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".     

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.     

Bacterially mediated precipitation in marine stromatolites

Stromatolites are laminated, lithified (CaCO₃) sedimentary deposits formed by precipitation and/or sediment accretion by cyanobacterial–bacterial mat communities. Stromatolites have been associated with these communities as far back as the Precambrian era some 2+ billion years ago. The means by which microbial communities mediate the precipitation processes have remained unclear, and are the subject of considerable debate and speculation. Two alternative explanations for microbially mediated precipitation include: (i) cyanobacterial photosynthesis increases pH in a system supersaturated in respect of CaCO₃, resulting in CaCO₃ precipitation and then laminated lithification, and (ii) decomposition of cyanobacterial extracellular organic matter (e.g. sheaths, mucilage and organic acids) by microheterotrophs leads to release of organic-bound Ca²⁺ ions and CaCO₃ precipitation. We evaluated these explanations by examining metabolically active, lithifying stromatolitic mat communities from Highborne Cay, Bahamas, using microautoradiography. Microautoradiographic detection of ¹⁴CO₂ fixation and ³H organic matter ( d -glucose and an amino acid mixture) utilization by photosynthetically active cyanobacteria and microheterotrophs, combined with community-level uptake experiments, indicate that bacteria, rather than cyanobacteria are the dominant sites of CaCO₃ deposition. In the oligotrophic waters in which stromatolites exist, microheterotrophs are reliant on the photosynthetic community as a main source of organic matter. Therefore, autotrophic production indirectly controls microbially mediated precipitation and stromatolite formation in these shallow marine environments.     

Microbial colonization and controls in dryland systems

Drylands constitute the most extensive terrestrial biome, covering more than one-third of the Earth's continental surface. In these environments, stress limits animal and plant life, so life forms that can survive desiccation and then resume growth following subsequent wetting assume the foremost role in ecosystem processes. In this Review, we describe how these organisms assemble in unique soil- and rock-surface communities to form a thin veneer of mostly microbial biomass across hot and cold deserts. These communities mediate inputs and outputs of gases, nutrients and water from desert surfaces, as well as regulating weathering, soil stability, and hydrological and nutrient cycles. The magnitude of regional and global desert-related environmental impacts is affected by these surface communities; here, we also discuss the challenges for incorporating the consideration of these communities and their effects into the management of dryland resources.     

Biomass recycling and the origin of phenotype in fungal mycelia

Fungi are one of the most important and widespread components of the biosphere, and are essential for the growth of over 90% of all vascular plants. Although they are a separate kingdom of life, we know relatively little about the origins of their ubiquitous existence. This reflects a wider ignorance arising from their status as indeterminate organisms epitomized by extreme phenotypic plasticity that is essential for survival in complex environments. Here we show that the fungal phenotype may have its origins in the defining characteristic of indeterminate organisms, namely their ability to recycle locally immobilized internal resources into a mobilized form capable of being directed to new internal sinks. We show that phenotype can be modelled as an emergent phenomenon resulting from the interplay between simple local processes governing uptake and remobilization of internal resources, and macroscopic processes associated with their transport. Observed complex growth forms are reproduced and the sensitive dependence of phenotype on environmental context may be understood in terms of nonlinearities associated with regulation of the recycling apparatus.     

'That which does not kill us only makes us stronger': the role of carbon monoxide in thermophilic microbial consortia

Carbon monoxide (CO), while a potent toxin, is also a key intermediate in major autotrophic pathways such as methanogenesis and acetogenesis. The ability of purple sulfur bacteria to use CO as an energy source was first described by Uffen in 1976. The prototype extremely thermophilic carboxydotroph Carboxydothermus hydrogenoformans was described in 1991. Eight bacteria and one archaeon that utilize CO have since been isolated and described from diverse geothermal environments. They derive energy from the oxidation of CO with water to form CO₂ and H₂. Most of these isolates thrive with headspace CO partial pressures around 1 atm, which is grossly elevated relative to CO concentrations in geothermal effluents. To account for this, we suggest that under consortial growth conditions the carboxydotrophs occupy microniches in which biogenic CO accumulates locally to high concentrations. CO oxidizers dissipate these potentially toxic CO hot spots with the production of H₂, CO₂ and acetate whose subsequent oxidation fuels other thermophiles. The identification of genes related to anaerobic CO oxidation in many metagenomic databases attests to widespread distribution of carboxydotrophs. Current evidence suggests that CO-oxidizing bacteria and archaea hold a vital niche in thermophilic ecosystems.     

