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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: 30 April 2025 | Viewed by 7287

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

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Keywords

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

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Published Papers (4 papers)

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Research

18 pages, 5089 KiB  
Article
Characteristics and Mechanism of Ammonia Nitrogen Removal by Heterotrophic Nitrification Bacterium Klebsiella pneumoniae LCU1 and Its Application in Wastewater Treatment
by Meng Xu, Lifei Chen, Yizhen Xin, Xiangyu Wang, Zhuoya Wang, Xueqiang Meng, Wenyu Zhang, Haoyang Sun, Yifan Li, Wenzhe Zhang, Peng Wan, Bingshuai Geng and Lusheng Li
Microorganisms 2025, 13(2), 297; https://doi.org/10.3390/microorganisms13020297 - 29 Jan 2025
Viewed by 1106
Abstract
In this study, a novel strain exhibiting heterotrophic nitrification was screened; subsequently, the strain was identified as Klebsiella pneumoniae LCU1 using 16S rRNA gene sequencing. The aim of the study was to investigate the effects of external factors on the NH4+ [...] Read more.
In this study, a novel strain exhibiting heterotrophic nitrification was screened; subsequently, the strain was identified as Klebsiella pneumoniae LCU1 using 16S rRNA gene sequencing. The aim of the study was to investigate the effects of external factors on the NH4+-N removal efficiency of strain LCU1 in order to elucidate the optimal conditions for NH4+-N removal by the strain and improve the removal efficiency. The findings indicated that the NH4+-N removal efficiency of the strain exceeded 80% under optimal conditions (sodium succinate carbon source, C/N ratio of 10, initial pH of 8.0, temperature of 30 °C, and speed of 180 rpm). The genome analysis of strain LCU1 showed that key genes involved in nitrogen metabolism, including narGHI, nirB, nxrAB, and nasAB, were successfully annotated; hao and amo were absent, but the nitrogen properties analysis determined that the strain had a heterotrophic nitrification ability. After 120 h, the NH4+-N removal efficiency of strain LCU1 was 34.5% at a high NH4+-N concentration of 2000 mg/L. More importantly, the NH4+-N removal efficiency of this strain was above 34.13% at higher Cu2+, Mn2+, and Zn2+ ion concentrations. Furthermore, strain LCU1 had the highest NH4+-N removal efficiency of 34.51% for unsterilised (LCU1-OC) aquaculture wastewater. This suggests that with intensive colonisation treatment, the strain has promising application potential in real wastewater treatment. Full article
(This article belongs to the Special Issue Microbial Nitrogen Cycle)
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18 pages, 2784 KiB  
Article
Bacterial Isolation from Natural Grassland on Nitrogen-Free Agar Yields Many Strains Without Nitrogenase
by Amrit Koirala, Nabilah Ali Alshibli, Bikram K. Das and Volker S. Brözel
Microorganisms 2025, 13(1), 96; https://doi.org/10.3390/microorganisms13010096 - 6 Jan 2025
Viewed by 1381
Abstract
Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely [...] Read more.
Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely on the use of semisolid agar or broth to limit oxygen exposure. Without physical separation, only the most competitive strains are obtained. The distance between strains provided by plating on solid media in reduced oxygen environments has been found to increase the diversity of culturable potential diazotrophic bacteria. To obtain diverse nitrogen-fixing isolates from natural grasslands, we plated soil suspensions from 27 samples onto solid nitrogen-free agar and incubated them under atmospheric and oxygen-reducing conditions. Putative nitrogen fixers were confirmed by subculturing in liquid nitrogen-free media and PCR amplification of the nifH genes. Streaking of the 432 isolates on nitrogen-rich R2A revealed many cocultures. In most cases, only one community member then grew on NFA, indicating the coexistence of nonfixers in coculture with fixers when growing under nitrogen-limited conditions. To exclude isolates able to scavenge residual nitrogen, such as that from vitamins, we used a stringent nitrogen-free medium containing only 6.42 μmol/L total nitrogen and recultured them in a nitrogen-depleted atmosphere. Surprisingly, PCR amplification of nifH using various primer pairs yielded amplicons from only 17% of the 442 isolates. The majority of the nifH PCR-negative isolates were Bacillus and Streptomyces. It is unclear whether these isolates have highly effective uptake systems or nitrogen reduction systems that are not closely aligned with known nitrogenase families. We advise caution in determining the nitrogen fixation ability of plants from growth on nitrogen-free media, even where the total nitrogen is very limited. Full article
(This article belongs to the Special Issue Microbial Nitrogen Cycle)
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28 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 2669
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
Cited by 1 | Viewed by 1305
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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