Microbial Ecosystems from the Deepest Regions of the Terrestrial Deep Biosphere

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Although recent discoveries from four continents support the existence of microbial ecosystems across vast regions of our planet's inner space, very little is known about the abundance, distribution, diversity, or ultimate depth limit of subsurface microbial life. These deep lithospheric inhabitants must contend with a variety of potential challenges including high temperature, pressure and salinity, extreme isolation, and low energy flux. Interestingly, although deep microbial ecosystems are assumed to be energy and nutrient limited, it is often difficult to identify any one limiting substrate and the energy for deep life is often present in relative abundance (e.g. as geologically-produced hydrogen or other reduced gases). Recently, the concept of radiation-supported deep microbial ecosystems has gained traction in the literature. In particular, one bacterium, a Firmicute denoted Candidatus Desulforudis audaxviator, has been shown to be prominent, and in cases dominate, in deep fracture fluids from across the Witwatersrand basin of South Africa, where it appears to persist by utilizing H2 and SO42- derived from radiochemical reactions in U-rich host rock. Until recently, these mines were thought to define the geographic limit of this genus and species; however, our recent North American detection of D. audaxviator in radioactive subsurface water resulting from underground nuclear tests both supports earlier assertions concerning the radiochemical lifestyle of D. audaxviator and greatly expands its range. Results such as these suggest that novel modes of life operating without inputs from the photosphere are possible, and thus may have implications for the likelihood of detecting life off the Earth (e.g. in the Martian subsurface). In addition to underground nuclear detonation cavities, this talk will consider insights gained from ongoing microbial ecology assessments from several to date unexplored deep ecosystems accessed via deep mines in the Black Hills (USA) and Canadian Shield (Canada) and exploratory boreholes in the Southern Great Basin (USA). The tantalizing possibility that several of these new potential habitats have exceeded some limit for life will be also be explored.

Microbial biofilm studies of the Environmental Control and Life Support System water recovery test for Space Station Freedom

NASA Technical Reports Server (NTRS)

Obenhuber, D. C.; Huff, T. L.; Rodgers, E. B.

1991-01-01

Analysis of biofilm accumulation, studies of iodine disinfection of biofilm, and the potential for microbially influenced corrosion in the water recovery test (WRT) are presented. The analysis of WRT components showed the presence of biofilms and organic deposits in selected tubing. Water samples from the WRT contained sulfate-reducing and acid-producing organisms implicated in corrosion processes. Corrosion of an aluminum alloy was accelerated in the presence of these water samples, but stainless steel corrosion rates were not accelerated.

The Earth Through Time: Implications for Searching for Habitability and Life on Exoplanets

NASA Technical Reports Server (NTRS)

Pilcher, Carl B.

2016-01-01

The Earth has been both a habitable and inhabited planet for around 4 billion years, yet distant observers studying Earth at different epochs in our history would have detected substantially different and probably varying conditions. Understanding Earth's history thus has much to tell us about how to interpret observations of potentially habitable exoplanets. In this talk I will review the history of life on Earth, from the earliest microbial biosphere living under a relatively methane-rich atmosphere to the modern world of animals, plants, and atmospheric oxygen, with a focus on how observable conditions on Earth changed as the planet and its biosphere evolved. I'll discuss the implications of this history for assessing the habitability of-or presence of life on-planets around other stars.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial metabolism of Tholin

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Mancinelli, R. L.; Boston, P. J.; Segal, W.; Khare, B. N.

1990-01-01

Tholin, a class of complex organic heteropolymers hypothesized to possess wide solar system distribution, is shown to furnish the carbon and energy requirements of a wide variety of common soil bacteria which encompasses aerobic, anaerobic, and facultatively anaerobic bacteria. Some of these bacteria are able to derive not merely their carbon but also their nitrogen requirements from tholin. The palatability of tholins to modern microbes is speculated to have implications for the early evolution of microbial life on earth; tholins may have formed the base of the food chain for an early heterotrophic biosphere, prior to the evolution of autotrophy on the early earth.

Hydrogen Fluxes from Photosynthetic Communities: Implications for Early Earth Biogeochemistry

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Bebout, Brad M.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

More than half the history of life on Earth was dominated by photosynthetic microbial mats, which must have represented the preeminent biological influence on global geochemical cycling during that time. In modem analogs of then ancient communities, hypersaline microbial mats from Guerrero Negro, Mexico, we have observed a large flux of molecular hydrogen originating in the cyanobacteria-dominated surface layers. Hydrogen production follows a distinct diel pattern and is sensitive to both oxygen tension and microbial species composition within the mat. On an early Earth dominated by microbial mats, the observed H2 fluxes would scale to global levels far in excess of geothermal emissions. A hydrogen flux of this magnitude represents a profound transmission of reducing power from oxygenic photosynthesis, both to the anaerobic biosphere, where H2 is an almost universally-utilized substrate and regulator of microbial redox chemistry, and to the atmosphere, where subsequent escape to space could provide an important mechanism for the net oxidation of Earth's surface.

Anaerobic psychrophiles from Alaska, Antarctica, and Patagonia: implications to possible life on Mars and Europa

NASA Astrophysics Data System (ADS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph D.

