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Microbial Life Under Extreme Energy Limitation

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Microbial Life Under Extreme Energy Limitation REVIEWS Microbial life under extreme energy limitation Tori M. Hoehler1* and Bo Barker Jørgensen2* Abstract | A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors. Deep biosphere The discovery of microbial life beneath the surface of states and the prominent organisms differ widely from The set of ecosystems and the continents and the seabed has shown that a large the Petri dish to the environment. Particularly when their organisms living beneath proportion of all the bacteria and archaea on Earth considering oligotrophic natural systems such as the the upper few metres of the live in the deep biosphere1 and that the energy supply deep biosphere, it is important to bear in mind that our solid earth surface. for microbial life that is present in this environment understanding of microbial energy metabolism stems Extended stationary phase spans many orders of magnitude. Even though so many primarily from studying populations that are charac- A phase of the batch culture microorganisms reside in the deep biosphere — about terized by rapid growth, high metabolic rates and high life cycle characterized by the 3 × 1029 cells according to the most recent census2 — the cell densities — characteristics that do not apply to most persistence of a small fraction energy flux available from buried organic carbon is less microorganisms in nature. of cells for months to years beyond the death of the than 1% of the photosynthetically fixed carbon on the 1 majority of the culture, without surface of our planet . These microorganisms generally The phases of life in batch culture. Populations in batch new addition of substrate. have no cultivated relatives, and their biochemistry and culture transition through lag phase, exponential phase, physiology are largely unknown. One of the greatest stationary phase, death phase and extended stationary enigmas, however, is how these vast communities can phase (FIG. 1). The most heavily studied aspects of the subsist in conditions that provide only marginal energy microbial life cycle are the growth (exponential) and for cell growth and division and seem to barely support stationary phases. Growth phase is characterized by cells the maintenance of basic cellular functions. operating at rates near the maximum allowed by their This Review explores the range of metabolic states in enzyme kinetics (growing in exponential fashion) and cultivated cell populations under feast and famine con- dividing with a time constant that is determined by the 1NASA Ames Research Center, Mail Stop 239–4, ditions and compares the lessons learned from labora- physiology of the organisms concerned and the growth Moffett Field, California tory cultures with our knowledge of energy-depleted conditions. Compilations across a broad range of cultured 94035-1000, USA. environ mental conditions. We present current estimates taxa3–7 show maximum growth rates that generally cluster 2Center for Geomicrobiology, of mean metabolic rates in natural communities and within a two orders of magnitude range, from less than Institute of Bioscience, −1 −1 Aarhus University, discuss whether highly energy-starved microorganisms 1 d to more than 30 d . At the high end of this range, Ny Munkegade 114, have previously unexplored physiological mechanisms to populations double in less than 30 minutes, and for the 8000 Aarhus C, Denmark. cope with low energy flux. discussion that follows it is useful to recall that a typical *The authors contributed culture of Escherichia coli has a doubling time of about equally to this work. Energy metabolism in culture 20 minutes and transitions through the lag-to-death batch Correspondence to T.M.H. 8 e-mail: Most of our knowledge about microbial physiology culture life cycle within about 3 days . [email protected] and metabolism is derived from the study of organisms Following stationary phase, most of the popula- doi:10.1038/nrmicro2939 in batch culture, but the pace of life, the physiological tion — typically 99% or more in batch cultures of E. coli NATURE REVIEWS | MICROBIOLOGY VOLUME 11 | FEBRUARY 2013 | 83 © 2013 Macmillan Publishers Limited. All rights reserved REVIEWS 1012 Cultures Natural populations second, batch culture conditions are not representative of the conditions found in low-energy environments. Thus 1010 it is not clear whether, or to what extent, the death that e occurs in batch cultures is part of microbial life under low energy flux. 4 108 (3×10 d) f The small fraction of cells that survive through the –1 (2 105 d) g death phase (which, even at a 99% attrition rate, can still × 6 7 −1 106 comprise cell densities of 10 –10 ml ) has been shown 5 6 Cells ml (10 –10 d) to