Biology subjects

Schoelmerich, M. C.

Publications and source records attributed to Schoelmerich, M. C..

14 recordsLinked to original sources

bioRxiv2026

Tandem repeats in methanogenic archaea and their viruses reveal a shared potential for rapid genomic diversification

Methanogenic archaea drive global methane emissions, yet the molecular basis of their physiological flexibility is unclear. Archaeal adaptation is typically attributed to horizontal gene transfer, which is episodic and cannot explain rapid, reversible change. Here we show that direct tandem repeats (TRs) offer an intrinsic alternative. By screening 50,567 prokaryotic genomes, we find TR densities in Methanosarcina more than 30-fold above the prokaryotic average, paralleling Borg extrachromosomal elements. These TRs recur at conserved loci while sharing almost no sequence identity between strains, indicating independent origin, and evolve during routine cultivation. Methanogen TRs are transcribed, show ribosome occupancy, and lie near regulatory and cofactor-related genes, whilst being depleted around core energy-conserving and translational machinery. Genic TRs generate intrinsically disordered regions in proteins carrying nucleotide-binding, protein-protein interaction and cell-surface domains, and occur in structural and surface proteins of methanogen-infecting viruses. TRs are therefore an overlooked source of variability and adaptation potential in methanogens and their viruses.

microbiology↗

bioRxiv2026

Virus {Psi}M2 enters a non-lytic lifecycle alternative to lysogeny during infection of Methanothermobacter marburgensis

Methanogens, a diverse group of archaea that produce methane during energy metabolism, are prevalent in anoxic habitats where they are exposed to viral infections. The head-tailed virus {Psi}M2 is one of few virus isolates that infect a methanogen host and was described as a lytic virus that lyses its host, Methanothermobacter marburgensis. Here, we present evidence that {Psi}M2 does not exclusively follow the classic lytic lifecycle but can also enter an alternative, chronic infection-like state. Growth experiments showed that infected cultures in minimal medium, optimized for the methanogen host (MS medium) did not exhibit complete lysis but continuously released infective virions. In contrast, in a suboptimal complex medium (SAB medium), the {Psi}M2-infected culture released virions in the exponential growth phase and eventually lysed after 14 hours post infection. Although the genome of {Psi}M2 encodes a putative integrase, a prerequisite for lysogeny, whole genome sequencing of {Psi}M2-infected M. marburgensis cultures revealed that the viral DNA remained extrachromosomal rather than integrating into the host genome, likely due to a mutation in the integrase gene. These findings suggest that {Psi}M2 enters a non-lytic lifecycle alternative to lysogeny under suboptimal host growth conditions. Sequencing further identified a heterogeneous viral population including previously undescribed variants. A high density of non-synonymous mutations and frameshift-inducing insertions was observed within ORFs predicted to encode a capsid protein and a major spike protein, suggesting these viral variants to differ in host recognition and infectivity. Overall, our results show more complex viral behavior and greater genetic variability than previously described.

microbiology↗

bioRxiv2026

Conserved multiheme cytochrome machinery for extracellular electron transfer is widespread and transcriptionally active across deep peat profiles

Northern peatlands store approximately one-third of global soil organic carbon, yet the anaerobic respiratory pathways governing carbon turnover remain unclear. In ombrotrophic bogs, the scarcity of inorganic terminal electron acceptors (TEAs) and high CO2:CH4 ratios indicate that methanogenesis alone cannot account for the observed CO2 production. Peat particulate organic matter (POM) has been proposed as an alternative TEA, but whether resident microorganisms encode and express extracellular electron transfer (EET) machinery required to use such extracellular TEAs remains unknown. Using depth-resolved metagenomics and metatranscriptomics across peat profiles from four ombrotrophic Swedish bogs, we identified conserved EET machinery in dominant yet uncultured Acidobacteriota and Verrucomicrobiota, comprising multiheme cytochromes and outer-membrane porins arranged in syntenic gene clusters. This machinery was transcriptionally active up to several meters depth, alongside broader anaerobic respiratory pathways, while methane-cycling processes were more prominent in the upper layers. These results provide systematic genomic and transcriptomic evidence for EET capacity in peatland microorganisms, establishing a molecular foundation for EET-based respiration and its potential role in suppressing methane formation and emissions.

