Knowledge ◽  
Polyaromatic Hydrocarbons ◽  
Oxidative Degradation ◽  
Deep Ocean ◽  
Metabolic Reconstruction ◽  
Regulatory Modules ◽  
Metabolic Plasticity ◽  
Wide Range ◽  
Metabolic Strategies

Abstract Background: The deep-sea harbors the majority of the microbial biomass in the Ocean, and it is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches - the deepest part of the ocean. Results: In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. Sixty-two metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in-situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g. benzoate), polyaromatic hydrocarbons (e.g. fluorene), polychlorobiphenyl (e.g. 4-chlorobiphenyl) and organochlorine compounds (e.g. chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g. trehalose), and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits lead us to postulate that the Chloroflexi may follow a “feast and famine” metabolic strategy, allowing them to efficiently consume labile OM and store the energy under OM rich conditions, and to survive under OM limitations by utilizing stored energy and degrading recalcitrant OM. Conclusion: This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi, and highlights their significance in deep-sea carbon, sulfur and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for the survival under variable and heterogenic OM inputs in the deep ocean.

Working Tools Study for JiaoLong Manned Submersible

2019 ◽  
Vol 53 (2) ◽  
pp. 56-64
Author(s):  
Xianpeng Shi ◽  
Yugang Ren ◽  
Jialing Tang ◽  
Wentao Fu ◽  
Baohua Liu
Keyword(s):  
Deep Sea ◽  
High Efficiency ◽  
Deep Ocean ◽  
Basic Research ◽  
Extreme Environment ◽  
The Past ◽  
Wide Range ◽  
Manned Submersible ◽  
Observation Function ◽  
Scientific Questions

AbstractThe remarkable progress in deep submergence science with manned submersibles in the past 50 years has made it possible for us to directly explore the inaccessible underwater extreme environment. Basic research carried out at depths over 1,000 m in the deep ocean has provided dramatic and unique insights into some of the most compelling scientific questions ever posed. Deep research manned submersibles have been widely recognized as indispensable platforms for conducting deep-sea research. Whereas all deep-sea submersibles share the unique feature of direct observation function by scientists and pilots from the cabin, all manned submersibles are equipped with different tools to implement a wide range of jobs in different exploration purposes. These can directly affect productivity and each dive's outcomes, such that it would be meaningful to study the samplers, sensors, and other devices that have been installed on the different deep-sea research manned submersibles around the world. This article will also introduce the research and development status of the JiaoLong manned submersible's operational tools, which have been researched and tested during the sea trials and test operational phase over the past 9 years. Based on developed technologies, state-of-the-art tools are essential to achieve a high-efficiency use for each dive. The article brings forward discussion and suggestions for the development of JiaoLong's operational tools, followed by a conclusion from the perspective of JiaoLong's operation team.

scholarly journals Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology

2020 ◽  
Author(s):  
Rikuan Zheng ◽  
Rui Liu ◽  
Yeqi Shan ◽  
Ruining Cai ◽  
Ge Liu ◽  
...  
Keyword(s):  
Deep Sea ◽  
Deep Ocean ◽  
Extracellular Dna ◽  
Phenotypic Traits ◽  
The Novel ◽  
Metabolic Potential ◽  
Free Living ◽  
Living Wall ◽  
First Time

AbstractCandidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes found in deep-sea methane seeps. Unfortunately, the paucity of marine isolates currently available has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we present a detailed description of the phenotypic traits, genomic data and central metabolisms tested in both laboratorial and deep-sea environments of the novel strain zrk13, which allows for the first time the reconstruction of the metabolic potential and lifestyle of a member of the tentatively defined Candidatus Izimaplasma. On the basis of the description of strain zrk13, the novel species and genus Xianfuyuplasma coldseepsis is proposed. Notably, DNA degradation driven by X. coldseepsis zrk13 was detected in both laboratorial and in situ conditions, strongly indicating it is indeed a key DNA degrader. Moreover, the putative genes determining degradation broadly distribute in the genomes of other Izimaplasma members. Given extracellular DNA is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor, Izimaplasma bacteria are thought to be important contributors to the biogeochemical cycling in the deep ocean.

