Crucial crises in biology: life in the deep biosphere.

The origin and evolution of life on Earth are the result of a series of crises that have taken place on the planet over about 4500 millions of years since it originated. Biopoiesis (origin of life), ecopoiesis (origin of ecosystems) and the first ecosystems (stromatolites and microbial mats), as well as eukaryopoiesis (origin of nucleated cells) are revised. The paper then focuses on the study of the deep biosphere, describing ecosystems never found before, which are independent of solar radiation and have changed previous assumptions about the requirements of life; even the concept of biosphere, as Vernadsky defined it, has increased its scope. Since the discovery, in 1987, of bacteria growing in the crevices of rocks at 500 m deep, in boreholes drilled near the Savanna River, Aiken, South Carolina, other bacteria have been found in the deep subsurface reaching depths of about 3 km (e.g., in the Columbia River Basalt Group, near Richland, Washington state), in an anaerobic, hot, high-pressure environment. Some kinds of microorganisms can thrive at such depths, living in many cases a geochemical existence, by using very specialized metabolisms, which depend on the local environments. The existence of organisms independent from photosynthetic production is the most outstanding, novel feature of the deep biosphere. Living beings might not need other energy and chemical sources than those which occur in the development of all planetary bodies. Life, therefore, could even be an ineluctable outcome of planetary evolution and, as a corollary, a natural continuation of the usual development of physical phenomena in the universe.     

LiGAPS-Beef,a mechanistic model to explore potential and feed-limited beef production 2: sensitivity analysis and evaluation of sub-models

The model LiGAPS-Beef (Livestock simulator for Generic analysis of Animal Production Systems – Beef cattle) has been developed to assess potential and feed-limited growth and production of beef cattle in different areas of the world and to identify the processes responsible for the yield gap. Sensitivity analysis and evaluation of model results with experimental data are important steps after model development. The first aim of this paper, therefore, is to identify which parameters affect the output of LiGAPS-Beef most by conducting sensitivity analyses. The second aim is to evaluate the accuracy of the thermoregulation sub-model and the feed intake and digestion sub-model with experimental data. Sensitivity analysis was conducted using a one-at-a-time approach. The upper critical temperature (UCT) simulated with the thermoregulation sub-model was most affected by the body core temperature and parameters affecting latent heat release from the skin. The lower critical temperature (LCT) and UCT were considerably affected by weather variables, especially ambient temperature and wind speed. Sensitivity analysis for the feed intake and digestion sub-model showed that the digested protein per kg feed intake was affected to a larger extent than the metabolisable energy (ME) content. Sensitivity analysis for LiGAPS-Beef was conducted for ¾ Brahman×¼ Shorthorn cattle in Australia and Hereford cattle in Uruguay. Body core temperature, conversion of digestible energy to ME, net energy requirements for maintenance, and several parameters associated with heat release affected feed efficiency at the herd level most. Sensitivity analyses have contributed, therefore, to insight which parameters are to be investigated in more detail when applying LiGAPS-Beef. Model evaluation was conducted by comparing model simulations with independent data from experiments. Measured heat production in experiments corresponded fairly well to the heat production simulated with the thermoregulation sub-model. Measured ME contents from two data sets corresponded well to the ME contents simulated with the feed intake and digestion sub-model. The relative mean absolute errors were 9.3% and 6.4% of the measured ME contents for the two data sets. In conclusion, model evaluation indicates the thermoregulation sub-model can deal with a wide range of weather conditions, and the feed intake and digestion sub-model with a variety of feeds, which corresponds to the aim of LiGAPS-Beef to simulate cattle in different beef production systems across the world.     

Feast and famine--microbial life in the deep-sea bed

The seabed is a diverse environment that ranges from the desert-like deep seafloor to the rich oases that are present at seeps, vents, and food falls such as whales, wood or kelp. As well as the sedimentation of organic material from above, geological processes transport chemical energy--hydrogen, methane, hydrogen sulphide and iron--to the seafloor from the subsurface below, which provides a significant proportion of the deep-sea energy. At the sites on the seafloor where chemical energy is delivered, rich and diverse microbial communities thrive. However, most subsurface microorganisms live in conditions of extreme energy limitation, with mean generation times of up to thousands of years. Even in the most remote subsurface habitats, temperature rather than energy seems to set the ultimate limit for life, and in the deep biosphere, where energy is most depleted, life might even be based on the cleavage of water by natural radioisotopes. Here, we review microbial biodiversity and function in these intriguing environments.     