2002-02-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryopreserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 degree(s)C. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep-sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep-sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph

2002-01-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryopreserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 C. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep-sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep-sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph; Six, N. Frank (Technical Monitor)

2001-01-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryo-preserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 T. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Protecting and Expanding the Richness and Diversity of Life, An Ethic for Astrobiology Research and Space Exploration

NASA Technical Reports Server (NTRS)

Randolph, Richard O.; McKay, Chris P.

2011-01-01

The ongoing search for life on other worlds and the prospects of eventual human exploration of the Moon and Mars indicate the need for new ethical guidelines to direct our actions as we search and how we respond if we discover microbial life on other worlds. Here we review how life on other worlds presents a novel question in environmental ethics. We propose a principle of protecting and expanding the richness and diversity of life as the basis of an ethic for astrobiology research and space exploration. There are immediate implications for the operational policies governing how we conduct the search for life on Mars and how we plan for human exploration throughout the Solar System.

Protecting and expanding the richness and diversity of life, an ethic for astrobiology research and space exploration

NASA Astrophysics Data System (ADS)

Randolph, Richard O.; McKay, Christopher P.

2014-01-01

The ongoing search for life on other worlds and the prospects of eventual human exploration of the Moon and Mars indicate the need for new ethical guidelines to direct our actions as we search and how we respond if we discover microbial life on other worlds. Here we review how life on other worlds presents a novel question in environmental ethics. We propose a principle of protecting and expanding the richness and diversity of life as the basis of an ethic for astrobiology research and space exploration. There are immediate implications for the operational policies governing how we conduct the search for life on Mars and how we plan for human exploration throughout the Solar System.

Transitory microbial habitat in the hyperarid Atacama Desert

PubMed Central

Schulze-Makuch, Dirk; Wagner, Dirk; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-01-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity. PMID:29483268

Transitory microbial habitat in the hyperarid Atacama Desert.

PubMed

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P; Mangelsdorf, Kai; Devine, Kevin G; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F; Arens, Felix L; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P; Meckenstock, Rainer U; Montgomery, Wren; Oberlin, Elizabeth A; Probst, Alexander J; Sáenz, Johan S; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-13

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: ( i ) a physico-chemical characterization of the soil habitability after an exceptional rain event, ( ii ) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], ( iii ) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and ( iv ) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity. Copyright © 2018 the Author(s). Published by PNAS.

Transitory microbial habitat in the hyperarid Atacama Desert

NASA Astrophysics Data System (ADS)

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P.; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Solís Cornejo, Francisco; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Siliceous Shrubs in Yellowstone's Hot Springs: Implications for Exobiological Investigations

NASA Technical Reports Server (NTRS)

Guidry, S. A.; Chafetz, H. S.

2003-01-01

Potential relict hot springs have been identified on Mars and, using the Earth as an analog, Martian hot springs are postulated to be an optimal locality for recognizing preserved evidence of extraterrestrial life. Distinctive organic and inorganic biomarkers are necessary to recognize preserved evidence of life in terrestrial and extraterrestrial hot spring accumulations. Hot springs in Yellowstone National Park, Wyoming, U.S.A., contain a wealth of information about primitive microbial life and associated biosignatures that may be useful for future exobiological investigations. Numerous siliceous hot springs in Yellowstone contain abundant, centimeter-scale, spinose precipitates of opaline silica (opal-A). Although areally extensive in siliceous hot spring discharge channel facies, these spinose forms have largely escaped attention. These precipitates referred to as shrubs, consist of porous aggregates of spinose opaline silica that superficially resemble miniature woody plants, i.e., the term shrubs. Shrubs in carbonate precipitating systems have received considerable attention, and represent naturally occurring biotically induced precipitates. As such, shrubs have great potential as hot spring environmental indicators and, more importantly, proxies for pre-existing microbial life.

Subseafloor fluid mixing and fossilized microbial life in a Cretaceous 'Lost City'-type hydrothermal system at the Iberian Margin

NASA Astrophysics Data System (ADS)

Klein, F.; Humphris, S. E.; Guo, W.; Schubotz, F.; Schwarzenbach, E. M.; Orsi, W.

2015-12-01

Subseafloor mixing of reduced hydrothermal fluids with seawater is believed to provide the energy and substrates needed to support autotrophic microorganisms in the hydrated oceanic mantle (serpentinite). Despite the potentially significant implications for the distribution of microbial life on Earth and other water-bearing planetary bodies, our understanding of such environments remains elusive. In the present study we examined fossilized microbial communities and fluid mixing processes in the subseafloor of a Cretaceous 'Lost City'-type hydrothermal system at the passive Iberia Margin (ODP Leg 149, Hole 897D). Brucite and calcite co-precipitated from mixed fluids ca. 65m below the Cretaceous palaeo-seafloor at temperatures of 32±4°C within steep chemical gradients (fO2, pH, CH4, SO4, ΣCO2, etc) between weathered, carbonate-rich serpentinite breccia and serpentinite. Mixing of oxidized seawater and strongly reducing hydrothermal fluid at moderate temperatures created conditions capable of supporting microbial activity within the oceanic basement. Dense microbial colonies are fossilized in brucite-calcite veins that are strongly enriched in organic carbon but depleted in 13C. We detected a combination of bacterial diether lipid biomarkers, archaeol and archaeal tetraethers analogous to those found in brucite-carbonate chimneys at the active Lost City hydrothermal field. The exposure of mantle rocks to seawater during the breakup of Pangaea fueled chemolithoautotrophic microbial communities at the Iberia Margin during the Cretaceous, possibly before the onset of seafloor spreading in the Atlantic. 'Lost City'-type serpentinization systems have been discovered at mid-ocean ridges, in forearc settings of subduction zones and at continental margins. It appears that, wherever they occur, they can support microbial life, even in deep subseafloor environments as demonstrated in the present study. Because equivalent systems have likely existed throughout most of Earth's history, fluid mixing may have provided the substrates and energy to support a unique subseafloor community of microorganisms over geological timescales.

