Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater

The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments

Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.

Dynamics of ammonia-oxidizing microorganisms in gradient temperature-regulated reactors under low ammonia loading condition

Ammonia-oxidizing microorganisms (AOMs) play a crucial role in nitrogen removal in engineered systems. However, temperature fluctuations can lead to ammonia oxidation failure. This study investigated the effects of a broad temperature range (10.5, 14, 17.5, 21, 26.4, 35, 38.5, 42, and 45.5 °C) on the distribution of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox together with Nitrospira and Nitrobacter in gradient temperature-regulated reactors operated under low ammonia loading condition. Quantitative PCR and high throughput sequencing revealed that the AOA amoA gene numbers (∼104 copies/ng DNA) were relatively high at 38.5 °C to 42 °C, suggesting AOA favoring higher temperature than lower temperature. The amoA genes of AOA (∼103 - 104 copies/ng DNA) outcompeted those of AOB (∼103 copies/ng DNA) and comammox ( Collapse

Key Words

• AOA
• AOB
• Comammox
• Nitrobacter
• Nitrospira
• Temperature

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MESH Headings

• Ammonia/metabolism
• Archaea/metabolism
• Bioreactors/microbiology
• Oxidation-Reduction
• Temperature
• Bacteria/metabolism

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Grants Collapse

Affiliation(s)

Prinpida Sonthiphand Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
Napong Songkriengkrai International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand
Nampetch Charanaipayuk International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand
Teerasit Termsaithong Learning Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand; Theoretical and Computational Physics (TCP) Group, Center of Excellence in Theoretical and Computational Science (TaCS-CoE), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
Benjaporn Boonchayaanant Suwannasilp Department of Environmental and Sustainable Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Unit, Chulalongkorn University, Bangkok, Thailand
Wuttichai Mhuantong National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
Tawan Limpiyakorn Department of Environmental and Sustainable Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Unit, Chulalongkorn University, Bangkok, Thailand.

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Pilot-scale experimental study on the enhanced natural attenuation of complex organic contaminants based on the recharge of electron acceptors

Anaerobic biodegradation plays a crucial role in attenuating organic contaminants in natural aquifers, where the concentration and type of electron acceptors directly determine the stages and rates of degradation progress. In this study, nitrate depletion was monitored in a simulated pilot-scale aquifer contaminated with toluene and trichloroethylene, while sulfate became the new periodic electron acceptor, accompanied by a decrease in the contaminant attenuation rate. Consequently, nitrate was injected into the contaminated plume in stages, and the hydro- and biochemical impacts were further monitored. The results revealed that the active recharge of nitrate became a new electron donor involved in anaerobic reduction processes, with contaminants attenuation rates increased by 2.48-3.88 times compared with that before injection. Moreover, the active recharge of nitrate inhibited further consumption of sulfate and oxidized pre-existing sulfides, which reduced the biological toxicity of the aquatic environment and provided favorable conditions for the growth of nitrate-reducing microorganisms. This study evaluated the enhancement of natural attenuation by recharging nitrate as an electron acceptor, providing a theoretical basis for environmentally friendly and economic remediation of petroleum-contaminated aquifers.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding

COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.

Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica

Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3-) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3- via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.