scholarly journals Marine ultra-small prokaryotes likely affect the cycling of Carbon, Methane, Nitrogen and Sulfur

2020 ◽  
Author(s):  
Romain Lannes ◽  
Louise Cavaud ◽  
Philippe Lopez ◽  
Eric Bapteste
Keyword(s):  
Metabolic Pathways ◽  
Redox Reactions ◽  
Carbon Fixation ◽  
Size Fraction ◽  
Biogeochemical Cycles ◽  
Sulfur Cycling ◽  
Coenzyme F420 ◽  
Genetic Components ◽  
First Finding ◽  
Genetic Potential

Abstract Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultra-small size fractions from marine samples (<0.22 micrometres) gathered worldwide by the Tara Oceans Expedition. This first finding suggested that prokaryotic nanoorganisms, phylogenetically distantly related to the known CPR and DPANN groups, could collectively impact carbon cycling and carbon fixation across the world’s ocean. To extend our mining of the functional and taxonomic microbial dark matter from the ultra-small size fraction from the Tara Oceans Expedition, we investigated the distribution of 28 metabolic pathways associated with the cycling of carbon, methane, nitrogen and sulfur. For all of these pathways, we report the existence of novel metabolic homologs in the ultra-small size fraction of the oceanic microbiome, associated with nanoorganisms belonging to the CPR and DPANN lineages, but also of metabolic homologs exclusively found in marine host taxa belonging to other (still unassigned) microbial lineages. Therefore, we conclude that marine nanoorganisms contribute to a greater diversity of key biogeochemical cycles than currently appreciated. In particular, we suggest that oceanic nanoorganisms may be involved in a metabolic loop around Acetyl-CoA, have an underappreciated genetic potential to degrade methane, contribute to sustaining redox-reactions by producing Coenzyme F420, and affect sulfur cycling, notably as they harbour a complete suite of homologs of enzymes of the SOX system.

scholarly journals DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

2019 ◽  
Vol 20 (13) ◽  
pp. 3349 ◽  
Author(s):  
Jose María Miralles-Robledillo ◽  
Javier Torregrosa-Crespo ◽  
Rosa María Martínez-Espinosa ◽  
Carmen Pire
Keyword(s):  
Redox Reactions ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Anaerobic Respiration ◽  
Biogeochemical Cycles ◽  
Free Software ◽  
Transfer Processes ◽  
Expression Of Genes ◽  
Potential Applications ◽  
Domains Of Life

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

scholarly journals Abiotic and biotic processes that drive carboxylation and decarboxylation reactions

2020 ◽  
Vol 105 (5) ◽  
pp. 609-615
Author(s):  
Cody S. Sheik ◽  
H. James Cleaves ◽  
Kristin Johnson-Finn ◽  
Donato Giovannelli ◽  
Thomas L. Kieft ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Subduction Zones ◽  
Carbon Fixation ◽  
Prebiotic Chemistry ◽  
Tricarboxylic Acid Cycle ◽  
Tricarboxylic Acid ◽  
Short Term ◽  
Planetary Evolution ◽  
Broad Overview

Abstract Carboxylation and decarboxylation are two fundamental classes of reactions that impact the cycling of carbon in and on Earth’s crust. These reactions play important roles in both long-term (primarily abiotic) and short-term (primarily biotic) carbon cycling. Long-term cycling is important in the subsurface and at subduction zones where organic carbon is decomposed and outgassed or recycled back to the mantle. Short-term reactions are driven by biology and have the ability to rapidly convert CO2 to biomass and vice versa. For instance, carboxylation is a critical reaction in primary production and metabolic pathways like photosynthesis in which sunlight provides energy to drive carbon fixation, whereas decarboxylation is a critical reaction in metabolic pathways like respiration and the tricarboxylic acid cycle. Early life and prebiotic chemistry on Earth likely relied heavily upon the abiotic synthesis of carboxylic acids. Over time, life has diversified (de)carboxylation reactions and incorporated them into many facets of cellular metabolism. Here we present a broad overview of the importance of carboxylation and decarboxylation reactions from both abiotic and biotic perspectives to highlight the importance of these reactions and compounds to planetary evolution.

scholarly journals Microbial Antimony Biogeochemistry: Enzymes, Regulation, and Related Metabolic Pathways

2016 ◽  
Vol 82 (18) ◽  
pp. 5482-5495 ◽  
Author(s):  
Jingxin Li ◽  
Qian Wang ◽  
Ronald S. Oremland ◽  
Thomas R. Kulp ◽  
Christopher Rensing ◽  
...  
Keyword(s):  
New Species ◽  
Metabolic Pathways ◽  
Redox Reactions ◽  
Industrial Applications ◽  
Aquatic Systems ◽  
Research Interest ◽  
Current Understanding ◽  
Mining Activities ◽  
Toxic Metalloid ◽  
Trace Concentrations

ABSTRACTAntimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction. We conclude that our current understanding of antimony biochemistry and biogeochemistry is roughly equivalent to where that of arsenic was some 20 years ago. This portends the possibility of future discoveries with regard to the ability of microorganisms to conserve energy for their growth from antimony redox reactions and the isolation of new species of “antimonotrophs.”

scholarly journals Importance of extremophilic microorganisms in biogeochemical cycles

2021 ◽  
Vol 9 (1) ◽  
pp. 082-093
Author(s):  
Arlette Galván González ◽  
Rocío Pérez y Terrón
Keyword(s):  
Metabolic Pathways ◽  
Biogeochemical Cycles ◽  
Extreme Conditions ◽  
Ammonium Oxidation ◽  
Carbon And Nitrogen ◽  
Extremophilic Microorganisms ◽  
Ecological Importance ◽  
Global Biogeochemical Cycles ◽  
Metabolic Activities ◽  
Life On Earth

Extremophilic microorganisms are organisms capable of proliferating under extreme conditions that are generally detrimental to most life on Earth. They are organisms considered of importance in different areas of research, due to their ability to produce proteins and enzymes under inhospitable conditions. Therefore, in the present work, the information on their participation in the processes of biogeochemical cycles was collected and analyzed in order to demonstrate their ecological importance. Recent studies on the metabolic pathways of the Extremophilic microorganisms and their environment have shown that most of the archaea, some bacteria and cyanobacteria carry out metabolic activities essential for the biogeochemical cycles of sulfur, carbon and nitrogen. Archaea and bacteria being one of the main microorganisms that participate in a variety of processes such as sulfidogenesis, methanogenesis, ANAMMOX (anaerobic ammonium oxidation), among others. This has suggested that Extremophilic microorganisms and extreme ecosystems have a significant impact on global biogeochemical cycles.

Cryptic biogeochemical cycles: unravelling hidden redox reactions

2017 ◽  
Vol 19 (3) ◽  
pp. 842-846 ◽  
Author(s):  
Andreas Kappler ◽  
Casey Bryce
Keyword(s):  
Redox Reactions ◽  
Biogeochemical Cycles

Prediction of FNR Regulated Genes and Metabolic Pathways Potentially Involved in Anaerobic Growth of Acidithiobacillus Ferrooxidans

2009 ◽  
Vol 71-73 ◽  
pp. 195-198 ◽  
Author(s):  
Hector Osorio ◽  
Juan Pablo Cárdenas ◽  
Jorge H. Valdés ◽  
David S. Holmes
Keyword(s):  
Acidithiobacillus Ferrooxidans ◽  
Metabolic Pathways ◽  
Sulfur Oxidation ◽  
Gene Clusters ◽  
Anaerobic Growth ◽  
Mineral Surfaces ◽  
Physiological Basis ◽  
Ambient Temperatures ◽  
Genetic Components ◽  
Oxygen Gradients

Efficient bioleaching requires adequate access to oxygen to drive the biochemical reactions that underpin iron and sulfur oxidation and ultimately copper solubilization. However, microaerophilic or anaerobic conditions may occur in certain parts of the heap, especially in areas of intense microbial activity or in biofilms where oxygen gradients occur. Microaerophilic conditions have also been detected in pristine acidic environments and in abandoned bioleaching operations. An important microorganism in bioleaching at ambient temperatures is the chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans. In addition to its well established role in oxidative processes, it has been shown to be capable of reducing metals such as iron and sulfur, and the products of these reactions may promote passivation of mineral surfaces and impede efficient solubilization of copper. In an effort to advance our understanding of the genetic and physiological basis of anaerobic metabolism, gene clusters controlled by the master anaerobic transcriptional regulator FNR were predicted in the genome of A. ferrooxidans using bioinformatics techniques. These clusters were found to be associated with energy metabolism, nitrogen fixation and carbohydrate metabolism. The results not only support previous evidence for proposed anaerobic metabolic pathways but also identify new genetic components and pathways that may be important for anaerobic or microaerophilic growth of this microorganism.

scholarly journals Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiangxu Meng ◽  
Jiahong Xu ◽  
Maoning Zhang ◽  
Ruyue Du ◽  
Wenxiu Zhao ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Candidate Genes ◽  
Aspartic Acid ◽  
Single Molecule ◽  
Metabolic Pathways ◽  
Carbon Fixation ◽  
Differentially Expressed ◽  
Metabolome Analysis ◽  
Differential Growth ◽  
Tropical Fruit

Abstract Background Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis. Results We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘glycolysis/gluconeogenesis’, and ‘TCA cycle’. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF–DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG–SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth. Conclusions Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.