microbiology↗

bioRxiv2026

Active microbial communities and their extrachromosomal elements link organic matter degradation to methane cycling in anoxic sediments

Anaerobic carbon transformation in freshwater sediments drives substantial methane emissions globally, yet the microbial taxa linking complex carbon degradation to methane production remain poorly characterized. Here, we combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno (Swiss Alps) to identify the active microbial clades, metabolic pathways, and extrachromosomal elements (ecDNA) across a depth gradient within the upper 56 cm of sediment. We recovered 802 species-level metagenome-assembled genomes (MAGs) spanning 66 phyla and identified a Bacteroidota clade (VadinHA17) as one of the most abundant and transcriptionally active populations in the sediment. This clade encodes and transcribes a broad range of diverse glycoside hydrolases (GH), indicating a central role in complex carbohydrate degradation. Transcriptional profiles suggest that this clade ferments organic substrates to acetate and hydrogen, which are key substrates for methanogenesis. In line with this, the acetoclastic methanogen Methanothrix and hydrogenotrophic Methanoregula were among the most abundant and transcriptionally active archaea in the same depth layers. Beyond microbial genomes, we detected 86,905 viral OTUs (vOTUs) and 2,136 plasmid OTUs (pOTUs), with free viruses and plasmids accounting for 5-10% and 0.2% of all sequencing reads, respectively. Notably, plasmids and viruses associated with Bacteroidota VadinHA17 encode and transcribe GHs that could augment host carbohydrate-degrading capacity. Together, these findings reveal new details on how methane production in anoxic lake sediments emerges from a network spanning primary fermentation, methanogenesis and ecDNA-mediated metabolisms.

ecology↗

bioRxiv2026

Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains

DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their hosts modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.

microbiology↗

bioRxiv2024

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

Borgs are huge extrachromosomal elements of anaerobic methane-oxidizing archaea. They exist in exceedingly complex microbiomes, lack cultivated hosts and have few protein functional annotations, precluding their classification as plasmids, viruses or other. Here, we used in silico structure prediction methods to investigate potential roles for [~]10,000 Borg proteins. Prioritizing analysis of multicopy genes that could signal importance for Borg lifestyles, we uncovered highly represented de-ubiquitination-like Zn-metalloproteases that may counter host targeting of Borg proteins for proteolysis. Also prevalent are clusters of multicopy genes for production of diverse glycoconjugates that could contribute to decoration of the host cell surface, or of putative capsid proteins that we predict multimerize into hexagonal arrays. Features including megabase-scale linear genomes with inverted terminal repeats, genomic repertoires for energy metabolism, central carbon compound transformations and translation, and pervasive direct repeat regions are shared with giant viruses of eukaryotes, although analyses suggest that these parallels arose via convergent evolution. If Borgs are giant archaeal viruses they would fill the gap in the tri(um)virate of giant viruses of all three domains of life. One Sentence SummaryProtein analyses, informed by in silico protein structure prediction, revealed that Borgs share numerous features with giant eukaryotic viruses, suggesting that Borgs have a viral-like lifestyle and evolutionary convergence of large extrachromosomal elements across the Domains of Life.

microbiology↗

bioRxiv2023

Asgard archaea modulate potential methanogenesis substrates in wetland soil

The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems are unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and the first complete genome of Freyarchaeia, and defined their metabolism in situ. Metatranscriptomics highlights high expression of [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway genes. Also highly expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and glycerol and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to be non-methanogenic acetogens, likely impacting reservoirs of substrates for methane production in terrestrial ecosystems. One-Sentence SummaryComplete genomes of Asgard archaea, coupled with metatranscriptomic data, indicate roles in production and consumption of carbon compounds that are known to serve as substrates for methane production in wetlands.