Subseafloor fluid mixing and fossilized microbial life in a Cretaceous 'Lost City'-type hydrothermal system at the Iberian Margin

NASA Astrophysics Data System (ADS)

Klein, F.; Humphris, S. E.; Guo, W.; Schubotz, F.; Schwarzenbach, E. M.; Orsi, W.

2014-12-01

Subseafloor mixing of reduced hydrothermal fluids with seawater is believed to provide the energy and substrates needed to support autotrophic microorganisms in the hydrated oceanic mantle (serpentinite). Despite the potentially significant implications for the distribution of microbial life on Earth and other water-bearing planetary bodies, our understanding of such environments remains elusive. In the present study we examined fossilized microbial communities and fluid mixing processes in the subseafloor of a Cretaceous 'Lost City'-type hydrothermal system at the passive Iberia Margin (ODP Leg 149, Hole 897D). Brucite and calcite co-precipitated from mixed fluids ca. 65m below the Cretaceous palaeo-seafloor at temperatures of 32±4°C within steep chemical gradients (fO2, pH, CH4, SO4, ΣCO2, etc) between weathered, carbonate-rich serpentinite breccia and serpentinite. Mixing of oxidized seawater and strongly reducing hydrothermal fluid at moderate temperatures created conditions capable of supporting microbial activity within the oceanic basement. Dense microbial colonies are fossilized in brucite-calcite veins that are strongly enriched in organic carbon but depleted in 13C. We detected a combination of bacterial diether lipid biomarkers, archaeol and archaeal tetraethers analogous to those found in brucite-carbonate chimneys at the active Lost City hydrothermal field. The exposure of mantle rocks to seawater during the breakup of Pangaea fueled chemolithoautotrophic microbial communities at the Iberia Margin during the Cretaceous, possibly before the onset of seafloor spreading in the Atlantic. 'Lost City'-type serpentinization systems have been discovered at mid-ocean ridges, in forearc settings of subduction zones and at continental margins. It appears that, wherever they occur, they can support microbial life, even in deep subseafloor environments as demonstrated in the present study. Because equivalent systems have likely existed throughout most of Earth's history, fluid mixing may have provided the substrates and energy to support a unique subseafloor community of microorganisms over geological timescales.

Morphology and Viability of Pleistocene Microbiota from the CRREL Permafrost Tunnel Near Fox, Alaska

NASA Technical Reports Server (NTRS)

Hoover, Richard B.

2000-01-01

The U. S. Army Cold Regions Research and Engineering Laboratory maintains the CRREL Permafrost Tunnel at Fox, Alaska (-10 miles north of Fairbanks.) The active microbial ecosystems and the cryopreserved anabiotic viable microorganisms and dead microbial remains and biomarkers frozen within the permafrost and ice of the CRREL Permafrost Tunnel are of direct relevance to Astrobiology. Microbial extremophiles from permafrost and ice provide information concerning where and how should we search for evidence of life elsewhere in the Cosmos. The permafrost and ice wedges of the Fox tunnel preserves a magnificent of record of Pliocene, Pleistocene and Holocene life on Earth spanning more than 2.5 million years. This record includes frozen fossil bacteria, archaea, algae, mosses, higher plants, insects and mammals. In this paper we present the preliminary results of studies of the morphology, ultramicrostructure and elemental distributions of Fox tunnel microbiota as determined in-situ by the Environmental Scanning Electron Microscope (ESEM) and the Field Emission Scanning Electron Microscope (FESEM) investigations. The long-term viability of cryopreserved microbiota and potential implications to Astrobiology will be discussed.

Cryptic oxygen oases: Hypolithic photosynthesis in hydrothermal areas and implications for Archean surface oxidation

NASA Astrophysics Data System (ADS)

Havig, J. R.; Hamilton, T. L.

2017-12-01

Mounting geochemical evidence suggests microorganisms capable of oxygenic photosynthesis (e.g., Cyanobacteria) colonized Archean continental surfaces, driving oxidative weathering of detrital pyrites prior to the 2.5 Ga great oxidation event. Modern terrestrial environments dominated by single-celled phototrophs include hydrothermal systems (e.g., Yellowstone National Park) and hypolithic communities found in arid to hyper-arid deserts (e.g., McMurdo Dry Valleys of Antarctica, Atacama Desert of Chile). Recent work indicates terrestrial hydrothermal systems date back at least as far as 3.5 Ga. Here, we explore phototrophic communities in both hypolithic (sub-sinter) and hydrothermal (subaqueous and subaerial) environments in Yellowstone National Park as potential analogs to Archean continental surfaces. Hydrothermal sub-sinter environments provide ideal conditions for phototrophic microbial communities, including blocking of harmful UV radiation, trapping and retention of moisture, and protection from erosion by rain and surface runoff. Hypolithic communities in geothermal settings were similar in both composition and carbon uptake rates to nearby hot spring communities. We hypothesize that hydrothermal area hypolithic communities represent modern analogs of phototrophic microbial communities that colonized Archean continental surfaces, producing oxygen locally and facilitating microbially-mediated pyrite oxidation prior to the presence of free oxygen in the global atmosphere. These results have implications for oxidation of the early Earth surface, the search for biosignatures in the rock record, as well as for potential harbors of past life on Mars and the search for life on Exoplanets.

