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Project Reports

• Describing the Anaerobic Thermophilic Microbial Community: A Metagenomic Strategy

  The ocean is one of the least explored parts of the microbial world, including at deep-sea hydrothermal vents, where the unique geochemistry creates many habitats for microbial and animal communities. These organisms encounter many conditions that we humans consider too extreme- too hot, too toxic, too little oxygen- but microbes seem to find a way and continue to push the limits of life. An impetus for studying life at deep-sea hydrothermal vents is that life may have originated and evolved near hydrothermal systems, and that organisms currently living in these likely analogues of early habitats may still harbor characteristics of early life. In addition, microbes unique to the hydrothermal vents could provide insight into metabolic processes, strategies for growth, and survival of life on solar bodies with a water history, such as Mars and Jupiter’s moon Europa. Our research on diffuse flow vents at deep-sea hydrothermal seamounts provides insight into the diversity, physiology, and genetic potential of these unique microbial communities within the context of their dynamic and complex geochemical habitat.

  ROADMAP OBJECTIVES: 4.1 5.1 5.2

• Biosignatures in Chemosynthetic and Photosynthetic Systems

  Our work examines the microbiology and geochemistry of microbial ecosystems on Earth in order to better understand the production of “biosignatures” — chemical or physical features or patterns that can only have been formed by the activities of life. More specifically, in photosynthetic (light-eating) microbial mats, we examine the factors that control the formation of biosignature gases (such as could be seen by telescope in the atmospheres of planets orbiting other stars) and isotopic and morphological features that could be preserved in the rock record (such as could be examined by rovers on Mars). Additionally, we study the formation of morphological and mineral signatures in chemotrophic (chemical-eating) systems that have no direct access to light or the products of photosynthesis. Such systems likely represent the only viable possibility for extant life on modern day Mars or Europa.

  ROADMAP OBJECTIVES: 2.1 4.1 5.1 5.2 6.1 7.1 7.2

• Application of U-Tube and Fiber-Optic Distributed Temperature Sensor to Characterize the Chemical and Physical Properties of a Deep Permafrost and Sub-Permafrost Environment at High Lake, Nunavut, Canada.

  Acquiring water samples for microbial and geochemical analyses from beneath hundreds of meters of frozen rock by conventional approaches are impossible because the water freezes in the tubing while transiting the permafrost and most down-hole pumps or bailers lack sufficient power to push up water that distance. Furthermore, to collect samples with representative trace gas concentrations the water needs to be kept under pressure as it rises to the surface. We utilized a new technology that combines a gas-lifting U-tube device with heat tracer tapes and a fiber-optic distributed temperature sensor (DTS) and successfully acquired a mixture of drilling water and fracture water from beneath 420 meters of permafrost. We also performed a thermal perturbation experiment and obtained a high resolution profile of the thermal conductivity of the permafrost zone, which in turn enabled us to invert the ambient geothermal profile to obtain this ground surface temperature history for the past 1000 years.

  ROADMAP OBJECTIVES: 2.1 5.2 5.3 7.1

• Genome-Genome Integration: Symbiosis, Genetic Assimilation, and Evolutionary Innovation

  Unlike single mutations, genome interactions can catalyze the acquisition of entirely new combinations of functions and drive major evolutionary transitions. Through studies of binary interactions between two species – i.e. a symbiont and its host- we can dissect the mechanisms of genome communication and coevolution. Through a comparative genomic approach, we are deciphering the 'language’ used to establish and maintain intimate associations between bacteria and animal hosts. Our ultimate objective is to understand how such interactions have contributed to organismal complexity and evolutionary novelty.

