On the early stages of the evolution of the geosphere and biosphere

The conditions necessary for the existence of nucleic-protein life are as follows: the presence of liquid water, an atmosphere, and a magnetic field (all of which protect from meteorites, abrupt changes in temperature, and a flow of charged particles from space) and the availability of nutrients (macro-and microelements in the form of dissolved compounds). In the evolution of the geosphere, complex interference of irreversible processes (general cooling, gravitational differentiation of the Earth’s interior, dissipation of hydrogen, etc.) with cyclic processes of varying natures and periodicities (from the endogenic cycles “from Pangea to Pangea” to Milankovitch cycles), these conditions have repeatedly changed; hence, in the coevolution of the geosphere and biosphere, the vector of irreversible evolution was determined by the geosphere. Only with the appearance of the ocean as a global system of homeostasis, which provided the maintenance and leveling of nutrient concentrations in the hydrosphere, and the conveyor of nutrients from the mantle, “the film of life” could begin its expansion from the source of the nutrients. Life itself is a system of homeostasis, but not due to the global size and a vast buffer capacity, but because of the high rate of reactions and presence of a program (genome) that allowed its development (ontogeny) independent from the outside environment. The early stages of the origin and evolution of the biosphere (from the RNA-world to the development of the prokaryotic ecosystems) were characterized by the domination of chemotrophic ecosystems. The geographical ranges of these ecosystems were directly or indirectly (through the atmosphere and hydrosphere) tied to the sources of nutrients in the geosphere, which were in turn connected to various sources of volcanic and geotectonic activity (geothermal waters, “black smokers” along the rift zones, etc.). This gave the biosphere consisting of chemotrophic ecosystems a mosaic appearance composed of separate local oases of life. The decrease of methane and accumulation of O₂ in the atmosphere in the geological evolution of the Earth caused the extinction of chemotrophic ecosystems and directed evolution of the biosphere toward autotrophy. Autotrophic photosynthesis gave the biosphere an energy source that was not connected to the geosphere, and for the first time allowed its liberation from the geosphere by developing its own vector of evolution. This vector resulted in the biosphere forming a continuous film of life on the planet by capturing the continents and occupying pelagic and abyssal zones, and the appearance of eukaryotes. The geosphere formed biogeochemical cycles in parallel to the geochemical ones, and comparable in the annual balances of participating matter.     

Open systems living in a closed biosphere: a new paradox for the Gaia debate

While energetically open, the biosphere is appreciably closed from the standpoint of matter exchange. Matter cycling and recycling is hence a necessary and emergent property of the global-scale system known as Gaia. But how can an aggregate of open-system life forms have evolved and persisted for billions of years within a planetary system that is largely closed to matter influx and outflow? The puzzling nature of a closed yet persistent biosphere draws our attention to the course of evolution of fundamental metabolic strategies and matter-capture techniques. It suggests a facet of the Gaia hypothesis, framed in terms of persistence. The oceans, atmosphere, soils and biota constitute a complex system which maintains and adjusts matter cycling and recycling within the constraints of planetary closure such that open-system forms of life can persist. This weaker version of the Gaia hypothesis may be useful because it readily lends itself to at least one form of test. What is the solution to the closed biosphere puzzle, and does it indicate that Gaia merits status as a discrete entity? We suggest several disciplines within the field of biology that might provide tools and perspectives toward reaching a solution. These disciplines include artificial closed ecosystems, prokaryote evolution, the nexus of thermodynamics and evolutionary biology, and hierarchy theory in ecosystem modeling and evolution theory.     

Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

Mesophotic and deeper reefs of the tropics are poorly known and underexplored ecosystems worldwide. Collectively referred to as the ‘twilight zone’, depths below ~30–50 m are home to many species of reef fishes that are absent from shallower depths, including many undescribed and endemic species. We currently lack even a basic understanding of the diversity and evolutionary origins of fishes on tropical mesophotic reefs. Recent submersible collections in the Caribbean have provided new specimens that are enabling phylogenetic reconstructions that incorporate deep‐reef representatives of tropical fish genera. Here, we investigate evolutionary depth transitions in the family Gobiidae (gobies), the most diverse group of tropical marine fishes. Using divergence‐time estimation coupled with stochastic character mapping to infer the timing of shallow‐to‐deep habitat transitions in gobies, we demonstrate at least four transitions from shallow to mesophotic depths. Habitat transitions occurred in two broad time periods (Miocene, Pliocene–Pleistocene), and may have been linked to the availability of underutilized niches, as well as the evolution of morphological/behavioural adaptations for life on deep reefs. Further, our analysis shows that at least three evolutionary lineages that invaded deep habitats subsequently underwent speciation, reflecting another unique mode of radiation within the Gobiidae. Lastly, we synthesize depth distributions for 95 species of Caribbean gobies, which reveal major bathymetric faunal breaks at the boundary between euphotic and mesophotic reefs. Ultimately, our study is the first rigorous investigation into the origin of Caribbean deep‐reef fishes and provides a framework for future studies that utilize rare, deep‐reef specimens.     