Detection of microbes in the subsurface

NASA Technical Reports Server (NTRS)

White, David C.; Tunlid, Anders

1989-01-01

The search for evidence of microbial life in the deep subsurface of Earth has implications for the Mars Rover Sampling Return Missions program. If suitably protected environments can be found on Mars then the instrumentation to detect biomarkers could be used to examine the molecular details. Finding a lipid in Martian soil would represent possibly the simplest test for extant or extinct life. A device that could do a rapid extraction possibly using the supercritical fluid technology under development now with a detection of the carbon content would clearly indicate a sample to be returned.

Microbial Contamination of Allende and Murchison Carbonaceous Chondrites; Developing a Protocol for Life Detection in Extraterrestrial Materials Using Biotechnology

NASA Technical Reports Server (NTRS)

Steele, A.; Whitby, C.; Griffin, C.; Toporski, J. K. W.; Westall, F.; Saunders, J. R.; McKay, D. S.

2001-01-01

The arguments used to refute the McKay et al., (1996) hypothesis of possible Martian life in ALH84001 failed to use contamination of the meteorite as a source. This has worrying implications for our ability to detect terrestrial microbiota in meteorites and therefore any potential extraterrestrial biosignatures in both meteorites and possible returned samples. We report on imaging and microbial culturing of both Allende and Murchison carbonaceous chondrites and on the use of molecular biology techniques on a sample of Allende. Contaminating fungi and bacteria were observed (in the case of Murchison) and cultured from both meteorites. DNA was successfully extracted and subsequent PCR showed the presence of both bacterial and fungal DNA although no Archaea were detected. These results show that it is possible to use molecular biological techniques on very small quantities (300 mg) of extraterrestrial material.

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

C. Doc Richardson; Nancy W. Hinman; Jill R. Scott

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compoundsmore » associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.« less

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

NASA Astrophysics Data System (ADS)

Richardson, C. Doc; Hinman, Nancy W.; Scott, Jill R.

2013-10-01

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compounds associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.

Acquisition and maturation of oral microbiome throughout childhood: An update

PubMed Central

Sampaio-Maia, Benedita; Monteiro-Silva, Filipa

2014-01-01

Traditional microbiology concepts are being renewed since the development of new microbiological technologies, such as, sequencing and large-scale genome analysis. Since the entry into the new millennium, a lot of new information has emerged regarding the oral microbiome. This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. Throughout childhood, the oral microbial load increases, but the microbial diversity decreases. The initial colonizers are related to the type of delivery, personal relationships, and living environment. These first colonizers seem to condition the subsequent colonization, which will lead to more complex and stable ecosystems in adulthood. These early oral microbial communities, therefore, play a major role in the development of the adult oral microbiota and may represent a source of both pathogenic and protective microorganisms in a very early stage of human life. The implications of this knowledge on the daily clinical practice of odontopediatrics are highlighted. PMID:25097637

Living together in biofilms: the microbial cell factory and its biotechnological implications.

PubMed

Berlanga, Mercedes; Guerrero, Ricardo

2016-10-01

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

Shallow transient liquid water environments on present-day mars, and their implications for life

NASA Astrophysics Data System (ADS)

Jones, Eriita G.

2018-05-01

The identification and characterisation of subsurface liquid water environments on Mars are of high scientific interest. Such environments have the potential to support microbial life, and, more broadly, to develop our understanding of the habitability of planets and moons beyond Earth. Given our current state of knowledge of life on Earth, three pre-requisites are necessary for an environment to be considered 'habitable' and therefore capable of supporting terrestrial-like life: energy, biogenic elements, and liquid water with a sufficiently high water activity. The surface of Mars today is predominately cold and dry, and any liquid water exposed to the atmosphere will vaporise or freeze on timescales of hours to days. These conditions have likely persisted for much of the last 10 million years, and perhaps longer. Despite this, briny liquid water flows (Recurrent Slope Linea) have been observed in a number of locations in the present-day. This review examines evidence from the Phoenix Lander (2008) and the Mars Science Laboratory (2012-current), to assess the occurrence of habitable conditions in the shallow Martian regolith. It will be argued that shallow, transient, liquid water brines are potentially habitable by microbial life, are likely a widespread occurrence on Mars, and that future exploration aimed at finding present-day habitable conditions and potential biology should 'follow the salt'.

Venus, Mars, and the ices on Mercury and the moon: astrobiological implications and proposed mission designs.

