Biomineralization of endolithic microbes in rocks from the McMurdo Dry Valleys of Antarctica: implications for microbial fossil formation and their detection

In some zones of Antarctica's cold and dry desert, the extinction of cryptoendolithic microorganisms leaves behind inorganic traces of microbial life. In this paper, we examine the transition from live microorganisms, through their decay, to microbial fossils using in situ microscopy (transmission electron microscopy, scanning electron microscopy in back-scattered electron mode) and microanalytical (energy dispersive X-ray spectroscopy) techniques. Our results demonstrate that, after their death, endolithic microorganisms inhabiting Commonwealth Glacier sandstone from the Antarctica McMurdo Dry Valleys become mineralized. In some cases, epicellular deposition of minerals and/or simply filling up of empty moulds by minerals leads to the formation of cell-shaped structures that may be considered biomarkers. The continuous deposition of allochthonous clay minerals and sulfate-rich salts fills the sandstone pores. This process can give rise to microbial fossils with distinguishable cell wall structures. Often, fossilized cell interiors were of a different chemical composition to the mineralized cell walls. We propose that the microbial fossil formation observed was induced by mineral precipitation resulting from inorganic processes occurring after the death of cryptoendolithic microorganisms. Nevertheless, it must have been the organic template that provoked the diffusion of mineral elements and gave rise to their characteristic distribution pattern inside the fossilized cells.     

New approaches to the study of Antarctic lithobiontic microorganisms and their inorganic traces,and their application in the detection of life in Martian rocks

Microbial life in the harsh conditions of Antarctica's cold desert may be considered an analogue of potential life on early Mars. In order to explore the development and survival of this epilithic and endolithic form of microbial life, our most sophisticated, state-of-the-art visualization technologies have to be used to their full potential. The study of any ecosystem requires a knowledge of its components and the processes that take place within it. If we are to understand the structure and function of each component of the microecosystems that inhabit lithic substrates, we need to be able to quantify and identify the microorganisms present in each lithobiontic ecological niche and to accurately characterize the mineralogical features of these hidden microhabitats. Once we have established the techniques that will allow us to observe and identify these microorganisms and mineral substrates in situ, and have confirmed the presence of water, the following questions can be addressed: How are the microorganisms organized in the fissures or cavities? Which microorganisms are present and how many are there? Additional questions that logically follow include: What are the existing water relationships in the microhabitat and what effects do the microorganisms have on the mineral composition? Mechanical and chemical changes in minerals and mineralization of microbial cells can give rise to physical and/or chemical traces (biomarkers) and to microbial fossil formation. In this report, we describe the detection of chains of magnetite within the Martian meteorite ALH84001, as an example of the potential use of SEM-BSE in the search for plausible traces of life on early Mars. Electronic Publication     

The Search for Biomarkers and Microbial Fossils in Antarctic Rock Microhabitats

The survival of lithobiontic microbial communities in Antarctica's extreme cold, dry environment is conditioned by changes in external climatic conditions that can lead to the death of these microorganisms. In the present study, granite samples from maritime Antarctica and sandstone from the Antarctic continental desert were collected with the aim of searching for biomarkers and microbial fossils at the microscopic level of observation. The results reveal the presence of inorganic biomarkers in the form of physicochemical bioweathering mineral patterns, and inorganic deposits such as calcium oxalates and silica. The presence of fossilised algae and other microorganisms within the sandstone rock was also confirmed. Identifying the internal cell structure within the fossilised cells is proposed as a new criterion for the biogenicity of biomorphs.     