Are microorganisms everywhere they can be?

Baas-Becking is famously attributed with the conjecture that ‘everything is everywhere, but the environment selects’. Although this aphorism is largely challenged by microbial biogeographical data, even weak versions of the claim leave unanswered the question about whether all environments that could theoretically support life contain life. In the last decade, the discovery of thermally sterilized habitable environments disconnected from inhabited regions, and habitats within organisms such as the sterile, but habitable human fetal gut, suggest the existence of a diversity of macroscopic habitable environments apparently devoid of actively metabolizing or reproducing life. Less clear is the status of such environments at the micron scale, for example, between colonies of organisms within rock interstices or on and within other substrates. I discuss recent evidence for these types of environments. These environments have practical uses in: (i) being negative controls for understanding the role of microbial processes in geochemical cycles and geological processes, (ii) yielding insights into the extent to which the biosphere extends into all spaces it theoretically can, (iii) suggesting caution in interpreting the results of life detection instrumentation, and (iv) being useful for establishing the conditions for the origin of life and its prevalence on other planetary bodies.     

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere.     

High-temperature deep-subsurface microbial communities as a possible equivalent of ancient ecosystems

Microbiological, molecular biological, and radioisotopic studies suggest that active and complex microbial communities exist in the deep layers of the subsurface biosphere. This review discusses only one group of such communities, i.e., those developing at high (above 60°C temperatures). Oil wells, subsurface water reservoirs (e.g., the Great Artesian Basin in Australia), deep mines (in South Africa), and high-temperature horizons below the seafloor in the areas of underwater volcanic activity contain the best-studied high-temperature subsurface ecosystems. These microbial communities differ considerably from one another in biodiversity, initial energy substrate, and major microbiological processes. However, before they can be considered as equivalents of the Earth’s primordial ecosystems, it is necessary to demonstrate that they are energetically independent of the modern biosphere.     

Genomics and the Ark: an ecocentric perspective on human history

Views of ourselves in relationship to the rest of the biosphere are changing. Theocentric and anthropocentric perspectives are giving way to more ecocentric views on the history, present, and future of humankind. Novel sciences, such as genomics, have deepened and broadened our understanding of the process of anthropogenesis, the coming into being of humans. Genomics suggests that early human history must be regarded as a complex narrative of evolving ecosystems, in which human evolution both influenced and was influenced by the evolution of companion species. During the agricultural revolution, human beings designed small-scale artificial ecosystems or evolutionary "Arks," in which networks of plants, animals, and microorganisms coevolved. Currently, our attitude towards this process seems subject to a paradoxical reversal. The boundaries of the Ark have dramatically broadened, and genomics is not only being used to increase our understanding of our ecological past, but may also help us to conserve, reconstruct, or even revivify species and ecosystems to whose degradation or (near) extinction we have contributed. This article explores the role of genomics in the elaboration of a more ecocentric view of ourselves with the help of two examples, namely the renaissance of Paleolithic diets and of Pleistocene parks. It argues that an understanding of the world in ecocentric terms requires new partnerships and mutually beneficial forms of collaboration and convergence between life sciences, social sciences, and the humanities.     

Maximum entropy production and general trends in biospheric evolution

The biosphere has greatly shaped the past evolution of the Earth system. Here I argue that life evolved to maximize planetary entropy production. The evolution of the Earth system through time has thus evolved as far away from thermodynamic equilibrium as possible. I describe the implications of this hypothesis for the evolution of the global cycles of water and carbon and the implied consequences for biospheric evolution. This thermodynamic perspective of Earth’s biospheric evolution extends the views of Vernadski and Lovelock and puts it on a quantitative foundation.     

A New Frontier for Palaeobiology: Earth's Vast Deep Biosphere

Diverse micro‐organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.     

