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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...

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Autores principales: Kikuchi, Shuta, Fujitani, Hirotsugu, Ishii, Kento, Isshiki, Rino, Sekiguchi, Yuji, Tsuneda, Satoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2023
Materias:
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.
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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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