Biology subjects

Dahle, H.

Publications and source records attributed to Dahle, H..

6 recordsLinked to original sources

bioRxiv2026

Aurora vent field is a hotspot for microbial hydrogen oxidation in the Arctic Ocean

Molecular hydrogen (H2) is a widespread, energetically efficient reductant supporting microbial metabolism across most known ecosystems. Although seafloor hydrothermal vents are major energy providers for H2-oxidizing microorganisms, the diversity of H2 oxidation potential in H2-rich systems remains poorly constrained. Here, we use a metagenomic approach to, for the first time, assess the genome-resolved microbial energy conservation potential within hydrothermal deposits and sediments from the ice-covered, extraordinarily H2-rich Aurora Vent Field in the Arctic Ocean. Community-wide analysis revealed broad taxonomic representation of microorganisms with the potential to consume H2 for energy conservation. Notably, we report the first genome belonging to the cosmopolitan Zetaproteobacteria genus Mariprofundus encoding the capacity for H2 oxidation. Additionally, novel, highly abundant Aquificota at Aurora encode uptake hydrogenases not previously characterized as central to H2 oxidation at deep sea vents. The encoded gene content of abundant taxa points to a preference for flexible rather than obligate lithotrophic energy metabolism. A substantial fraction of inferred H2-oxidizing potential is associated with presumed heterotrophs, potentially enhancing carbon transfer efficiency within the Aurora microbial food web. Overall, this study sheds new light on the importance of H2 availability for shaping microbial communities in hydrothermal systems. ImportanceHydrogen oxidation is a potent energy source for microorganisms that contributes to shaping and sustaining food webs in marine and terrestrial habitats, with particular importance in deep-sea chemosynthetic communities. This study provides detailed insights into how exceptionally high hydrogen availability at the Aurora Vent Field may influence microbial community structure, revealing that hydrogen oxidation potential is widespread among diverse, metabolically versatile taxa rather than obligate hydrogen oxidizers. Our findings refine current understanding of microbial energy flow and carbon cycling in hydrogen-rich hydrothermal systems. These results inform future efforts to model microbial food webs, predict ecosystem responses to changing geochemical conditions, and explore metabolic interactions in deep-sea chemosynthetic habitats more broadly.

microbiology↗

bioRxiv2024

Optimizing alkalinity control in Recirculating Aquaculture Systems (RAS): a dynamic modelling approach

Maintaining good water quality is essential for successful fish production in land-based recirculating aquaculture systems (RAS). Numerous interdependent factors influence water quality parameters, making it difficult to evaluate which operational strategies are most favorable. Mathematical models and model simulations have proven to be powerful tools to evaluate how RAS design and operation are linked to RAS dynamics, but these models rarely implement pH and carbonate species as dynamic variables. Here, we present a dynamic model for RAS (dynRAS) that combines rates of TAN (total ammonia nitrogen) removal, fish growth, and CO2 and TAN excretion, with a reaction model for pH and the carbonate system formulated based on the law of mass action. A novel aspect of our approach is the incorporation of a dosage system modelled by a Hill-function, enabling the exploration of diverse dosing strategies for pH and alkalinity management. The model was validated based on empirical data from a pilot scale RAS system operated with a feeding regime involving 12 hours of feeding per day. We found that model simulations could be used to accurately predict diurnal cycling patterns in RAS water quality parameters. Furthermore, we made use of simulations to assess how diurnal cycling varies with changing pH and alkalinity levels. Model results emphasize the complexity of pH and alkalinity control in RAS in relation to overall water quality management. Based on our simulations, we argue that what should be considered as optimal pH and alkalinity in RAS depends on the state of the system. Accordingly, optimal pH and alkalinity thresholds may vary between different RAS units and between different time points of a rearing cycle. More generally, we demonstrate how modelling and model simulations can be an effective way of getting insights into the dynamics of complex RAS interactions and provide a valuable tool to efficiently explore effects of different operational strategies on water quality parameters.

systems biology↗

bioRxiv2024

Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine-freshwater barrier

Iron-oxidizing Betaproteobacteria and Zetaproteobacteria are generally associated with freshwater and marine environments, respectively. Despite repeated cross-environment observations of these taxa, there has been no focused exploration of genomes of marine Gallionella (Betaproteobacteria) to understand transitions between freshwater and marine habitats. Consequently, their roles in these environments remain uncertain. Here, we present strong evidence for co-occurrence of Gallionella and Zetaproteobacteria at deep-sea hydrothermal vents at the Arctic Mid-Ocean Ridges through metagenomic analyses. Phylogenomics analysis of Gallionella metagenome-assembled genomes (MAGs) suggests that seawater adaptation is an evolutionary event which occurred multiple times in distinct lineages. Similarly, several distinct evolutionary events for freshwater and terrestrial Mariprofundus and other Zetaproteobacteria are predicted. The presence of cyc2 iron oxidation genes in co-occurring marine Betaproteobacteria and Zetaproteobacteria implies an overlap in niches of these iron-oxidizers. Functional enrichment analyses reveal genetic differences between marine MAGs of both iron-oxidizing groups and their terrestrial aquatic counterparts linked to salinity adaptation. Though scanning electron microscopy confirms the presence of Fe(III) oxyhydroxide stalks where Gallionella and Mariprofundus co-occur, Gallionella MAGs from hydrothermal vents lack evidence of putative stalk formation genes. Mariprofundus is therefore the likely sole stalk-producing iron-oxidizer in this environment. Conversely, discovery of putative stalk formation genes in Mariprofundus MAGs across the marine-freshwater barrier suggests that Fe(III) oxyhydroxide stalks might not be an exclusive signature for single iron-oxidizing taxa in marine and freshwater environments. Our research provides novel insights into the iron-oxidizing capacities, stalk production, environmental adaptation, and evolutionary transitions between marine and freshwater habitats for Gallionella and Zetaproteobacteria. ImportanceIron-oxidizing bacteria play an important role in the global cycling of iron, carbon, and other metals. While it has previously been assumed that bacterial evolution does not frequently involve crossing the salinity barrier, recent studies indicate that such occurrences are more common than previously thought. Our study offers strong evidence that this also happens among iron-oxidizing bacteria, with new insights into how these bacteria adapt to the new environment, including hydrothermal vents and freshwater habitats. In addition, we emphasize the importance of accurate iron-oxidizing taxa identification through sequencing, rather than relying solely on the morphology of Fe(III) oxyhydroxides and environment. On a larger scale, microorganisms within established communities needing to respond to changes in salinity due to events like seawater intrusion in coastal aquifers underscore the importance of knowledge of transitions across habitat types with different salt concentration.

