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Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus‐level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the gen...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10472526/ https://www.ncbi.nlm.nih.gov/pubmed/37078228 http://dx.doi.org/10.1111/1758-2229.13158 |
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author | Kikuchi, Shuta Fujitani, Hirotsugu Ishii, Kento Isshiki, Rino Sekiguchi, Yuji Tsuneda, Satoshi |
author_facet | Kikuchi, Shuta Fujitani, Hirotsugu Ishii, Kento Isshiki, Rino Sekiguchi, Yuji Tsuneda, Satoshi |
author_sort | Kikuchi, Shuta |
collection | PubMed |
description | Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus‐level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia‐oxidising bacteria (AOB). The apparent half‐saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH(3) + NH(4) (+) and 18.5 ± 1.8 μmol N (mg protein)(−1) h(−1), respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1‐like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia‐oxidising Nitrosomonas. |
format | Online Article Text |
id | pubmed-10472526 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-104725262023-09-02 Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer Kikuchi, Shuta Fujitani, Hirotsugu Ishii, Kento Isshiki, Rino Sekiguchi, Yuji Tsuneda, Satoshi Environ Microbiol Rep Brief Reports Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus‐level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia‐oxidising bacteria (AOB). The apparent half‐saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH(3) + NH(4) (+) and 18.5 ± 1.8 μmol N (mg protein)(−1) h(−1), respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1‐like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia‐oxidising Nitrosomonas. John Wiley & Sons, Inc. 2023-04-20 /pmc/articles/PMC10472526/ /pubmed/37078228 http://dx.doi.org/10.1111/1758-2229.13158 Text en © 2023 The Authors. Environmental Microbiology Reports published by Applied Microbiology International and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Brief Reports Kikuchi, Shuta Fujitani, Hirotsugu Ishii, Kento Isshiki, Rino Sekiguchi, Yuji Tsuneda, Satoshi Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title | Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title_full | Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title_fullStr | Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title_full_unstemmed | Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title_short | Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer |
title_sort | characterisation of bacteria representing a novel nitrosomonas clade: physiology, genomics and distribution of missing ammonia oxidizer |
topic | Brief Reports |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10472526/ https://www.ncbi.nlm.nih.gov/pubmed/37078228 http://dx.doi.org/10.1111/1758-2229.13158 |
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