Microbial ecology of the cryosphere: sea ice and glacial habitats

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City

Automated teller machine (ATM) keypads represent a specific and unexplored microhabitat for microbial communities. Although the number of built environment and urban microbial ecology studies has expanded greatly in recent years, the majority of research to date has focused on mass transit systems, city soils, and plumbing and ventilation systems in buildings. ATM surfaces, potentially retaining microbial signatures of human inhabitants, including both commensal taxa and pathogens, are interesting from both a biodiversity perspective and a public health perspective. By focusing on ATM keypads in different geographic areas of New York City with distinct population demographics, we aimed to characterize the diversity and distribution of both prokaryotic and eukaryotic microbes, thus making a unique contribution to the growing body of work focused on the “urban microbiome.” In New York City, the surface area of urban surfaces in Manhattan far exceeds the geographic area of the island itself. We have only just begun to describe the vast array of microbial taxa that are likely to be present across diverse types of urban habitats.

In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the “urban microbiome” may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes.

IMPORTANCEAutomated teller machine (ATM) keypads represent a specific and unexplored microhabitat for microbial communities. Although the number of built environment and urban microbial ecology studies has expanded greatly in recent years, the majority of research to date has focused on mass transit systems, city soils, and plumbing and ventilation systems in buildings. ATM surfaces, potentially retaining microbial signatures of human inhabitants, including both commensal taxa and pathogens, are interesting from both a biodiversity perspective and a public health perspective. By focusing on ATM keypads in different geographic areas of New York City with distinct population demographics, we aimed to characterize the diversity and distribution of both prokaryotic and eukaryotic microbes, thus making a unique contribution to the growing body of work focused on the “urban microbiome.” In New York City, the surface area of urban surfaces in Manhattan far exceeds the geographic area of the island itself. We have only just begun to describe the vast array of microbial taxa that are likely to be present across diverse types of urban habitats.

Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China

In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups.

Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates

Diatom-bacteria aggregates are key for the vertical transport of organic carbon in the ocean. Sinking aggregates also represent pelagic microniches with intensified microbial activity, oxygen depletion in the center, and anaerobic nitrogen cycling. Since some of the aggregate-forming diatom species store nitrate intracellularly, we explored the fate of intracellular nitrate and its availability for microbial metabolism within anoxic diatom-bacteria aggregates. The ubiquitous nitrate-storing diatom Skeletonema marinoi was studied as both axenic cultures and laboratory-produced diatom-bacteria aggregates. Stable 15N isotope incubations under dark and anoxic conditions revealed that axenic S. marinoi is able to reduce intracellular nitrate to ammonium that is immediately excreted by the cells. When exposed to a light:dark cycle and oxic conditions, S. marinoi stored nitrate intracellularly in concentrations >60 mmol L-1 both as free-living cells and associated to aggregates. Intracellular nitrate concentrations exceeded extracellular concentrations by three orders of magnitude. Intracellular nitrate was used up within 2-3 days after shifting diatom-bacteria aggregates to dark and anoxic conditions. Thirty-one percent of the diatom-derived nitrate was converted to nitrogen gas, indicating that a substantial fraction of the intracellular nitrate pool of S. marinoi becomes available to the aggregate-associated bacterial community. Only 5% of the intracellular nitrate was reduced to ammonium, while 59% was recovered as nitrite. Hence, aggregate-associated diatoms accumulate nitrate from the surrounding water and sustain complex nitrogen transformations, including loss of fixed nitrogen, in anoxic, pelagic microniches. Additionally, it may be expected that intracellular nitrate not converted before the aggregates have settled onto the seafloor could fuel benthic nitrogen transformations.

Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies. Key Words: In situ measurement-Biosignatures-Microbiology-Europa-Ice. Astrobiology 16, 755-774.

Polar Marine Microorganisms and Climate Change

The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.

Microbial mercury methylation in Antarctic sea ice

Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces

Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers, providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules, which otherwise would be respired. Furthermore, data suggest that CO₂ could be produced also by microbiologically mediated oxidation of CO, which may be produced by photodegradation of organic matter.

The subzero microbiome: microbial activity in frozen and thawing soils

Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula

Environmental viruses constitute the most abundant biological entities on earth, and harbor an enormous genetic diversity. While their strong influence on the ecosystem is widely acknowledged, current knowledge about their diversity and distribution remains limited. Here we present the metagenomic study of viral communities from freshwater bodies located along a transect of the Antarctic Peninsula. These ecosystems were chosen on the basis of environmental and biogeographical variation. The results obtained indicate that the virus assemblages were diverse, and that the larger fraction represented viruses with no close relatives in the databases. Comparisons to existing metaviromes showed that the communities studied were dissimilar to other freshwater viromes including those from the Arctic. Finally, we observed no indication of there being a reduction in either viral richness or diversity estimates with increasing latitude along the studied transect, further adding to the controversy regarding the possible existence of latitudinal gradients of diversity in the microbial world.