Ecosphere,biosphere, or Gaia? What to call the global ecosystem

The terms biosphere, ecosphere, and Gaia are used as names for the global ecosystem. However, each has more than one meaning. Biosphere can mean the totality of living things residing on the Earth, the space occupied by living things, or life and life-support systems (atmosphere, hydrosphere, lithosphere, and pedosphere). Ecosphere is used as a synonym of biosphere and as a term for zones in the universe where life as we know it should be sustainable. Gaia is similar to biosphere (in the sense of life and life-support systems) and ecosphere (in the sense of biosphere as life and life-support systems), but, in its most extreme form, refers to the entire planet as a living entity. A case is made for avoiding the term Gaia (at least as a name for the planetary ecosystem), restricting biosphere to the totality of living things, and adopting the ecosphere as the most apt name for the global ecosystem.     

Ophel: a groundwater biome based on chemoautotrophic resources. The global significance of the Ayyalon cave finds,Israel

The discovery, in the inner coastal plain of Israel, of a deep, secluded subterranean ecosystem, supported by chemosynthetis producing by sulfide-oxidizing bacteria, suggests the existence of a new biome, “Ophel”, with an autonomous energy basis. This biome could provide an ecological and historical basis for explaining the high taxonomic diversity of subterranean faunas, especially of crustaceans. A continuum with the anchialine ecosystems, in which chemoautotrophy is also encountered, as well as with marine hot vents and cold seeps, implies the existence of a second, parallel chemosynthesis-based eukaryotic biosphere. Handling editor: K. Martens Dedicated to my teacher, the active nonagerian Acad. Prof. Nicolaie Botnariuc, Bucharest.     

Exploration of deep intraterrestrial microbial life: current perspectives

Intraterrestrial life has been found at depths of several thousand metres in deep sub-sea floor sediments and in the basement crust beneath the sediments. It has also been found at up to 2800-m depth in continental sedimentary rocks, 5300-m depth in igneous rock aquifers and in fluid inclusions in ancient salt deposits from salt mines. The biomass of these intraterrestrial organisms may be equal to the total weight of all marine and terrestrial plants. The intraterrestrial microbes generally seem to be active at very low but significant rates and several investigations indicate chemolithoautotrophs to form a chemosynthetic base. Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of our planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems. Several prospective research areas are foreseen to focus on the importance of microbial communities for metabolic processes such as anaerobic utilisation of hydrocarbons and anaerobic methane oxidation.     

Origin of biosphere

Concepts of origin of life on the planet are briefly considered. The problem of origin of biosphere is discussed, with a suggestion that the origin of living organisms and biosphere are two aspects of the same process. There is put forward a hypothesis of embryosphere—the primary medium, in which preorganisms could appear. The ecosystemic approach to origin of life poses question about sources of the matter and energy used by the primary life as well as about causes of the biochemical unity that exists in all Earth organisms.     

Deep-sea nematode biodiversity in the Mediterranean basin: testing for longitudinal, bathymetric and energetic gradients

The knowledge of the processes controlling the spatial distribution of species diversity is one of the main challenges of the present ecological research. Spatial patterns of benthic biodiversity in the deep sea are poorly known in comparison with other ecosystems and this limits our understanding of the mechanisms controlling the distribution and maintenance of high biodiversity in the largest ecosystems of our biosphere. Although the Mediterranean basin covers <1% of the world ocean surface, none the less it hosts >7.5% of the global biodiversity. The high biogeographic complexity and the presence of steep ecological gradients contribute in making the Mediterranean a region of very high diversity. Here we report the results of an investigation on the patterns of nematode biodiversity in the deep-Mediterranean Sea, in relation with bathymetric, longitudinal and energetic gradients. Our results indicate that benthic biodiversity in the deep-Mediterranean decreases significantly with increasing depth. Moreover, at equally deep sites, nematode diversity decreased from the western to the eastern basin and longitudinal gradients were evident when comparing sites at 4000-m depth, with 3000-m depth. The analysis of the available energy (measured as labile organic matter content of the sediments) suggests that biodiversity patterns are not controlled by the amounts of food resources, but instead bio-availability is the key factor. A more detailed analysis revealed an extremely high deep-sea beta-diversity (turnover diversity), both among sites at different depths as well as at similar depths of different longitude or within the same basin. This new finding has not only important implications on the estimates of the overall regional diversity (gamma diversity), but also suggests the presence of high biogeographic complexity in the deep benthic domain of the Mediterranean Sea.     