Relationship between morphometrics and trophic levels in deep-sea fishes

2020 ◽  
Vol 637 ◽  
pp. 225-235 ◽  
Author(s):  
MA Ladds ◽  
MH Pinkerton ◽  
E Jones ◽  
LM Durante ◽  
MR Dunn
Keyword(s):  
Stable Isotopes ◽  
Trophic Level ◽  
Deep Sea ◽  
Strong Relationship ◽  
Ecosystem Model ◽  
Trophic Levels ◽  
Fish Size ◽  
Wide Range ◽  
Gape Size ◽  
Morphological Variables

Marine food webs are structured, in part, by predator gape size. Species found in deep-sea environments may have evolved such that they can consume prey of a wide range of sizes, to maximise resource intake in a low-productivity ecosystem. Estimates of gape size are central to some types of ecosystem model that determine which prey are available to predators, but cannot always be measured directly. Deep-sea species are hypothesized to have larger gape sizes than shallower-water species relative to their body size and, because of pronounced adaptive foraging behaviour, show only a weak relationship between gape size and trophic level. Here we present new data describing selective morphological measurements and gape sizes of 134 osteichthyan and chondrichthyan species from the deep sea (200-1300 m) off New Zealand. We describe how gape size (height, width and area) varied with factors including fish size, taxonomy (class and order within a class) and trophic level estimated from stable isotopes. For deep-sea species, there was a strong relationship between gape size and fish size, better predicted by body mass than total length, which varied by taxonomic group. Results show that predictions of gape size can be made from commonly measured morphological variables. No relationship between gape size and trophic level was found, likely a reflection of using trophic level estimates from stable isotopes as opposed to the commonly used estimates from FishBase. These results support the hypothesis that deep-sea fish are generalists within their environment, including suspected scavenging, even at the highest trophic levels.

Safety assessment of biological raw materials in the system of medicines quality assurance

2020 ◽  
pp. 63-72
Author(s):  
Yu. Olefir ◽  
E. Sakanyan ◽  
I. Osipova ◽  
V. Dobrynin ◽  
M. Smirnova ◽  
...  
Keyword(s):  
Raw Materials ◽  
State Level ◽  
The State ◽  
Spongiform Encephalopathy ◽  
Safety Standards ◽  
Wide Range ◽  
The Russian Federation ◽  
Key Aspects ◽  
First Time ◽  
Medicines Quality

The entry of a wide range of biotechnological products into the pharmaceutical market calls for rein-forcement of the quality, efficacy and safety standards at the state level. The following general monographs have been elaborated for the first time to be included into the State Pharmacopoeia of the Russian Federation, XIV edition: "Viral safety" and "Reduction of the risk of transmitting animal spongiform encephalopathy via medicinal products". These general monographs were elaborated taking into account the requirements of foreign pharmacopoeias and the WHO recommendations. The present paper summarises the key aspects of the monographs.

Innovation in Byzantine Medicine

2020 ◽  
Author(s):  
Petros Bouras-Vallianatos
Keyword(s):  
Human Physiology ◽  
Medical Literature ◽  
Cultural Exchange ◽  
Significant Degree ◽  
Medieval Medicine ◽  
Medieval Latin ◽  
Main Thesis ◽  
Wide Range ◽  
Comprehensive Examination ◽  
First Time

Byzantine medicine is still a little-known and misrepresented field not only in the wider arena of debates on medieval medicine but also among Byzantinists. Byzantine medical literature is often viewed as ‘stagnant’ and mainly preserving ancient ideas; and our knowledge of it continues to be based to a great extent on the comments of earlier authorities, which are often repeated uncritically. This book presents the first comprehensive examination of the medical corpus of, arguably, the most important late Byzantine physician John Zacharias Aktouarios (c.1275–c.1330). The main thesis is that John’s medical works show an astonishing degree of openness to knowledge from outside Byzantium combined with a significant degree of originality, in particular, in the fields of uroscopy, pharmacology, and human physiology. The analysis of John’s edited (On Urines and On Psychic Pneuma) and unedited (Medical Epitome) works is supported for the first time by the consultation of a large number of manuscripts. The study is also informed by evidence from a wide range of medical sources, including previously unpublished ones, and texts from other genres, such as epistolography and merchants’ accounts. The contextualization of John’s works sheds new light on the development of Byzantine medical thought and practice, and enhances our understanding of the late Byzantine social and intellectual landscape. Finally, John’s medical observations are also examined in the light of examples from the medieval Latin and Islamic worlds, placing his medical theories in the wider Mediterranean milieu and highlighting the cultural exchange between Byzantium and its neighbours.

Rebels, Believers, Survivors

2020 ◽  
Author(s):  
Noel Malcolm
Keyword(s):  
Catholic Church ◽  
Religious Conversion ◽  
Late Nineteenth Century ◽  
Napoleonic Wars ◽  
Conversion To Islam ◽  
Wide Range ◽  
History Of ◽  
External Powers ◽  
First Time ◽  
Modern Myth