  ROADMAP OBJECTIVES: 5.1 5.2 6.2

• Modeling Early Earth Environments

  In this project, scientists from different disciplines model the conditions likely to have been found on the Early Earth, prior to 2.3 billion years ago. Specific areas of research include understanding the gases, many biologically produced, and mechanisms that controlled early Earth’s surface temperature, the nature of hazes that shielded the planetary surface from UV and may be responsible for signatures in sulfur isotopes that were left in the rock record, the chemical nature of the Earth’s environment during and after a planet-wide glaciation (a “Snowball event”), the evolution of planetary atmospheres over time due to loss of atmosphere to space, and the use of iron isotopes as a tracer of the oxidative state of the Earth’s ocean over time.

  ROADMAP OBJECTIVES: 1.1 1.2 2.1 4.1 4.2 5.1 5.2 5.3 6.1 7.2

• Design, Construction and Testing of a Cavity-Ring Down Spectrometer for Determination of the Concentration and Isotopic Composition of Methane

  The recent detection of CH₄ in the Martian atmosphere and observations suggesting that it varies both temporally and spatially argues for dynamic sources and sinks. CH₄ is a gaseous biomarker on Earth that is readily associated with methanogens when its H and C isotopic composition falls within a certain range. It is imperative that a portable instrument be developed that is capable of measuring the C and H isotopic composition of CH₄ at levels comparable to that on Mars with a precision similar to that of an isotope ratio mass spectrometer and that such an instrument be space flight capable. Such an instrument could guide a rover to a site on Mars where emission of biogenic gases is occurring and samples could be collected for Mars sample return.

  ROADMAP OBJECTIVES: 2.1 2.2 3.3 4.1 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Carbon Flow Between Organisms in Complex Communities

  ROADMAP OBJECTIVES: 4.2 5.2

• Examination of the Microbial Diversity Found in Ice Cores (Brenchley)

  Our goal is to discover microorganisms surviving in cold or frozen environments and to use this information to understand how different microorganisms survive extreme habitats. Our recent results demonstrated that abundant populations, including many bacteria representing novel taxa, exist frozen in a Greenland glacier ice core for at least 120,000 years. Current isolates are being characterized as new species of ultra-small celled bacteria. This research provides insight into microbial survival in extreme environments that might exist elsewhere in the solar system.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 6.1 6.2 7.1

• Microbial Diversity and Population Structure Studies in the Rio Tinto

  As part of our Microbial diversity and population structure studies in the Rio Tinto, we hope to better understand how environmental conditions such as pH and metal concentrations help shape the underlying microbial community structures in extreme environments that serve as terrestrial analogs for Mars. The iron-based mineralogy found in the Rio Tinto coupled with low pH are two characteristics that tie this extreme environment to Mars. To this end, we have been sampling stations along the river that differ in the concentration and oxidation state of iron and other metals (see http://amarallab.mbl.edu/rt_main/rt.html for more detailed information and photographs of the study locations) and using molecular techniques coupled with physicochemical measurements to investigate microbial diversity in the water column at both spatial and temporal scales. When possible, determination of as many in situ physico-chemical parameters are made on biofilms as well, using microelectrodes available for field measurements. This allows for the correlation of biological diversity information with physicochemical parameters of the river. The outcome of this study will provide a comprehensive view of the microbial ecology of the system, a first step towards establishing an ecological genomics project for the Rio Tinto.

  ROADMAP OBJECTIVES: 3.3 5.1 5.2

• DDF: Geomicrobiology of a Unique Ice-Sulfur Spring Ecosystem in the High Arctic

  A glacial, active sulfide spring environment at Borup Fiord Pass on Ellesmere Island in the Canadian High Arctic provides an excellent opportunity to study microbial life at a site that may be an analog to Europa, an ice-covered moon of Jupiter. During the past year we have collected samples from the extensive mats of sulfur-minerals that precipitate in discharge channels to identify the microbial communities hosted in the sulfur-ice, and to cultivate key key organisms mediating the oxidation of H2S to elemental sulfur.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 7.1 7.2

• Environmental Genomics Reveals a Single Species Ecosystem Deep Within the Earth.

