Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River

Abstract

Nitrogen cycling microbes, including nitrite-oxidizing bacteria (NOB), perform critical ecosystem functions that help mitigate anthropogenic stresses and maintain ecosystem health. Activity of these beneficial nitrogen cycling microbes is dictated in part by the microorganisms’ response to physicochemical conditions, such as temperature, pH, and nutrient availability. NOB from the newly described Candidatus Nitrotoga genus have been detected in a wide range of habitats across the globe, yet only a few organisms within the genus have been physiologically characterized. For freshwater systems where NOB are critical for supporting aquatic life, Ca. Nitrotoga have been previously detected but little is known about the physiological potential of these organisms or their response to changing environmental conditions. Here, we determined functional response to environmental change for a representative freshwater species of Ca. Nitrotoga (Ca. Nitrotoga sp. CP45, enriched from a Colorado river). The physiological findings demonstrated that CP45 maintained nitrite oxidation at pH levels of 5–8, at temperatures from 4 to 28°C, and when incubated in the dark. Light exposure and elevated temperature (30°C) completely halted nitrite oxidation. Ca. Nitrotoga sp. CP45 maintained nitrite oxidation upon exposure to four different antibiotics, and potential rates of nitrite oxidation by river sediment communities were also resilient to antibiotic stress. We explored the Ca. Nitrotoga sp. CP45 genome to make predictions about adaptations to enable survival under specific conditions. Overall, these results contribute to our understanding of the versatility of a representative freshwater Ca. Nitrotoga sp. Identifying the specific environmental conditions that maximize NOB metabolic rates may ultimately direct future management decisions aimed at restoring impacted systems.

Some like it cold: the cellular organization and physiological limits of cold‐tolerant nitrite‐oxidizing Nitrotoga

“…In competition with Nitrospira , Nitrotoga was flourishing when either temperature (Alawi et al ., 2007; Karkman et al ., 2011; Achberger et al ., 2016; Saunders et al ., 2016; Liu et al ., 2017; Wegen et al ., 2019), pH (Hüpeden et al ., 2016; Vieira et al ., 2019), or both were low (Ma et al ., 2017). However, some Nitrotoga were found to proliferate also in mesophilic ecosystems and culture conditions (Kitzinger et al ., 2018; Zheng et al ., 2020; Lantz et al ., 2021), challenging the paradigm of cold‐adaptation of Nitrotoga .…”

Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake

“…While some bacteria can perform complete oxidation of ammonia (Daims et al, 2015; van Kessel et al, 2015), this process is typically completed in two steps by chemolithoautotrophic microorganisms: ammonia‐oxidizing archaea (AOA) or bacteria (AOB) first oxidize NH 3 to nitrite (NO 2 − ), followed by the oxidation of NO 2 − to NO 3 − by nitrite‐oxidizing bacteria (NOB; e.g., Dworkin & Gutnick, 2012; Könneke et al, 2005). Nitrifiers present in freshwater habitats can include the AOA Nitrososphaerota (commonly known as Thaumarchaeota), AOB of the genera Nitrosomonas and Nitrosospira within the Nitrosomonadaceae, and NOB of the phylum Nitrospirota, genus Nitrobacter , and genus Nitrotoga (e.g., Alfreider et al, 2018; Boddicker & Mosier, 2018; Cabello‐Yeves et al, 2018, 2020; Hayden & Beman, 2014; Herber et al, 2019; Klotz et al, 2022; Lantz et al, 2021; Podowski et al, 2022; Ngugi et al, 2023). These lineages can represent large (>30%) proportions of lake and ocean prokaryotic communities (e.g., Francis et al, 2005; Karner et al, 2001; Ngugi et al, 2023), highlighting the importance of these organisms to both N and carbon cycles.…”

Vertical Distribution and Seasonal Patterns of <i>Candidatus</i> Nitrotoga in a Sub-Alpine Lake

“…Ca. Nitrotoga is an important representative of NOB in rivers, being present in the water column and sediments characterized by a wide range of environmental conditions ( Fan et al , 2016 ; Boddicker and Mosier, 2018 ; Lantz et al , 2021 ). Previous studies also investigated Ca.…”

“…The primer set has since been successfully used in various environmental and engineered systems, including samples obtained from aquatic environments. ( Nowka et al , 2015 ; Figdore et al , 2018 ; Ishii et al , 2020 ; Li et al , 2020 ; Lantz et al , 2021 ). At both sampling depths of PIB, 21 and 24 m, the evaluation of the primer combination Ntg200F/840R generated PCR products of the correct length.…”