PubMed

Schulze-Makuch, Dirk; Dohm, James M; Fairén, Alberto G; Baker, Victor R; Fink, Wolfgang; Strom, Robert G

2005-12-01

Venus and Mars likely had liquid water bodies on their surface early in the Solar System history. The surfaces of Venus and Mars are presently not a suitable habitat for life, but reservoirs of liquid water remain in the atmosphere of Venus and the subsurface of Mars, and with it also the possibility of microbial life. Microbial organisms may have adapted to live in these ecological niches by the evolutionary force of directional selection. Missions to our neighboring planets should therefore be planned to explore these potentially life-containing refuges and return samples for analysis. Sample return missions should also include ice samples from Mercury and the Moon, which may contain information about the biogenic material that catalyzed the early evolution of life on Earth (or elsewhere). To obtain such information, science-driven exploration is necessary through varying degrees of mission operation autonomy. A hierarchical mission design is envisioned that includes spaceborne (orbital), atmosphere (airborne), surface (mobile such as rover and stationary such as lander or sensor), and subsurface (e.g., ground-penetrating radar, drilling, etc.) agents working in concert to allow for sufficient mission safety and redundancy, to perform extensive and challenging reconnaissance, and to lead to a thorough search for evidence of life and habitability.

Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life.

PubMed

Stevenson, Andrew; Burkhardt, Jürgen; Cockell, Charles S; Cray, Jonathan A; Dijksterhuis, Jan; Fox-Powell, Mark; Kee, Terence P; Kminek, Gerhard; McGenity, Terry J; Timmis, Kenneth N; Timson, David J; Voytek, Mary A; Westall, Frances; Yakimov, Michail M; Hallsworth, John E

2015-02-01

Since a key requirement of known life forms is available water (water activity; aw ), recent searches for signatures of past life in terrestrial and extraterrestrial environments have targeted places known to have contained significant quantities of biologically available water. However, early life on Earth inhabited high-salt environments, suggesting an ability to withstand low water-activity. The lower limit of water activity that enables cell division appears to be ∼ 0.605 which, until now, was only known to be exhibited by a single eukaryote, the sugar-tolerant, fungal xerophile Xeromyces bisporus. The first forms of life on Earth were, though, prokaryotic. Recent evidence now indicates that some halophilic Archaea and Bacteria have water-activity limits more or less equal to those of X. bisporus. We discuss water activity in relation to the limits of Earth's present-day biosphere; the possibility of microbial multiplication by utilizing water from thin, aqueous films or non-liquid sources; whether prokaryotes were the first organisms able to multiply close to the 0.605-aw limit; and whether extraterrestrial aqueous milieux of ≥ 0.605 aw can resemble fertile microbial habitats found on Earth. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

A Comparison of Microbial Communities from Deep Igneous Crust

NASA Astrophysics Data System (ADS)

Smith, A. R.; Flores, G. E.; Fisk, M. R.; Colwell, F. S.; Thurber, A. R.; Mason, O. U.; Popa, R.

2013-12-01

Recent investigations of life in Earth's crust have revealed common themes in organism function, taxonomy, and diversity. Capacities for hydrogen oxidation, carbon fixation, methanogenesis and methanotrophy, iron and sulfur metabolisms, and hydrocarbon degradation often predominate in deep life communities, and crustal mineralogy has been hypothesized as a driving force for determining deep life community assemblages. Recently, we found that minerals characteristic of the igneous crust harbored unique communities when incubated in the Juan de Fuca Ridge flank borehole IODP 1301A. Here we present attached mineral biofilm morphologies and a comparison of our mineral communities to those from a variety of locations, contamination states, and igneous crustal or mineralogical types. We found that differences in borehole mineral communities were reflected in biofilm morphologies. Olivine biofilms were thick, carbon-rich films with embedded cells of uniform size and shape and often contained secondary minerals. Encrusted cells, spherical and rod-shaped cells, and tubes were indicative of glass surfaces. We also found that the attached communities from incubated borehole minerals were taxonomically more similar to native, attached communities from marine and continental crust than to communities from the aquifer water that seeded it. Our findings further support the hypothesis that mineralogy selects for microbial communities that have distinct phylogenetic, morphological, and potentially functional, signatures. This has important implications for resolving ecosystem function and microbial distributions in igneous crust, the largest deep habitat on Earth.

Geobiology: A Conceptual Framework for Understanding Earth's Surface

NASA Astrophysics Data System (ADS)

Sumner, D. Y.

2016-12-01

A topic of study becomes a new field when it provides a useful conceptual framework for understanding suites of important processes. Geobiology integrates microbial biology with Earth sciences in a way that allows us to ask - and answer - deeper questions about Earth and the life on it. Recent studies of the oxidation of Earth's surface exemplify the impact of Geobiology as a new field. For decades, scientists have understood that Earth's surface was oxidized by photosynthesis. Geochemical records indicate dramatic redox changes both globally, e.g. the loss of MIF sulfur signatures due to formation of an ozone layer, and locally, as preserved in sedimentary rocks. However, these records depend critically on the dynamics of both the global biosphere and local microbial ecology. For example, an increase in global redox due to photosynthetic iron oxidation has different biogeochemical implications than an increase from oxygenic photosynthesis; O2 reacts very differently with organic matter and minerals than iron oxyhydroxides do, influencing microbial ecology as well as potential geochemical signatures in sedimentary rocks. Thus, studies of modern microbial communities provide insights into the interactions among metabolisms and geochemical gradients that have shaped Earth's redox history. For example, the ability of cyanobacteria to create O2 oases in benthic mats and soils on land provides a new framework for evaluating redox-sensitive elemental fluxes to the ocean. Similarly, genomic studies of Cyanobacteria have revealed close relatives, Melainabacteria, that are mostly obligate anaerobes. The evolutionary relationships between these two groups, as preserved in their genomes, reflect important microbial processes that led to oxidation of Earth's surface. By combining insights from microbial biology and sedimentary geochemistry, geobiologists will develop significantly more accurate models of the interactions between life and Earth.

