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".     

Abiotic formation of bioorganic compounds in space--preliminary experiments on ground and future exobiology experiments in space.

Simulation experiments on ground have shown that "amino acid precursors", which give amino acids after acid-hydrolysis, can be formed when an ice mixture simulating ice mantles of interstellar dust particles (lSDs) is irradiated with high energy particles or UV light. It is strongly suggested that such bioorganic compounds were delivered by comets for the first biosphere on the Earth. It is of great interest to confirm this hypothesis in actual space conditions, such as in an exposed facility of JEM. Fundamental designs for such exobiology experiments in earth orbit (EEEO) will be discussed.     

A source-sink hypothesis for abyssal biodiversity

Bathymetric gradients of biodiversity in the deep-sea benthos constitute a major class of large-scale biogeographic phenomena. They are typically portrayed and interpreted as variation in alpha diversity (the number of species recovered in individual samples) along depth transects. Here, we examine the depth ranges of deep-sea gastropods and bivalves in the eastern and western North Atlantic. This approach shows that the abyssal molluscan fauna largely represents deeper range extensions for a subset of bathyal species. Most abyssal species have larval dispersal, and adults live at densities that appear to be too low for successful reproduction. These patterns suggest a new explanation for abyssal biodiversity. For many species, bathyal and abyssal populations may form a source-sink system in which abyssal populations are regulated by a balance between chronic extinction arising from vulnerabilities to Allee effects and immigration from bathyal sources. An increased significance of source-sink dynamics with depth may be driven by the exponential decrease in organic carbon flux to the benthos with increasing depth and distance from productive coastal systems. The abyss, which is the largest marine benthic environment, may afford more limited ecological and evolutionary opportunity than the bathyal zone.     

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.     

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.     

Biodiversity and distribution of the genus Gromia (Protista, Rhizaria) in the deep Weddell Sea (Southern Ocean)

We present a survey of morphospecies of Gromia, a genus of testate protists, from bathyal and abyssal depths in the Weddell Sea and adjacent areas of the Southern Ocean. This material represents the most extensive and diverse available collection of deep-sea gromiids so far recorded. The twelve species, nine of which are undescribed, are recognized on the basis of morphological criteria, including the test size and shape, the appearance and structure of the oral capsule, and the characteristics of the test wall. Most species have a single oral capsule, which is circular in plan view with a conical nipple-like shape in lateral view. One morphospecies has three oral capsules. The appearance and structure of the wall displays great variability among Gromia species, ranging from very delicate and transparent with highly reflective highlights to relatively thick with distinct patterns of ridges covering the surface. More often, however, differences in wall structure are more subtle. Most morphospecies were distributed at bathyal depths along the continental margin, but one was sampled at ~4,800 m, representing the first record of an abyssal gromiid. Concurrent with findings from other regions of the World’s oceans, the Weddell Sea gromiids were mostly found in surficial sediments in areas of elevated organic input, suggesting that deep-sea gromiids are likely to play an important role in carbon cycling in bathyal eutrophic regions through the ingestion and degradation of fresh organic matter.     

Ecological and Biochemical Evaluation of the Environment of Modern Foraminifers of the White Sea

Current ecological conditions in the regions of Bol'shoi Keretskii raid and Glubokaya Salma (Kandalaksha Bay, White Sea) were evaluated on the basis of structural and dynamic indices of the upper sediments in the context of specific composition of the benthic foraminiferal community. The distribution of the main species of living foraminifers was determined for the shallow and deep-sea groups. The relationship between populations of the most abundant species of living benthic foraminifers and hydrolytic enzyme activities providing for destruction of bottom organic matter at biochemical rates has been revealed.     

Nitric Oxide Cycle in Mammals and the Cyclicity Principle

This paper continues a series of reports considering nitric oxide (NO) and its cyclic conversions in mammals. Numerous facts are summarized with the goal of developing a general concept that would allow the statement of the multiple effects of NO on various systems of living organisms in the form of a short and comprehensive law. The current state of biological aspects of NO research is analyzed in term of elucidation of possible role of these studies in the system of biological sciences. The general concept is based on a notion on cyclic conversions of NO and its metabolites. NO cycles in living organisms and nitrogen turnover in the biosphere and also the Bethe nitrogen–carbon cycle in star matter are considered. A hypothesis that the cyclic organization of processes in living organisms and the biosphere reflects the evolution of life is proposed: the development of physiological functions and metabolism are suggested to be closely related to space and evolution of the Earth as a planet of the Solar System.     

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.     

Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.     

