Biology subjects

Kallmeyer, J.

Publications and source records attributed to Kallmeyer, J..

6 recordsLinked to original sources

bioRxiv2026

Deep Microbial Colonization in 2-Billion-Year-Old Ultramafic Rock from the Bushveld Complex

Archean cratons may provide stable microbial habitats in the deep subsurface, as evidenced by the discovery of billion-year-old crustal fluids1,2. However, the long-term habitability of these cratonic environments is uncertain, as polymetamorphic evolution in most cratons typically destroys microbial habitats through mineral reactions and porosity loss3,4. Preservation of deep microbial habitats is more likely where mantle-derived magma intruded the craton after metamorphic overprinting4. Here we report the discovery of dense microbial colonization at 814 m depth within the 2.05-billion-year-old, unmetamorphosed Bushveld Igneous Complex intrusion, South Africa5. Using advanced contamination-control protocols6,7 and synchrotron-based X-ray spectroscopy, we identified indigenous microbial cells localized at the rims of phlogopite, a hydrous phyllosilicate mineral. Our study reveals that microbial colonization is associated with Fe(III) derived from the structure of phlogopite, where the dehydrogenation likely oxidizes Fe(II) to Fe(III) coupled to H2 generation8. Despite the absence of fracture-driven fluid ingress in the unfractured rock matrix, aqueous alteration evidenced at the rims by potassium removal indicates a self-sustaining habitat driven by an internal redox gradient9. These findings demonstrate that aqueous alteration of ultramafic rocks can sustain isolated microbial life over geological timescales, significantly expanding the potential for long-term habitability on both Earth and Mars4,10.

microbiology↗

bioRxiv2025

Microbial Diversity and Community Shifts in a Petroleum Reservoir under Production: Effects of Water Breakthrough and Anthropogenic Alterations

Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production processes like water injection, which introduces external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough in the Edvard Grieg oil reservoir offshore Norway using 16S rRNA gene and metagenomic sequencing. We found clear regional heterogeneity in community composition, with low diversity dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while well A07 showed a distinct microbial signature. The dominant genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not due to widespread replacement by injected microbes, but via the increase of sulfate-reducing bacteria. Metagenomic data supported these observations and suggested rapid microbial transport between injection water and the water separator. These findings support the use of microbial signatures as cost-effective tools for monitoring oil reservoir processes and integrity.

microbiology↗

bioRxiv2025

Microbial Worlds Apart: Distinct Communities in Crude Oil and Production Waters

Genomic analyses of microbial community composition are used to improve oil reservoir engineering and monitor reservoir dynamics. Given the challenges of extracting nucleic acids from oil, production water samples are often used as proxies from which to infer microbial community information from oil reservoirs. We employed 16S rRNA gene amplicon and metagenomic sequencing on samples of crude oil and production water from four North Sea oil fields. Taxonomic profiling revealed differences in microbial compositions and functions between production water and crude oil. Production water was more homogeneous, less diverse, harboured taxa associated with conditions non-native to the reservoir (e.g., seawater), and exhibited evidence of contact with atmospheric oxygen, most likely from passing through the water separators. Conversely, crude oil samples harboured microbial taxa typically associated with oil reservoirs. Despite long-term production and, in some cases, re-injection of production waters, the putative native microbial communities were still present in the oil. These findings demonstrate that crude oil samples are much more representative of oil reservoir microbiomes than their production water proxies.

microbiology↗

bioRxiv2024

Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Igneous Rock from the Bushveld 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 rockwater 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 2-billion-year-old igneous rock in the Bushveld 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 smectite. The entry and exit of microbial cells in the veins are severely limited by tight packing with smectite, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.

microbiology↗

bioRxiv2022

Microbial diversity and community dynamics in an active, high CO2 subsurface rift ecosystem

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2 concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2 during earthquakes may provide substrates for methanogenic and chemolithotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 240 m deep drill core, running across six lithostratigraphic zones. In addition, we evaluated diversity as well as metabolic attributes of bacterial and archaeal communities. Our investigation revealed a distinct low biomass community, with a surprisingly diverse Archaea population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis revealed sulfate and sodium concentrations as high as 1000 mg L-1 in sediment samples from a depth between 50 and 100 m and in weathered rock samples collected below 200 m. Most microbial signatures could be assigned to common soil and water bacteria, which together with the occurrence of freshwater Cyanobacteria at specific depths, emphasize the heterogenous, groundwater movement driven nature of this terrestrial subsurface environment. Although not as frequently and abundantly as initially expected, our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2 and when available H2, as a primary energy source.

microbiology↗

bioRxiv2022

Anaerobic methane oxidizing archaea offset sediment methane concentrations in Arctic thermokarst lagoons

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, and lipid biomarkers. We specifically assessed whether sulfate-driven anaerobic methane oxidation (S-AOM) through anaerobic methanotrophic archaea (ANMEs), common in marine sediments with constant supply of sulfate and methane, establish after thermokarst lagoon development and whether sulfate-driven ANMEs consequently oxidize CH4 that would be emitted to the water column under thermokarst lake conditions. The marine-influenced lagoon environment had fundamentally different methane-cycling microbial communities and metabolic pathways compared to the freshwater lakes, suggesting a substantial reshaping of microbial and carbon dynamics during lagoon formation. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow. CH4 concentrations in the freshwater-influenced sediments averaged 1.34{+/-}0.98 {micro}mol g-1, with highly depleted {delta}13C-CH4 values ranging from -89{per thousand} to -70{per thousand}. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011{+/-}0.005 {micro}mol g-1 with comparatively enriched {delta}13C-CH4 values of -54{per thousand} to -37{per thousand} pointing to substantial methane oxidation. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate-poor sediments. Our study shows that S-AOM in lagoon sediments can effectively reduce sediment CH4 concentrations and we conclude that thermokarst lake to lagoon transitions have the potential to mitigate terrestrial methane fluxes before thermokarst lakes fully transition to a marine environment.

microbiology↗