Biology subjects

Lloyd, K. G.

Publications and source records attributed to Lloyd, K. G..

14 recordsLinked to original sources

bioRxiv2026

Global carbon fixation in Earth's subsurface biosphere

The subsurface of our planet hosts 15% of Earths biomass and plays a key role in mediating the exchange of volatiles and elements between deep, long-residence-time geological reservoirs and rapidly cycling surface environments, influencing planetary climate and habitability. While a significant fraction of subsurface microorganisms rely on surface-derived organic carbon, an unknown portion is sustained through chemolithotrophic carbon fixation. Despite its importance, the global diversity and distribution of microbial carbon fixation pathways in the subsurface, and the environmental drivers shaping them, remain poorly constrained. Here we systematically characterise carbon fixation pathways for 412 subsurface metagenomes, including 242 new metagenomes, and compare them to surface-derived datasets. We find that subsurface environments span a broader physicochemical space than surface systems and support a higher abundance and diversity of carbon fixation strategies. Using colocated geochemical data spanning >50 variables, we show that the reductive tricarboxylic acid cycle and the reductive acetyl-CoA pathway are enriched in reducing, geochemically evolved fluids. We use the metagenomic results together with previously published carbon fixation rates in the subsurface to derive a global continental subsurface carbon fixation rate of [~]2.65 Pg C yr-1 (range: 0.31-2.99). This represents [~]2% of terrestrial photosynthetic primary production, and is an order of magnitude higher than geological fluxes between the surface and the subsurface. These results identify the subsurface as a reservoir of autotrophic strategies organized along geochemical gradients, contributing substantially to the global carbon cycle. One Sentence SummaryThe subsurface is a widespread, environmentally and functionally diverse reservoir of autotrophic carbon fixation pathways that can contribute substantially to the global carbon cycle, fixing [~]2.65 Pg C yr-1 in continental settings alone.

microbiology↗

bioRxiv2025

Tectonic setting shapes microbial biosynthetic potential across global geothermal environments

Microbial communities in geothermal environments constitute an underexplored reservoir of biosynthetic gene clusters with significant biotechnological potential. Here, we investigate the secondary metabolite potential of 219 microbial communities across marine and continental geothermal field sites, encompassing broad environmental gradients in temperature (4.7{degrees}C to 93.5{degrees}C), pH (0.85 to 10.3), and tectonic setting, including volcanic arcs, backarcs, divergent margins at on-axis mid-ocean ridges, post-subduction extensional arcs, and paleo-convergent intraplate plume systems. We identified 9,019 putative new biosynthetic gene cluster families, mostly lacking similarity to known biosynthetic gene clusters. Volcanic arc systems consistently exhibit the highest diversity of biosynthetic repertoires, whereas intraplate plume systems showed a greater representation of terpene-associated gene cluster families. In contrast, divergent margin systems were primarily characterized by nonribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides pathways, together accounting for a large fraction of their predicted biosynthetic diversity. These findings suggest that tectonic context could be associated with large-scale patterns in microbial biosynthetic potential and provide a geobiological framework for guiding natural product discovery in geothermal ecosystems.

microbiology↗

bioRxiv2025

Functional genomic signatures predict microbial culturability across the tree of life

Most microbial taxa on Earth remain uncultivated, limiting our ability to study their physiology, ecology, and roles in environmental processes. Although metagenome-assembled genomes (MAGs) have expanded access to uncultured phylogenetic diversity, the functional basis for culturability remains poorly understood. Here, we analyze the 52,515 MAGs from the Genomes from Earths Microbiomes (GEM) catalog to test two hypotheses: 1) genomes from uncultured microbes encode more functionally novel genes than those from cultured taxa, and 2) specific genomic features are systematically associated with culturability across phyla. To assess functional novelty, we aligned predicted proteins to SwissProt and measured sequence dissimilarity to the nearest curated homolog. We find that uncultured MAGs, particularly among Archaea, harbor substantially more divergent proteins. To identify genomic traits predictive of culturability, we combined pathway-level enrichment with LASSO regression and permutation-based feature importance. Cultured MAGs were consistently enriched in Clusters of Orthologous Groups (COG) pathways related to vitamin and cofactor biosynthesis (e.g., thiamine, folate, B12), energy metabolism (e.g., TCA cycle), and CRISPR-Cas systems--functions often depleted in uncultured counterparts. LASSO models identified a subset of these pathways as strong predictors of cultured status even in poorly sampled phyla, suggesting conserved genomic signatures of culturability. In contrast, pathways such as purine biosynthesis and NADH dehydrogenase were associated with uncultured lineages, highlighting potential barriers to cultivation. These results 1) demonstrate the great functional novelty of uncultured microbes, potentially offering unprecedented opportunities for discoveries of novel function, and 2) identify metabolic traits associated with culturability to inform future cultivation strategies. ImportanceThe vast majority of microbes are uncultured, which means they have never been characterized under laboratory conditions. We showed that genomic sequences of uncultured microbes have less similarity to characterized proteins compared to cultured microbes, revealing that there may be fundamental biological reasons why they are not cultured. We also showed that certain metabolic pathways, such as those related to vitamin and cofactor biosynthesis, can predict the ability of microbes to grow under laboratory conditions, and these pathways are abundant in highly cultured phyla, indicating how metabolic pathways can influence cultivation strategies.