Ecophysiological properties of photosynthesizing bacteria from the Black Sea chemocline zone

In May 1998, during the fifty-first voyage on board the research vessel Professor Vodyanitskii, a comparative study was conducted of the species diversity of green and purple sulfur bacteria in the water column of the chemocline zone at deep-sea stations and on the bottom surface of the Black Sea shallow regions. At three deep-sea stations, the accumulation of photosynthesizing bacteria in the chemocline zone at a depth of 85-115 m was revealed on the basis of the distribution of potential values of carbon dioxide light fixation. The location of the site of potential carbon dioxide light fixation suggests that the photosynthesis may be determined by the activity of the brown Chlorobium sp., revealed earlier at these depths. Enrichment cultures of brown sulfur bacteria were obtained from samples taken at the deep-sea stations. By morphology, these bacteria, assigned to Chlorobium sp., appear as nonmotile straight or slightly curved rods 0.3-0.5 x 0.7-1.2 microm in size; sometimes, they form short chains. Ultrathin sections show photosynthesizing antenna-like structures, chlorosomes, typical of Chlorobiaceae. The cultures depended on the presence of NaCl (20 g/l) for growth, which corresponds to the mineralization of Black Sea water. The bacteria could grow photoautotrophically, utilizing sulfide, but the Black Sea strains grew much more slowly than the known species of brown sulfur bacteria isolated from saline or freshwater meromictic lakes. The best growth of the strains studied in this work occurred in media containing ethanol (0.5 g) or sodium acetate (1 g/l) and low amounts of sulfide (0.4 mM), which is consistent with the conditions of syntrophic growth with sulfidogens. The data obtained allow us to conclude that the cultures of brown sulfur bacteria are especially adapted to developing at large depths under conditions of electron donor deficiency owing to syntrophic development with sulfate reducers. The species composition of the photosynthetic bacteria developing in the bottom sediments of shallow stations differed substantially from that observed at deep-sea stations. Pure cultures of the green Chlorobium sp. BS 1C and BS 2C (chlorobactin as the carotenoid), purple sulfur bacteria Chromatium sp. BS 1Ch (containing spirilloxanthine series pigments), and Thiocapsa marina BS 2Tc (containing the carotenoid okenone) were obtained from samples of sediments at shallow-water stations. Brown sulfur bacteria were absent in the sediment samples obtained from the Black Sea shallow-water stations 1 and 2.     

Ecophysiological properties of photosynthetic bacteria from the Black Sea chemocline zone

In May 1998, during the fifty-first voyage on board the research vessel Professor Vodyanitskii, a comparative study was conducted of the species diversity of green and purple sulfur bacteria in the water column of the chemocline zone at deep-sea stations and on the bottom surface of the Black Sea shallow regions. At three deep-sea stations, the accumulation of photosynthetic bacteria in the chemocline zone at a depth of 85–115 m was revealed on the basis of the distribution of potential values of carbon dioxide light fixation. The location of the site of potential carbon dioxide light fixation suggests that the photosynthesis may be determined by the activity of the brown Chlorobium sp., earlier revealed at these depths. Enrichment cultures of brown sulfur bacteria were obtained from samples taken at the deep-sea stations. By morphology, these bacteria, assigned to Chlorobium sp., appear as nonmotile straight or slightly curved rods 0.3–0.5 × 0.7–1.2 µm in size; sometimes, they form short chains. Ultrathin sections show photosynthetic antenna-like structures, chlorosomes, typical of Chlorobiaceae. The cultures depended on the presence of NaCl (20 g/l) for growth, which corresponds to the mineralization of Black Sea water. The bacteria could grow photoautotrophically, utilizing sulfide, but the Black Sea strains grew much more slowly than the known species of brown sulfur bacteria isolated from saline or freshwater meromictic lakes. The best growth of the strains studied in this work occurred in media containing ethanol (0.5 g) or sodium acetate (1 g/l) and low amounts of sulfide (0.4 mM), which is consistent with the conditions of syntrophic growth with sulfidogens. The data obtained allow us to conclude that the cultures of brown sulfur bacteria are especially adapted to developing at large depths under conditions of electron donor deficiency owing to syntrophic development with sulfate reducers. The species composition of the photosynthetic bacteria developing in the bottom sediments of shallow stations differed substantially from that observed at deep-sea stations. Pure cultures of the green Chlorobium sp. BS 1C and BS 2C (chlorobactin as the carotenoid), purple sulfur bacteria Chromatium sp. BS 1Ch (containing spirilloxanthine series pigments), and Thiocapsa marina BS 2Tc (containing the carotenoid okenone) were obtained from samples of sediments at shallow-water stations. Brown sulfur bacteria were absent in the sediment samples obtained from the Black Sea shallow-water stations 1 and 2.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 239–247.Original Russian Text Copyright © 2005 by Gorlenko, Mikheev, Rusanov, Pimenov, Ivanov.     

Population differentiation decreases with depth in deep-sea bivalves

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by phiST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530-3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864-4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.     

