effective strategy; however, low levels of microbial activity, sufficient to carry out
survival functions such as DNA repair, may be a superior strategy for microbial
viability on long timescales (Price and Sowers 2004; Johnson et al. 2007).
For example, in a relatively young Alaskan chronosequence aged 19 to 33 Ka, the
relative abundance of spore-forming bacteria increased from 13% to 79%
(Mackelprang et al. 2017). In contrast, in an Antarctic chronosequence, sporeforming Clostridia were observed to increase in soils from present day to 30 Ka;
however, the Clostridia had accumulated DNA damage (as measured by nicks in the
DNA structure), as opposed to non-spore-forming Actinobacteria from the same
samples. In soils dated 400–600 Ka, the Clostridia could no longer be detected via
molecular methods, and the Actinobacteria were still present, sustaining relatively
little DNA damage (Johnson et al. 2007).
6.2.2 Microbial Vital Signs?: Evidence for Activity
and Replication at Sub-zero Temperatures
Though no microbial activity can be measured in University Valley soils in situ or in
the lab, and there is evidence for enriched dormancy traits in the soils, hints that
active microbiota, or at the very least cells in a maintenance or survival state can be
found. In addition to genes associated with dormancy, there were genes associated
with cold adaptation at sub-zero temperatures (e.g. cold shock proteins, stress
response, reactive oxygen species tolerance) (Goordial et al. 2017). Though conditions for laboratory cultivation of microbial isolates are significantly different from
those experienced in the environment, the sub-zero growth demonstrated by the
isolated (non-sporulating) Rhodococcus sp. JG3 and Rhodotorula sp. JG1b raises the
question of whether such microbial life may be active at similar temperatures in the
permafrost environment but remain undetected due to low biomass or slow metabolic rates.
The genome of Rhodococcus sp. JG3 demonstrates traits consistent with cold
adaptation which would allow activity at cold temperatures. The genome encodes a
higher copy number of genes associated with stress response and cold shock,
compared to closely related mesophilic relatives (Goordial et al. 2016). At the
amino acid level, protein-coding genes have residue substitutions which likely
confer increased flexibility and fluidity to those proteins, advantageous in sub-zero
environments. In many cases, numerous isozymes (enzymes encoding for the same
function) are present with slightly different amino acid compositions. Numerous
isozymes which are “hot” or “cold” adapted have been identified and are thought to
be advantageous for carrying out the same function at different temperatures.
The temperature limit for cellular replication of Rhodococcus sp. JG3 is À5
C,
with a doubling time of 14 days. When cultured Rhodococcus sp. JG3 cells in
exponential growth were rinsed and added without nutrients to sterilized University
Valley permafrost in high abundance (final load 10
6 cells/g), microbial respiration
6 When the Vital Signs of Microbial Life Go Cold, Does That Mean the Pulse Is. . .
121
survival functions such as DNA repair, may be a superior strategy for microbial
viability on long timescales (Price and Sowers 2004; Johnson et al. 2007).
For example, in a relatively young Alaskan chronosequence aged 19 to 33 Ka, the
relative abundance of spore-forming bacteria increased from 13% to 79%
(Mackelprang et al. 2017). In contrast, in an Antarctic chronosequence, sporeforming Clostridia were observed to increase in soils from present day to 30 Ka;
however, the Clostridia had accumulated DNA damage (as measured by nicks in the
DNA structure), as opposed to non-spore-forming Actinobacteria from the same
samples. In soils dated 400–600 Ka, the Clostridia could no longer be detected via
molecular methods, and the Actinobacteria were still present, sustaining relatively
little DNA damage (Johnson et al. 2007).
6.2.2 Microbial Vital Signs?: Evidence for Activity
and Replication at Sub-zero Temperatures
Though no microbial activity can be measured in University Valley soils in situ or in
the lab, and there is evidence for enriched dormancy traits in the soils, hints that
active microbiota, or at the very least cells in a maintenance or survival state can be
found. In addition to genes associated with dormancy, there were genes associated
with cold adaptation at sub-zero temperatures (e.g. cold shock proteins, stress
response, reactive oxygen species tolerance) (Goordial et al. 2017). Though conditions for laboratory cultivation of microbial isolates are significantly different from
those experienced in the environment, the sub-zero growth demonstrated by the
isolated (non-sporulating) Rhodococcus sp. JG3 and Rhodotorula sp. JG1b raises the
question of whether such microbial life may be active at similar temperatures in the
permafrost environment but remain undetected due to low biomass or slow metabolic rates.
The genome of Rhodococcus sp. JG3 demonstrates traits consistent with cold
adaptation which would allow activity at cold temperatures. The genome encodes a
higher copy number of genes associated with stress response and cold shock,
compared to closely related mesophilic relatives (Goordial et al. 2016). At the
amino acid level, protein-coding genes have residue substitutions which likely
confer increased flexibility and fluidity to those proteins, advantageous in sub-zero
environments. In many cases, numerous isozymes (enzymes encoding for the same
function) are present with slightly different amino acid compositions. Numerous
isozymes which are “hot” or “cold” adapted have been identified and are thought to
be advantageous for carrying out the same function at different temperatures.
The temperature limit for cellular replication of Rhodococcus sp. JG3 is À5
C,
with a doubling time of 14 days. When cultured Rhodococcus sp. JG3 cells in
exponential growth were rinsed and added without nutrients to sterilized University
Valley permafrost in high abundance (final load 10
6 cells/g), microbial respiration
6 When the Vital Signs of Microbial Life Go Cold, Does That Mean the Pulse Is. . .
121