ILSI Southeast Asia Region conference proceedings: The gut, its microbes and health: relevance for Asia.

PubMed

Lee, Yuan Kun; Conway, Patricia; Pettersson, Sven; Nair, G Balakrish; Surono, Ingrid; Egayanti, Yusra; Amarra, Maria Sofia

2017-01-01

The human being is a complex entity, involving interaction between microbes and the human host. Evidence shows that the nutritional value of food is influenced in part by the structure and operations of an individual's gut microbial community, and food in turn shapes the individual's microbiome. A conference was held to promote understanding of the intestinal microbiome and its implications for health and disease, particularly among Asian populations. Papers describing 1) the intestinal ecosystem in Asian populations, 2) changes in intestinal microbiota through life and its effects, 3) the Asian gut microbiota in disease conditions, 4) indigenous probiotics to maintain a healthy gut microbiota, 5) probiotic regulation in an Asian country, and 6) the results of a panel discussion are included in this report. The gut microbial inhabitants of Asian people differ from those of Europe and North America. Geographic location, diet, and ethnic background influence intestinal microbial composition. Urbanization and economic development have brought changes in traditional Asian diets, which in turn affected the gut microbiome, contributing to a shift in the region's health burden from infectious diseases to non-communicable chronic diseases. Novel probiotic strains of Indonesian origin demonstrated significant enhancement of humoral immune response in human studies. Knowledge gaps and implications for research to further understand the Asian gut microbiome were discussed.

Extremely halophilic archaea and the issue of long-term microbial survival

PubMed Central

2011-01-01

Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, the Dead Sea, alkaline salt lakes and marine solar salterns; they have also been isolated from rock salt of great geological age (195–250 million years). An overview of their taxonomy, including novel isolates from rock salt, is presented here; in addition, some of their unique characteristics and physiological adaptations to environments of low water activity are reviewed. The issue of extreme long-term microbial survival is considered and its implications for the search for extraterrestrial life. The development of detection methods for subterranean haloarchaea, which might also be applicable to samples from future missions to space, is presented. PMID:21984879

Exploration of a Subsurface Biosphere in a Volcanic Massive Sulfide: Results of the Mars Analog Rio Tinto Drilling Experiment

NASA Astrophysics Data System (ADS)

Stoker, C. R.; Stevens, T.; Amils, R.; Fernandez, D.

2005-12-01

Biological systems on Earth require three key ingredients-- liquid water, an energy source, and a carbon source, that are found in very few extraterrestrial environments. Previous examples of independent subsurface ecosystems have been found only in basalt aquifers. Such lithotrophic microbial ecosystems (LME) have been proposed as models for steps in the early evolution of Earth's biosphere and for potential biospheres on other planets where the surface is uninhabitable, such as Mars and Europa.. The Mars Analog Rio Tinto Experiment (MARTE) has searched in a volcanic massive sulfide deposit in Rio Tinto Spain for a subsurface biosphere capable of living without sunlight or oxygen and found a subsurface ecosystem driven by the weathering of the massive sulfide deposit (VMS) in which the rock matrix provides sufficient resources to support microbial metabolism, including the vigorous production of H2 by water-rock interactions. Microbial production of methane and sulfate occurred in the sulfide orebody and microbial production of methane and hydrogen sulfide continued in an anoxic plume downgradient from the sulfide ore. Organic carbon concentrations in the parent rock were too low to support microbes. The Rio Tinto system thus represents a new type of subsurface ecosystem with strong relevance for exobiological studies. Commercial drilling was used to reach the aquifer system at 100 m depth and conventional laboratory techniques were used to identify and characterize the biosphere. Then, the life search strategy that led to successful identification of this biosphere was applied to the development of a robotic drilling, core handling, inspection, subsampling, and life detection system built on a prototype planetary lander that was deployed in Rio Tinto Spain in September 2005 to test the capability of a robotic drilling system to search for subsurface life. A remote science team directed the simulation and analyzed the data from the MARTE robotic drill. The results of this experiment have important implications for the strategy for searching for life on Mars.

Pathways for abiotic organic synthesis at submarine hydrothermal fields.

PubMed

McDermott, Jill M; Seewald, Jeffrey S; German, Christopher R; Sylva, Sean P

2015-06-23

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond.

Pathways for abiotic organic synthesis at submarine hydrothermal fields

PubMed Central

McDermott, Jill M.; Seewald, Jeffrey S.; German, Christopher R.; Sylva, Sean P.

2015-01-01

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond. PMID:26056279

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

PubMed Central

Xiong, Weili; Olm, Matthew R.; Thomas, Brian C.; Baker, Robyn; Firek, Brian; Morowitz, Michael J.; Hettich, Robert L.

