Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms]

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".     

An inorganic geochemical argument for coupled anaerobic oxidation of methane and iron reduction in marine sediments

Here, we present results from sediments collected in the Argentine Basin, a non‐steady state depositional marine system characterized by abundant oxidized iron within methane‐rich layers due to sediment reworking followed by rapid deposition. Our comprehensive inorganic data set shows that iron reduction in these sulfate and sulfide‐depleted sediments is best explained by a microbially mediated process—implicating anaerobic oxidation of methane coupled to iron reduction (Fe‐AOM) as the most likely major mechanism. Although important in many modern marine environments, iron‐driven AOM may not consume similar amounts of methane compared with sulfate‐dependent AOM. Nevertheless, it may have broad impact on the deep biosphere and dominate both iron and methane cycling in sulfate‐lean marine settings. Fe‐AOM might have been particularly relevant in the Archean ocean, >2.5 billion years ago, known for its production and accumulation of iron oxides (in iron formations) in a biosphere likely replete with methane but low in sulfate. Methane at that time was a critical greenhouse gas capable of sustaining a habitable climate under relatively low solar luminosity, and relationships to iron cycling may have impacted if not dominated methane loss from the biosphere.     

Microbes on the edge of global biosphere]

The search for life on the edge of global biosphere is a frontier to bridge conventional bio/ecology and exo/astrobiology. This communication reviews the foci of microbiological studies on the inhabitants of the selected "edges", i.e., deep-sea, deep subsurface and Antarctic habitats. The deep-sea is characterized as the no-light (non-photosynthetic) habitat, and the primary production is mostly due to the chemosynthetic autotrophy at the hydrothermal vents and methane-rich seeps. Formation of the chemosynthesis-dependent animal communities in the deep leads to the idea that such communities may be found in "ocean" of the Jovian satellite, Europa. The oxygen minimal layer (OML) in mid-water provides another field of deep-sea research. Modern OML is a relatively thin layer, found between the water depth of 200 and 1000 m, but was much thicker during the periods of oceanic anoxia events (OAEs) in the past. The history of oceanic biosphere is regarded as the cycle of OAE and non-OAE periods, and the remnants of the past OAEs may be seen in the modem OML. Anoxic (no-O2) condition is also characteristic of deep subsurface biosphere. Microorganisms in deep subsurface biosphere exploit every available oxidant, or terminal electron acceptor (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Subsurface of hydrothermal vents, or sub-vent biosphere, may house brine (high salt) habitats and halophilic microorganisms. Some sub-vent halophiles were phylogenetically closely similar to the ones found in the Antarctic habitats which are extremely dry by the liophilizing climate. 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, has been a target of "life in extreme environments" and is about to be drill-penetrated for microbiological studies. These 'microbiological platforms' will provide new knowledge about the diversity and potential of the Earth's life and facilitate the capability of astrobiologial exploration.     

Cyclism revisited: extinction and ‘Achilles’ Heels' keep diversification in check on macroevolutionary time scales

Mass extinctions of varying magnitude prune the continuous diversification predicted by Darwinian evolutionary processes. They are caused by events that are too rare to become adaptatively accommodated. Their effects depend not only on the nature and magnitude of the triggering event but also on the state of the biosphere at the particular time. This is most clearly shown by the existence of Golden Ages preceding all Phanerozoic mass extinctions. These coincide with greenhouse periods, in which doomed clades gave rise to heteromorphs, deviating in strange ways from established bauplans. When critically examined, the seemingly ‘decadent’ morphologies of Schindewolf's ‘typolytic stages’ turn out to have been highly functional. The paradoxical link between adaptive peaks and evolutionary failure can now be explained. Specialisation tends to increase vulnerability (1) by narrowing niches and (2) by the retention of clade-specific conservative features that happen to become fatal Achilles’ Heels for entire clades in the face of a particular perturbation. Following extinctions, the availability of open niches favoured relatively rapid diversification of more innovative clades and their rise to ecological dominance (Schindewolf's ‘typogenetic stage’). Although the long-term changes can be observed only in the fossil record, Golden Biotopes in the present biosphere show that the Darwinian process may also be promoted by ecological isolation. As a result, clade histories do resemble individual biographies, but for ecological rather than orthogenetic reasons. This insight may help us to deal with the present mass extinction caused by our own species.     

The science of the biosphere

This paper considers the needs and potentials for the development of the biosphere. An emphasis is placed on the unusual qualities of the biosphere, such as important time lags, interactions between life and its environment at large scales, and biological evolution, which has led to large scale changes in the environment during the Earth's history. These qualities require a different approach to the development of a theory for this large scale system than has been used in the past, when the biosphere was treated as a steady-state, quasilinear system. Other aspects of the development of the science of the biosphere, including the use of remote sensing, are reviewed, and the application of these techniques to the estimation of certain biological variables is discussed.     

