Biology subjects

Mankowski, A.

Publications and source records attributed to Mankowski, A..

8 recordsLinked to original sources

bioRxiv2026

A global genomic survey of prokaryotic carbon fixation reveals an oxygen-tolerant rTCA cycle in the surface ocean

Autotrophic carbon fixation, the conversion of inorganic carbon into biomass, underpins life on Earth. Prokaryotes can carry out this process via at least seven biochemically distinct pathways, yet the phylogenetic and environmental distribution of most remains poorly resolved. Screening approximately 40 billion genes from reference genomes, metagenome-assembled genomes (MAGs) and unbinned metagenomic contigs, we provide a global assessment of the phylogeny and ecophysiology of prokaryotic autotrophs. Most pathway marker genes occurred in unbinned contigs and low-quality MAGs, representing phylogenetically distinct lineages absent from isolate genomes and quality filtered MAGs. Established autotrophs accounted for the large majority of pathway detections in quality filtered MAGs, largely recapitulating known biology from cultivated model organisms. Against this backdrop, the reductive TriCarboxylic Acid (rTCA) cycle, long considered restricted to anoxic environments, was detected in three phylogenetically distinct Campylobacterota lineages from oxygenated surface seawater, suggesting a previously unrecognized and unexpected niche for this pathway. We show that all three MAGs share an enzyme variant, previously described in other oxygen-tolerant lineages, that likely underlies their presence in the oxygenated surface ocean. Read mapping across global ocean metagenomes indicates that the organisms carrying it could be far more widespread than the scarcity of recovered MAGs alone would suggest. Together, these findings illustrate that the current view of global autotrophic carbon fixation is largely shaped by what genome-resolved methods can readily recover, while the true phylogenetic and ecological distribution of autotrophic carbon fixation appears to be much broader.

microbiology↗

bioRxiv2026

Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential

Biological nitrogen fixation sustains productivity across Earths ecosystems, yet the diversity, distribution and ecological drivers of nitrogen-fixing prokaryotes (diazotrophs) remain incompletely resolved. Here we screened approximately 40 billion genes to generate a catalogue of 21,157 diazotroph genomes. Using this catalogue, we quantified diazotroph diversity and abundance across 9,163 metagenomes spanning diverse environments. Diazotrophy was distributed across the prokaryotic tree of life, but both gene diversity and metagenomic abundance were dominated by heterotrophic lineages. Freshwater and sedimentary ecosystems emerged as major reservoirs of nitrogen-fixation potential beyond the environments that have historically anchored the field. Diazotroph-rich assemblages were associated with nitrogen and phosphorus limitation together with carbohydrate-rich metabolic regimes, revealing distinct nutrient and energy niches for cyanobacterial and heterotrophic diazotrophs. Together, this framework unifies disparate views of diazotroph diversity, abundance and ecology, providing a foundation for improved prediction of biological nitrogen fixation across Earths ecosystems.

microbiology↗

bioRxiv2025

Chemosynthetic Symbioses as Hidden Hubs of DMSP and Organosulfur Cycling in Marine Sediments

Chemosynthetic symbioses between animals and bacteria are known to underpin productivity in the deep sea, yet the diversity of energy and carbon sources sustaining these associations in shallow-water environments remains poorly understood. Dimethylsulfoniopropionate (DMSP) is highly abundant in coastal habitats, where it is produced by seagrasses, phytoplankton, and heterotrophic bacteria, and occurs together with its breakdown product dimethyl sulfide (DMS) in shallow-water sediments. Here we show, supported by genomic and transcriptomic evidence, that DMSP and DMS cycling are integral to the energy and carbon metabolism of the gutless oligochaete Olavius algarvensis and its chemosynthetic symbionts. By assigning DMSP degradation pathways to individual members of the hosts microbial community, we reconstructed a network integrating demethylation and cleavage with energy conservation, methionine biosynthesis, and acetate assimilation into polyhydroxyalkanoates. We also identified a host-encoded methanethiol oxidase (MtoX) suggesting host participation in MeSH detoxification. Comparative metagenomic analyses of more than 60 gutless oligochaete species from globally distributed habitats showed that key DMSP- and DMS-processing genes (dddP, dmdA, tmm, dmsA) are widespread, indicating that organosulfur metabolism is a conserved feature of these symbioses. Our findings expand the recognized metabolic repertoire of shallow-water chemosynthetic symbioses and provide evidence that these associations directly contribute to marine DMSP and DMS cycling.

microbiology↗

bioRxiv2025

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from equator to poles, are a pervasive macroecological pattern, yet their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed layer microbiomes exhibited diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) showed no latitudinal diversity structuring. Taxonomic resolution revealed that the mixed layer LDG was underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibited distinct or contrasting LDGs. Diversity structuring also varied by seasons and regions, governed by temperature and nutrient availability. Together, these findings highlight that within the ocean microbiome, LDGs are not universal, but lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.

microbiology↗

bioRxiv2025

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 73,082 samples from humans (including 58,506 of the gut microbiome), 10,703 animal samples, 5,146 ocean water samples, and 21,802 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status and medication for humans, host species and captivity status for animals, and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.

microbiology↗

bioRxiv2025

Evolutionary history of the widespread association between placozoans and diverse Rickettsiales symbionts

