Biology subjects

Hodgskiss, L. H.

Publications and source records attributed to Hodgskiss, L. H..

8 recordsLinked to original sources

bioRxiv2026

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the evolutionary origins of this regulatory machinery are unknown. Here, we show that the key molecular components of histone-based chromatin regulation are present in the Asgard archaea, the closest prokaryotic relatives of eukaryotes. Asgard histones are abundant and have extended N-terminal tails rich in lysine residues that can be post-translationally modified, all of which are features shared with eukaryotic histones. In line with these findings, we identify enzymes from Asgard archaea that deposit or remove lysine acetylation on histone tails in vitro. Moreover, Asgard sirtuin deacetylases (SIR2 proteins) restore chromatin silencing in yeast, demonstrating the functional compatibility of Asgard enzymes with eukaryotic histone substrates. Our findings establish that the foundations of histone-based chromatin predate eukaryogenesis and place Asgard archaea as an evolutionary intermediate in the emergence of eukaryotic chromatin.

evolutionary biology↗

bioRxiv2026

Biofilm Lifestyle Drives Ecophysiological Niche Expansion in an Archaeal Soil Nitrifier

As key drivers of nitrification, ammonia-oxidizing archaea (AOA) play a central role in the global nitrogen cycle and contribute significantly to the emissions of the potent greenhouse gas nitrous oxide (N2O). However, the ecological implications of AOA growth as biofilms, remain poorly understood. Since nitrite production can be used to follow cellular activities directly we were able to compare biofilms with planktonic cells of the terrestrial model AOA Nitrososphaera viennensis at ecologically and agriculturally relevant conditions. Biofilms were more resistant across nearly all tested conditions and remained active at lower temperatures, acidic pH, and high ammonium concentrations. Collectively, activities in biofilm help reconcile discrepancies between earlier laboratory and environmental observations of soil AOA. Additionally, biofilms showed a high general resilience and lowered sensitivities to nitrification inhibitors. Although in situ biofilms grown in microrespiratory chambers exhibited activity and ammonia affinity similar to planktonic cells, biofilm cultures produced only half as much N2O. The enhanced fitness of biofilms across all tested conditions vastly expands the potential ecophysiological niche of AOA and supports the hypothesis that biofilm growth represents the in situ phenotype of AOA in soil environments.

microbiology↗

bioRxiv2026

Common nitrification inhibitors exhibit varied physiological mechanisms on an ammonia-oxidizing microorganism

Microbial ammonia oxidation, the first and rate-limiting step of nitrification, plays a central role in soil nitrogen cycling. It is most relevant in agricultural soils as nitrifiers compete with crops for ammonia-based fertilizers. Therefore, synthetic nitrification inhibitors are widely used alongside fertilizers to reduce the activities of dominant drivers of this process, i.e. ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the physiological responses of ammonia oxidizers remain poorly resolved. Here the response of the AOA Nitrososphaera viennensis to the nitrification inhibitors 3,4-dimethylpyrazole phosphate (DMPP) and allylthiourea (ATU) were investigated using a combination of functional genomics, physiological assays, and relief experiments. The results overturn earlier assumptions that DMPP and ATU act by chelating free copper. Both compounds affected ammonia oxidation and triggered broader shifts in energy metabolism and stress-response pathways, which diverged markedly between the two inhibitors. We propose a competitive inhibition of the ammonia monooxygenase complex with DMPP as it can be alleviated by additional ammonia and elicits activation of urea acquisition, while ATU acted as a non-competitive inhibitor generally inducing quiescence. Both modes of inhibition were associated with clear transcriptomic and proteomic signals that will be advantageous for the identification of mechanisms of other nitrification inhibitors in the future. Key word: Ammonia-oxidizing archaea, nitrification, nitrification inhibitors, archaea, nitrogen cycle