Adaptation to high CO2 concentration in an optimal environment: radiation capture, canopy quantum yield and carbon use efficiency

The effect of elevated [CO₂] on wheat (Triticum aestivum L. Veery 10) productivity was examined by analysing radiation capture, canopy quantum yield, canopy carbon use efficiency, harvest index and daily C gain. Canopies were grown at either 330 or 1200 μ mol mol^–1[CO₂] in controlled environments, where root and shoot C fluxes were monitored continuously from emergence to harvest. A rapidly circulating hydroponic solution supplied nutrients, water and root zone oxygen. At harvest, dry mass predicted from gas exchange data was 102·8 ± 4·7% of the observed dry mass in six trials. Neither radiation capture efficiency nor carbon use efficiency were affected by elevated [CO₂], but yield increased by 13% due to a sustained increase in canopy quantum yield. CO₂ enrichment increased root mass, tiller number and seed mass. Harvest index and chlorophyll concentration were unchanged, but CO₂ enrichment increased average life cycle net photosynthesis (13%, P < 0·05) and root respiration (24%, P < 0·05). These data indicate that plant communities adapt to CO₂ enrichment through changes in C allocation. Elevated [CO₂] increases sink strength in optimal environments, resulting in sustained increases in photosynthetic capacity, canopy quantum yield and daily C gain throughout the life cycle.     

The survival of Salmonella enterica serovar Typhimurium DT104 and total viable counts on beef surfaces at different relative humidities and temperatures

Aims:  The aim of this study was to investigate changes in Salmonella and total viable count (TVC) survival on beef carcass surfaces stored for 72 h under different combinations of relative humidity (i.e. RH 75% or 96%) and temperature (5°C or 10°C).
Methods and Results:  The influence of low water activity ( a _w) and temperature on the survival and growth of Salmonella enterica serovar Typhimurium DT104 and the aerobic mesophilic flora on meat pieces from different sites on beef carcasses was investigated, under controlled conditions (75% or 96% RH; 5 or 10°C) in an environmental cabinet. Salmonella counts declined during storage at low a _w (75% RH) conditions at 5°C or 10°C. Salmonella counts increased during storage at high a _w (96% RH) at 10°C only. At 5°C, TVCs increased during storage at high a _w, but not at low a _w. TVCs increased on all samples from carcasses stored at high or low a _w at 10°C, except those samples taken from areas of surface fat.
Conclusions:  This suggests that substrate composition dictates growth rates under low a _w conditions. The results are discussed in terms of the possible protective effects of substrate osmolyte accumulation in bacterial survival and/or growth.
Significance and Impact of the Study:  The data obtained in this study provides useful insights on the influence of a _w and temperature on pathogen survival on meat surfaces at chill temperature.     

Species-specific responses to atmospheric carbon dioxide and tropospheric ozone mediate changes in soil carbon

We repeatedly sampled the surface mineral soil (0–20 cm depth) in three northern temperate forest communities over an 11-year experimental fumigation to understand the effects of elevated carbon dioxide (CO₂) and/or elevated phyto-toxic ozone (O₃) on soil carbon (C). After 11 years, there was no significant main effect of CO₂ or O₃ on soil C. However, within the community containing only aspen ( Populus tremuloides Michx.), elevated CO₂ caused a significant decrease in soil C content. Together with the observations of increased litter inputs, this result strongly suggests accelerated decomposition under elevated CO_2. In addition, an initial reduction in the formation of new (fumigation-derived) soil C by O₃ under elevated CO₂ proved to be only a temporary effect, mirroring trends in fine root biomass. Our results contradict predictions of increased soil C under elevated CO₂ and decreased soil C under elevated O₃ and should be considered in models simulating the effects of Earth's altered atmosphere.     

Review: from chemosphere to biosphere

An understanding of how the Earth's chemosphere was transformed to a biosphere is central to our understanding of the origin of life and the search for extraterrestrial life or life signatures. Once early prokaryotic life originated and colonized the Earth, the biosphere was well on its way to being formed. In this paper, information and knowledge is integrated to examine the possibility how life first self-assembled and transformed a lifeless chemosphere into a complex biosphere that we still do not understand today.     

Microbial diversity--insights from population genetics

Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N_e, is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10³ and 10⁷ suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N_e of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.     

Age and growth of the striped mullet, Mugil platanus (Actinopterygii, Mugilidae), in a southwestern Atlantic coastal lagoon (37°32'S–57°19'W): a proposal for a life-history model

Species of Mugilidae are an important economic resource supporting several small communities in Argentina and Brazil through fishing. The growth parameters of the von Bertalanffy model, age limit ( t _0.95) and natural mortality ( M ) for the striped mullet ( Mugil platanus ) Günther, 1880, in the Mar Chiquita coastal lagoon (37°32'S–57°19'W) were estimated. These results constitute the first estimated values for the species as: L _∞ (cm) = 563.82; K (years⁻¹) = 0.30; t ₀ (years) = −0.057 (age groups 1–8); t _0.95 = 10.07 years and M  = 0.30. Moreover, a hypothetical model is proposed for the life history of the adult stock of M. platanus from the Mar Chiquita coastal lagoon based on CPUE data, environmental parameters, ovarian maturity stages, gonadosomatic indexes, the allometric growth coefficient b and deposition of hyaline or opaque rings in the otholiths. Mugil platanus is therefore regarded as a species of moderate to rapid growth rate, with a relatively low longevity and a high natural mortality rate, compared to other species of Mugilidae.     

