Biology subjects

Gwak, J.-H.

Publications and source records attributed to Gwak, J.-H..

5 recordsLinked to original sources

bioRxiv2025

Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase

Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. Nitrobacter winogradskyi Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent Km (25.9 M) and a high specific affinity a{degrees} (440.5 l g cells-1 h-1), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that Nitrobacter can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both r-and K-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.

microbiology↗

bioRxiv2025

Hypoosmolarity inhibits archaeal ammonia oxidation

Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels ([~]120 S/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by "Ca. Nitrosotenuis" of the Nitrosopumilaceae family, was stimulated by high salinity ([~]760 S/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low ([~]170 S/cm) and high salinity ([~]850 S/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.

microbiology↗

bioRxiv2024

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOM), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and an ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, H2O2-induced oxidative stress defense, and ammonia oxidation, including ammonia monooxygenase subunit C (amoC3) and the multicopper oxidases. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

ecology↗

bioRxiv2024

Nitrous oxide respiration in acidophilic methanotrophs

Methanotrophic bacteria mitigate methane (CH4) emissions from natural environments. Although aerobic methanotrophs are considered strict aerobes, they are often highly abundant in extremely hypoxic and even anoxic environments. Despite the presence of denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we revealed that two acidophilic methanotrophs encoding N2O reductase (clade I and type II nosZ, respectively): Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6, respired N2O and grew anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. However, NO3 - and NO2 - could be reduced during methanol oxidation in Methylocella tundrae T4 and Methylocella silvestris BL2 without significantly increasing cell biomass. The lack of growth on methanol + NO3- or NO2- was likely due to the production of toxic reactive nitrogen species and C1 metabolites. However, the oxidation of pyruvate, a C3 electron donor, combined with NO3- or NO2- reduction resulted in anaerobic growth of Methylocella tundrae T4 and Methylocella silvestris BL2. In the extreme acidophile, Methylacidiphilum caldifontis IT6, N2O respiration supported cell growth at an extremely acidic pH of 2.0. In Methylocella tundrae T4, simultaneous consumption of N2O and CH4 was observed in suboxic conditions, both in microrespirometry and growth experiments, indicating the robustness of its N2O reductase activity in the presence of O2. Furthermore, CH4 oxidation per O2 reduced in O2-limiting conditions increased when N2O was added, indicating that cells of T4 can direct more O2 towards methane monooxygenase when respiring N2O as a terminal electron acceptor. Upregulation of nosZ and distinct repertories of methanol dehydrogenase-encoding genes (XoxF- and MxaFI-type) in Methylocella tundrae T4 cells grown anaerobically on methanol with N2O as the sole electron acceptor indicated adaptation mechanisms to anoxia. Our findings demonstrate that some methanotrophs can respire N2O independently or in tandem with O2, significantly expanding their potential ecological niche and paving the way for enhanced growth and survival in dynamic environments. This metabolic capability has application potential for simultaneously mitigating the emissions of the key greenhouse gases, CO2, CH4, and N2O, from natural and engineered environments.

microbiology↗

bioRxiv2024

Candidatus Nitrosocosmicus members are the dominant archaea associated with pepper (Capsicum annuum L.) and ginseng (Panax ginseng C.A. Mey.) plants rhizospheres

BackgroundAlthough archaea are widespread in terrestrial environments, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. The ammonia-oxidizing archaea (AOA), which are abundant in soil environments, catalyze the first step of nitrification and have the potential to influence plant growth and development significantly. ResultsBased on archaeal 16S rRNA and amoA gene (encoding the ammonia monooxygenase subunit A) amplicon sequencing analysis, distinct archaeal communities dominated by AOA were found to be associated with the root systems of pepper (Capsicum annuum L.) and ginseng (Panax ginseng C.A. Mey.) plants compared to bulk soil not penetrated by roots. AOA related to "Candidatus Nitrosocosmicus", which, unlike most other AOA, harbor genes encoding manganese catalase (MnKat), dominated rhizosphere soils, and thus contributed to the development of distinct archaeal communities in rhizospheres. Accordingly, for both plant species, the copy number ratios of AOA MnKat genes to amoA genes were significantly higher in rhizosphere soils than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. ConclusionsDue to their abundance, "Ca. Nitrosocosmicus" members can be considered key players mediating the nitrification process in rhizospheres. The selection of this MnKat-containing AOA in rhizospheres of several agriculturally important plants hints at a previously overlooked AOA-plant interaction. For additional mechanistic analyses of the interaction, this key clade of AOA with cultured representatives can be employed.

microbiology↗