Evolutionary stasis of a deep subsurface microbial lineage

Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.

Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem

Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.

Microbial ecology of the deep terrestrial subsurface

The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.

A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA

The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.

Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production

The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm-3 day-1. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm-3 day-1 at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.

Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments

Introduction

Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.

Methods

Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.

Results and Discussion

The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.

Unearthing terrestrial extreme microbiomes for searching terrestrial-like life in the Solar System

The possibility of life elsewhere in the universe has fascinated humankind for ages. To the best of our knowledge, life, as we know it, is limited to planet Earth; yet current investigation suggests that life might be more common than previously thought. In this review, we explore extreme terrestrial analogue environments in the search for some notable examples of extreme organisms, including overlooked microbial groups such as viruses, fungi, and protists, associated with limits of life on Earth. This knowledge is integral to provide the foundational principles needed to predict what sort of Earth-like organisms we might find in the Solar System and beyond, and to understand the future and origins of life on Earth.

Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.

86Kr excess and other noble gases identify a billion-year-old radiogenically-enriched groundwater system

Deep within the Precambrian basement rocks of the Earth, groundwaters can sustain subsurface microbial communities, and are targets of investigation both for geologic storage of carbon and/or nuclear waste, and for new reservoirs of rapidly depleting resources of helium. Noble gas-derived residence times have revealed deep hydrological settings where groundwaters are preserved on millions to billion-year timescales. Here we report groundwaters enriched in the highest concentrations of radiogenic products yet discovered in fluids, with an associated ⁸⁶Kr excess in the free fluid, and residence times >1 billion years. This brine, from a South African gold mine 3 km below surface, demonstrates that ancient groundwaters preserved in the deep continental crust on billion-year geologic timescales may be more widespread than previously understood. The findings have implications beyond Earth, where on rocky planets such as Mars, subsurface water may persist on long timescales despite surface conditions that no longer provide a habitable zone.

Noble gases confirm billion-year groundwater residence times and external fluxes in deep crustal settings globally with implications for subsurface habitability and economic reservoir formation over planetary timescales both on Earth and beyond

Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments

To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28–73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere.

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The genome of subseafloor Schizophyllum commune is distinct from that of other environmental isolates

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The divergence time between strains 20R-7-F01 and H4-8 of S. commune is 28–73 Mya

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S. commune experiences an evolutionary stasis in the subseafloor environment

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DNA repair, transposons, and CAZymes help fungi adapt to the subseafloor environment

Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume

Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml-1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to 'omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.

Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO₂ along with other reduced and oxidized gases to the atmosphere 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 perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.

Thermochronologic perspectives on the deep-time evolution of the deep biosphere

The Earth's deep biosphere hosts some of its most ancient chemolithotrophic lineages. The history of habitation in this environment is thus of interest for understanding the origin and evolution of life. The oldest rocks on Earth, formed about 4 billion years ago, are in continental cratons that have experienced complex histories due to burial and exhumation. Isolated fracture-hosted fluids in these cratons may have residence times older than a billion years, but understanding the history of their microbial communities requires assessing the evolution of habitable conditions. Here, we present a thermochronological perspective on the habitability of Precambrian cratons through time. We show that rocks now in the upper few kilometers of cratons have been uninhabitable (>∼122 °C) for most of their lifetime or have experienced high-temperature episodes, such that the longest record of habitability does not stretch much beyond a billion years. In several cratons, habitable conditions date back only 50 to 300 million years, in agreement with dated biosignatures. The thermochronologic approach outlined here provides context for prospecting and interpreting the little-explored geologic record of the deep biosphere of Earth's cratons, when and where microbial communities may have thrived, and candidate areas for the oldest records of chemolithotrophic microbes.

Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment

Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years.