‘Follow the Water’: Hydrogeochemical Constraints on Microbial Investigations 2.4 km Below Surface at the Kidd Creek Deep Fluid and Deep Life Observatory

Abstract

Microbiological and geochemical data are presented to characterize the hydrogeochemistry and to investigate extant microbial life in fracture waters 2.4?km below surface, at the Kidd Creek Observatory in Canada. Previous studies identified the world’s oldest groundwaters with mean residence times on the order of millions to billions of years trapped in fractures in Precambrian host rock here. In this study, major ion chemistry, δ¹⁸O and δ²H isotopic signatures and dissolved gases in the fracture waters are shown to be distinct from potential contamination end-members, demonstrating the fracture waters are not impacted by waters used in mining operations. A previous work on sulfur isotope signatures suggested a longstanding indigenous population of sulfate-reducing bacteria in these highly reducing fluids and sufficient sulfate to support microbial activity. Here, we report the first evidence for extant visible and cultivable microbial life at this location. Anaerobic metabolisms were investigated using the Most Probable Number (MPN) method. The fracture fluids contained extant cells at low biomass density (～10³–10⁴ cells/mL) and showed a strong response from autotrophic sulfate-reducers and alkane-oxidizing sulfate reducers. These lines of evidence provide the interpretational framework (chemical, hydrogeologic, and microbiologic) essential to the on-going genomic and metagenomic investigations at the Kidd Creek Observatory – the world’s most longstanding location for investigation of subsurface fluids and deep life at such profound depth.     

The digestive performance of mammalian herbivores: why big may not be that much better

1. A traditional approach to the nutritional ecology of herbivores is that larger animals can tolerate a diet of lesser quality due to a higher digestive efficiency bestowed on them by comparatively long ingesta retention times and lower relative energy requirements. 2. There are important physiological disadvantages that larger animals must compensate for, namely a lower gut surface : gut volume ratio, larger ingesta particle size and greater losses of faecal bacterial material due to more fermentation. Compensating adaptations could include an increased surface enlargement in larger animals, increased absorption rates per unit of gut surface, and increased gut motility to enhance mixing of ingesta. 3. A lower surface : volume ratio, particularly in sacciform forestomach structures, could be a reason for the fact that methane production is of significant scope mainly in large herbivores and not in small herbivores with comparably long retention times; in the latter, the substrate for methanogenesis – the volatile fatty acids – could be absorbed faster due to a more favourable gut surface : volume ratio. 4. Existing data suggest that in herbivores, an increase in fibre digestibility is not necessarily accompanied by an increase in overall apparent dry matter digestibility. This indicates a comparative decrease of the apparent digestibility of non-fibre material, either due to a lesser utilization of non-fibre substrate or an increased loss of endogenous/bacterial substance. Quantitative research on these mechanisms is warranted in order to evaluate whether an increase in body size represents a net increase of digestive efficiency or just a shift of digestive focus.     

Life's utilization of B vitamins on early Earth

Coenzymes are essential across all domains of life. B vitamins (B₁‐thiamin, B₂‐riboflavin, B₃‐niacin, B₅‐pantothenate, B₆‐pyridoxine, B₇‐biotin, and B₁₂‐cobalamin) represent the largest class of coenzymes, which participate in a diverse set of reactions including C₁‐rearrangements, DNA repair, electron transfer, and fatty acid synthesis. B vitamin structures range from simple to complex heterocycles, yet, despite this complexity, multiple lines of evidence exist for their ancient origins including abiotic synthesis under putative early Earth conditions and/or meteorite transport. Thus, some of these critical coenzymes likely preceded life on Earth. Some modern organisms can synthesize their own B vitamins de novo while others must either scavenge them from the environment or establish a symbiotic relationship with a B vitamin producer. B vitamin requirements are widespread in some of the most ancient metabolisms including all six carbon fixation pathways, sulfate reduction, sulfur disproportionation, methanogenesis, acetogenesis, and photosynthesis. Understanding modern metabolic B vitamin requirements is critical for understanding the evolutionary conditions of ancient metabolisms as well as the biogeochemical cycling of critical elements such as S, C, and O.     

