Biology subjects

Probst, A. J.

Publications and source records attributed to Probst, A. J..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism

BackgroundCandidate Phyla Radiation (CPR) bacteria are commonly detected yet enigmatic members of diverse microbial communities. Their host associations, metabolic capabilities, and potential roles in biogeochemical cycles remain under-explored. We studied chemoautotrophically-based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs using bulk geochemical analysis, genome-resolved metagenomics and scanning transmission x-ray microscopy (STXM) at room temperature and 87{degrees} K. ResultsCPR-affiliated Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria are members of two biofilm communities dominated by chemolithotrophic sulfur-oxidizing bacteria including Thiothrix or Beggiatoa. STXM imaging revealed ultra-small cells along the surfaces of filamentous bacteria that we interpret are CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show protein-encapsulated elemental sulfur spherical granules associated with filamentous bacteria, indicating that they are sulfur-oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially underpin a symbiosis involving Berkelbacteria and/or Moranbacteria and filamentous sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. ConclusionsOur combined metagenomic, geochemical, spectromicroscopic and structural bioinformatics analyses link some CPR bacteria to sulfur-oxidizing Proteobacteria, likely Thiothrix, and indicate roles for CPR bacteria in sulfur and hydrogen cycling.

microbiology↗

bioRxiv2022

Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities

Microbial communities are significant drivers of global biogeochemical cycles, yet accurate function prediction of their proteome and discerning their activity in situ for bioprospecting remains challenging. Here, we present environmental activity-based protein profiling (eABPP) as a novel proteomics-based approach bridging the gap between environmental genomics, correct function annotation and in situ enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases by combining genome-resolved metagenomics and mass spectrometry-based eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. eABPP does not only advance current methodological approaches by providing evidence for enzyme and microbial activity in situ but also represents an alternative approach to sequence homology-guided biocatalyst discovery from environmental ecosystems.

biochemistry↗

bioRxiv2022

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Marine viruses have thoroughly been studied in seawater, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2 % of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols and rain. Viruses detected in rain and aerosols showed a significantly higher percent G/C base content compared to marine viruses, and a genetically distinct rain virome supports that those viruses could inhabit higher air masses. CRISPR spacer matches of marine prokaryotes to "foreign" viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization and long-range atmospheric dispersal implicate virus-mediated carbon turnover in remote areas, viral dispersal mechanisms relevant to human health, and involvement of viruses in atmospheric processes like ice-nucleation.

microbiology↗

bioRxiv2022

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes, and viruses from metagenomes exist. However, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool accessible for non-bioinformaticians that make it easy to recover genomes of prokaryotes, eukaryotes, and viruses from metagenomes, either alone or in combination. We tested MuDoGer using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.

bioinformatics↗

bioRxiv2021

Host-associated phages disperse across the extraterrestrial analogue Antarctica

Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating or prophages) across the Antarctic continent can be tracked via their genetic signatures aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria including Ralstonia spp. We reconstructed the complete genome of a temperate phage with near-complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula in distance of 5538 km to the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for Astrobiology. ImportanceHost-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to presence of these bacteria carrying genome-integrated prophages on space-related equipment, and the here demonstrated potential for dispersal of host-associated phages, our work has implications for Planetary Protection, a discipline in Astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.

microbiology↗

bioRxiv2021

Rates of primary production in groundwater rival those in oligotrophic marine systems

The terrestrial subsurface contains nearly all of Earths freshwater reserves1 and harbors upwards of 60% of our planets total prokaryotic biomass2,3. While genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the translocation of photosynthetically derived organic carbon4-6, corroborating measurements of carbon fixation in the subsurface are absent. Using a novel ultra-low level 14C-labeling technique, we show that in situ carbon fixation rates in a carbonate aquifer reached 10% of the median rates measured in oligotrophic marine surface waters, and were up to six-fold greater than those observed in lower euphotic zone waters where deep chlorophyll levels peak. Empirical carbon fixation rates were substantiated by both nitrification and anammox rate data. Metagenomic analyses revealed a remarkable abundance of putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria - the first representatives of this class expected to fix carbon via the Wood-Ljungdahl pathway. Based on these fixation rates, we extrapolate global primary production in carbonate groundwaters to be 0.11 Pg of carbon per year.