persist for months or years without further addition of substrate, forming what has been referred to as an 104 d 8,10,11 c h extended stationary phase . Among the states repre- b sented in batch culture, extended stationary phase would 102 seem the most relevant for understanding life in low- a energy environments, but it must be borne in mind that there are key differences in the nature of energy provision 100 and the relevant timescales and thus, potentially, also in –2 0 2 4 6 8 10 10 10 10 10 10 10 10 the prevailing physiological states. Extended stationary Duration of activity (d) phase in E. coli is characterized by the rapid emergence Figure 1 | Timescales, population sizes and biomass turnover times associated with of at least four distinct mutations that enhance the abil- 12–14 culture-based and natural environment studies. Blue pointsNature represent Reviews a |hypothetical Microbiology ity to catabolize amino acids — that is, to subsist on batch culture experiment for an organism with a 1 h doubling time (after Finkel8). Red the remains of dead predecessors — and thereby confer points reflect measurements in natural systems. Values in parentheses represent estimates a growth advantage relative to wild-type cells or even of carbon turnover in terms comparable to doubling time. Time points of note are (a) earlier generations of survivors9,10. The emergence and b succession of these growth advantage in stationary phase (cd e (GASP) mutants drives population turnover that occurs 20 cmbsf (centimetres below sea floor)70,71f on monthly or shorter timescales and that can persist for 10,15 (metres below sea floor)70,71g65 more than a year . Such dynamic overturn in the pop- (h16. The majority of our ulation (with relatively high rates of growth replacing cell knowledge about microbial physiology derives from the region approximated by a, attrition) reflects an energy-intensive state that is driven whereas a large proportion of bacteria and archaea on Earth live in circumstances by the initial availability of 100–1,000 dead cells’ worth approximated by e–h. of energy for each survivor of death phase. Because it seems unlikely that such dynamism could be supported over the much longer timescales that are characteristic of — becomes non-viable8. The onset and extent of cell sustained microbial activity in natural settings16, caution death within a given species is reproducible9,10, but the is warranted in considering even the extended stationary mechanisms responsible are not well understood. Finkel8 phase as a model for life in low-energy settings. suggests two possibilities. Cell death might simply result from exhaustion of resources and consequent inability to Energy partitioning: YATP, growth and maintenance. support a high-density population, or by accumulation of The energy yield of substrate catabolism is partitioned inhibitory substances; the energy and nutrients provided among various cellular functions, including both those by the death and lysis of a fraction of the cells can then that are related to and those that are not related to support the remaining viable fraction. Alternatively, cell growth17–19. The demonstration that energy is diverted death could be a programmed response that is induced by to processes other than growth is well illustrated by 20 the sensing of high cell density and resource limitation, the growth yield parameter YATP . Equating growth with subsequent sensing of newly sustainable conditions to the catabolic yield of ATP, rather than to substrate following the death of most of the population inducing consumption, facilitates direct comparison of growth the survivors to exit the programmed death pathway. yield across different taxa and substrates18,20, and permits The cause and rate of cell death are crucially important theoretical estimates of the biomass yield if ATP were in the context of low-energy environments because the used exclusively for growth21. The many determinations energy required to support a steady-state population of YATP in cultures have demonstrated that the true yield varies dramatically depending on the level of cell turn- almost always falls significantly short of the theoretical over within that population. Biosynthesis is energetically maximum (in E. coli, YATP is about one-third of theo- costly. The need to constantly resynthesize whole cells retical maximum21), meaning that a substantive fraction (as opposed to coping with molecular attrition within a of energy is diverted to functions other than growth22. cell) would greatly increase the effective per-cell energy Reported values for YATP vary by fivefold across different needed to support a steady-state population and might organisms and growth conditions21,23, indicating that the exclude many low-energy environments from habitation.
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