Exhaustive Analysis of a Genotype Space Comprising 1015 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation

All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism’s potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10¹⁵ metabolisms that encodes all possible subsets of 51 reactions in central carbon metabolism. Using flux balance analysis, we predict the viability of these metabolisms on 10 different carbon sources which give rise to 1024 potential metabolic phenotypes. Although viable metabolisms with any one phenotype comprise a tiny fraction of genotype space, their absolute numbers exceed 10⁹ for some phenotypes. Metabolisms with any one phenotype typically form a single network of genotypes that extends far or all the way through metabolic genotype space, where any two genotypes can be reached from each other through a series of single reaction changes. The minimal distance of genotype networks associated with different phenotypes is small, such that one can reach metabolisms with novel phenotypes – viable on new carbon sources – through one or few genotypic changes. Exceptions to these principles exist for those metabolisms whose complexity (number of reactions) is close to the minimum needed for viability. Increasing metabolic complexity enhances the potential for both evolutionary conservation and evolutionary innovation.     

Efficiency of energy utilisation and voluntary feed intake in ruminants

Energy requirements of animals are most readily expressed in terms of net energy (NE), while the energy yield of feed is, at least initially, expressed in terms of metabolisable energy (ME). Energy evaluation systems 'translate' NE requirements into ME requirements (ME systems) or assign NE values to feeds (NE systems). Efficiency of ME utilisation is higher for maintenance than for production and the NE yield of a feed varies, therefore, with ME intake. In addition, energetic efficiency for maintenance and production is thought to be different for lactating and non-lactating animals and to be affected by diet quality. As a result, there are currently many national energy evaluation systems that are complex, differ in their approach and are, as a result, difficult to compare. As ruminants in most production systems are fed ad libitum, this is also the most appropriate intake level at which to estimate energetic efficiency. Analyses of older as well as more recent data suggest that ad libitum feeding (i) abolishes the effects of diet quality on energetic efficiency (almost) completely, (ii) abolishes the differences between lactating and non-lactating animals (almost) entirely and (iii) results in overall energetic efficiencies that are always close to 0.6. The paper argues that there is now sufficient information to develop an international energy evaluation system for ad libitum fed ruminants. Such a system should (i) unify ME and NE systems, (ii) avoid the systematic bias and large errors that can be associated with current systems (iii) be simpler than current systems and (iv) have as a starting point a constant efficiency of ME utilisation, with a value of around 0.6. The remarkably constant efficiency of ME utilisation in ad libitum fed ruminants could be the result of energetic efficiency as well as feed intake regulation being affected by the same variables or of a direct role of energetic efficiency in feed intake regulation. Models to predict intake on the basis of the latter hypothesis are already available for non-reproducing ruminants but remain to be developed for reproducing animals.     

Possible origin of a membrane in the subsurface of the Earth

A location for the origin of life on Earth could have been an oil/water interface in the warm, subsurface environment of the Earth. The physico-chemical conditions of the subsurface would include elevated, but eventually cooling temperatures, anaerobic conditions, and protection from intense surface radiation. This type of subsurface oil/water environment may have been ideal for the assembly of the first simple membrane(s), where no enzyme catalysis was needed. Once a stable, simple, continuous closed membrane was formed, one central component of the first cell(s) would have been present; a semi-permeable open system that allowed the passage of both matter and energy in and out of the cell. Such an open system could also acquire novel functions, whereas a closed system would be unable to evolve.     

Mass-energy balance for microbial product synthesis-biochemical and cultural aspects

Interrelations between the rates of the product synthesis, cell biomass growth, respiration, and organic substrate consumption have been studied by the mass-energy balance method. This method is based on the utilization of a special unit of substance reducity, namely redoxon. Biochemical parameters have been found which are involved in these interrelations and which describe the processes of high-energy bond gain and energy expenditure during metabolism. In order to find these, the separation of the whole metabolism into several partial metabolisms has been applied. Equations have been obtained describing the dependences of the product yield and process specific productivity on the biochemical parameters and two macroscopic rates (e.g., rates of dilution and substrate consumption). Both aerobic and anaerobic product syntheses have been considered. The estimate of the upper limit of process productivity has been obtained. Mechanisms of the influence of the producer's intracellular characteristics on the rates of physiological processes and the culture productivity are discussed.     