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities

Endospores of thermophilic bacteria are found in cold and temperate sediments where they persist in a dormant state. As inactive endospores that cannot grow at the low ambient temperatures, they are akin to tracer particles in cold sediments, unaffected by factors normally governing microbial biogeography (e.g., selection, drift, mutation). This makes thermophilic endospores ideal model organisms for studying microbial biogeography since their spatial distribution can be directly related to their dispersal history. To assess dispersal histories of estuarine bacteria, thermophilic endospores were enriched from sediments along a freshwater‐to‐marine transect of the River Tyne in high temperature incubations (50°C). Dispersal histories for 75 different taxa indicated that the majority of estuarine endospores were of terrestrial origin; most closely related to bacteria from warm habitats associated with industrial activity. A subset of the taxa detected were marine derived, with close relatives from hot deep marine biosphere habitats. These patterns are consistent with the sources of sediment in the River Tyne being predominantly terrestrial in origin. The results point to microbial communities in estuarine and marine sediments being structured by bi‐directional currents, terrestrial run‐off and industrial effluent as vectors of passive dispersal and immigration.     

Migration-Induced Architectures of Planetary Systems

The recent increase in number of known multi-planet systems gives a unique opportunity to study the processes responsible for planetary formation and evolution. Special attention is given to the occurrence of mean-motion resonances, because they carry important information about the history of the planetary systems. At the early stages of the evolution, when planets are still embedded in a gaseous disc, the tidal interactions between the disc and planets cause the planetary orbital migration. The convergent differential migration of two planets embedded in a gaseous disc may result in the capture into a mean-motion resonance. The orbital migration taking place during the early phases of the planetary system formation may play an important role in shaping stable planetary configurations. An understanding of this stage of the evolution will provide insight on the most frequently formed architectures, which in turn are relevant for determining the planet habitability. The aim of this paper is to present the observational properties of these planetary systems which contain confirmed or suspected resonant configurations. A complete list of known systems with such configurations is given. This list will be kept by us updated from now on and it will be a valuable reference for studying the dynamics of extrasolar systems and testing theoretical predictions concerned with the origin and the evolution of planets, which are the most plausible places for existence and development of life.     

Search for life in deep biospheres]

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.     

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (∼14 Ma old) and the most oligotrophic subsurface sediments of the world''s oceans (South Pacific Gyre (SPG)). The numbers of viruses (10⁴–10⁹ cm⁻³, counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.     

The begginning of photosynthesis.

There is no evolutionary continuity between photochemical abiosynthesis and bacterial photosynthesis. Rather, the photosynthetic bacteria are descendants of fermenters that did not use light. Photosynthesis and respiration, both using electron flow coupled with phosphorylation, have a common origin ('conversion hypothesis'), but photosynthesis came first. Anaerobic (nitrate or sulphate) respiration cannot have preceded photosynthesis as neither nitrate nor sulphate existed on the early earth. Sulphate was made first by photosynthetic sulphur bacteria. Nitrate arose even later, namely, in the aerobic biosphere produced by the blue-green algae, the first 'phytotrophs'. Photophosphorylation may have originated through the combination with membrane function of substrate level phosphorylation in reactionsand function of substrate level phosphorylation in reactions of photoproducts. Cyclic photophosphorylation arose while the biosphere was still reducing. It was supplemented later by processes for the light-based production of reducing power (NADH), ATP-powered electron flow, and subsequently light-powered electron flow with ATP production (noncyclic photophosphoryaltion). These later processes served the assimilation of CO2.     

Non-light based ecosystems and bioastronomy.

The possibility of the existence of life beyond planet Earth has always fascinated humans. However, due to certain circumstances such as the failure of the Viking expeditions to detect any sign of biotic activity on Mars, and the understanding that the presence of life would lead to drastic alterations in the atmosphere of the host planet (alterations that have never been detected on other planets or planetoids of the solar system), the belief that our planet is the only planet to sustain life inside the solar system originated. During the last three decades a series of new complex biological communities have been discovered, in the deep sea, inside caves isolated from the external biosphere, and deep inside the crust of our planet, and found to depend on geothermal energy instead of solar energy for their survival. These discoveries give us new evidence and hope that life might exist not only on other planets, but perhaps even in other planetoids of our solar system. Life may exist in regions other than the surface of a planet, and these areas would be extremely difficult to identify.