A large population of king crabs in Palmer Deep on the west Antarctic Peninsula shelf and potential invasive impacts

Lithodid crabs (and other skeleton-crushing predators) may have been excluded from cold Antarctic continental shelf waters for more than 14 Myr. The west Antarctic Peninsula shelf is warming rapidly and has been hypothesized to be soon invaded by lithodids. A remotely operated vehicle survey in Palmer Deep, a basin 120 km onto the Antarctic shelf, revealed a large, reproductive population of lithodids, providing the first evidence that king crabs have crossed the Antarctic shelf. DNA sequencing and morphology indicate the lithodid is Neolithodes yaldwyni Ahyong & Dawson, previously reported only from Ross Sea waters. We estimate a N. yaldwyni population density of 10 600 km(-2) and a population size of 1.55 × 10(6) in Palmer Deep, a density similar to lithodid populations of commercial interest around Alaska and South Georgia. The lithodid occurred at depths of more than 850 m and temperatures of more than 1.4°C in Palmer Deep, and was not found in extensive surveys of the colder shelf at depths of 430-725 m. Where N. yaldwyni occurred, crab traces were abundant, megafaunal diversity reduced and echinoderms absent, suggesting that the crabs have major ecological impacts. Antarctic Peninsula shelf waters are warming at approximately 0.01°C yr(-1); if N. yaldwyni is currently limited by cold temperatures, it could spread up onto the shelf (400-600 m depths) within 1-2 decades. The Palmer Deep N. yaldwyni population provides an important model for the potential invasive impacts of crushing predators on vulnerable Antarctic shelf ecosystems.     

HSP70 heat shock proteins and environmental stress in Antarctic marine organisms: A mini-review

The ability to understand and predict the effects of environmental stress on biodiversity is becoming increasingly important in our changing environment. Antarctic marine species are some of the most stenothermal on the planet and many inhabit the waters off the Antarctic Peninsula which is one of the areas where there is rapid regional climate change. Therefore these animals are highly vulnerable to changing environmental temperatures and clearly we need to understand the complexities of their response, not just at the individual species level, but also the implications for the ecosystem as a whole. Heat shock proteins have a long history of use in studies of organism stress responses and have frequently been proposed as potential universal molecular biomarkers, especially for non-model species. In this mini-review, the heat shock response and heat shock proteins (specifically the HSP70 family) are examined in Antarctic marine species alongside their physiological capabilities and limits to answer a series of questions: do these animals have a heat shock response which includes the expression of HSP70 genes? What is the relationship between their heat shock response and physiological capabilities? Can HSP70 genes be used as molecular biomarkers for these species?     

Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.     

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.     

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.     

Bacterial Exopolysaccharides from Extreme Marine Environments with Special Consideration of the Southern Ocean, Sea Ice, and Deep-Sea Hydrothermal Vents: A Review

Exopolysaccharides (EPSs) are high molecular weight carbohydrate polymers that make up a substantial component of the extracellular polymers surrounding most microbial cells in the marine environment. EPSs constitute a large fraction of the reduced carbon reservoir in the ocean and enhance the survival of marine bacteria by influencing the physicochemical environment around the bacterial cell. Microbial EPSs are abundant in the Antarctic marine environment, for example, in sea ice and ocean particles, where they may assist microbial communities to endure extremes of temperature, salinity, and nutrient availability. The microbial biodiversity of Antarctic ecosystems is relatively unexplored. Deep-sea hydrothermal vent environments are characterized by high pressure, extreme temperature, and heavy metals. The commercial value of microbial EPSs from these habitats has been established recently. Extreme environments offer novel microbial biodiversity that produces varied and promising EPSs. The biotechnological potential of these biopolymers from hydrothermal vent environments as well as from Antarctic marine ecosystems remains largely untapped.     

Mercury (micro)biogeochemistry in polar environments

The contamination of polar regions with mercury that is transported as inorganic mercury from lower latitudes has resulted in the accumulation of methylmercury in the food chain of polar environments, risking the health of humans and wildlife. This problem is likely to be particularly severe in coastal marine environments where active cycling occurs. Little is currently known about how mercury is methylated in polar environments. Relating observations on mercury deposition and transport through polar regions to knowledge of the microbiology of cold environments and considering the principles of mercury transformations as have been elucidated in temperate aquatic environments, we propose that in polar regions (1) variable pathways for mercury methylation may exist, (2) mercury bioavailability to microbial transformations may be enhanced, and (3) microbial niches within sea ice are sites where active microorganisms are localized in proximity to high concentrations of mercury. Thus, microbial transformations, and consequently mercury biogeochemistry, in the Arctic and Antarctic are both unique and common to these processes in lower latitudes, and understanding their dynamics is needed for the management of mercury-contaminated polar environments.     