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.     

Selective chirality — A closer examination

The recent suggestion (Root-Bernstein, 1982) that the homochirality of amino acids and sugars in the current biosphere may have originated as a result of novel organic selector molecules is examined critically. It is concluded that such selector molecules are non-existent as described, and that their postulation is based on chemical and stereochemical misconceptions.     

Secondary host choice by the autoparasitoid Encarsia pergandiella

Autoparasitoids are species of parasitic wasps in the family Aphelinidae which produce females as solitary primary endoparasitoids of homopterans such as whitefly and scale insects (primary hosts), and males as solitary hyperparasitoids. Males generally develop on immature conspecific females or on individuals of other primary parasitoid species (secondary hosts). Encarsia pergandiella is an autoparasitoid that has been introduced to Italy for control of greenhouse whitefly Trialeurodes vaporariorum, in greenhouses and field crops. In this study we examined the secondary host selection behaviour of this species with regard to conspecific females and females of two thelytokous species, E. formosa and E. meritoria. Encarsia formosa has been used successfully for greenhouse whitefly control in Northern Europe, but has not been effective in Southern Italy in winter crops in unheated greenhouses. E. meritoria has recently spread in Italy, and may have potential for biological control of whitefly in the greenhouse environment. In the first experiment, female E. pergandiella were exposed to one of three pair-wise combinations of the three species in petri dish arenas. Parasitism was determined by dissection of the hosts. The number of hosts parasitized by E. pergandiella females did not differ with host species. However, significantly greater numbers of eggs were laid in E. meritoria in both treatments in which it was present; these hosts were more likely to be superparasitized. In a second experiment, observations of females in arenas with equal numbers of all three host species indicated that females encountered and parasitized all host species with approximately equal frequency, although the length of time females spent in the oviposition posture differed with host species.     

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.     

Peculiarities of the brain organization and fine structure in small insects related to miniaturization. 4. Thrips (Thysanoptera,Thripidae)

This article describes the morphology and ultrastructure of the brain of the greenhouse thrips, Heliothrips haemorrhoidalis (Thripidae), studied in a series of histological sections with the use of 3D reconstructions and TEM. The structural peculiarities of the brain organization and its features associated with body miniaturization as well as its quantitative characteristics (the number of cells and the volume of individual centers) are described for the first time in both the adult and the first-instar nymph of H. haemorrhoidalis. It is suggested that the limits of the nervous system miniaturization may be different in holo- and hemimetabolous insects.     

Raising consciousness in ecosystem health

New knowledge and theory developed by physicists in the first half of the 20th century radically changed our concepts of the nature of reality and the place of the human species in it. This information has not yet penetrated the other natural sciences nor day-to-day life. This paper argues that it is essential that we leave behind the World as Machine world view, or paradigm, which has led us to global crisis. Instead we must more rapidly incorporate the information from the 20th century new physics, and shift the dominant social paradigm to a Systems view of the world, in our efforts towards defining and implementing ecosystem health and the closely-related sustainable development. Some of the key implications of new physics to ecosystem health are that the biosphere and the surrounding universe is an indivisible whole; that the human species, especially our consciousness, is integral to the biosphere; that nothing is static; and that dynamism and function are primary, whereas structure is secondary. It is suggested that the understanding of the connectedness of humans to the rest of the biosphere will alter the behaviour of the human species towards more ecologically sustainable actions.     

Is woody bioenergy carbon neutral? A comparative assessment of emissions from consumption of woody bioenergy and fossil fuel

Under the current accounting systems, emissions produced when biomass is burnt for energy are accounted as zero, resulting in what is referred to as the ‘carbon neutrality’ assumption. However, if current harvest levels are increased to produce more bioenergy, carbon that would have been stored in the biosphere might be instead released in the atmosphere. This study utilizes a comparative approach that considers emissions under alternative energy supply options. This approach shows that the emission benefits of bioenergy compared to use of fossil fuel are time‐dependent. It emerges that the assumption that bioenergy always results in zero greenhouse gas (GHG) emissions compared to use of fossil fuels can be misleading, particularly in the context of short‐to‐medium term goals. While it is clear that all sources of woody bioenergy from sustainably managed forests will produce emission reductions in the long term, different woody biomass sources have various impacts in the short‐medium term. The study shows that the use of forest residues that are easily decomposable can produce GHG benefits compared to use of fossil fuels from the beginning of their use and that biomass from dedicated plantations established on marginal land can be carbon neutral from the beginning of its use. However, the risk of short‐to‐medium term negative impacts is high when additional fellings are extracted to produce bioenergy and the proportion of felled biomass used for bioenergy is low, or when land with high C stocks is converted to low productivity bioenergy plantations. The method used in the study provides an instrument to identify the time‐dependent pattern of emission reductions for alternative bioenergy sources. In this way, decision makers can evaluate which bioenergy options are most beneficial for meeting short‐term GHG emission reduction goals and which ones are more appropriate for medium to longer term objectives.     

Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor

Oceanography is inherently interdisciplinary and, since its inception, has included the study of microbe-mineral interactions. From early studies of manganese nodules, to the discovery of hydrothermal vents, it has been recognized that microorganisms are involved at various levels in the transformation of rocks and minerals at and below the seafloor. Recent studies include mineral weathering at low temperatures and microbe-mineral interactions in the subseafloor "deep biosphere". A common characteristic of seafloor and subseafloor geomicrobiological processes that distinguishes them from terrestrial or near-surface processes is that they occur in the dark, one or more steps removed from the sunlight that fuels the near-surface biosphere on Earth. This review focuses on geomicrobiological studies and energy flow in dark, deep-ocean and subseafloor rock habitats.     

The third age of phage

The third age of phage has begun with the recognition that phages may be key to the great planetary biogeochemical cycles and represent the greatest potential genetic resource in the biosphere.     

Biogenic Enhancement of Weathering and the Stability of the Ecosphere

A dynamic model of the global carbon cycle is used to determine the influence of biotic amplification of weathering on the overall stability of the biosphere. It takes into account the most important processes for the long-term evolution of the Earth. The model is solved under the condition of slow changing luminosity, volcanic activity, and continental area. We find that for large enough amplification factors the system has two stable states, the abiotic and biotic solution. Furthermore, this leads to an extension of the life span of the biosphere by 0.7 Gyr compared to previous studies underestimating the effect of biogenic enhancement of weathering. It can be shown that the biosphere is resilient to random perturbation of the global carbon cycle for the next 0.5-1.0 Gyr.     

"Bioplutonism" and the evolutionary implications of beneficial genes from another biosphere

Could exogenous genes from another biosphere have aided the evolution of life on Earth's surface over the last half-billion years? That possibility was considered by Thomas Gold in 1992, when he hypothesized that a “deep hot biosphere” (DHB) resides independently well below its cooler surface counterpart. And he suggested that “… in the long term … there may occasionally be beneficial exchanges of genetic material between microbial life at depth and the surface life.” Thus, the question: what evidence is there to support Gold's notion that exogenous genes from the DHB – let us call them “bioplutons” – ever bestowed benefits on the evolution of surface life? In pursuit of this question I drafted a null hypothesis: “Nothing beyond our own biosphere, as we know it today, renders any kind of genetic benefits to biological evolution.” After objectively analyzing the evidence and arguments pro and con I failed to reject the null hypothesis, given what we know today, especially the fact that no genetic imprint from the DHB has been identified in eukaryotic genomes. But my conclusion is regarded as tentative, because the fundamentals of Gold's argument, collectively referred to herein as “bioplutonism,” might be confirmed eventually with successful probes into the DHB, and with the sampling of its alleged genetic material.     

Dynamics of numerical changes in human population in terms of animal population ecology

The author uses data concerning the natural regulation of population size and growth among animals to consider possible future scenarios for human population growth. Four possible variants are considered: "numerical stabilization and its consequences connected with density effect; sharp slump caused by a global ecological catastrophe; limited slump brought about by exhaustion of resources and environmental pollution; numerical decrease through birth regulation. It has been shown that only the last variant can, in [the] case of the human population being 1.2-1.5 billion people, ensure restoration of [the] biosphere with keeping [the] existing tempo of scientific-technological progress." (SUMMARY IN ENG)     

Thinking at the global scale

The noosphere concept was originally proposed as a sphere of mind or thought that has emerged from the biosphere over the course of human evolution. Two versions of the noosphere concept were developed in the 20th century and they differed with respect to whether the noosphere was to be considered separate from the biosphere or a new form of the biosphere. Both versions shared an assumption that collective human thought based on a scientific epistemology would achieve a benevolent relationship with the biosphere. Research in global ecology continues to reveal the growing influence of humanity on the biota and on the global biogeochemical cycles, but recent history has not confirmed humanity's ability to self‐regulate. Nevertheless, the noosphere concept remains useful because it acknowledges the uniquely subjective aspect of human brain functioning and the propensity for humans to share ideas and work collaboratively. Both of these features will be needed to develop a structured coupling of humanity and the biosphere that preserves the biophysical processes sustaining the ecosphere.