Complete nitrification: insights into the ecophysiology of comammox  Nitrospira

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Abstract

Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.

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Most cited references 83

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The microbial nitrogen-cycling network

Boran Kartal, Marcel M. M. Kuypers, Hannah Marchant (2018)

Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth. The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms. In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.

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UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction.

Jongsik Chun, Inwoo Baek, Sung-Min Ha … (2018)

Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.

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Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling.

Alexander Treusch, Sven Leininger, Arnulf Kletzin … (2005)

Mesophilic crenarchaeota are frequently found in terrestrial and marine habitats worldwide, but despite their considerable abundance the physiology of these as yet uncultivated archaea has remained unknown. From a 1.2 Gb large-insert environmental fosmid library of a calcareous grassland soil, a 43 kb genomic fragment was isolated with a ribosomal RNA that shows its affiliation to group 1.1b of crenarchaeota repeatedly found in soils. The insert encoded a homologue of a copper-containing nitrite reductase with an unusual C-terminus that encoded a potential amicyanin-like electron transfer domain as well as two proteins related to subunits of ammonia monooxygenases or particulate methane monooxygenases (AmoAB/PmoAB) respectively. Expression of nirK and the amoA-like gene was shown by reverse transcription polymerase chain reaction (PCR) analyses in soil samples, the latter being found at higher levels when the soil was incubated with ammonia (measured by quantitative PCR). Further variants of both genes were amplified from soil samples and were found in the environmental database from the Sargasso Sea plankton. Taken together, our findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions.

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Author and article information

Contributors

Sebastian Lücker:

ORCID: http://orcid.org/0000-0003-2935-4454

S.luecker@science.ru.nl

Journal

Journal ID (nlm-ta): Appl Microbiol Biotechnol

Journal ID (iso-abbrev): Appl. Microbiol. Biotechnol

Title: Applied Microbiology and Biotechnology

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0175-7598

ISSN (Electronic): 1432-0614

Publication date (Electronic): 10 November 2018

Publication date PMC-release: 10 November 2018

Publication date (Print): 2019

Volume: 103

Issue: 1

Pages: 177-189

Affiliations

ISNI 0000000122931605, GRID grid.5590.9, Department of Microbiology, , Radboud University Nijmegen, ; Nijmegen, The Netherlands

Author information

Sebastian Lücker http://orcid.org/0000-0003-2935-4454

Article

Publisher ID: 9486

DOI: 10.1007/s00253-018-9486-3

PMC ID: 6311188

PubMed ID: 30415428

SO-VID: 92954633-0973-407d-979e-5373993a2c2a

License:

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

History

Date received : 3 September 2018

Date revision received : 26 October 2018

Date accepted : 27 October 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100003246, Nederlandse Organisatie voor Wetenschappelijk Onderzoek;

Award ID: 024.002.002

Award ID: 863.14.019

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ScienceOpen disciplines: Biotechnology

Keywords: nitrification,comammox,nitrospira,complete nitrification,nitrite-oxidizing bacteria,ammonia-oxidizing microorganisms

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ScienceOpen disciplines: Biotechnology

Keywords: nitrification, comammox, nitrospira, complete nitrification, nitrite-oxidizing bacteria, ammonia-oxidizing microorganisms

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

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Preventive and Emergency Medicine Insights

Most cited references 83

The microbial nitrogen-cycling network

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction.

Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling.

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