This book of essays covers a wide range of topics in the history of Albania and Kosovo. Many of the essays illuminate connections between the Albanian lands and external powers and interests, whether political, military, diplomatic or religious. Such topics include the Habsburg invasion of Kosovo in 1689, the manoeuvrings of Britain and France towards the Albanian lands during the Napoleonic Wars, the British interest in those lands in the late nineteenth century, and the Balkan War of 1912. On the religious side, essays examine ‘crypto-Christianity’ in Kosovo during the Ottoman period, the stories of conversion to Islam revealed by Inquisition records, the first theological treatise written in Albanian (1685), and the work of the ‘Apostolic Delegate’ who reformed the Catholic Church in early twentieth-century Albania. Some essays bring to life ordinary individuals hitherto unknown to history: women hauled before the Inquisition, for example, or the author of the first Albanian autobiography. The longest essay, on Ali Pasha, tells for the first time the full story of the role he played in the international politics of the Napoleonic Wars. Some of these studies have been printed before (several in hard-to-find publications, and one only in Albanian), but the greater part of this book appears here for the first time. This is not only a contribution to Albanian and Balkan history it also engages with many broader issues, including religious conversion, methods of enslavement within the Ottoman Empire, and the nature of modern myth-making about national identity.

Recycling and Reuse in the Roman Economy

2020 ◽  
Keyword(s):  
Building Materials ◽  
Computational Modelling ◽  
Late Antique ◽  
Roman Economy ◽  
Wide Range ◽  
The Status ◽  
Recent Developments ◽  
Methodological Approaches ◽  
First Time ◽  
Site Types

The recycling and reuse of materials and objects were extensive in the past, but have rarely been embedded into models of the economy; even more rarely has any attempt been made to assess the scale of these practices. Recent developments, including the use of large datasets, computational modelling, and high-resolution analytical chemistry, are increasingly offering the means to reconstruct recycling and reuse, and even to approach the thorny matter of quantification. Growing scholarly interest in the topic has also led to an increasing recognition of these practices from those employing more traditional methodological approaches, which are sometimes coupled with innovative archaeological theory. Thanks to these efforts, it has been possible for the first time in this volume to draw together archaeological case studies on the recycling and reuse of a wide range of materials, from papyri and textiles, to amphorae, metals and glass, building materials and statuary. Recycling and reuse occur at a range of site types, and often in contexts which cross-cut material categories, or move from one object category to another. The volume focuses principally on the Roman Imperial and late antique world, over a broad geographical span ranging from Britain to North Africa and the East Mediterranean. Last, but not least, the volume is unique in focusing upon these activities as a part of the status quo, and not just as a response to crisis.

scholarly journals A Virtual Telescope for the Open University Science Foundation Course

1998 ◽  
Vol 162 ◽  
pp. 100-105
Author(s):  
Andrew J. Norton ◽  
Mark H. Jones
Keyword(s):  
Social Science ◽  
Open University ◽  
Distance Teaching ◽  
The Arts ◽  
Wide Range ◽  
University Science ◽  
First Time ◽  
Degree Level ◽  
Selection Of

The Open University is the UK's foremost distance teaching university. For over twenty five years we have been presenting courses to students spanning a wide range of degree level and vocational subjects. Since we have no pre-requisites for entry, a major component of our course profile is a selection of foundation courses comprising one each in the Arts, Social Science, Mathematics, Technology and Science faculties. The Science Faculty's foundation course is currently undergoing a substantial revision. The new course, entitled “S103: Discovering Science”, will be presented to students for the first time in 1998.

scholarly journals Autophagy Deficiency by Atg4B Loss Leads to Metabolomic Alterations in Mice

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 481
Author(s):  
Gemma G. Martínez-García ◽  
Raúl F. Pérez ◽  
Álvaro F. Fernández ◽  
Sylvere Durand ◽  
Guido Kroemer ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Amino Acids ◽  
Mammalian Cells ◽  
Tissue Homeostasis ◽  
In Vivo Studies ◽  
Protective Mechanism ◽  
Cardiac Damage ◽  
Wide Range ◽  
First Time

Autophagy is an essential protective mechanism that allows mammalian cells to cope with a variety of stressors and contributes to maintaining cellular and tissue homeostasis. Due to these crucial roles and also to the fact that autophagy malfunction has been described in a wide range of pathologies, an increasing number of in vivo studies involving animal models targeting autophagy genes have been developed. In mammals, total autophagy inactivation is lethal, and constitutive knockout models lacking effectors of this route are not viable, which has hindered so far the analysis of the consequences of a systemic autophagy decline. Here, we take advantage of atg4b−/− mice, an autophagy-deficient model with only partial disruption of the process, to assess the effects of systemic reduction of autophagy on the metabolome. We describe for the first time the metabolic footprint of systemic autophagy decline, showing that impaired autophagy results in highly tissue-dependent alterations that are more accentuated in the skeletal muscle and plasma. These changes, which include changes in the levels of amino-acids, lipids, or nucleosides, sometimes resemble those that are frequently described in conditions like aging, obesity, or cardiac damage. We also discuss different hypotheses on how impaired autophagy may affect the metabolism of several tissues in mammals.

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