Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.

The Origin of Life in the Early Continental Crust: A Comprehensive Model

Continental rift zones on the early Earth provided essential conditions for the emergence of the first cells. These conditions included an abundant supply of raw materials, cyclic fluctuations in pressure and temperature over millions of years, and transitions of gases between supercritical and subcritical phases. While evidence supports vesicle formation and the chemical evolution of peptides, the mechanism by which information was stored remains unresolved. This study proposes a model illustrating how interactions among organic molecules may have enabled the encoding of amino acid sequences in RNA. The model highlights the interplay between three key molecular components: a proto-tRNA, the vesicle membrane, and short peptides. The vesicle membrane acted as a reservoir for hydrophobic amino acids and facilitated their attachment to proto-tRNA. As a single strand, proto-tRNA also served as proto-mRNA, enabling it to be read by charged tRNAs. By replicating this information and arranging RNA strands, the first functional peptides such as pore-forming proteins may have formed, thus improving the long-term stability of the vesicles. This model further outlines how these vesicles may have evolved into the earliest cells, with enzymes and larger RNA molecules giving rise to tRNA and ribosomal structures. Shearing forces may have facilitated the first cellular divisions, representing a pre-LUCA stage.

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.

Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle

BACKGROUND

Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS

We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS

We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.

Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa

Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.

Time-series metaproteogenomics of a high-CO2 aquifer reveals active viruses with fluctuating abundances and broad host ranges

Ecosystems subject to mantle degassing are of particular interest for understanding global biogeochemistry, as their microbiomes are shaped by prolonged exposure to high CO2 and have recently been suggested to be highly active. While the genetic diversity of bacteria and archaea in these deep biosphere systems have been studied extensively, little is known about how viruses impact these microbial communities. Here, we show that the viral community in a high-CO2 cold-water geyser (Wallender Born, Germany) undergoes substantial fluctuations over a period of 12 days, although the corresponding prokaryotic community remains stable, indicating a newly observed "infect to keep in check" strategy that maintains prokaryotic community structure. We characterized the viral community using metagenomics and metaproteomics, revealing 8 654 viral operational taxonomic units (vOTUs). CRISPR spacer-to-protospacer matching linked 278 vOTUs to 32 hosts, with many vOTUs sharing hosts from different families. High levels of viral structural proteins present in the metaproteome (several structurally annotated based on AlphaFold models) indicate active virion production at the time of sampling. Viral genomes expressed many proteins involved in DNA metabolism and manipulation, and encoded for auxiliary metabolic genes, which likely bolster phosphate and sulfur metabolism of their hosts. The active viral community encodes genes to facilitate acquisition and transformation of host nutrients, and appears to consist of many nutrient-demanding members, based on abundant virion proteins. These findings indicate viruses are inextricably linked to the biogeochemical cycling in this high-CO2 environment and substantially contribute to prokaryotic community stability in the deep biosphere hotspots.

Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective

Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.

Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere

Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.

A predicted CRISPR-mediated symbiosis between uncultivated archaea

CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.

Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments

Introduction

Long-term stability of underground CO₂ storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO₂ makes the Eger Rift in the Czech Republic a natural analogue to underground CO₂ storage. The Eger Rift is a seismically active region and H₂ is produced abiotically during earthquakes, providing energy to indigenous microbial communities.

Methods

To investigate the response of a microbial ecosystem to high levels of CO₂ and H₂, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H₂/CO₂ headspace to simulate a seismically active period with elevated H₂.

Results and discussion

Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H₂ and CO₂, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO₂ driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO₂ and H₂-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO₂ concentrations, similar to those found in CCS sites.

Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater

Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.

Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis

BACKGROUND

The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition.

RESULTS

Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaCl_w/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs.

CONCLUSIONS

Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.