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Microorganisms
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Microbial Nitrogen Cycle
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Microbial Nitrogen Cycle

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 15 October 2024 | Viewed by 1959

Special Issue Editor

Prof. Dr. Volker Brozel

E-Mail Website
Guest Editor
Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
Interests: diazotroph; nitrogen fixation; soil; biofilm
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The microbial nitrogen cycle is a crucial environmental process that involves the transformation and cycling of nitrogen by microorganisms. Nitrogen is essential for all living organisms, and its availability as either ammonium, nitrate or as part of amino acids greatly affects the growth and development of plants and animals. Diverse microbes catalyze the transformation of nitrogenous compounds through reduction, oxidation or hydrolysis, shifting the amount of nitrogen available to support life. All nitrogen conversions contribute to the nitrogen cycle and include nitrogen fixation, nitrification, denitrification, ammonification and other processes. While nitrogen in the form of ammonia or nitrate is needed in soil to support plant growth, excess nitrogen in water can lead to eutrophication and harm aquatic life. Understanding the microbial nitrogen cycle is important for various fields, including agriculture, ecology, and environmental science. This Special Issue aims to delve into the diverse aspects of the microbial nitrogen cycle. Through research articles, reviews, and case studies, this Special Issue aims to provide a comprehensive understanding of the role of microorganisms in cycling nitrogen in various environments. By delving into this topic, we hope to shed light on the crucial role of microbial communities in sustaining and regulating nitrogen availability in ecosystems.

Prof. Dr. Volker Brozel
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial nitrogen cycle
  • nitrogen fixation
  • nitrification
  • denitrification
  • ammonification

Published Papers (2 papers)

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Research

30 pages, 8640 KiB  
Article
Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential
by Raphael D. Isokpehi, Yungkul Kim, Sarah E. Krejci and Vishwa D. Trivedi
Microorganisms 2024, 12(4), 791; https://doi.org/10.3390/microorganisms12040791 - 13 Apr 2024
Viewed by 1064
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the [...] Read more.
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities. Full article
(This article belongs to the Special Issue Microbial Nitrogen Cycle)
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17 pages, 3647 KiB  
Article
Seasonal Variability of Cultivable Nitrate-Reducing and Denitrifying Bacteria and Functional Gene Copy Number in Fresh Water Lake
by Jörg Böllmann and Marion Martienssen
Microorganisms 2024, 12(3), 511; https://doi.org/10.3390/microorganisms12030511 - 2 Mar 2024
Viewed by 612
Abstract
This study describes the seasonal course of denitrifying and nitrate-reducing bacteria in a dimictic mesotrophic lake (Lake Scharmützelsee, Brandenburg, Germany) within a three-year period from 2011 to 2013. The bacterial cell numbers were quantified by the fluorescence microscopy, most probable number (MPN) and [...] Read more.
This study describes the seasonal course of denitrifying and nitrate-reducing bacteria in a dimictic mesotrophic lake (Lake Scharmützelsee, Brandenburg, Germany) within a three-year period from 2011 to 2013. The bacterial cell numbers were quantified by the fluorescence microscopy, most probable number (MPN) and PCR-dependent quantification of the chromosomal 16S rDNA and of the nirS and nirK gene copy number. The highest seasonal differences (up to three orders of magnitudes) have been measured using MPN in the epilimnion. This variation was not reflected by PCR-dependent approaches or direct microscopical enumeration. At adverse conditions (low temperature and/or low nitrate concentrations), the differences between MPN and gene copy numbers increased by up to five orders of magnitudes and decreased to one magnitude at favourable environmental conditions. These results can be explained best by an increasing ratio of viable but not cultivable (VBNC) cells or dead cells at impairing conditions. In the hypolimnion, the courses of MPN and nir gene copy numbers were similar. This can be explained by a higher feeding pressure and therefore smaller amounts of dormant cells. In the pelagial in general, the total cell numbers enumerated by either microscopical or molecular approaches were similar. In the sediment, more than 99% of the DNA was obviously not related to viable bacteria but was rather DNA in dead cells or adsorbed to particle surfaces. Full article
(This article belongs to the Special Issue Microbial Nitrogen Cycle)
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