A flexible,two-component feeding system derived from Blaxter's three-component,metabolisable-energy system

A flexible, energy-system is described based on Blaxter's three-component metabolisable-energy (ME) system, in which animal energy requirements are expressed as net energy (NE), the value of feeds is given as ME, and there is a third component comprising a set of experimentally derived rules for converting the ME values of different feeds to NE. The proposed system retains NE as the method of defining animal energy requirements and combines the ME values for different feeds with conversion of ME to NE for maintenance, growth and lactation using the most appropriate conversion for the particular feeding situation.The system retains all the essential features of Blaxter's three-component system, but allows rations for both dairy and beef production to be calculated by the same procedure. Four examples are given for rationing lactating cows and beef cattle.It is suggested that this system should permit easier calculation of rations and the rapid incorporation of new information and should lead to a better understanding by producers, advisers, students and scientists of the principles and limitations of energy rationing.     

A metagenomic window into carbon metabolism at 3?km depth in Precambrian continental crust

Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H₂ and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)—by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.     

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species (Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar – 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days – 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.     

Biological relativity to water–energy dynamics

Climate has long been related to geographical differences in the distribution and diversity of life. What has eluded explanation is why this should be so. One emerging possibility is biological relativity to water–energy dynamics: the relative nature of biotic dynamics to changes in energy/matter conditions caused by changes in water (all states) while doing work, especially liquid water. The dynamic parameters involved – liquid water and optimal energy conditions – are independent of life, and have been shown to provide a simple, globally predictive explanation for co‐variation between climate and the species richness of woody plants. Here I elaborate on what I mean by ‘biological relativity to water–energy dynamics’ and how it should relate to the geography and evolution of life in general (terrestrial, subterranean, marine/aquatic biota). Working through a natural hierarchy of physical, geographical, ecological and biological first principles, I outline the hierarchical, abiotic → biotic conceptual framework within which this idea operates. The implications of this idea include the following. First, the biosphere is better conceptualized as a ‘subsphere’ of the liquid hydrosphere – a system within a system, wherein ‘life’ has all the unique physical properties of liquid water, plus unique emergent properties of its own. Second, the fundamental capacity for life to exist and be dynamic in all biotic systems is determined by the abiotic capacity for liquid water to exist and be dynamic, which is always relative to the capacity for water–energy dynamics in general. Third, liquid water–energy dynamics acts as a fundamental mechanism of evolution, while being a constant mechanism of natural selection. Fourth, over space and time, there should be first‐order predictable and/or systematic differences in the capacity for, operation and outcomes of, biotic dynamics globally (e.g. species richness), that necessarily dissolve into apparent chaos locally. Fifth, biological relativity to water–energy dynamics provides a fundamental and natural framework for operationalizing hierarchy theory and developing trans‐scalar explanations for the geography and evolution of life's diversity.     

Self-assembly of the first cells in a hydrophobic environment with hydrogen as the energy source.

Two fundamental questions in biology are how and where the first cell(s) self-assembled under anoxic conditions on the Earth. The possibility is explored that life first self-assembled in a hydrophobic environment in the subsurface protected from radiation with ubiquitous hydrogen as the likely universal energy source.     