An approach to the nonlinear dynamics of Russian wheat aphid population growth with the cusp catastrophe model

Many insect field populations, especially aphids, often exhibit irregular and even catastrophic fluctuations. The objective of the present study is to explore whether or not the population intrinsic rates of growth ( r _m) obtained under laboratory conditions can shed some light on the irregular changes of insect field populations. We propose to use the catastrophe theory, one of the earliest nonlinear dynamics theories, to answer the question. To collect the necessary data, we conducted a laboratory experiment to investigate population growth of the Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), in growth chambers. The experiment was designed as the factorial combinations of five temperatures and five host plant-growth stages (25 treatments in total): 1800 newly born RWA nymphs arranged in the 25 treatments (each treatment with 72 repetitions) were observed for their development, reproduction and survival through their entire lifetimes. After obtaining the population intrinsic rates of growth ( r _m) from the experimental data under various environmental conditions, we built a cusp catastrophe model for RWA population growth by utilizing r _m as the system state variable, and temperature and host plant-growth stage as control variables. The cusp catastrophe model suggests that RWA population growth is intrinsically catastrophic , and dramatic jumps from one state to another might occur even if the temperature and plant-growth stage change smoothly . Other basic behaviors of the cusp catastrophe model, such as catastrophic jumps , hystersis and divergence , are also expected in RWA populations. These results suggest that the answer to the previously proposed question should be "yes".     

Bacteria beneath the West Antarctic Ice Sheet

Subglacial environments, particularly those that lie beneath polar ice sheets, are beginning to be recognized as an important part of Earth's biosphere. However, except for indirect indications of microbial assemblages in subglacial Lake Vostok, Antarctica, no sub-ice sheet environments have been shown to support microbial ecosystems. Here we report 16S rRNA gene and isolate diversity in sediments collected from beneath the Kamb Ice Stream, West Antarctic Ice Sheet and stored for 15 months at 4°C. This is the first report of microbes in samples from the sediment environment beneath the Antarctic Ice Sheet. The cells were abundant (∼10⁷ cells g⁻¹) but displayed low diversity (only five phylotypes), likely as a result of enrichment during storage. Isolates were cold tolerant and the 16S rRNA gene diversity was a simplified version of that found in subglacial alpine and Arctic sediments and water. Although in situ cell abundance and the extent of wet sediments beneath the Antarctic ice sheet can only be roughly extrapolated on the basis of this sample, it is clear that the subglacial ecosystem contains a significant and previously unrecognized pool of microbial cells and associated organic carbon that could potentially have significant implications for global geochemical processes.     

Resistance of Enterobacter sakazakii (Cronobacter spp.) to environmental stresses

Aim:  To gain a better understanding of the survival and persistence of Enterobacter sakazakii in severe environments.
Methods and Results:  We evaluated the resistance of Ent. sakazakii to various environmental stresses, including heating, drying, water activity ( a _w), and pH. The resistance of Ent. sakazakii to heat varies widely among strains. Most tested strains of Ent. sakazakii exhibited unusual resistance to dry stress, which depends on drying media. Growth of most strains occurred within 24 h at 37°C when the initial a _w of the medium was adjusted to 0·94 with sucrose or sodium chloride. The minimum pH for growth within 24 h at 37°C was 3·9 or 4·1 for most strains tested. Additionally, there did not appear to be any relationship between resistance to stresses and biofilm-forming ability in Ent. sakazakii planktonic cells.
Conclusions:  These results indicate that Ent. sakazakii is much more resistant than other Enterobacteriaceae to environmental stresses. Moreover, it is likely that Ent. sakazakii has cross-resistance to dry and thermal stresses.
Significance and Impact of the Study:  The findings of this study will contribute to an improved understanding of the survival and behaviour of Ent. sakazakii , which will lead to improved strategies for preventing outbreaks of Ent. sakazakii infection.     