microbiology↗

bioRxiv2021

Label-free Raman microspectroscopy for identifying virocells

Raman microspectroscopy has been thoroughly used to assess growth dynamics and heterogeneity of prokaryotic cells. Yet, little is known about how the chemistry of individual cells changes during infection with lytic viruses, resulting in so-called virocells. Here, we investigate biochemical changes of bacterial and archaeal cells of three different species in laboratory cultures before and after addition of their respective viruses using single-cell Raman microspectroscopy. By applying multivariate statistics, we identified significant differences in the spectra of single cells and cells after addition of lytic phage (phi6) for Pseudomonas syringae. A general ratio of wavenumbers that contributed the greatest differences in the recorded spectra was defined as an indicator for virocells. Based on reference spectra, this difference is likely attributable to an increase in nucleic acid vs. protein ratio of virocells. This method proved also successful for identification of Bacillus subtilis cells infected with phi29 displaying a decrease in respective ratio but failed for archaeal virocells (Methanosarcina mazei with Methanosarcina Spherical Virus) due to autofluorescence. Multivariate and univariate analyses suggest that Raman spectral data of infected cells can also be used to explore the complex biology behind viral infections of bacteria. Using this method, we confirmed the previously described two-stage infection of P. syringaes phi6 and that infection of B. subtilis by phi29 results in a stress response within single cells. We conclude that Raman microspectroscopy is a promising tool for chemical identification of Gram-positive and Gram-negative virocells undergoing infection with lytic DNA or RNA viruses. ImportanceViruses are highly diverse biological entities shaping many ecosystems across Earth. Yet, understanding the infection of individual microbial cells and the related biochemical changes remains limited. Using Raman microspectroscopy in conjunction with univariate and unsupervised machine learning approaches, we established a marker for identification of infected Gram-positive and Gram-negative bacteria. This non-destructive, label-free analytical method at single-cell resolution paves the way for future studies geared towards analyzing complex biological changes of virus-infected cells in pure culture and natural ecosystems.

microbiology↗

bioRxiv2021

Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling

Methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Other than its two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), there exist other genes called "methanogenesis markers" that are believed to participate in methane metabolism. Many of them are Domains of Unknown Function. Here we show that these markers emerged together with methanogenesis. Even if Mcr is lost, the markers and Mtr can persist resulting in intermediate metabolic states related to the Wood-Ljungdahl pathway. Beyond the markers, the methanogenic ancestor was hydrogenotrophic, employing the anaplerotic hydrogenases Eha and Ehb. The selective pressures acting on Eha, Ehb, and Mtr partially depend on their subunits membrane association. Integrating the evolution of all these components, we propose that the ancestor of all methane metabolizers was an autotrophic H2/CO2 methanogen that could perhaps use methanol but not oxidize alkanes. Hydrogen-dependent methylotrophic methanogenesis has since emerged multiple times independently, both alongside a vertically inherited Mcr or from a patchwork of ancient transfers. Through their methanogenesis genomic remnants, Thorarchaeota and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeota act as metabolically versatile players in carbon cycling of anoxic environments across the globe.

microbiology↗

bioRxiv2021

The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate to environmental drivers or host organisms. Their metabolic traits to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges. Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes obtained from sequential 0.2 and 0.1 {micro}m filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 {micro}m fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 {micro}m fractions. Patescibacteria enriched in the smaller 0.1 {micro}m filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher fraction of rod-shape determining proteins, and genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed based on oxygen concentrations. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. However, only 8% of MAGs showed highly significant one-to-one association, mostly with Omnitrophota. Genes coding for motility and transport functions in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota). Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we propose that the majority of Patescibacteria can attach to multiple hosts just long enough to loot or exchange supplies with an economic lifestyle of little preference for geochemical conditions.