2018-01-01

ABSTRACT During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context. PMID:29636439

Ignimbrite as a substrate for endolithic life in the hyper-arid Atacama Desert: Implications for the search for life on Mars

NASA Astrophysics Data System (ADS)

Wierzchos, Jacek; Davila, Alfonso F.; Artieda, Octavio; Cámara-Gallego, Beatriz; de los Ríos, Asunción; Nealson, Kenneth H.; Valea, Sergio; Teresa García-González, M.; Ascaso, Carmen

2013-06-01

The hyper-arid core of the Atacama Desert in Chile is considered the driest and most life-limited place on Earth, with few habitats capable of sustaining an active microbial ecosystem. As such, it is one of the best terrestrial analogues of the extreme arid conditions on Mars, and an ideal environment to explore survival and biological adaptation strategies as the environment becomes increasingly dry. Here we show that weakly welded rhyolitic ignimbrites in this desert are abundantly colonized by endolithic cyanobacteria and associated heterotrophic bacteria. We propose that the porous ignimbrite interior provides protection from damaging UV radiation and excessive levels of visible light. Rock porosity also favors cell hydration through water retention after scarce rainfall events, even when the surrounding environment remains stubbornly dry. This is the first known example of an endolithic microbial community colonizing ignimbrite rocks in an extremely dry environment. The existence of a habitat capable of supporting abundant phototrophic and heterotrophic communities in an environment that precludes most life forms suggests that, if similar deposits are found on Mars, these should be considered important targets in the search for life. Indeed, ignimbrite rocks have been tentatively identified in Gale Crater, the landing site of the Mars Science Laboratory (MSL) mission and could be directly analyzed by its rover Curiosity.

Methane origin in the Samail ophiolite: Comment on "Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability" [Geochim. Cosmochim. Acta 179 (2016) 217-241

NASA Astrophysics Data System (ADS)

Etiope, Giuseppe

2017-01-01

Miller et al. (2016) report a new study of fluids in the peridotites of the Samail ophiolite in Oman related to modern serpentinization (olivine hydration), a process that can provide energy and raw materials for chemosynthetic microbial life. The authors, in particular, report an isotopic composition for methane (CH4) in groundwater near Ibra (up to 1.4 mM) that is unusually 13C-enriched (δ13CCH4 ∼ +2.4 and +3‰ VPDB), and consider the gas origin to be uncertain, i.e., abiotic or microbial, and to be modulated by significant fractionation due to oxidation or diffusion. The purpose of this comment is to clarify and correct a few points concerning the possible origin of the δ13CCH4 values, with the intention to promote a fruitful and constructive debate, considering the interest that there is for serpentinization and the associated formation of various gases.

The Infant Microbiome: Implications for Infant Health and Neurocognitive Development

PubMed Central

Yang, Irene; Corwin, Elizabeth J.; Brennan, Patricia A.; Jordan, Sheila; Murphy, Jordan R.; Dunlop, Anne

2015-01-01

Background Beginning at birth, the microbes in the gut perform essential duties related to the digestion and metabolism of food, the development and activation of the immune system, and the production of neurotransmitters that affect behavior and cognitive function. Objectives The objectives of this review are to: (a) provide a brief overview of the microbiome and the “microbiome-gut-brain axis”; (b) discuss factors known to affect the composition of the infant microbiome: mode of delivery, antibiotic exposure, and infant feeding patterns; and (c) present research priorities for nursing science, and clinical implications for infant health and neurocognitive development. Discussion The gut microbiome influences immunological, endocrine, and neural pathways and plays an important role in infant development. Several factors influence colonization of the infant gut microbiome. Different microbial colonization patterns are associated with vaginal versus surgical birth, exposure to antibiotics, and infant feeding patterns. Because of extensive physiological influence, infant microbial colonization patterns have the potential to impact physical and neurocognitive development and life course disease risk. Understanding these influences will inform newborn care and parental education. PMID:26657483

Microbial contributions to chronic inflammation and metabolic disease.

PubMed

Shanahan, Fergus; Sheehan, Donal

2016-07-01

It is long known that immune and metabolic cascades intersect at various cross-points. More recently, the regulatory influence of the microbiota on both of these cascades has emerged. Advances with therapeutic implications for chronic immunologic and metabolic disorders are examined. Disturbances of the microbiota, particularly in early life, may be the proximate environmental risk factor in socioeconomically developed societies for development of chronic immune-allergic and metabolic disorders, including obesity. Antibiotics and dietary factors contribute to this risk. Multiple microbial signalling molecules mediate host-microbe interactions including bacterial metabolites such as short-chain fatty acids, bile salts and others. New strategies for manipulating the composition and metabolic activity of the gut microbiota have emerged and offer a realistic prospect of personalized therapeutic options in immune and metabolic diseases.

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

PubMed

Wierzchos, Jacek; Sancho, Leopoldo García; Ascaso, Carmen

2005-04-01

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.

Potential for microbial oxidation of ferrous iron in basaltic glass.

PubMed

Xiong, Mai Yia; Shelobolina, Evgenya S; Roden, Eric E

2015-05-01

Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and utilization of dissolved Fe(II) as an energy source is not likely to take place.

Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars.

PubMed

Mickol, Rebecca L; Laird, Sarah K; Kral, Timothy A

2018-04-23

Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii , were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

Microfossils in the Antarctic cold desert: Possible implications for Mars

NASA Technical Reports Server (NTRS)

Friedmann, E. I.; Ocampo-Friedmann, R.

1986-01-01

In the Ross Desert of Antarctica, the principal life form is the cryptoendolithic microbial community in the near-surface layers of porous sandstone rocks. Biological, geological, and climatic factors interact in a complex and precarious balance, making life possible in an otherwise hostile environment. Once this balance is tipped, fossilization sets in. In the reverse case, new colonization of the rock surface may be initiated. As a result, fossilization is contemporary with modern life and both may be simultaneously present in a mosaic pattern. Also, different stages of fossilization are present. The process of fossilization takes place in a nonaquatic environment. If primitive life ever appeared on Mars, it is possible that with increasing aridity, life withdrew into an endolithic niche similar to that in the Antarctic desert. Fossilization in a nonaquatic environment may have set in with the result that traces of past life could be preserved. If such was the case, the study of the fossilization process in Antarctica may hold useful information for the analysis of Martian samples for microfossils.

