| 1. |
- Lopez-Fernandez, Margarita, et al.
(författare)
-
Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield
- 2023
-
Ingår i: npj Biofilms and Microbiomes. - : Nature Publishing Group. - 2055-5008. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the aspo Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.
|
|
| 2. |
- Lorenz, Henning, Dr. 1972-, et al.
(författare)
-
COSC-2 – drilling the basal décollement and underlying margin of palaeocontinent Baltica in the Paleozoic Caledonide Orogen of Scandinavia
- 2022
-
Ingår i: Scientific Drilling. - Göttingen : Copernicus Publications. - 1816-8957 .- 1816-3459. ; 30, s. 43-57
-
Tidskriftsartikel (refereegranskat)abstract
- Abstract.The Collisional Orogeny in the Scandinavian Caledonides (COSC) scientific drilling project aims to characterise the structure and orogenic processes involved in a major collisional mountain belt by multidisciplinary geoscientific research. Located in western central Sweden, the project has drilled two fully cored deep boreholes into the bedrock of the deeply eroded Early Paleozoic Caledonide Orogen. COSC-1 (2014) drilled a subduction-related allochthon and the associated thrust zone. COSC-2 (2020, this paper) extends this section deeper through the underlying nappes (Lower Allochthon), the main Caledonian décollement, and the upper kilometre of basement rocks. COSC-2 targets include the characterisation of orogen-scale detachments, the impact of orogenesis on the basement below the detachment, and the Early Paleozoic palaeoenvironment on the outer margin of palaeocontinent Baltica. This is complemented by research on heat flow, groundwater flow, and the characterisation of the microbial community in the present hard rock environment of the relict mountain belt. COSC-2 successfully, and within budget, recovered a continuous drill core to 2276 m depth. The retrieved geological section is partially different from the expected geological section with respect to the depth to the main décollement and the expected rock types. Although the intensity of synsedimentary deformation in the rocks in the upper part of the drill core might impede the analysis of the Early Paleozoic palaeoenvironment, the superb quality of the drill core and the borehole will facilitate research on the remaining targets and beyond. Protocols for sampling in the hard rock environment and subsequent sample preservation were established for geomicrobiological research and rock mechanical testing. For the former, a sparse sample series along the entire drill core was taken, while the target of the latter was the décollement. COSC-2 was surveyed by a comprehensive post-drilling downhole logging campaign and a combined borehole/land seismic survey in autumn 2021. This paper provides an overview of the COSC-2 (International Continental Scientific Drilling Project – ICDP 5054_2_A and 5054_2_B boreholes) operations and preliminary results. It will be complemented by a detailed operational report and data publication.
|
|
| 3. |
- Westmeijer, George, et al.
(författare)
-
Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities
- 2022
-
Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 5:1
-
Tidskriftsartikel (refereegranskat)abstract
- The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.
|
|
| 4. |
- Westmeijer, George, et al.
(författare)
-
Continental scientific drilling and microbiology : (extremely) low biomass in bedrock of central Sweden
- 2024
-
Ingår i: Biogeosciences. - : Copernicus Publications. - 1726-4170 .- 1726-4189. ; 21:2, s. 591-604
-
Tidskriftsartikel (refereegranskat)abstract
- Scientific drilling expeditions offer a unique opportunity to characterize microbial communities in the subsurface that have long been isolated from the surface. With subsurface microbial biomass being low in general, biological contamination from the drilling fluid, sample processing, or molecular work is a major concern. To address this, characterization of the contaminant populations in the drilling fluid and negative extraction controls are essential for assessing and evaluating such sequencing data. Here, rock cores down to 2250 m depth, groundwater-bearing fractures, and the drilling fluid were sampled for DNA to characterize the microbial communities using a broad genomic approach. However, even after removing potential contaminant populations present in the drilling fluid, notorious contaminants were abundant and mainly affiliated with the bacterial order Burkholderiales. These contaminant microorganisms likely originated from the reagents used for isolating DNA despite stringent quality standards during the molecular work. The detection of strictly anaerobic sulfate reducers such as Candidatus Desulforudis audaxviator suggested the presence of autochthonous deep biosphere taxa in the sequenced libraries, yet these clades represented only a minor fraction of the sequence counts ( < 0.1 %), hindering further ecological interpretations. The described methods and findings emphasize the importance of sequencing extraction controls and can support experimental design for future microbiological studies in conjunction with continental drilling operations.
|
|
| 5. |
- Westmeijer, George, et al.