microbiology↗

bioRxiv2023

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

Methane emissions that contribute to climate change can be mitigated by anaerobic methane-oxidizing archaea such as Methanoperedens. Some Methanoperedens have huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is little studied. Here, we report small enigmatic linear ECEs, circular viruses and unclassified ECEs, that we predict replicate within Methanoperedens. The linear ECEs have features such as inverted terminal repeats, pervasive tandem repeats, and coding patterns that are strongly reminiscent of Borgs, but they are only 52 kb to 145 kb in length. They share proteins with Borgs and Methanoperedens. Thus, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and we assign them to at least five family-level groups. We also identify eight novel families of Methanoperedens viruses, some of which encode multiheme cytochromes, and unclassified circular ECEs that encode TnpB genes. A population-heterogeneous CRISPR array is in close proximity to the TnpB and has spacers that target other Methanoperedens ECEs including previously reported plasmids. The diverse groups of ECEs exchange genetic information with each other and with Methanoperedens, likely impacting the activity and evolution of these environmentally important archaea.

microbiology↗

bioRxiv2023

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding OmcZ nanowire-like electron-exporting cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

microbiology↗

bioRxiv2023

Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species

Human milk oligosaccharides (HMOs) ensure proper infant gut microbiome establishment. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigated microbiome responses to 2-fucosyllactose (2FL), a prevalent HMO and infant formula additive, by establishing individualized microbiomes using fecal samples from three different infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2FL. Using metagenomic data, we predicted that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2FL breakdown, thus critical for B. breves growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrated that HMO utilization can vary with an individuals microbiome.

microbiology↗

bioRxiv2022

Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of tandem repeats in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg-host associations and possibly co-speciation.

microbiology↗

bioRxiv2022

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Anaerobic methanotrophic (ANME) archaea conserve energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME archaea are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus. These have been maintained in two bioreactors that contain enrichment cultures dominated by different Methanoperedens species and co-occur with Methanoperedens species in other anoxic environments. By manual curation we show that two of the plasmids are large (155,607 bp and 191,912 bp), circular, and replicate bidirectionally. The group of Methanoperedens species that carry these plasmids is related to "Ca. Methanoperedens nitroreducens", "Ca. Methanoperedens ferrireducens", "Ca. Methanoperedens manganicus" and the plasmids occur in the same copy number as the main chromosome. The larger plasmid encodes transporters that potentially enhance access to Ni, which is required for the methyl-CoM reductase (Mcr), Co required for the cobalamin cofactor needed for methyltransferases, and amino acid uptake. We show that many plasmid genes are actively transcribed, including genes involved in plasmid chromosome maintenance and segregation, a Co2+/Ni2+ transporter and cell protective proteins. Notably, one plasmid carries three tRNAs and two colocalized genes encoding ribosomal protein uL16 and elongation factor eEF2. These are not encoded in the host Methanoperedens genome and uL16 and eEF2 were highly expressed, indicating an obligate interdependence between this plasmid and its host. The finding of plasmids of Methanoperedens opens the way for the development of genetic vectors that could be used to probe little understood aspects of Methanoperedens physiology. Ultimately, this may provide a route to introduce or alter genes that may enhance growth and overall metabolism to accelerate methane oxidation rates.

microbiology↗

bioRxiv2021

Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria

Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare members. Laboratory enrichments can select for subsystems of interacting organisms and enable genome recovery for enriched populations. Here, a reactor inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4{degrees}C for 31 months enriched for diverse Planctomycetes and Candidate Phyla Radiation (CPR) bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage Peribacter (1.239 Mbp) was curated to completion, and unexpectedly, encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some Planctomycetes and CPR bacteria were active under the culture conditions. We also reconstructed genomes and obtained transmission electron microscope images for numerous phages, including one with a >300 kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes may act as hubs for interaction networks that include symbiotic CPR bacteria and phages.

microbiology↗

bioRxiv2021

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as "Borgs". We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.

microbiology↗