Rickettsiales are an enigmatic clade of strictly host-associated bacteria with some very common phylotypes in aquatic habitats. Despite amplicon- and metagenomic sequencing-based observations, the roles of these aquatic Rickettsiales are still unknown, as their genomes feature both beneficial and parasitic traits. In placozoans, microscopy-based observations of intracellular and Rickettsia-like-organisms point to Rickettsiales as common and abundant symbionts. We therefore systematically studied the microbiomes of placozoans to understand the eco-evolutionary dynamics of their associated Rickettsiales. Single-animal metagenomics revealed a widespread association of placozoans with Rickettsiales from three clades of Ca. Midichloriaceae, which were present in all but two placozoan lineages. A comparative phylogenetic analysis of placozoans and their Rickettsiales symbionts revealed host species-specific switches among Rickettsiales clades in several placozoan lineages. Our combination of evolutionary analyses, genome annotations, and expression data indicate different functional roles of these Rickettsiales clades, with some clearly diverging from a classical parasitic lifestyle by the loss of all ATP scavenging machinery. One of placozoan lineages that lacked Ca. Midichloriaceae was instead associated with Rickettsiaceae symbionts, while another was completely devoid of Rickettsiales symbionts. Our imaging data of fibre cells entirely free of Rickettsiales underscores previously unrecognized variation in placozoan-microbe associations. Early-branching invertebrates, including placozoans as well as many corals, are gaining increasing traction as emerging models across the life sciences. Our data and analyses show that it is important to consider the specific endosymbiont groups and their ecology in a given host, as these symbionts likely influence the hosts cellular and organismal biology.

microbiology↗

bioRxiv2024

Genomic and proteomic characterization of sulfate-reducing symbionts of gutless marine annelids

Sulfate-reducing bacteria (SRB) are widespread in marine and terrestrial environments, where they often form syntrophic associations with bacteria, archaea, and eukaryotes. Among the most intimate of these are multipartite symbioses in gutless marine oligochaete worms, which host SRB and sulfur-oxidizing endosymbionts that engage in a syntrophic exchange of sulfur compounds. Despite decades of research on free-living SRB, the metabolic traits that enable SRB to persist in symbiosis, and how these differ across hosts and environments, remain poorly understood. Here, we show that a globally distributed clade of symbiotic SRB has a conserved core metabolism that diverges markedly from free-living relatives. Using comparative genomics and metaproteomics, we reveal that these endosymbionts retain key traits of SRB such as sulfate reduction, complete oxidation of acetate to CO2, amino acid degradation for nitrogen acquisition, and transport of essential nutrients. However, they exhibit a more oxygen-tolerant metabolism and lack typical nutrient-scavenging mechanisms of free-living SRB. One symbiont-specific trait, the glyoxylate bypass, was consistently expressed in situ and may serve both in reactive oxygen species defence and in biomass generation. The enrichment and expression of oxygen-tolerant pathways, coupled with the loss of nutrient-scavenging functions, indicate specialization to a host-associated, redox-fluctuating environment distinct from that of free-living SRB. Consistent with this shift, symbiont genomes are larger than those of free-living relatives, contrasting with genome reduction in many endosymbionts and reinforcing the importance of metabolic versatility. Our findings provide a framework for understanding how metabolic flexibility enables SRB to persist in long-term multipartite symbioses across diverse marine ecosystems.

microbiology↗

bioRxiv2021

Highly variable fidelity drives symbiont community composition in an obligate symbiosis

Multipartite symbioses, which involve intimate interactions among three or more species, have evolved independently numerous times in convergent evolution, and enable functional complexity and ecological flexibility. How stability is maintained in such relationships remains, however, poorly understood, and can only be fully understood by integrating processes across both micro- and macroevolutionary scales. In this study, we bridge these scales by examining the symbiotic communities of gutless marine oligochaetes - annelid worms that have become obligately dependent on their bacterial partners for nutrition and waste removal over the past 150 million years. Using metagenomic sequencing of 231 individuals from 63 host species, collected across 17 marine environments worldwide, we reconstructed host and symbiont phylogenies to investigate the composition, specificity, and evolutionary history of their symbiotic communities from the strain to genus level. Our results show that each gutless oligochaete harbors up to 10 symbiont species drawn from a restricted pool of 33 marine bacterial genera. Community composition was strongly shaped by host species at 90% explanatory power, and much less by geography or environment. Symbiont communities were highly stable within host species but shifted rapidly at short macroevolutionary scales as host species diverged. Ancestral state reconstructions revealed that the primary symbiont, Candidatus Thiosymbion, was an early and persistent acquisition, while secondary symbionts were gained multiple times through convergent evolution, enhancing the diversity and metabolic flexibility of the symbiotic communities. By linking fine-scale microevolutionary dynamics with broader macroevolutionary patterns, our study reveals how gutless oligochaetes achieve both stability and flexibility in their symbiotic partnerships - enabling long-term host dependency while driving innovation and adaptation. This evolutionary trajectory may underpin the ecological success and diversification of gutless oligochaetes in marine sediments, and may help explain the repeated emergence and persistence of other multipartite associations.

evolutionary biology↗