microbiology↗

bioRxiv2025

Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are widespread in nature and contribute to global carbon and nitrogen cycling. Although their energy production is an aerobic process, AOA occur in environments of low oxygen and in fully anoxic zones. Recently, oxygen production under anoxic conditions was demonstrated, raising the hypothesis that this activity can sustain oxygen dependent ammonia oxidation. In the work presented here, Nitrososphaera viennensis produces high amounts of oxygen in anoxia in dependence of nitrite but not ammonia. Rather than conferring a physiological benefit, oxygen production impaired recovery from anoxia. Produced oxygen is mostly not consumed and therefore cannot sustain ammonia oxidation in the absence of external oxygen. Instead, it is tightly linked to the amount of available redox equivalents. These observations indicate that oxygen production represents a general physiological strategy for alleviating the potential accumulation of reactive intermediates in the ammonia oxidation pathway, analogous to nitrifier denitrification in ammonia-oxidizing bacteria. TeaserOxygen production in ammonia-oxidizing archaea is not an adaptation to anoxia, but rather an electron overflow pathway that is detectable in anoxic conditions.

microbiology↗

bioRxiv2025

Metabolic Response of a Chemolithoautotrophic Archaeon to Carbon Limitation

The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach of the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modelling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon even in the absence of available genetic tools.

microbiology↗

bioRxiv2024

Biofilm lifestyle as a common trait of ammonia-oxidizing archaea

Although widespread in nature, growth in biofilms has been relatively little explored in the globally distributed ammonia oxidizing archaea (AOA). Here we investigated six representatives of three different terrestrial and marine clades of AOA in a longitudinal and quantitative study for their ability to form biofilm and studied gene expression patterns of three representatives. While all strains grew on a solid surface, soil strains exhibited the highest capacity for biofilm formation. Based on microscopic and gene expression data, two different colonization strategies could be distinguished. S-layer containing AOA (from both soil and marine habitats) initialized attachment as single cells and subsequently formed denser layers and three-dimensional structures, while the S-layer free species of the Nitrosocosmicus clade attached as suspended aggregates to the surface and henceforth showed fastest establishment of biofilm. Transcription profiles were significantly different between planktonic and biofilm growth in all strains and revealed individual reactions, often fulfilling shared functions. In particular the strong expression of different types of multicopper oxidases was observed in all strains indicating modifications of their cell coats. S-layer carrying AOA each additionally expressed a set of adhesion proteins supporting attachment. Detoxification of nitrous compounds, copper acquisition as well as the expression of transcription factor B were also shared reactions among biofilm producing strains. However, the majority of differentially expressed protein families was distinct among the three strains illustrating that individual solutions have evolved for the shared growth mode of biofilm formation in AOA, probably driven by the different ecological niches.

microbiology↗

bioRxiv2024

The type III-B CRISPR-Cas System Affects Energy Metabolism and Adaptation in the Archaeon Saccharolobus solfataricus

Type III CRISPR-Cas immune systems that recognize and cleave extrachromosomal RNA when active, are particularly widespread in archaea. Mechanistically, these systems have the potential to regulate gene expression of host genes on a post-transcriptional level, but very little is known about any potential accessory roles of type III-B systems beyond immunity. We have created knockout mutants of a type III-B CRISPR-Cas complex in the thermoacidophilic archaeon Saccharolobus solfataricus to investigate potential secondary functions of the type III-B system. Deletion mutants exhibited an accelerate growth but were less quickly adaptable to changes in carbon sources in their growth media. In line with this phenotype, upregulated genes were significantly enriched in functional categories of energy production and conversion, as well as with carbohydrate or amino acid transport and metabolism in RNAseq studies. Generally, a significant accumulation of genes encoding transmembrane proteins in the upregulated proportion of the transcriptome suggests interconnections between the type III-B CRISPR-Cas system and various membrane-associated processes. Notably, the deletion mutants did not lose their general virus- or plasmid defense activities indicating that this particular system might have been partially adopted for cellular regulatory roles.

microbiology↗

bioRxiv2022

Unexpected Complexity of the Ammonia Monooxygenase in Archaea

Ammonia oxidation as the first step of nitrification constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase is lacking, in particular for the environmentally abundant ammonia oxidizing archaea (AOA). Here, the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Beside the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modelling and in gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase indicating that AmoY and AmoZ serve an important structural and functional role. These data open avenues for further structure-function studies of this ecologically important key nitrification complex.

microbiology↗