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Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.
Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT, Shah, BS
Biochemical Society transactions. 2021;(6):2465-2481
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Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
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2.
The ambivalent role of water at the origins of life.
do Nascimento Vieira, A, Kleinermanns, K, Martin, WF, Preiner, M
FEBS letters. 2020;(17):2717-2733
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Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
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Vibrio vulnificus infection: a persistent threat to public health.
Yun, NR, Kim, DM
The Korean journal of internal medicine. 2018;(6):1070-1078
Abstract
Vibrio vulnificus is a gram-negative bacterium that can cause serious, potentially fatal infections. V. vulnificus causes three distinct syndromes: an overwhelming primary septicemia caused by consuming contaminated seafood, wound infections acquired when an open wound is exposed to contaminated warm seawater, and gastrointestinal tract-limited infections. Case-fatality rates are higher than 50% for primary septicemia, and death typically occurs within 72 hours of hospitalization. Risk factors for V. vulnificus infection include chronic liver disease, alcoholism, and hematological disorders. When V. vulnificus infection is suspected, appropriate antibiotic treatment and surgical interventions should be performed immediately. Third-generation cephalosporin with doxycycline, or quinolone with or without third-generation cephalosporin, may be potential treatment options for patients with V. vulnificus infection.
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Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms.
Mapelli, F, Scoma, A, Michoud, G, Aulenta, F, Boon, N, Borin, S, Kalogerakis, N, Daffonchio, D
Trends in biotechnology. 2017;(9):860-870
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Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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Patterns of deoxygenation: sensitivity to natural and anthropogenic drivers.
Oschlies, A, Duteil, O, Getzlaff, J, Koeve, W, Landolfi, A, Schmidtko, S
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 2017;(2102)
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Abstract
Observational estimates and numerical models both indicate a significant overall decline in marine oxygen levels over the past few decades. Spatial patterns of oxygen change, however, differ considerably between observed and modelled estimates. Particularly in the tropical thermocline that hosts open-ocean oxygen minimum zones, observations indicate a general oxygen decline, whereas most of the state-of-the-art models simulate increasing oxygen levels. Possible reasons for the apparent model-data discrepancies are examined. In order to attribute observed historical variations in oxygen levels, we here study mechanisms of changes in oxygen supply and consumption with sensitivity model simulations. Specifically, the role of equatorial jets, of lateral and diapycnal mixing processes, of changes in the wind-driven circulation and atmospheric nutrient supply, and of some poorly constrained biogeochemical processes are investigated. Predominantly wind-driven changes in the low-latitude oceanic ventilation are identified as a possible factor contributing to observed oxygen changes in the low-latitude thermocline during the past decades, while the potential role of biogeochemical processes remains difficult to constrain. We discuss implications for the attribution of observed oxygen changes to anthropogenic impacts and research priorities that may help to improve our mechanistic understanding of oxygen changes and the quality of projections into a changing future.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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Factors affecting virus dynamics and microbial host-virus interactions in marine environments.
Mojica, KD, Brussaard, CP
FEMS microbiology ecology. 2014;(3):495-515
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Abstract
Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host-virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.
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Marine microbial metagenomics: from individual to the environment.
Tseng, CH, Tang, SL
International journal of molecular sciences. 2014;(5):8878-92
Abstract
Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. Studies using next-generation sequencing techniques on single genomes and collections of genomes have not only led to novel insights into microbial genomics, but also revealed a close association between environmental niches and genome evolution. Herein, we review studies investigating microbial genomics (largely in the marine ecosystem) at the individual and community levels to summarize our current understanding of microbial ecology in the environment.
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Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.
Merchant, SS, Helmann, JD
Advances in microbial physiology. 2012;:91-210
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Abstract
Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes.
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Marine viruses and global climate change.
Danovaro, R, Corinaldesi, C, Dell'anno, A, Fuhrman, JA, Middelburg, JJ, Noble, RT, Suttle, CA
FEMS microbiology reviews. 2011;(6):993-1034
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Sea-surface warming, sea-ice melting and related freshening, changes in circulation and mixing regimes, and ocean acidification induced by the present climate changes are modifying marine ecosystem structure and function and have the potential to alter the cycling of carbon and nutrients in surface oceans. Changing climate has direct and indirect consequences on marine viruses, including cascading effects on biogeochemical cycles, food webs, and the metabolic balance of the ocean. We discuss here a range of case studies of climate change and the potential consequences on virus function, viral assemblages and virus-host interactions. In turn, marine viruses influence directly and indirectly biogeochemical cycles, carbon sequestration capacity of the oceans and the gas exchange between the ocean surface and the atmosphere. We cannot yet predict whether the viruses will exacerbate or attenuate the magnitude of climate changes on marine ecosystems, but we provide evidence that marine viruses interact actively with the present climate change and are a key biotic component that is able to influence the oceans' feedback on climate change. Long-term and wide spatial-scale studies, and improved knowledge of host-virus dynamics in the world's oceans will permit the incorporation of the viral component into future ocean climate models and increase the accuracy of the predictions of the climate change impacts on the function of the oceans.
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[Research on search of the carotenoid-producing microorganisms in marine area and the improvement of production ratio].
Sakagami, Y, Sumiya, Y, Komemushi, S
Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan. 2010;(11):1445-51
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Abstract
Carotenoids are liposoluble pigments widely distributed in nature. More than 750 carotenoids are isolated from natural sources, but only a few kinds are used industrially. The production of carotenoid by microorganisms is to be expected, but few carotenoids originate from living things on land. And there is little knowledge about carotenoid-producing microorganisms in the oceans. The possibility still exists of discovering new carotenoid-producing microorganisms. Sunlight is very strong in subtropical regions. The surface of the sea and coral reefs in these regions is a severe environment for growth of microorganisms. While such conditions produce reactive oxygen species, the continuing strong irradiation can also lead to damaging and lethal photo-oxidative reactions. Many undiscovered microorganisms may possess protective mechanisms such as anti-oxidative activities for survival in this environment. This study focused on marine microorganisms inhabiting coral reefs in the Okinawa area, especially carotenoid-producing bacteria possessing anti-oxidative activities. Many carotenoid-producing microorganisms were collected from subtropical ocean areas (a total of 334 strains of pigmented microorganisms), and the chemical composition, some culture conditions and genetic characteristics of the carotenoids from these microorganisms were examined. Furthermore, similar research was performed using some creatures from the ocean surrounding Kochi Prefecture.