  The first metagenome sequence from a deep subsurface environment of South Africa has not only described the genetic composition of a new genera/species of sulfate reducing bacteria, Desulforudis Audaxviator, but has also revealed that it is by far the most dominant and most likely the sole resident of its environment. A single species ecosystem has never been reported before and runs counter to the prevalent concept that microorganisms live and evolve as communities of mixed species. Whether this bacterial species occurs in other deep subsurface environments around the world or whether other deep subsurface environments are also occupied by single species remains to be determined.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 6.2

• Planetary Surface and Interior Models and Super Earths

  In this task we are developing and using models of a terrestrial planet’s surface and interior to understand
  the evolution of planetary environments. These models allow us to understand how interactions between the
  planetary surface and interior, and life, affect a planet’s atmosphere. New models are also exploring the possible habitability of “super-Earths”, rocky planets that have been found around other stars that can be up to 10 times more massive than our own Earth.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 5.2 6.1 7.2

• High Lake Gossan Deposit: An Arctic Analogue for Ancient Martian Surficial Processes?

  The massive sulfide deposit at High Lake is covered by a ~1 meter thick layer of Fe oxides and sulfate minerals. The minerals have formed within the last 8,000 years in the active zone of the permafrost and as such the site provides a good analog to those terranes on Mars that contain similar mineral assemblages, e.g. Terra Meridiana, and may have formed under similar, acidic conditions. The minerals present in the High Lake gossan were characterized by XRD, SEM and Mössbauer.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 6.1 7.1

• Planetary-Scale Transition From Abiotic to Biotic Nitrogen Cycle

  Nitrogen is an essential element for life. Understanding the planetary nitrogen cycle is critical to understanding the origin and evolution of life. The earth’s atmosphere is full of nitrogen gas (N2). However, this large pool of nitrogen is unavailable to most of the life on earth except a few microbes capable of “fixing” nitrogen into a form that can be used by other organisms (e.g., NH3, NH4+, NOx, organic-N). Without fixed nitrogen life would not have originated on earth and would most likely not occur on any other planet. The Atacama Desert in Chile is an enigma in that it contains vast nitrate (a type of fixed nitrogen) deposits. Elsewhere on earth, nitrate is either denitrified (transformed into N2 and released back into the atmosphere) through the activity of microorganisms, or is dissolved and leached from the system. Although the Atacama is the driest desert in the world we have shown that lack of water alone cannot account for the lack of nitrogen cycling in this desert. Preliminary data suggest that it may be due to the high oxidation level of the soil in combination with a lack of organic material in the soil.

  ROADMAP OBJECTIVES: 1.1 2.1 3.2 4.1 5.1 5.2 5.3 6.1

• Identifying Microbial Life at Crustal Rock-Water Interfaces

  We are working to cultivate and characterize microorganisms which directly derive energy from reactions between mafic rocks and water. We are particularly targeting organisms that colonize the surfaces of the rocks during alteration. Thus we are also developing high-resolution chemical measurements capable of detecting reaction fronts and mineral by-products that form over time at the microbe-mineral interface.

  ROADMAP OBJECTIVES: 5.2 5.3 6.1 6.2 7.2

• Laboratory Microbial Simulations: Astrobiological Signatures

  We aim to use laboratory and field environments to investigate microorganisms and their biogeochemical signatures. We have investigated methanotrophic seeps and deeply-buried marine environments, as well as used laboratory pure-cultures to further our understanding of diverse metabolisms.

  ROADMAP OBJECTIVES: 2.1 4.1 5.1 5.2 5.3 7.1

• Microbial Diversity of a Hypersaline Microbial Mat

  The goal of this project is to survey the microbial life that comprises a hypersaline microbial mat at Guerrero Negro, Mexico using culture independent technology (ribosomal and other gene sequences). The results have expanded significantly our knowledge of microbial diversity, bacterial, archaeal and eucaryotic.