Evidence for marine origin and microbial-viral habitability of sub-zero hypersaline aqueous inclusions within permafrost near Barrow, Alaska

Cryopegs are sub-surface hypersaline brines at sub-zero temperatures within permafrost; their global extent and distribution are unknown. The permafrost barrier to surface and groundwater advection maintains these brines as semi-isolated systems over geological time. A cryopeg 7 m below ground near Barrow, Alaska, was sampled for geochemical and microbiological analysis. Sub-surface brines (in situtemperature of -6 °C, salinity of 115 ppt), and an associated sediment-infused ice wedge (melt salinity of 0.04 ppt) were sampled using sterile technique. Major ionic concentrations in the brine corresponded more closely to other (Siberian) cryopegs than to Standard seawater or the ice wedge. Ionic ratios and stable isotope analysis of water conformed to a marine or brackish origin with subsequent Rayleigh fractionation. The brine contained ∼1000× more bacteria than surrounding ice, relatively high viral numbers suggestive of infection and reproduction, and an unusually high ratio of particulate to dissolved extracellular polysaccharide substances. A viral metagenome indicated a high frequency of temperate viruses and limited viral diversity compared to surface environments, with closest similarity to low water activity environments. Interpretations of the results underscore the isolation of these underexplored microbial ecosystems from past and present oceans.

Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax

The Svalbard archipelago (Spitsbergen Island) is the northernmost landmass in the European Arctic and has a variety of small- and medium-sized glaciers. The plasmidome of eleven psychrophilic strains of Variovorax spp. isolated from the ice surface of Hans and Werenskiold Glaciers of Spitsbergen Island, was defined. This analysis revealed the presence of six plasmids whose nucleotide sequences have been determined. Four of them, exhibiting high reciprocal sequence similarity, possess unique structures, since their genomes lack any recognized genes. These miniature replicons, not exceeding 1 kb in size, include pHW69V1 (746 bp), which is the smallest autonomous replicon so far identified in free-living bacteria. The miniature plasmids share no similarity with known sequences present in the databases. In silico and experimental analyses identified conserved DNA regions essential for the initiation of replication of these replicons.

Bridging the divide: a model-data approach to Polar and Alpine microbiology

Advances in microbial ecology in the cryosphere continue to be driven by empirical approaches including field sampling and laboratory-based analyses. Although mathematical models are commonly used to investigate the physical dynamics of Polar and Alpine regions, they are rarely applied in microbial studies. Yet integrating modelling approaches with ongoing observational and laboratory-based work is ideally suited to Polar and Alpine microbial ecosystems given their harsh environmental and biogeochemical characteristics, simple trophic structures, distinct seasonality, often difficult accessibility, geographical expansiveness and susceptibility to accelerated climate changes. In this opinion paper, we explain how mathematical modelling ideally complements field and laboratory-based analyses. We thus argue that mathematical modelling is a powerful tool for the investigation of these extreme environments and that fully integrated, interdisciplinary model-data approaches could help the Polar and Alpine microbiology community address some of the great research challenges of the 21st century (e.g. assessing global significance and response to climate change). However, a better integration of field and laboratory work with model design and calibration/validation, as well as a stronger focus on quantitative information is required to advance models that can be used to make predictions and upscale processes and fluxes beyond what can be captured by observations alone.

Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge

Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

The deep ocean floor covers more than 60% of the Earth's surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000-5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.

A Submersible, Off-Axis Holographic Microscope for Detection of Microbial Motility and Morphology in Aqueous and Icy Environments

Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples taken directly from sea ice at several locations near Nuuk, Greenland. In all samples, the appearance and motility of eukaryotes were conclusive signs of life. The appearance of prokaryotic cells alone was not sufficient to confirm life, but when prokaryotic motility occurred, it was rapid and conclusive. Warming the samples to above-freezing temperatures or supplementing with serine increased the number of motile cells and the speed of motility; supplementing with serine also stimulated chemotaxis. These results show that DHM is a useful technique for detection of active organisms in extreme environments, and that motility may be used as a biosignature in the liquid brines that persist in ice. These findings have important implications for the design of missions to icy environments and suggest ways in which DHM imaging may be integrated with chemical life-detection suites in order to create more conclusive life detection packages.