microbiology↗

bioRxiv2023

Novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Favne deep-sea hydrothermal vent field

Iron oxidizing Zetaproteobacteria are well-known to colonize deep-sea hydrothermal vent fields around the world where iron-rich fluids are discharged into oxic seawater. How inter-field and intra-field differences in geochemistry influence the diversity of Zetaproteobacteria, however, remains largely unknown. Here, we characterize Zetaproteobacteria phylogenomic diversity, metabolic potential, and morphologies of the iron oxides they form, with a focus on the recently discovered F[a]vne vent field. Located along the Mohns ridge in the Arctic, this vent field is a unique study site with vent fluids containing both iron and hydrogen with thick iron microbial mats (Fe mats) covering porously venting high-temperature (227-267 {degrees}C) black smoker chimneys. Through genome-resolved metagenomics and microscopy, we demonstrate that the Fe mats at F[a]vne are dominated by tubular iron oxide sheaths, likely produced by Zetaproteobacteria of genus Ghiorsea. With these structures, Ghiorsea may provide a surface area for members of other abundant taxa such as Campylobacterota, Gammaproteobacteria and Alphaproteobacteria. Furthermore, Ghiorsea likely oxidizes both iron and hydrogen present in the fluids, with several Ghiorsea populations co-existing in the same niche. Homologues of Zetaproteobacteria Ni,Fe hydrogenases and iron oxidation gene cyc2 were found in genomes of other community members, suggesting exchange of these genes could have happened in similar environments. Our study provides new insights into Zetaproteobacteria in hydrothermal vents, their diversity, energy metabolism and niche formation. ImportanceKnowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen oxidizing Zetaproteobacteria representative belonging to ZetaOTU9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

microbiology↗

bioRxiv2020

The genome of a persistent giant algal virus encodes an unprecedented number of genes involved in energy metabolism

Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions--the synthesis of which is energetically demanding. Here, we unveil peculiar phenotypic and genomic features of Prymnesium kappa virus RF01 (PkV RF01), a giant virus of the Mimiviridae family. We found that this virus encodes an unprecedented number of proteins involved in energy metabolism, such as all four succinate dehydrogenase (SDH) subunits (A-D) as well as key enzymes in the {beta}-oxidation pathway. The SDHA gene was transcribed upon infection, indicating that the viral SDH is actively used by the virus-- potentially to modulate its hosts energy metabolism. We detected orthologous SDHA and SDHB genes in numerous genome fragments from uncultivated marine Mimiviridae viruses, which suggests that the viral SDH is widespread in oceans. PkV RF01 was less virulent compared with other cultured prymnesioviruses, a phenomenon possibly linked to the metabolic capacity of this virus and suggestive of relatively long co-evolution with its hosts. It also has a unique morphology, compared to other characterized viruses in the Mimiviridae family. Finally, we found that PkV RF01 is the only alga-infecting Mimiviridae virus encoding two aminoacyl-tRNA synthetases and enzymes corresponding to an entire base-excision repair pathway, as seen in heterotroph-infecting Mimiviridae. These Mimiviridae encoded-enzymes were found to be monophyletic and branching at the root of the eukaryotic tree of life. This placement suggests that the last common ancestor of Mimiviridae was endowed with a large, complex genome prior to the divergence of known extant eukaryotes. ImportanceViruses on Earth are tremendously diverse in terms of morphology, functionality, and genomic composition. Over the last decade, the conceptual gap separating viruses and cellular life has tightened because of the detection of metabolic genes in viral genomes that express complex virus phenotypes upon infection. Here, we describe Prymnesium kappa virus RF01, a large alga-infecting virus with a unique morphology, an atypical infection profile, and an unprecedented number of genes involved in energy metabolism (such as the tricarboxylic (TCA) cycle and the {beta}-oxidation pathway). Moreover, we show that the gene corresponding to one of these enzymes (the succinate dehydrogenase subunit A) is transcribed during infection and is widespread among marine viruses. This discovery provides evidence that a virus has the potential to actively regulate energy metabolism with its own gene.

microbiology↗

bioRxiv2020

On the diversity of chemical power supply as a determinant of biological diversity

Understanding how environmental factors shape biological communities is a fundamental problem in microbial ecology. Patterns of microbial diversity have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and its biological diversity and community structure. We reveal a strong mechanistic coupling between biological diversity and the diversity of chemical power supply, but also find that different properties of power supply, such as substrate fluxes and flow and Gibbs energies of reactions, affect community structure in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of biodiversity across physicochemical gradients, such as pH gradients. Our findings demonstrate the importance of taking into account energy fluxes in order to reveal fundamental connections between community structure and environmental variability, and to obtain a better understanding of microbial population dynamics and diversity in natural environments.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