  ROADMAP OBJECTIVES: 3.2 3.3 5.1 5.2 5.3 7.2

• The High Lakes Project (HLP)

  The High Lakes Project is a multi-disciplinary astrobiological investigation studying high-altitude lakes between 4,200 m and 5,916 m elevation in the Central Andes of Bolivia and Chile. Its primary objective is to understand the impact of increased environmental stress on lake habitats and their evolution during rapid climate change as an analogy to early Mars. Their unique geophysical environment and mostly uncharted ecosystems have added new objectives to the project, including the assessment of the impact of low ozone/high solar irradiance in non-polar aquatic environments, the documentation of poorly known ecosystems, and the quantification of the impact of climate change on lake environment and ecosystem.
  Data from 2003 to 2007 show that solar irradiance is 165% that of sea level with instantaneous UV-B flux reaching 17W/m2. Short UV wavelengths (260-270 nm) were recorded and peaked at 14.6 mW/m2. High solar irradiance occurs in an atmosphere permanently depleted in ozone falling below ozone hole definition for 33-36 days and between 30-35% depletion the rest of the year. The impact of strong UV-B and UV erythemally-weighted daily dose on life is compounded by broad daily temperature variations with sudden and sharp fluctuations. Lake habitat chemistry is highly dynamical with notable changes in yearly ion concentrations and pH resulting from low and variable yearly precipitation. The year-round combination of environmental variables define these lakes as end-members. In such an environment, they host surprisingly abundant and diverse ecosystems including a significant fraction of previously undescribed species of zooplankton, cyanobacterial, and bacterial populations.

  ROADMAP OBJECTIVES: 1.1 2.1 4.1 4.3 5.1 5.2 5.3 6.1 6.2 7.1

• Stromatolites in the Desert: Analogs to Other Worlds

  Field work at Cuatro Ciénegas, Mexico has focused on understanding unique
  structures called microbialites. These are colonies of bacteria that have
  been encased by minerals that have precipated out of the water surrounding
  them. This process have been going on for 2 and a half billion years on
  earth. The work we are doing is using experiments to see how the environment
  can affect the genes in these bacteria to create the microbialites. We do
  this to improve our understanding of how they utilize two very important atoms, carbon and nitrogen. By studying these Earth bacteria we can better understand how microbialites interact with their environemnt, and whether or not microbialites might exist and be detectable in extrasolar environments.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3

• Mars Forward Contamination Studies Utilizing a Mars Environmental Simulation Chamber

  A variety of microorganisms have been selected for experimental culturing in a Mars environmental simulation chamber. The test organisms are adapted on Earth to desiccation resistance and cold tolerance so they are suitable for exposure to simulated surface conditions on Mars. The test chamber is capable of reproducing temperatures, solar radiation, and atmospheric conditions inferred for Mars. Results from these tests will provide critical information for the design and engineering of sampling and caching equipment on a future mission to sample rocks and sediments on Mars and return those samples to Earth for laboratory study.

  ROADMAP OBJECTIVES: 2.1 3.2 3.3 5.1 5.2 5.3 6.1 6.2 7.1

• Origin of Multicellularity and Complex Land-Based Ecosystem

  80-90% of all land plants have mutualistic symbiotic associations with fungi where the fungal symbionts provide increased access to essential minerals and the fungal symbionts gain fixed carbon. We are characterizing the fungal symbionts in early lineages of land plants (over 300 million years old) that have a life cycle where one phase is above ground and photosynthetic and another phase is completely underground for as long as fifteen years. This subterranean phase in these poorly understood plants is completely dependant on a set of fungal symbionts to provide a source of fixed carbon. Establishing the identity of the fungal symbionts in these diverse underground plants is fundamental to understanding the broader co-evolutionary and ecological history of plant-fungal associations across the almost 500 million year history of land plants.