scholarly journals Sulfur intermediates as new biogeochemical hubs in an aquatic model microbial ecosystem

2020 ◽  
Author(s):  
Adrien Vigneron ◽  
Perrine Cruaud ◽  
Alexander I. Culley ◽  
Raoul-Marie Couture ◽  
Connie Lovejoy ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Pathways ◽  
Sulfide Oxidation ◽  
Chemical Oxidation ◽  
Sulfur Cycle ◽  
Sulfur Compounds ◽  
Organic Sulfur ◽  
Sulfur Cycling ◽  
Microbial Ecosystem ◽  
Wide Range

Abstract BackgroundThe sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules, and plays a fundamental role in cellular and ecosystems level-processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways involved in these transformations remain poorly understood, notably for inorganic sulfur compounds of intermediate oxidation states (thiosulfate, tetrathionate, sulfite, polysulfides). Isolated and highly stratified, the extreme geochemical and environmental contexts of the meromictic ice-capped Lake A, in the Canadian High Arctic, provides an outstanding model ecosystem to resolve the distribution and metabolism of aquatic sulfur cycling microorganisms along redox and salinity gradients. ResultsApplying complementary molecular approaches, we identified sharply contrasting microbial communities and metabolic potentials among the distinct water layers of the Lake A, with homologies to diverse fresh, brackish and saline water microbiomes. Sulfur cycling genes were abundant at all depths, with oxidative processes in the oxic freshwater layers, reductive reactions in the anoxic and sulfidic bottom waters and genes for both transformations at the chemocline, and co-varied with bacterial abundance. Up to 154 different genomic bins with potential for sulfur transformation were recovered, revealing a panoply of taxonomically diverse microorganisms with complex metabolic pathways for biogeochemical sulfur reactions. Metabolism of sulfur cycle intermediates was widespread throughout the water column, co-occurring with sulfate reduction or sulfide oxidation pathways. The genomic bin composition suggested that in addition to chemical oxidation, these intermediate sulfur compounds were likely produced by the predominant sulfur chemo- and photo-oxidizers at the chemocline and by diverse microbial organic sulfur molecule degraders. ConclusionsThe Lake A microbial ecosystem provided an ideal opportunity to identify new features of the biogeochemical sulfur cycle. Our detailed metagenomic analyses across the broad physico-chemical gradients of this highly stratified lake extend the known diversity of microorganisms and metabolic pathways involved in sulfur transformations over a wide range of environmental conditions. The results identify the importance of sulfur cycle intermediates and organic sulfur molecules as major sources of electron donors and acceptors for aquatic and sedimentary microbial communities in association with the classical sulfur cycle.

scholarly journals Evaluation of Photosynthetic Characters and Regulation Pattern of Photosynthesis Associated Gene in Two Mulberry Varieties

2021 ◽  
Vol 25 (04) ◽  
pp. 863-872
Author(s):  
Yong Li
Keyword(s):  
Net Photosynthetic Rate ◽  
Photosynthetic Rate ◽  
Metabolic Pathways ◽  
Carbon Fixation ◽  
Expression Patterns ◽  
Photochemical Efficiency ◽  
High Yield ◽  
Photochemical Quenching ◽  
Chlorophyll Metabolism ◽  
Photosynthetic Organisms

Photosynthetic characteristics and expression patterns of the photosynthesis-related genes in the high-yield mulberry variety E’Sang 1 (E1) and normal mulberry variety Husang 32 (H32) were investigated in this study. The observation of daily variation of photosynthesis in E1 and H32 indicated that the peak of net photosynthetic rate(Pn)inE1 variety was significantly higher than that inH32 (P <0.05). Meanwhile, the Pn-PAR and Pn-Ci responses of E1 and H32 were evaluated, and the results showed that the carboxylation efficiency and compensation saturation point were much higher in E1 rather thanH32. Importantly, the photosystem II actual photochemical efficiency and photochemical quenching coefficient in the leaves of E1 were significantly higher than those in H32 (P<0.05). Also, the activity of RuBP in E1 was higher than that in H32 (P >0.05). Based on the RNA-seq data, a total of 3,356 differentially expressed genes (DEGs) were detected among different time points between E1 and H32. Of these, 1,136 DEGs were involved in the metabolic pathways, including three main photosynthesis-related metabolic pathways (i.e., carbon fixation in photosynthetic organisms, carbon metabolism, and porphyrin and chlorophyll metabolism). Meanwhile, 10 novel DEGs related to photosynthesis were detected, and four potential key genes of them could account for the differences in net photosynthetic rate and yield betweenH32 and E1.This study could provide important insights into the molecular breeding of mulberry varieties with high photosynthetic efficiency and contribute to understanding the genetic mechanism of photosynthesis.© 2021 Friends Science Publishers

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