microbiology↗

bioRxiv2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating the individual microbes that respond to specific changes has been difficult. To address that, we implemented BONCAT-Live, by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient enriched conditions. From a Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human oral microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities. ImportanceDynamic microbial activity transforms environments and impacts health and disease in associations with plants and animals, including humans. Identifying the contribution of individual microbes to those processes in real time has not been generally compatible with their selective cultivation. BONCAT-Live tracks which microbes in environmental samples are translationally active and couples it with single cell isolation and cultivation. By studying the response of individual community member to specific natural or induced physical or chemical changes in the environment and culturing those organisms, BONCAT-Live enables further insights into microbial metabolic strategies, community dynamics and environmental adaptations.

microbiology↗

bioRxiv2025

Traits enabling persistence of living Promethearchaeota in marine sediments frozen for over 100 kyr

The phylum Promethearchaeota (formerly "Asgard" archaea), the microbial progenitors of all Eukaryotes, are abundant throughout Earths subsurface, who have been hypothesized to persist over geological timescales in stable environments with little cell division. We therefore examined the genetic adaptations of Promethearchaeota after being frozen for >100 kyr by comparing metagenome-assembled genomes (MAGs) from the Kolyma Lowland, Siberia, to MAGs from other marine and terrestrial sediments worldwide. We reconstructed 22 Promethearchaeota MAGs from 5 classes (Heimdallarchaeia, Gerdarchaeia, Lokiarchaeia, Helarachaeia and Thorarchaeia). Six MAGs from the intracellular DNA fraction were > 70% complete before and after DNA repair, and therefore likely represent living Promethearchaeota that have maintained high DNA integrity under cryogenic conditions through geological time. These 6 MAGs were also over 7 times more abundant than all other Promethearchaeota MAGs based on read recruitment. These permafrost Promethearchaeota MAGs are closely related to other non-permafrost Promethearchaeota lineages at the family or genus level and share metabolic potential and genes for DNA and protein repair with them. This suggests that the ability to survive for >100 kyr in permafrost is a trait that is widespread within the Promethearchaeota. No genes were more prevalent in our permafrost MAGs compared to Promethearchaeota MAGs from other environments. The lack of detectable genetic change since these groups were frozen is consistent with the predicted state of inactivity. Furthermore, although DNA repair mechanisms were present in the Promethearchaeota/Eukaryote lineage before the eukaryotic split, Promethearchaeota protein repair mechanisms emerged after the split, suggesting that adaptations to long term dormancy, or aeonophily, may set modern Promethearchaeota apart from eukaryotes. Collectively, our study expands the known habitat range of many subgroups of Promethearchaeota to ancient marine permafrost and suggests they may have extraordinary long-term survivability under cryogenic conditions through geological time.

microbiology↗

bioRxiv2024

Nitrous Oxide Formation and Consumption in Thawing Permafrost: A Microcosm Study

Nitrous oxide (N2O) emissions contribute to stratospheric ozone depletion and global warming. Climate warming causes permafrost thawing and decomposition of the dormant nitrogenous compounds, releasing N2O; however, understanding of the microbial formation and consumption of N2O in permafrost is still limited. Permafrost soils collected at two depths (5.4 m and 16.9 m) from the East Siberian Sea coast of Russia were used to establish microcosms assessing N2O formation and consumption in the presence of either nitrate (NO3-, 1 mM) or N2O (1 mM), respectively, during incubation at 4 and 20{degrees}C. Rapid N2O formation was observed in NO3--amended microcosms, but N2O consumption was slow and incomplete over a 1-year incubation period in all microcosms. Twenty-six quality-filtered metagenome-assembled genomes (MAGs) harboring genes involved in the reduction of NO3- and/or N2O were recovered from 16 metagenomes obtained from duplicate NO3-- and N2O-amended microcosms. None of the MAGs carried a complete set of genes to perform canonical denitrification (i.e., NO3-[->]N2) indicating N2O formation and consumption is likely driven by non-denitrifying bacteria. While coastal permafrost microbiomes harbor nosZ genes, activity monitored in the microcosms indicates N2O formation exceeds N2O consumption, emphasizing the need for integrated approaches to assess and predict N turnover in thawing permafrost.