Microorganisms in the atmosphere over Antarctica

Antarctic microbial biodiversity is the result of a balance between evolution, extinction and colonization, and so it is not possible to gain a full understanding of the microbial biodiversity of a location, its biogeography, stability or evolutionary relationships without some understanding of the input of new biodiversity from the aerial environment. In addition, it is important to know whether the microorganisms already present are transient or resident – this is particularly true for the Antarctic environment, as selective pressures for survival in the air are similar to those that make microorganisms suitable for Antarctic colonization. The source of potential airborne colonists is widespread, as they may originate from plant surfaces, animals, water surfaces or soils and even from bacteria replicating within the clouds. On a global scale, transport of air masses from the well-mixed boundary layer to high-altitude sites has frequently been observed, particularly in the warm season, and these air masses contain microorganisms. Indeed, it has become evident that much of the microbial life within remote environments is transported by air currents. In this review, we examine the behaviour of microorganisms in the Antarctic aerial environment and the extent to which these microorganisms might influence Antarctic microbial biodiversity.     

Ecophysiology of Antarctic vascular plants

Most of the ice and snow-free land in the Antarctic summer is found along the Antarctic Peninsula and adjacent islands and coastal areas of the continent. This is the area where most of the Antarctic vegetation is found. Mean air temperature tends to be above zero during the summer in parts of the Maritime Antarctic. The most commonly found photosynthetic organisms in the Maritime Antarctic and continental edge are lichens (around 380 species) and bryophytes (130 species). Only two vascular plants, Deschampsia antarctica Desv. and Colobanthus quitensis (Kunth) Bartl., have been able to colonize some of the coastal areas. This low species diversity, compared with the Arctic, may be due to permanent low temperature and isolation from continental sources of propagules. The existence of these plants in such a permanent harsh environment makes them of particular interest for the study of adaptations to cold environments and mechanisms of cold resistance in plants. Among these adaptations are high freezing resistance, high resistance to light stress and high photosynthetic capacity at low temperature. In this paper, the ecophysiology of the two vascular plants is reviewed, including habitat characteristics, photosynthetic properties, cold resistance, and biochemical adaptations to cold.     

Bacteriophage in polar inland waters

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.     

Non-indigenous microorganisms in the Antarctic: assessing the risks

The Antarctic continent is frequently cited as the last pristine continent on Earth. However, this view is misleading for several reasons. First, there has been a rapid increase in visitors to Antarctica, with large increases at research bases and their environs and to sites of major tourist interest (e.g. historical sites and concentrations of megafauna). Second, although substantial efforts are made to avoid physical disturbance and contamination by chemical, human and other wastes at these sites, little has been done to prevent the introduction of non-indigenous microorganisms. Here, we analyse the extent and significance of anthropogenic introduction of microbial 'contaminants' to the Antarctic continent. We conclude that such processes are unlikely to have any immediate gross impact on microbiological community structure or function, but that increased efforts are required to protect the unique ecosystems of Antarctica from microbial and genetic contamination and homogenisation.     

Antarctic microbial diversity: the basis of polar ecosystem processes

Microorganisms are fundamental to the functioning of Antarctic ecosystems. Although microbial biomass can be immense in Southern Ocean blooms and freshwater cyanobacterial mats, species richness is generally more restricted than it is in temperate regions. However, there are representatives of a broad variety of taxa providing a diverse gene pool. Species diversity may be low while metabolic flexibility is high so that a few strains can provide most necessary functions. In this context, biodiversity is the sum of biological potential. This Special Issue highlights aspects of microbial ecology that can be studied only in Antarctica or which are defined most clearly in Antarctic habitats. Relatively simple microbial communities, or conspicuous species within them, can be used as indicators of microbial processes and responses to environmental change. These include the palaeological record of benthic diatoms and response of soil cyanobacterial communities to regional warming and UV-B stress. The climatic conditions and relict babitats of the Antarctic dry valleys are a valuable analogue for detecting microbial life and diversity on Mars. The global microbial biodiversity initiative Diversitas and international Antarctic networks such as BIOTAS (Biological Investigations of Terrestrial Antarctic Systems) harness taxonomic and ecophysiological expertize to understand better these unique polar ecosystems.     