Non-pollen palynomorphs in the Black Sea corridor

There have been few studies of non-pollen palynomorphs (NPP) in Holocene brackish water environments. The Black Sea is one of the world’s largest and deepest bodies of stable brackish water and a natural laboratory for study of marine carbon cycling to anoxic sediments. The main NPP in the modern sediments of this brackish water sea are dinoflagellate cysts (dinocysts), acritarchs (mainly the prasinophytes Cymatiosphaera, Micrhystridium, Sigmopollis and Pseudoschizaea) and diverse fungal remains. Other NPP include colonial algae, tintinnids, copepod and cladoceran egg covers, testate amoebae and microforaminiferal linings. These NPP assemblages are similar to those in the marginal marine environment of the Pliocene St. Erth Beds (England), but have more abundant NPP, and virtually lack scolecodonts. In the Black Sea corridor, modern assemblages from areas with salinity >22‰ have higher percentages of microforaminiferal linings and fewer prasinophytes, colonial algae and fungal spores. Prasinophytes dominate only in mid-Holocene sediments, during a 2000 years interval of sea level transgression and sapropel deposition. Early Holocene sediments have lower dinocyst diversity, increased fresh–brackish water colonial algae (Pediastrum spp. and Botryococcus braunii), zygnemataceous spores and desmids (including Zygnema, Cosmarium), ostracod linings and fewer foraminiferal linings. These assemblages are similar to those in the Baltic Sea where the annual salinity is about 6–8‰.     

Deep-Sea Biodiversity in the Mediterranean Sea: The Known,the Unknown,and the Unknowable

Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.     

Deep-sea ecosystem variability of the Aegean Sea during the past 22 kyr as revealed by Benthic Foraminifera

Specific responses of the regional deep-sea ecosystems to climatic and oceanographic processes during the last 22 kyr are revealed by benthic foraminiferal faunas from two cores in the northern and southern Aegean Sea. Under glacial boundary conditions, high-diversity benthic foraminiferal faunas and elevated benthic foraminiferal numbers indicate enhanced organic matter availability and well-ventilated deep-water masses in the whole Aegean Sea. The glacial termination is accompanied by significant fluctuations in productivity and deep-water ventilation. In the northern Aegean Sea, meltwater inflow from mountain glaciers during the Bølling/Allerød warm period resulted in a restriction of local deep-water formation, as mirrored by a dominance of bolivinids. During the deposition of sapropel S1, drops in benthic foraminiferal number and diversity are more significant in the southern Aegean Sea when compared to the north. This suggests the persistence of local deep-water formation in the northern Aegean Sea during S1 deposition. In addition, faunal fluctuations within S1 at both sites suggest the repeated influence of short-term cooling events on the re-ventilation and re-colonization of Aegean deep-sea ecosystems. During the middle and late Holocene, benthic foraminiferal faunas document the establishment of oligotrophic and well-ventilated conditions in the southern Aegean Sea. The corresponding faunas from the northern Aegean Sea reflect generally mesotrophic conditions and variable deep-water oxygenation. During the entire Holocene, the deep-sea ecosystems of this region responded very sensitively to short-term changes in humidity and temperature. These abrupt climate changes controlled the inflow of nutrients from rivers and the Black Sea and the formation of local deep-water masses.     

Revision of the bathyal fish genusHomostolus (Ophidiiformes,Ophidiidae)

The ophidiid fish genusHomostolus is revised on the basis of 44 specimens. Meristic and morphometric characters strongly indicate that the genus as presently known contains a single species,Homostolus acer Smith et Radcliffe, 1913, withHomostolus japonicus Matsubara, 1943, reduced to synonymy. Geographical variations found in certain meristic characters indicate thatH. acer expanded its range from Philippine waters into both northern and southern waters. The species is distributed on deep-sea floors from the Pacific Ocean off central Japan, to the Indian Ocean off northern Western Australia, and to the Tasman Sea off New South Wales, at bathyal depths from about 400 to 700 m.     

Bionics, Biological Systems and the Principle of Optimal Design

The living world is an exciting and inexhaustible source of high performance solutions to the multitude of biological problems, which were attained as a result of a natural selection, during the millions and millions years evolution of life on Earth. This work presents and comments some examples of high performances of living beings, in the light of the universal principle governing the realm of living matter: Optimal Design Principle. At the same time, the transfer of these optimal solutions, from living matter to the technologies, is also discussed. This transfer is offering new and fertile perspectives to future technologies, which must be more efficient, cheaper and in perfect harmony with the biosphere.     

Methane content in bottom sediments and water mass of the Black Sea

The methane content in bottom sediments and water column of the Black Sea was determined using various methods of desorption and analysis of gases and various methods of calculating their concentrations. The head-space method with the use of salting out and calculation by internal standard proved to be the most accurate procedure for the analysis of methane concentration in bottom sediments. The methane content in bottom sediments increased with the depth of sediment sampling. In the upper 50-70 cm of shelf sediments, two minimums of methane concentration were revealed; in deep-sea sediments, only one minimum was recorded (in the 20-50 cm horizons). In the water column, methane concentrations slowly grew from the surface to a depth of 150-200 m and abruptly increased to a depth of 700-1200 m, remaining virtually constant in underlying layers. In certain deep-sea regions, peaks of methane content in the 1000-1200 m horizons of the water column were revealed, which were most probably due to local influx of abyssal waters enriched with this gas.