Toward a new practical energy evaluation system for dairy cows

Energy evaluation systems translate an animal's net energy (NE) requirements into feed metabolisable energy requirements (MER). The Feed into Milk (FiM) project (Agnew RE, Yan T, France J, Kebreab E and Thomas C 2004. Energy requirement and supply. In Feed into Milk. A new applied feeding system for dairy cows (ed. C Thomas), pp. 11-20. Nottingham University Press, Nottingham, UK) proposed a new system to predict MER of dairy cows that is, in contrast to previous energy evaluation systems for cattle, independent of feed quality. The FiM system shares this characteristic with an energy evaluation system for ad libitum-fed cattle proposed in 1994 by Tolkamp and Ketelaars (T&K). The FiM system requires nine parameters to translate requirements for NE into MER for dairy cows, while the T&K system for cattle requires only two for the same purpose. This paper analyses the contribution of each of the parameters to the final MER predictions, the differences in MER prediction between the two systems and the underlying causes of these differences. The systems differ considerably in their estimates of the NE that is required for maintenance and in their (implicit) assumptions about the partial efficiency of ME utilisation for lactation. The T&K system is based on a constant partial efficiency of ME utilisation, but in the FiM system this efficiency changes with milk yield (MY) and shows a sharp discontinuity that is at odds with the underlying biology. These are the two main causes of the differences in MER predictions. Nevertheless, over a range of MYs between 10 and 40 kg, and for cows maintaining, gaining or losing weight, the MER predictions of the two systems are very similar with maximum differences of up to ±2% only. FiM predictions of MER are systematically higher than T&K predictions for cows with very low and very high MY. It is concluded that the FiM system could reduce parameter requirements with negligible effects on MER predictions. The combination of a very high maintenance NE parameter and a curvilinear model with two subsequent corrections leads to internal inconsistencies in the FiM system. The T&K system is much simpler but it might benefit from including more recent information for the estimation of its parameters.     

Temperature‐dependence of minimum resource requirements alters competitive hierarchies in phytoplankton

Resource competition theory is a conceptual framework that provides mechanistic insights into competition and community assembly of species with different resource requirements. However, there has been little exploration of how resource requirements depend on other environmental factors, including temperature. Changes in resource requirements as influenced by environmental temperature would imply that climate warming can alter the outcomes of competition and community assembly. We experimentally demonstrate that environmental temperature alters the minimum light and nitrogen requirements – as well as other growth parameters – of six widespread phytoplankton species from distinct taxonomic groups. We found that species require the most nitrogen at the highest temperatures while light requirements tend to be lowest at intermediate temperatures, although there are substantial interspecific differences in the exact shape of this relationship. We also experimentally parameterize two competition models, which we use to illustrate how temperature, through its effects on species’ traits, alters competitive hierarchies in multispecies assemblages, determining community dynamics. Developing a mechanistic understanding of how temperature influences the ability to compete for limiting resources is a critical step towards improving forecasts of community dynamics under climate warming.     

Deep subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt revealed through geochemistry and molecular biomarkers

The Iberian Pyrite Belt (IPB, southwest of Spain), the largest known massive sulfide deposit, fuels a rich chemolithotrophic microbial community in the Río Tinto area. However, the geomicrobiology of its deep subsurface is still unexplored. Herein, we report on the geochemistry and prokaryotic diversity in the subsurface (down to a depth of 166 m) of the Iberian Pyritic belt using an array of geochemical and complementary molecular ecology techniques. Using an antibody microarray, we detected polymeric biomarkers (lipoteichoic acids and peptidoglycan) from Gram‐positive bacteria throughout the borehole. DNA microarray hybridization confirmed the presence of members of methane oxidizers, sulfate‐reducers, metal and sulfur oxidizers, and methanogenic Euryarchaeota. DNA sequences from denitrifying and hydrogenotrophic bacteria were also identified. FISH hybridization revealed live bacterial clusters associated with microniches on mineral surfaces. These results, together with measures of the geochemical parameters in the borehole, allowed us to create a preliminary scheme of the biogeochemical processes that could be operating in the deep subsurface of the Iberian Pyrite Belt, including microbial metabolisms such as sulfate reduction, methanogenesis and anaerobic methane oxidation.     

Understanding the bioreactor

Analysis of bioreactors is central for successful design and operation of biotechnical processes. The bioreactor should provide optimum conditions, with respect to temperature, pH and substrate condition, for example, besides its basic function of containment. The ability to control the substrate concentration is an important function of the bioreactor. The substrate concentration can be subject to spatial variation – advertently or inadvertently – and may also change with time in batch or fed-batch operation. The cellular metabolism will depend on local concentrations in the reactor, as well as on the physiological status of the cell. In order to understand the bioreactor operation, cellular metabolism must be considered together with the flow profile and the mass transfer characteristics of the bioreactor. Some fundamental aspects of bioreactor operation for yeast and bacterial cultivations are discussed in this short review.