Altered kelp (Laminariales) phlorotannins and growth under elevated carbon dioxide and ultraviolet-B treatments can influence associated intertidal food webs

Due to the importance of brown algae, such as kelp (Laminariales, Phaeophyta), within most cool nearshore environments, any direct responses of kelp to multiple global changes could alter the integrity of future coastal marine systems. Fifty-five-day manipulation of carbon dioxide (CO₂) and ultraviolet light (UVB) within outdoor sea-tanks, approximating past, present and two predicted future levels, examined the direct influences on Saccharina latissima (= Laminaria saccharina ) and Nereocystis luetkeana development and biochemistry, as well as the indirect influences on a marine herbivore ( Tegula funebralis ; Gastropoda, Mollusca) and on naturally occurring intertidal detritivores. Kelp species displayed variable directional (negative and positive growth) and scale responses to CO₂ and UVB manipulations, which was influenced by interactions. Kelp phlorotannin (phenolic) production in blade tissues was induced by elevated UVB levels, and especially enhanced (additively) by elevated CO₂, further suggesting that some actively growing kelp species are carbon limited in typical nearshore environments. Negative indirect effects upon detritivore consumers fed CO₂-manipulated kelp blade tissues were detected, however, no statistical relationships existed among UVB-treated tissues, and test herbivores did not distinguish between phlorotannin-altered CO₂: UVB-treated kelp blade tissues. Results suggest that past and future conditions differentially benefit these kelp species, which implies a potential for shifts in species abundance and community composition. Higher CO₂ conditions can indirectly impede marine decay processes delaying access to recycled trace nutrients, which may be disruptive to the seasonal regrowth of algae and/or higher trophic levels of nearshore ecosystems.     

A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling

Molecular oxygen (O₂) is a potent inhibitor of key microbial processes, including photosynthesis, N₂ fixation, denitrification, sulfate reduction, methanogenesis, iron, and metal reduction reactions. Prokaryote survival and proliferation in aquatic environments is often controlled by the ability to tolerate exposure to oxic conditions. Many prokaryotes do not have subcellular organelles for isolating O₂-producing from O₂-consuming processes and have developed consortial associations with other prokaryotes and eukaryotes that alleviate metabolic constraints of high O₂. Nutrient transformations often rely on appropriate cellular and microenvironmental, or microzonal, redox conditions. The spatial and temporal requirements for microenvironmental overlap among microbial groups involved in nutrient transformations necessitates close proximity and diffusional exchange with other biogeochemically distinct, yet complementary, microbial groups. Microbial consortia exist at different levels of community and metabolic complexity, as shown for detrital, microbial mat, biofilm, and planktonic microalgal-bacterial assemblages. To assess the macroscale impacts of consortial interactions, studies should focus on the range of relevant temporal (minutes to hours) and spatial (microns to centimeters) scales controlling microbial production, nutrient exchange, and cycling. In this review, we discuss the utility and application of techniques suitable for determining microscale consortial activity, production, community composition, and interactions in the context of larger scale aquatic ecosystem structure and function. Correspondence to: Hans W. Paerl.     

A simple regression model to assess environmental effects on fish growth

Multiple regression was used to assess relationships between annular growth and environmental variables. This approach (1) tests for the significance of environmental changes on fish growth and (2) can be successfully used to predict fish growth using different environmental conditions. Age usually explains a large proportion of the variation in growth increments measured in length, and these two variables are inversely related. Since length increments decline as age increases, environmental impacts on growth will be reduced as fish grow older. To account for within-age growth variation and incorporate this age-dependent factor, the inverse of age (1/age in years) is multiplied by the value of an environmental variable (ENV) that may be related to growth. This interaction term and age are regressed against mean annular growth increments in length (TLINC; l _{t +1}— l ₁):
TLINC = b₀—b₁AGE±b₂(1/AGE)*ENV
where b₀, b₁, and b₂ are the regression coefficients for intercept and slope, respectively. Additional variables that measure environmental factors can be added to the model. Environmental effects associated with growth rates of black crappie, Pomoxis nigromaculatus (LeSueur), are presented as an example.     

Ecophysiological and morphological parameters related to survival in grass species exposed to an extreme climatic event

An experiment was performed to elucidate interspecific differences in survival time of grass species subjected to an extreme climatic event. We exposed eight grass species to a simulated heat wave in the field ('free air' temperature increase at 11°C above ambient) combined with drought. We determined whether interspecific differences in survival time were related to the responses of the species to the imposed stress or could be explained by their ecophysiological or morphological characteristics in unstressed conditions. Surprisingly, there was no effect of specific leaf area, but species with a higher total leaf area survived longer. This may arise from a greater water reserve in the plant as a whole, which could delay the desiccation of the meristem, or from reduced evaporation due to a higher leaf area index. Species in which the decrease in light-saturated stomatal conductance ( g _s ) and photosynthetic CO₂ uptake rate ( A _max ) was strongly related to the decrease in soil water availability (measured as soil relative water content and stress duration) survived longer than species in which g _s and A _max likewise declined but responded more to daily fluctuations in irradiance, temperature, and vapor pressure deficit during the heat wave. We, therefore, hypothesize that interspecific differences in stress survival time might be related to the extent to which stomata react to changes in soil water conditions relatively to changes in other environmental and physiological factors. The results suggest that resistance to extremes is governed by other mechanisms than resistance to moderate drought.     

Extreme environments and exobiology

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as "absolute extreme". Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.