(författare)
-
Continental scientific drilling and microbiology: (extremely) low biomass in crystalline bedrock of central Sweden
- 2023
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Scientific drilling expeditions offer a unique opportunity to characterize the microbial communities in the subsurface that have been long-term isolated from the surface. With subsurface microbial biomass being low in general, biological contamination from the drilling fluid, sample processing, or molecular work is a major concern. To address this, characterization of the contaminant populations in the drilling fluid and negative extraction controls are essential for assessing and evaluating such sequencing data. Here, crystalline rock cores down to 2250 m depth, groundwater-bearing fractures, and the drilling fluid were sampled for DNA to characterize the microbial communities using a broad genomic approach. However, even after removing potential contaminant populations present in the drilling fluid, notorious contaminants were abundant and mainly affiliated with the bacterial order Burkholderiales. These contaminant microorganisms likely originated from the reagents used for isolating and amplifying DNA despite stringent quality standards during the molecular work. The detection of strictly anaerobic sulfate reducers such as Candidatus Desulforudis audaxviator suggested the presence of autochthonous deep biosphere taxa in the sequenced libraries, yet these clades represented only a minor fraction of the sequence counts (< 0.1 %), hindering further ecological interpretations. The described methods and findings emphasize the importance of sequencing extraction controls and can support experimental design for future microbiological studies in conjunction with continental drilling operations.
|
|
| 6. |
- Westmeijer, George
(författare)
-
Microbial life deep underground : From anaerobic cultures to reconstructed genomes
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The deep biosphere refers to the vast ecosystem of life beneath the Earth’s surface, residing in the fractured bedrock and pores of rocks, largely isolated from solar energy. These fractures enclose an important reservoir of groundwater that contains microorganisms active in processes such as the uptake of inorganic carbon, sulfur cycling, or the degradation of organic matter. However, there is still much knowledge to be gained on the diversity and function of these subsurface microorganisms, and how the surface influences subsurface life. In this work, I explored interactions among subsurface microorganisms, studied subsurface microbial diversity in the light of surface recharge, and characterized microbial populations residing in biofilms.Potential interactions among microorganisms were explored with anaerobic cultures using groundwaters from the Äspö Hard Rock Laboratory. By removal of larger cells (> 0.45 ?m in diameter), an inoculum enriched in ultra-small bacteria (nanobacteria) was obtained. Despite the presence of various sources of energy and nutrients, these nanobacteria did not grow over prolonged incubation times up to four months. Reconstructed genomes confirmed this group of bacteria to have a low metabolic potential, indicative of a symbiotic lifestyle.Characterization of microbial communities in subsurface groundwaters and overlying environments on Äspö island revealed that a substantial proportion of the subsurface community was also detected in soil-hosted groundwaters. Considering the unidirectional water flow, this showed that part of the subsurface diversity between 70 and 460 m depth could originate from surface recharge, especially for the shallower groundwaters. In contrast to the high microbial diversity observed in Äspö groundwaters, characterization of a fracture fluid at 975 m depth in central Sweden revealed a microbial community dominated by a single population, adapted to the energy-limited conditions in the deep subsurface, namely the bacterium Candidatus Desulforudis audaxviator.Furthermore, the activity (based on RNA transcripts) of attached microbial populations was measured using flow-cells that facilitated biofilm formation. An elevated number of genes involved in the transition from a planktonic to an attached lifestyle was observed. Interestingly, comparing the microbial activity in the biofilm to the planktonic community revealed Thiobacillus denitrificans to have a principal role in the biofilm formation. Combined, these findings help understand the magnitude of microbial diversity in the continental subsurface as well as how these microorganisms are adapted to cope with the energy limitations in this subsurface ecosystem.
|
|