  ROADMAP OBJECTIVES: 4.2 5.2

• Microbial Communities in Subpermafrost Saline Fracture Water at the Lupin Au Mine, Nunavut, Canada

  As scientists prepare to search for life in the subsurface of Mars, it is increasingly clear that we have little experience characterizing microbial life in permafrost environments on Earth. Lupin gold mine in Nunavut Territory Canada provides scientists with an opportunity to collect samples of ground water beneath 500 meters of permafrost. These subpermafrost water samples contain extant microbial communities that are dominated by sulfate-reducing bacteria. It remains to be determined how and when this microbial community became established.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 7.1

• Molecular Signatures of Life on the Edge (DDF Project)

  We have investigated the Dead Sea, as a possible analog of early Mars environments — slightly acidic and highly saline. We have used metagenomics, lipid analysis, and amino acid analysis.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 7.1

• Sulfur Biogeochemistry of the Early Earth

  Sulfur is widespread in surface geochemical systems and is abundant in many rock types. It is present in volcanic gases and marine waters, and has served a key role in geobiological processes since the origin of life. Like other low atomic number elements, sulfur isotope ratios in various compounds usually follow predictable mass-dependent fractionation laws; these different mass-dependent isotope fractionations serve as powerful tracers for igneous, metamorphic, sedimentary, hydrothermal and biological processes. Mass-independent sulfur isotope fractionation is a short-wavelength photolytic effect that occurs in space, as well as in gas-phase reactions in atmospheres transparent to deep penetration by ultraviolet light. Crucial aspects of the chemical evolution of the early atmosphere — and the surface zone as a whole — can be followed by mass-independent sulfur isotopes in Archean metasedimentary rocks. Metabolic styles of organisms in response to global changes in surface redox over geologic time can also be traced with multiple S isotopes.

  We have concluded from our various studies over the last year and before to the very inception of the NAI node at Colorado, that all Archean sulfur minerals previously documented for their 34S/32S compositions warrant a comprehensive re-examination of their 32S, 33S, 34S (and 36S), sulfur isotope systematics.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 5.3 6.1 7.1 7.2

• Ecology of a Hawaiian Lava Cave Microbial Mat

  We have been studying a microbial biofilm (Figure 1) growing at very low light intensities and high temperature and humidity below the entrance of a lava cave in Kilauea Crater, Hawai’i Volcanoes National Park. (Figure 2)
  The cave presents an oligotrophic environment, but condensation of geothermally heated groundwater that vents at the rear of the cave has promoted the development of a complex microbial community, similar in higher order taxonomic structure to copiotrophic soil environments. Given the existence of lava tubes of similar geologic composition on Mars, geothermal activity there may have allowed the existence, or persistence, of complex microbial communities in similar Martian environments, wherein they would be shielded from the effects of harmful UV radiation.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1

• Mechanisms of Marine Microbial Community Structuring

  The sub-tropical open ocean is an extreme environment that presents the opportunity to examine the factors affecting microbial community structure across a number of environmental gradients. We have developed and utilized a novel assay that allows us to simultaneously determine the taxonomic composition of Archaea, Bacteria and microbial Eucarya in DNA extracted from environmental samples. Samples analyzed represent the epi-, meso- and bathy-pelagic zones of the ocean, which display gradients in temperature, pressure, oxygen content, nutrient content and photosynthetically available radiation.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1

• Sediment-Buried Basement Deep Biosphere

  There is growing evidence that a substantial subseafloor biosphere extends throughout the immense volume of aging basement (basaltic rock) of the ocean crust. Since most ocean basement rock is buried under thick, impermeable layers of sediment, the fluids circulating within the underlying ocean basement are usually inaccessible for direct studies. Circulation Obviation Retrofit Kit (CORK) observatories affixed to Integrated Ocean Drilling Program (IODP) boreholes offer an unprecedented opportunity to study biogeochemical properties and microbial diversity in circulating fluids from deep ocean basement. UH-NAI post doctoral fellows (e.g., Brian Glazer, Andrew Boal)

  ROADMAP OBJECTIVES: 1.1 3.3 4.1 5.1 5.2 5.3 6.1 6.2