microbiology↗

bioRxiv2021

Virus-associated organosulfur metabolism in human and environmental systems

Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically-derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. While microbial organosulfur metabolism is well-studied, the role of viruses in organosulfur metabolism is unknown. Here we report the discovery of 39 gene families involved in organosulfur metabolism encoded by 3,749 viruses from diverse ecosystems, including human microbiomes. The viruses infect organisms from all three domains of life. Six gene families encode for enzymes that degrade organosulfur compounds into sulfide, while others manipulate organosulfur compounds and may influence sulfide production. We show that viral metabolic genes encode key enzymatic domains, are translated into protein, are maintained after recombination, and that sulfide provides a fitness advantage to viruses. Our results reveal viruses as drivers of organosulfur metabolism with important implications for human and environmental health.

microbiology↗

bioRxiv2020

Viruses carrying genes for microbial extremotolerance are abundant and widely dispersed in the Atacama Desert hyperarid soil

Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage, spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment. ImportanceDeserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.

microbiology↗

bioRxiv2020

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

The functioning, health, and productivity of soil is intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and non-rhizosphere soil at six and nine weeks of plant growth and extracted DNA that was then separated by density using gradient centrifugation. Thirty-two fractions from each sample were grouped by density, sequenced, assembled, and binned to generate 55 unique microbial genomes that were >70% complete. The complete 18S rRNA sequences of several micro-eukaryotic bacterivores and fungi were enriched in 13C. We generated several circularized bacteriophage (phage) genomes, some of which were the most labelled entities in the rhizosphere. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genomes for traits known to be used in interactions involving bacteria, micro-eukaryotes and plant roots and found that heavily isotopically-labeled bacteria have the ability to modulate plant signaling hormones, possess numerous plant pathogenicity factors, and produce toxins targeting micro-eukaryotes. Overall, 13C stable isotope-informed genome-resolved metagenomics revealed that very active bacteria often have the potential for strong interactions with plants and directly established that phage can be important agents of turnover of plant-derived carbon in soil.

microbiology↗

bioRxiv2020

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth's crust

The continental subsurface houses a major portion of lifes abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we used a combination of metagenomics and genome-informed microscopy to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches displayed resistances of Ca. Altiarchaea against eight predicted viral clades, which showed genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tagged and imaged a putatively viral genome rich in protospacers using fluorescence microscopy. Virus-targeted genomeFISH revealed a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

microbiology↗

bioRxiv2020

Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core

The hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus, found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.

genomics↗

bioRxiv2020

uBin - a manual refining tool for metagenomic bins designed for educational purposes

Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earths biomes, yet producing high quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high-throughput, their manual refinement has been slow and sometimes difficult. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was specifically designed for educational purposes. When applied to the public CAMI dataset, refinement of bins was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate active proliferation of microbes in Earths lower orbit. uBin is an easy to install software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software is open source and available under https://github.com/ProbstLab/uBin.

genomics↗

bioRxiv2020

Geological degassing enhances microbial metabolism in the continental subsurface

Mantle degassing provides a substantial amount of reduced and oxidized gases shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we characterized deep subsurface fluids from a cold-water geyser driven by mantle degassing using genome-resolved metagenomics to investigate how the gases impact the metabolism and activity of indigenous microbes compared to non-impacted sites. While species-specific analyses of Altiarchaeota suggest site-specific adaptations and a particular biogeographic pattern, chemolithoautotrophic core features of the communities appeared to be conserved across 17 groundwater ecosystems between 5 and 3200 m depth. We identified a significant negative correlation between ecosystem depth and bacterial replication, except for samples impacted by high amounts of subsurface gases, which exhibited near-surface activity. Our results suggest that geological degassing leads to higher nutrient flows and microbial activity in the deep subsurface than previously estimated.

microbiology↗

bioRxiv2019

Clades of huge phage from across Earth’s ecosystems

Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty-four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPR-Cas systems have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phage may repurpose bacterial CRISPR-Cas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earths ecosystems.

microbiology↗

bioRxiv2018

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.

microbiology↗