Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

Fujitani, Hirotsugu; Momiuchi, Kengo; Nomachi, Manami; Kikuchi, Shuta; Ushiki, Norisuke; Sekiguchi, Yuji; Tsuneda, Satoshi

doi:10.3389/fmicb.2020.545190

Cited by 14 publications

(14 citation statements)

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“…High FA concentrations were proposed to inhibit the activities of NOB, such as Nitrospira, facilitating partial nitrification to accumulate nitrite for anammox in PN−A systems. 53 Although the tolerance to ammonia concentrations varied between different species, 21,26 the FA inhibition to the canonical Nitrospira was observed at the concentration as low as 0.7 mg-NH 3 −N/L, 55 which was comparable with the FA concentration (0.34−0.76 mg-N/L) in stage III. Despite the level lower than those (>1.4 mg-N/L) used in the batch assay, the FA in stage III, confounding with oxygen limitation and increased anammox activity due to increased nitrite availability, likely posed a more inhibitory effect on the nitrite oxidation than on the ammonia oxidation of Nitrospira, leading to dominance of comammox Nitrospira but decrease of strictly nitrite-oxidizing Nitrospira.…”

Section: Discussionmentioning

confidence: 89%

“…In addition, free ammonia (FA), the unionized form of ammonium, inhibits the activities of nitrifying − and anammox bacteria . The inhibition effect of FA on nitrite oxidizers had been reported as early as 1976, while several Nitrospira species were found to be inhibited at low concentrations of FA. ,, Recent studies suggested the low tolerance to ammonium for the ammonia oxidation of a new comammox bacteria, Ca. Nitrospira kreftii, whereas the inhibition effects of ammonium were not observed with N.…”

Section: Introductionmentioning

confidence: 99%

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Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Shao

2021

Environ. Sci. Technol.

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Bacteria capable of complete ammonia oxidation (comammox) are widespread and contribute to nitrification in wastewater treatment facilities. However, their roles in partial nitrification–anaerobic ammonium oxidation (anammox) systems remain unclear. In this study, a bench-scale bioreactor with continuous stirring was operated for more than 1000 days with limited oxygen supply to achieve efficient nitrogen removal (70.1 ± 2.7%) at a low ammonium loading of 35.2 mg-N/L/day. High-throughput amplicon sequencing analysis of the comammox ammonia monooxygenase subunit A (amoA) gene revealed seven sequence types from two clusters in clade A of comammox Nitrospira. Quantitative polymerase chain reaction analyses suggested that the comammox species dominated the ammonia-oxidizing community, with an abundance as high as 89.2 ± 7.9% in total prokaryotic amoA copies. Multiple linear regression further revealed the substantial contribution of the comammox Nitrospira to ammonia oxidation in the bioreactor. The investigation with bioreactor and batch experiments consistently showed that activities of comammox Nitrospira were inhibited by free ammonia far more severely than other ammonia-oxidizing microbes. Overall, this study provided new insight into the ecology of comammox Nitrospira under hypoxic conditions and suggested comammox-associated partial nitrification–anammox as a potential method for treating low-strength ammonium-containing wastewater.

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Section: Discussionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Shao

2021

Environ. Sci. Technol.

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“…The predominant prokaryotes in the high-quality soil were Nitrospira, Polycyclovorans, Geobacter, Candidatus Nitrososphaera, Geothrix, Bacillus, and Candidatus Nitrosotalea. Nitrospira inhabits a variety of environments, including soil, ground water, and fresh water, and can cause nitrification by oxidizing ammonia and nitrite [23]. Polycyclovorans inhabits phytoplankton and can utilize hydrocarbons as an energy source [24].…”

Section: Characteristics Of Prokaryotesmentioning

confidence: 99%

Comparison of Microbial Gene Diversity in Grassland Topsoil Depending on Soil Quality

Lee¹,

Kim

Yang

et al. 2021

Applied Sciences

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Soil has multiple functions, including the provision of habitat to organisms, and most biological activities occur in the surface soil. Due to the negative effects of soil erosion, efforts for soil conservation are being made, including the development of a reliable index that can help assess soil quality. In this study, the physical and chemical properties and biological genes from grassland topsoil were analyzed, in order to identify surface soil organism markers that could be used as a soil quality index. Six spots of grassland topsoil were analyzed, one high-quality and five low-quality, based on a web-based soil quality assessment module. Consequently, eukaryotes and prokaryotes with different soil quality ratios were compared and examined. The following bacteria and archaea have the potential to be used in soil quality assessment: circulation of materials including nitrogen, Nitrospira spp., Candidatus Nitrososphaera, and Candidatus Nitrosotalea; biological purification, Geobacter spp.; pathogens, Burkholderia spp., Paraburkholderia spp., Pseudomonas brassicacearum, and Rhizobacter spp.; antibiotic secretion, Candidatus Udaeobacter; and material degradation Steroidobacter spp. and Rhodanobacter spp. This study provides primary data for identifying biological markers for soil quality evaluation. In the future, a wider variety of data need to be accumulated to develop a highly reliable index related to soil quality.

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“…Further reductions in thermophilic archaea and bacteria occurred between Aged phase and mature Compost, including M. thermoacetophila , T. terrifontis , R. profundi and R. marinus as well as the transient Ignavibacterium album and the extremophile and nematode pathogen Leucobacter chromiireducens ( Muir & Tan, 2008 ). Within highly diverse mature compost, large increases were observed in specialized species such as the obligate methanotroph Methylosarcina lacus and the nitrite-oxidizing bacteria Nitrospira japonica ( Fujitani et al, 2020 ; Kalyuzhnaya et al, 2005 ), but the community was best characterized by increases in 51 ESVs annotated as taxa within the order Rhizobiales which increased when compared to Aged phase, such as the methanotroph Methylocystis rosea , the nodule associated Mesorhizobium tamadayense and Rhizobium helanshanense , suggestive of a compost community which could benefit soil health and plant rhizosphere associations ( Qin et al, 2012 ; Rahalkar et al, 2018 ; Ramírez-Bahena et al, 2012 ).…”

Section: Discussionmentioning

confidence: 99%

“…The ESV Nitrospira_1 shared 100% sequence identity with an uncultured soil bacterium (GenBank EF667461.1) and was most closely related to N. japonica strain NJ11 (98.01%), while the ESV Nitrospira_2 shared 100% sequence identity with an uncultured soil bacterium (GenBank EU012235.1) and shared most sequence similarity to Nitrospira sp. KM1 (97.61%), a novel nitrite-oxidizing Nitrospira strain isolated from a drinking water treatment plant ( Fujitani et al, 2020 ). While caution is necessary when speculating as to the function based on culture independent sequencing, these putative uncultured bacteria could represent new thermotolerant/thermophilic nitrite oxidizing Nitrospira species which could be responsible for the increase in nitrite-nitrate concentrations during the Middle phase.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Grenier

González

Brereton

et al. 2023

PeerJ

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Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

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Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

Cited by 14 publications

References 78 publications

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Comparison of Microbial Gene Diversity in Grassland Topsoil Depending on Soil Quality

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

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