Biology subjects

Kjeldsen, K. U.

Publications and source records attributed to Kjeldsen, K. U..

5 recordsLinked to original sources

bioRxiv2025

Genome-centric metagenomics reveals novel electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments

Conductive particles are abundant in coastal sediments, yet the organisms and pathways that use them for methane production remain unclear. We applied long-read, genome-resolved metagenomics to a sediment-derived consortium that remained dependent on granular activated carbon (GAC) for a decade. We identified a particle-obligate food web of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The dominant SAO electrogen was a new genus, Candidatus Geosyntrophus acetoxidans (<70% ANI/AAI to described taxa), encoding a streamlined extracellular electron-transfer system: one porin-cytochrome conduit (PCC), 47 multiheme cytochromes, conductive pili, and acetate uptake/utilization genes. A second SAO electrogen, Lentimicrobium sp., carried two giant PCC-like clusters, suggesting an alternative acetate-oxidation route. Electrons flowed via GAC to a Methanosarcina (<89% ANI/AAI to described taxa) equipped with the multiheme cytochrome MmcA and a Rnf/Fpo/HdrDE circuit for EET-driven CO2-reducing methanogenesis. Particle-free lines lost both partners and methanogenic activity, establishing particles as the determinant of persistence. This first genomic blueprint of a natural CIET-SAO consortium identifies potential genomic markers (distinct PCCs, MmcA) for in-situ detection and reveals a particle-bound route from acetate to methane likely operating as a fundamental electron-transfer unit in geoconductor-rich anoxic sediments.

microbiology↗

bioRxiv2023

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here, we analyze distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea, as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree/species tree reconciliation approaches, we show that, in analogy to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared to other archaea. Finally, we infer that the last common ancestor of Asgard archaea likely was a thermophilic chemolithotroph, and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and the platform for the emergence of cellular complexity in eukaryotic cells.

evolutionary biology↗

bioRxiv2019

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group have been identified based on culture-independent approaches with several metagenome-assembled genomes (MAGs) reconstructed to date. However, most of these genomes consist of several relatively small contigs, and, until recently, no complete Asgard archaea genome is yet available. Large scale phylogenetic analyses suggest that Asgard archaea represent the closest archaeal relatives of eukaryotes. In addition, members of this superphylum encode proteins that were originally thought to be specific to eukaryotes, including components of the trafficking machinery, cytoskeleton and endosomal sorting complexes required for transport (ESCRT). Yet, these findings have been questioned on the basis that the genome sequences that underpin them were assembled from metagenomic data, and could have been subjected to contamination and other assembly artefacts. Even though several lines of evidence indicate that the previously reported findings were not affected by these issues, having access to high-quality and preferentially fully closed Asgard archaea genomes is needed to definitively close this debate. Current long-read sequencing technologies such as Oxford Nanopore allow the generation of long reads in a high-throughput manner making them suitable for their use in metagenomics. Although the use of long reads is still limited in this field, recent analyses have shown that it is feasible to obtain complete or near-complete genomes of abundant members of mock communities and metagenomes of various level of complexity. Here, we show that long read metagenomics can be successfully applied to obtain near-complete genomes of low-abundant members of complex communities from sediment samples. We were able to reconstruct six MAGs from different Lokiarchaeota lineages that show high completeness and low fragmentation, with one of them being a near-complete genome only consisting of three contigs. Our analyses confirm that the eukaryote-like features previously associated with Lokiarchaeota are not the result of contamination or assembly artefacts, and can indeed be found in the newly reconstructed genomes.

microbiology↗

bioRxiv2019

Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization, and will be increasingly important as climate warming causes more rapid glacial melt. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godth[a]bsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had young sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates, and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with sulfate reduction rates, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.\n\nContribution to the Field StatementIn most coastal marine sediments organic matter turnover and total energy flux are highest at the surface and decrease significantly with increasing sediment depth, causing depth-dependent changes in the microbial community composition. Glacial runoff in arctic and subarctic fjords alters the composition of the microbial community at the surface, mainly due to different availabilities of organic matter and metals. Here we show that glacial runoff also modifies microbial community assembly with sediment depth. Sediment age was a key driver of microbial community composition in six-meter-long marine sediment cores from the Godth[a]bsfjord region, south-western Greenland. High sedimentation rates at glacier-influenced sediment stations enabled a complex community of sulfur-cycling-associated microorganisms to continuously thrive at high relative abundances from the surface into the sediment subsurface. These communities consisted of putative fermenters, sulfate reducers and sulfur oxidizers, which likely depended on high metal concentrations in the relatively young, glacier-influenced sediments. In non-glacier-influenced sediments with lower sedimentation rates, these sulfur-cycling-associated microorganisms were only present near the surface. With increasing sediment depth these surface microorganisms were largely replaced by other surface microorganisms that positively correlated with sediment age and belong to known taxa of the energy-limited, marine deep biosphere.

microbiology↗

bioRxiv2019

Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g. Chloroflexi & Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.

microbiology↗