microbiology↗

bioRxiv2024

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments constitute one of Earths largest habitats for microbial life, yet differences between surface and subsurface microbiomes and between marine and terrestrial microbiomes remain unclear. We analyzed 478 archaeal and 1054 bacterial amplicon sequence datasets and 147 metagenomes from diverse and globally distributed surface and subsurface environments. Taxonomic analyses show that archaeal and bacterial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between marine and terrestrial microbiomes, suggesting a horizontal phylogenetic divide between sea and land that mirrors patterns in plant and animal diversity. In contrast, community composition overlapped from surface to subsurface environments indicating vertical diversity continua rather than a discrete subsurface biosphere. Diversity of terrestrial microbiomes decreases from surface to subsurface environments. Marine subsurface diversity and phylogenetic novelty rivaled (bacteria) or even exceeded (archaea) that of surface environments, suggesting that the marine subsurface holds a considerable and underestimated fraction of Earths archaeal and bacterial diversity. TeaserSubsurface ecosystems within Earths crust and seafloor harbor diverse and distinct microbiomes featuring many unknown lineages.

microbiology↗

bioRxiv2024

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBAs versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.

bioinformatics↗

bioRxiv2022

Implications of taxonomic bias for microbial differential-abundance analysis

Differential-abundance (DA) analyses enable microbiome researchers to assess how microbial species vary in relative or absolute abundance with specific host or environmental conditions, such as health status or pH. These analyses typically use sequencing-based community measurements that are taxonomically biased to measure some species more efficiently than others. Understanding the effects that taxonomic bias has on the results of a DA analysis is essential for achieving reliable and translatable findings; yet currently, these effects are unknown. Here, we characterized these effects for DA analyses of both relative and absolute abundances, using a combination of mathematical theory and data analysis of real and simulated case studies. We found that, for analyses based on species proportions, taxonomic bias can cause significant errors in DA results if the average measurement efficiency of the community is associated with the condition of interest. These errors can be avoided by using more robust DA methods (based on species ratios) or quantified and corrected using appropriate controls. Wide adoption of our recommendations can improve the reproducibility, interpretability, and translatability of microbiome DA studies. This manuscript was rendered from commit 7412a36 of https://github.com/mikemc/differential-abundance-theory. Supporting data analyses can be found in the accompanying computational research notebook. Please post comments or questions on GitHub. The manuscript is licensed under a CC BY 4.0 License. See the GitHub Releases or Zenodo record for earlier versions.

bioinformatics↗

bioRxiv2020

Novel taxa of Acidobacteriota involved in seafloor sulfur cycling

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, sub-division 23) and Ca. Polarisedimenticola ( sub-division 22), with distinct genetic properties that may explain their distributions in biogeochemically distinct fjord sediments. Ca. Sulfomarinibacter encodes flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen and acetate. A Ca. Polarisedimenticola MAG encodes enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

microbiology↗

bioRxiv2020

Woeseiales transcriptional response in Arctic fjord surface sediment

Distinct lineages of Gammaproteobacteria clade Woeseiales are globally-distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79{degrees}N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.

microbiology↗

bioRxiv2020

Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily-metabolized organic compounds and total microbial cell abundance decrease steadily. However, it is unknown whether some microbial clades increase with depth, despite the overall trend of abundance decrease. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often anaerobic, uncultured, or common in deep marine sediments relative to those that decreased. Minimum turnover times (which are minimum in situ doubling times of growth rates) were estimated to be 2-25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the Fraction Read Abundance of 16S rRNA genes and total Cell counts (FRAxC). Turnover times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28 {+/-} 19%). qPCR and FRAxC in WOR cores and FRAxC in CLB incubations produced similar turnover times for key deep subsurface uncultured clades Bathyarchaeota (8.7 {+/-} 1.9 years) and Thermoprofundales/MBG-D (4.1 {+/-} 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for natural selection of traits for long-term subsistence after resuspension events. Significance statementThe current dogma is that the deeply-branching uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments - rather they exist in a sort of prolonged torpor for thousands of years. This is because no evidence has ever been found that these clades actually increase population sizes, or grow, as they are gradually buried. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This changes our dogma about marine sediments as a vast repository of non-growing microbes, to a vast repository of non-growing microbes with a thin and relatively rapid area of growth in the upper 10 centimeters.

microbiology↗

bioRxiv2020

ANME-1 archaea drive methane accumulation and removal in estuarine sediments

Uncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide. Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

microbiology↗

bioRxiv2018

Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

To unequivocally determine a microbes physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 x 1029 (81%) and 2.2 x 1029 (25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

microbiology↗