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Extreme Microorganisms in the Nitrogen Cycle

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 31125

Special Issue Editors


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Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, E-03080 Alicante, Spain
Interests: extremophiles; omics-based technologies; gene regulation; microbial metabolism; carotenoids; polyhydroxyalkanoates; biogeochemical cycles; system biology
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Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Spain
Interests: archaeal; denitrification; nitrogen cycle
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Assistant Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain

Special Issue Information

Dear Colleagues,

The nitrogen cycle is one of the most important biogeochemical cycles on the planet and involves a wide range of nitrogen species and biochemical transformations. Microorganisms play a key role in this cycle. Recent investigations have revealed that N-cycle is relevant in marine and other extreme environments like salterns, very dry deserts, volcanoes, deep ocean trencheso or upper atmosphere.

Articles (original research, commentaries, opinions, reviews) to be published in this Special Issue of IJMS should contribute to understanding the role of moderate and extreme microbes in the N-cycle from interdisciplinary approaches.

Topics include, but are not limited to:

  • N-cycle pathways (biochemical, molecular biology, microbiological, ecological approaches)
  • Nitrogen assimilation, fixation and respiration
  • Nitrogenous gasses emissions and climate change
  • Ammonification/nitrification
  • Dissimilatory nitrate reduction to ammonia
  • Annamox and denitrification

Dr. Rosa María Martínez-Espinosa
Dr. Carmen Lucía Pire-Galiana
Guest Editors

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Published Papers (6 papers)

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Research

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22 pages, 4856 KiB  
Article
Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen
by Sungmin Hwang, Nikita E. Chavarria, Rylee K. Hackley, Amy K. Schmid and Julie A. Maupin-Furlow
Int. J. Mol. Sci. 2019, 20(19), 4784; https://doi.org/10.3390/ijms20194784 - 26 Sep 2019
Cited by 4 | Viewed by 3535
Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as [...] Read more.
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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15 pages, 1165 KiB  
Article
Cyanate Assimilation by the Alkaliphilic Cyanide-Degrading Bacterium Pseudomonas pseudoalcaligenes CECT5344: Mutational Analysis of the cyn Gene Cluster
by Lara Paloma Sáez, Purificación Cabello, María Isabel Ibáñez, Víctor Manuel Luque-Almagro, María Dolores Roldán and Conrado Moreno-Vivián
Int. J. Mol. Sci. 2019, 20(12), 3008; https://doi.org/10.3390/ijms20123008 - 20 Jun 2019
Cited by 17 | Viewed by 3248
Abstract
The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 can grow with cyanate, cyanide, or cyanide-containing industrial residues as the sole nitrogen source, but the assimilation of cyanide and cyanate takes place through independent pathways. Therefore, cyanide degradation involves a chemical reaction between cyanide and oxaloacetate [...] Read more.
The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 can grow with cyanate, cyanide, or cyanide-containing industrial residues as the sole nitrogen source, but the assimilation of cyanide and cyanate takes place through independent pathways. Therefore, cyanide degradation involves a chemical reaction between cyanide and oxaloacetate to form a nitrile that is hydrolyzed to ammonium by the nitrilase NitC, whereas cyanate assimilation requires a cyanase that catalyzes cyanate decomposition to ammonium and carbon dioxide. The P. pseudoalcaligenes CECT5344 cynFABDS gene cluster codes for the putative transcriptional regulator CynF, the ABC-type cyanate transporter CynABD, and the cyanase CynS. In this study, transcriptional analysis revealed that the structural cynABDS genes constitute a single transcriptional unit, which was induced by cyanate and repressed by ammonium. Mutational characterization of the cyn genes indicated that CynF was essential for cynABDS gene expression and that nitrate/nitrite transporters may be involved in cyanate uptake, in addition to the CynABD transport system. Biodegradation of hazardous jewelry wastewater containing high amounts of cyanide and metals was achieved in a batch reactor operating at an alkaline pH after chemical treatment with hydrogen peroxide to oxidize cyanide to cyanate. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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9 pages, 591 KiB  
Article
Metabolic Pathway Analysis of Nitrogen and Phosphorus Uptake by the Consortium between C. vulgaris and P. aeruginosa
by A. Suggey Guerra-Renteria, M. Alberto García-Ramírez, César Gómez-Hermosillo, Abril Gómez-Guzmán, Yolanda González-García and Orfil González-Reynoso
Int. J. Mol. Sci. 2019, 20(8), 1978; https://doi.org/10.3390/ijms20081978 - 23 Apr 2019
Cited by 10 | Viewed by 2869
Abstract
Anthropogenic activities have increased the amount of urban wastewater discharged into natural aquatic reservoirs containing a high amount of nutrients such as phosphorus (Pi and PO 4 3 ), nitrogen (NH 3 and NO 3 ) and organic contaminants. Most of [...] Read more.
Anthropogenic activities have increased the amount of urban wastewater discharged into natural aquatic reservoirs containing a high amount of nutrients such as phosphorus (Pi and PO 4 3 ), nitrogen (NH 3 and NO 3 ) and organic contaminants. Most of the urban wastewater in Mexico do not receive any treatment to remove nutrients. Several studies have reported that an alternative to reduce those contaminants is using consortiums of microalgae and endogenous bacteria. In this research, a genome-scale biochemical reaction network is reconstructed for the co-culture between the microalga Chlorella vulgaris and the bacterium Pseudomonas aeruginosa. Metabolic Pathway Analysis (MPA), is applied to understand the metabolic capabilities of the co-culture and to elucidate the best conditions in removing nutrients. Theoretical yields for phosphorus removal under photoheterotrophic conditions are calculated, determining their values as 0.042 mmol of PO 4 3 per g DW of C. vulgaris, 19.43 mmol of phosphorus (Pi) per g DW of C. vulgaris and 4.90 mmol of phosphorus (Pi) per g DW of P. aeruginosa. Similarly, according to the genome-scale biochemical reaction network the theoretical yields for nitrogen removal are 10.3 mmol of NH 3 per g DW of P. aeruginosa and 7.19 mmol of NO 3 per g DW of C. vulgaris. Thus, this research proves the metabolic capacity of these microorganisms in removing nutrients and their theoretical yields are calculated. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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Review

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19 pages, 727 KiB  
Review
Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments
by Rosa María Martínez-Espinosa
Int. J. Mol. Sci. 2020, 21(12), 4228; https://doi.org/10.3390/ijms21124228 - 13 Jun 2020
Cited by 34 | Viewed by 7317
Abstract
Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting [...] Read more.
Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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23 pages, 2216 KiB  
Review
Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review
by Pierre Albina, Nadège Durban, Alexandra Bertron, Achim Albrecht, Jean-Charles Robinet and Benjamin Erable
Int. J. Mol. Sci. 2019, 20(20), 5163; https://doi.org/10.3390/ijms20205163 - 18 Oct 2019
Cited by 84 | Viewed by 6890
Abstract
Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the [...] Read more.
Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO2) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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22 pages, 3214 KiB  
Review
DMSO Reductase Family: Phylogenetics and Applications of Extremophiles
by Jose María Miralles-Robledillo, Javier Torregrosa-Crespo, Rosa María Martínez-Espinosa and Carmen Pire
Int. J. Mol. Sci. 2019, 20(13), 3349; https://doi.org/10.3390/ijms20133349 - 8 Jul 2019
Cited by 28 | Viewed by 6626
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Extreme Microorganisms in the Nitrogen Cycle)
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