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Microorganisms
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Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria
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Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 12861

Special Issue Editor

Dr. Andreas Pommerening-Röser

E-Mail Website
Guest Editor
Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
Interests: Ammonia-oxidizing bacteria; ecology and phylogeny; genome sequencing; in situ-impact and fields of application; culturing and next-generation isolation

Special Issue Information

Dear Colleagues,

The lithoautotrophic ammonia-oxidizing bacteria (AOB) are characterized by their shared ability to utilize ammonia as a sole energy source and carbon dioxide as the main source of carbon. They initiate the so-called nitrification process that is considered to be of key importance in natural nitrogen cycling. Even though it is now known that AOB are no longer the only microorganisms doing this, nonetheless they remain of particular importance for microbial ecology and biogeochemistry. Due to their ecological importance, their physiological uniqueness and their phylogenetic structure, AOB are virtually predestined for environmental studies. Due their adaptation to diverse site conditions, a large number of AOB species has evolved. What is still missing, however, is information about the equally large number of environmental factors or ecophysiological properties that might have shaped speciation within this group of bacteria. All attempts, be it whole genome analysis or pure culture bases studies, to explore this issue will certainly advance our knowledge of factors affecting AOB in natural and man-made environments and their significance in nitrification and the global nitrogen cycle.

For this Special Issue of Microorganisms, you are cordially invited to submit contributions related on any aspects outlined above.

Dr. Andreas Pommerening-Röser
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.

Published Papers (4 papers)

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Research

25 pages, 3192 KiB  
Article
High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution
by Lin Wang, Chee Kent Lim and Martin G. Klotz
Microorganisms 2020, 8(5), 693; https://doi.org/10.3390/microorganisms8050693 - 08 May 2020
Cited by 3 | Viewed by 3442
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and [...] Read more.
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)
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14 pages, 2120 KiB  
Article
Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo
by Ann-Kathrin Kniggendorf, Regina Nogueira, Somayeh Nasiri Bahmanabad, Andreas Pommerening-Röser and Bernhard Wilhelm Roth
Microorganisms 2020, 8(3), 432; https://doi.org/10.3390/microorganisms8030432 - 19 Mar 2020
Cited by 8 | Viewed by 2516
Abstract
The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth [...] Read more.
The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth rates of stressed AOB, making the sample volumes required to monitor the internal stress response of AOB prohibitive to repeated analysis. In a proof-of-concept study, confocal Raman microscopy with excitation resonant to the heme c moiety of cytochrome c was used to compare the cytochrome c content and activity of stressed and unstressed Nitrosomonas europaea (Nm 50), Nitrosomonas eutropha (Nm 57), Nitrosospira briensis (Nsp 10), and Nitrosospira sp. (Nsp 02) in vivo. Each analysis required no more than 1000 individual cells per sampling; thus, the monitoring of cultures with low cell concentrations was possible. The identified spectral marker delivered reproducible results within the signal-to-noise ratio of the underlying Raman spectra. Cytochrome c content was found to be elevated in oxygen-deprived and previously oxygen-deprived samples. In addition, cells with predominantly ferrous cytochrome c content were found in deprived Nitrosomonas eutropha and Nitrosospira samples, which may be indicative of ongoing electron storage at the time of measurement. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)
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14 pages, 1428 KiB  
Article
Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities
by Jack K. Beltz, Hayley McMahon, Isis Torres Nunez and Anne E. Bernhard
Microorganisms 2020, 8(1), 9; https://doi.org/10.3390/microorganisms8010009 - 19 Dec 2019
Cited by 3 | Viewed by 2160
Abstract
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three [...] Read more.
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)
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21 pages, 4497 KiB  
Article
Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia
by Tina Sanders, Claudia Fiencke, Jennifer Hüpeden, Eva Maria Pfeiffer and Eva Spieck
Microorganisms 2019, 7(12), 699; https://doi.org/10.3390/microorganisms7120699 - 14 Dec 2019
Cited by 14 | Viewed by 4046
Abstract
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved [...] Read more.
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)
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