11:30 AM - 11:45 AM
[AHW20-04] How do we understand the life of Prokaryotes in a hidden habitat?
★Invited Papers
Keywords:MicrobialDNA, tracer , groundwater, microbial ecology
If the examined groundwater water with 15℃ throughout a year contains some amount of thermophilic bacteria detected by DNA, we may discuss at least some portion of the water comes from deep environment where temperature exceeds about 40℃, based on the microbiological understanding of the growth condition for thermophiles. An environment of 40℃ is calculated to be found at a depth exceeding 500m if an increase in temperature is taken to be 3 to 4℃ per 100m there. The examined groundwater, thus, can be considered to contain such deep water. Previous studies conducted at the foot of Mt. Fuji showed microbial DNA could be used as a new tracer for chasing groundwater (Segawa et al. 2015, Sugiyama et al. 2018). The potential is confirmed by “Revisiting Mt. Fuji’s groundwater origins” (Schilling et al., 2023). Appling microbial DNA analysis as a tracer of groundwater, however, needs to take into consideration the microbial ecology (ME) in the subsurface environment.
How deep?
A deep subsurface ecological study was launched from marine subseafloor expedition (e.g., Parkes et al. 1994). The extended microbial distribution showed that the penetrated seawater harvested microbes over 2 km below the seafloor (Inagaki et al. 2015). In contrast, the microbial distribution for the terrestrial subsurface habitat was found to reach a depth greater than 1.1 km in the Island Arc (Sugiyama & Kato, submitted). Microbes are thus found to be distributed down to deep environments, however the microbial ecological question is whether they are active therein. This represents whether “the particles” really come from the deep.
Who are they?
Deep groundwater contains 104~6 prokaryotic cells/ml, and far more cells may exist in a form attached and embedded to or in sediments and fractures. However, ME reveals a limited portion of the detected cells are active depending upon the condition necessary for the growth of the given prokaryotes. Environmental DNA studies extended quickly during the last decade owing to the development of DNA techniques and an accumulation of environmental data. Prokaryotes (bacteria and archaea), however, cannot be identified by using only DNA sequencing because of their metabolic huge diversity and asexual multiplication with high mutation rate. Their biochemical properties must be elucidated through the cultivation in microbiology. Additionally, the great majority of the clones retrieved by DNA from a given soil or water are not cultivated yet.
In order to grow organisms, being not merely microbes but ourselves, need both electron donor and acceptor. In dark and oxygen depleted subsurface environment denitrification (mainly nitrate acting as the electron acceptor), sulfur reduction (sulfate) and fermentation (organic compounds) are the major heterotrophic machineries for the prokaryotes utilizing organic compounds as an electron donor (Chemoorganotroph). On the other side, Chemolithotroph produces energy from H2, CH4, H2S or others as an electron donor. If the retrieved clones (DNA sequences) are found to be closely related to the prokaryotes for which their energy producing machinery are known, we may predict the inhabiting environment for the retrieved clones. In addition to temperature, reduction potential is a useful measure to characterize and predict the environment where the given prokaryotes inhabit. The retrieved DNA sequences from the sample is recommended to analyze at the Genus level to find out their ecological properties.
Archaea are the target for deep environment
If you ask me which sort of primer (to retrieve DNA from the sample) do you recommend?
“Archaeal” is my quick answer in search of microbes for the deep biosphere.
Inagaki et al. Science, 349:420424 (2015).
Parkes et al. Nature 371: 410-413 (1994).
Schilling et al., Nature water, vol.1, 60-73 (2023).
Seagawa et al. Geomicrobiol. J. 32: 677-688 (2015).
Sugiyama et al. Biogeosciences 15: 721-732 (2018).
How deep?
A deep subsurface ecological study was launched from marine subseafloor expedition (e.g., Parkes et al. 1994). The extended microbial distribution showed that the penetrated seawater harvested microbes over 2 km below the seafloor (Inagaki et al. 2015). In contrast, the microbial distribution for the terrestrial subsurface habitat was found to reach a depth greater than 1.1 km in the Island Arc (Sugiyama & Kato, submitted). Microbes are thus found to be distributed down to deep environments, however the microbial ecological question is whether they are active therein. This represents whether “the particles” really come from the deep.
Who are they?
Deep groundwater contains 104~6 prokaryotic cells/ml, and far more cells may exist in a form attached and embedded to or in sediments and fractures. However, ME reveals a limited portion of the detected cells are active depending upon the condition necessary for the growth of the given prokaryotes. Environmental DNA studies extended quickly during the last decade owing to the development of DNA techniques and an accumulation of environmental data. Prokaryotes (bacteria and archaea), however, cannot be identified by using only DNA sequencing because of their metabolic huge diversity and asexual multiplication with high mutation rate. Their biochemical properties must be elucidated through the cultivation in microbiology. Additionally, the great majority of the clones retrieved by DNA from a given soil or water are not cultivated yet.
In order to grow organisms, being not merely microbes but ourselves, need both electron donor and acceptor. In dark and oxygen depleted subsurface environment denitrification (mainly nitrate acting as the electron acceptor), sulfur reduction (sulfate) and fermentation (organic compounds) are the major heterotrophic machineries for the prokaryotes utilizing organic compounds as an electron donor (Chemoorganotroph). On the other side, Chemolithotroph produces energy from H2, CH4, H2S or others as an electron donor. If the retrieved clones (DNA sequences) are found to be closely related to the prokaryotes for which their energy producing machinery are known, we may predict the inhabiting environment for the retrieved clones. In addition to temperature, reduction potential is a useful measure to characterize and predict the environment where the given prokaryotes inhabit. The retrieved DNA sequences from the sample is recommended to analyze at the Genus level to find out their ecological properties.
Archaea are the target for deep environment
If you ask me which sort of primer (to retrieve DNA from the sample) do you recommend?
“Archaeal” is my quick answer in search of microbes for the deep biosphere.
Inagaki et al. Science, 349:420424 (2015).
Parkes et al. Nature 371: 410-413 (1994).
Schilling et al., Nature water, vol.1, 60-73 (2023).
Seagawa et al. Geomicrobiol. J. 32: 677-688 (2015).
Sugiyama et al. Biogeosciences 15: 721-732 (2018).