Supplementation of Poultry Feeds with Dietary Zinc and Other Minerals and Compounds to Mitigate Nitrogen Emissions—A Review

One of the environmental challenges that the poultry industry has been faced with is ammonia emission from manure. One way to reduce nitrogen excretion and emissions is supplementing dietary trace minerals to inhibit the activity of microbial uricase, a key enzyme converting nitrogen compounds in the manure into ammonia. Several dietary minerals are commercially available as economic alternatives for reducing ammonia emissions in poultry. In this review, we discuss different mineral elements including zinc as feed amendment minerals that could be used to reduce ammonia emission. Issues discussed include potential for inhibiting microbial uricase, dietary supplementation levels, growth performance, toxicity, their influence on manure nitrogen emission, and potential mineral accumulation in soil. In addition, we discuss other minerals and compounds that have the potential to reduce ammonia volatilization by inhibiting microbial uricase and growth of uric acid-utilizing microorganisms.     

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper‐arid polar desert

Permafrost in the high elevation McMurdo Dry Valleys of Antarctica ranks among the driest and coldest on Earth. Permafrost soils appear to be largely inhospitable to active microbial life, but sandstone lithic microhabitats contain a trophically simple but functional cryptoendolithic community. We used metagenomic sequencing and activity assays to examine the functional capacity of permafrost soils and cryptoendolithic communities in University Valley, one of the most extreme regions in the Dry Valleys. We found metagenomic evidence that cryptoendolithic microorganisms are adapted to the harsh environment and capable of metabolic activity at in situ temperatures, possessing a suite of stress response and nutrient cycling genes to fix carbon under the fluctuating conditions that the sandstone rock would experience during the summer months. We additionally identified genes involved in microbial competition and cooperation within the cryptoendolithic habitat. In contrast, permafrost soils have a lower richness of stress response genes, and instead the metagenome is enriched in genes involved with dormancy and sporulation. The permafrost soils also have a large presence of phage genes and genes involved in the recycling of cellular material. Our results underlie two different habitability conditions under extreme cold and dryness: the permafrost soil which is enriched in traits which emphasize survival and dormancy, rather than growth and activity; and the cryptoendolithic environment that selects for organisms capable of growth under extremely oligotrophic, arid and cold conditions. This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities.     

Prokaryotic Diversity in the Antarctic: The Tip of the Iceberg

In contrast to the rather limited diversity of plants and animals to be found in the Antarctic, the microbial diversity of this continent has been shown to be "surprisingly" diverse. Apparently barren soil and rock landscapes, as well as the numerous and diverse lakes found at the edges of the continent, harbor a range of prokaryotes which indicate that the extremely low temperatures which prevail seasonally are no obstacle to microbial colonization. Both direct cultivation methods and modern molecular genetic methods have contributed to our understanding of the range of organisms to be found. Cultivation based studies are often hampered by constraints inherent in the methods selected for the isolation of organisms. Molecular-based approaches do not suffer from the same cultivation-based biases, but other problems need to be taken into consideration. It has rarely been possible to combine both techniques in a single study, nor has it usually been possible to take the results and conclusions drawn from the study of one environment and apply this knowledge to a further series of experiments on the same environment. The Antarctic may be considered to be a geographically well isolated area to study. Comparison with other environments that may also be "isolated" from their surroundings (i.e., hot springs or highly saline lakes) allows parallels to be drawn. The conclusions drawn provide important insights into the way the Antarctic may have been colonized and the microbiota diversified. Much work still needs to be done beyond the simple task of making an inventory. The functioning of complex communities, such as mat systems, requires an understanding of the ecology of the systems, not only at the level of the whole system, but also the role of localized environments within that system. Perhaps these ecosystems have, in the absence of plant and animal communities, a role to play in the monitoring of polar climate change. The information available at present clearly indicates that the Antarctic is deserving of further study at the microbial level.