Ionic Strength Is a Barrier to the Habitability of Mars.

PubMed

Fox-Powell, Mark G; Hallsworth, John E; Cousins, Claire R; Cockell, Charles S

2016-06-01

The thermodynamic availability of water (water activity) strictly limits microbial propagation on Earth, particularly in hypersaline environments. A considerable body of evidence indicates the existence of hypersaline surface waters throughout the history of Mars; therefore it is assumed that, as on Earth, water activity is a major limiting factor for martian habitability. However, the differing geological histories of Earth and Mars have driven variations in their respective aqueous geochemistry, with as-yet-unknown implications for habitability. Using a microbial community enrichment approach, we investigated microbial habitability for a suite of simulated martian brines. While the habitability of some martian brines was consistent with predictions made from water activity, others were uninhabitable even when the water activity was biologically permissive. We demonstrate experimentally that high ionic strength, driven to extremes on Mars by the ubiquitous occurrence of multivalent ions, renders these environments uninhabitable despite the presence of biologically available water. These findings show how the respective geological histories of Earth and Mars, which have produced differences in the planets' dominant water chemistries, have resulted in different physicochemical extremes which define the boundary space for microbial habitability. Habitability-Mars-Salts-Water activity-Life in extreme environments. Astrobiology 16, 427-442.

Microbial biofilm studies of the environmental control and life support system water recovery test for Space Station Freedom

NASA Technical Reports Server (NTRS)

Rodgers, E. B.; Obenhuber, D. C.; Huff, T. L.

1992-01-01

NASA is developing a water recovery system (WRS) for Space Station Freedom to reclaim human waste water for reuse by astronauts as hygiene or potable water. A water recovery test (WRT) currently in progress investigates the performance of a prototype of the WRS. Analysis of biofilm accumulation, the potential for microbially influenced corrosion (MIC) in the WRT, and studies of iodine disinfection of biofilm are reported. Analysis of WRT components indicated the presence of organic deposits and biofilms in selected tubing. Water samples for the WRT contained acid-producing and sulfate-reducing organisms implicated in corrosion processes. Corrosion of an aluminum alloy was accelerated in the presence of these water samples; however, stainless steel corrosion rates were not accelerated. Biofilm iodine sensitivity tests using an experimental laboratory scale recycled water system containing a microbial check valve (MCV) demonstrated that an iodine concentration of 1 to 2 mg/L was ineffective in eliminating microbial biofilm. For complete disinfection, an initial concentration of 16 mg/L was required, which was gradually reduced by the MCV over 4 to 8 hours to 1 to 2 mg/L. This treatment may be useful in controlling biofilm formation.

Genomic evidence for the Wood-Ljungdahl pathway for carbon fixation in warm basaltic ocean crust

NASA Astrophysics Data System (ADS)

Smith, A. R.; Fisk, M. R.; Mueller, R.; Colwell, F. S.; Mason, O. U.; Popa, R.

2016-12-01

Microbial life in the deep suboceanic aquifer can harness geochemical energy resulting from water-rock reactions and contribute to carbon cycling in the ocean via primary production, or chemosynthesis. Iron-bearing minerals such as olivine in oceanic crust can produce molecular hydrogen, small molecular weight hydrocarbons, and hydrogen sulfide as they react with seawater. Although this generally occurs in serpentinizing systems at very high temperatures deep in the subsurface, it has also been hypothesized to drive the subseafloor microbial ecosystems present in shallower basaltic aquifers. We present genome-based evidence for chemolithoautotrophic microbes present on the surface of olivine incubated in Juan de Fuca Ridge basaltic ocean crust for a 4-year period. These metagenome-derived genomes show dominant taxa capable of using both branches of the Wood-Ljungdahl pathway for carbon fixation and energy generation. This pathway uses molecular hydrogen potentially derived from the olivine surface as it reacts with seawater and CO2 which is inherent to seawater. These taxa were not reported from aquifer fluid samples, but have been found only in association with mineral surfaces in this study location. Most taxa in this simple community are distant relatives of cultured taxa; therefore this genome information is crucial to understanding how the subseafloor aquifer community is structured, how it obtains energy, how it cycles carbon, and gives us keys to help cultivate these organisms in the laboratory. Our findings also support the Subsurface Lithoautotrophic Microbial Ecosystem (SLiME) hypothesis and have implications for understanding life on early Earth and the potential for life in the Martian subsurface.

Perspective: researching the transition from non-living to the first microorganisms: methods and experiments are major challenges.

PubMed

Trevors, J T

2010-06-01

Methods to research the origin of microbial life are limited. However, microorganisms were the first organisms on the Earth capable of cell growth and division, and interactions with their environment, other microbial cells, and eventually with diverse eukaryotic organisms. The origin of microbial life and the supporting scientific evidence are both an enigma and a scientific priority. Numerous hypotheses have been proposed, scenarios imagined, speculations presented in papers, insights shared, and assumptions made without supporting experimentation, which have led to limited progress in understanding the origin of microbial life. The use of the human imagination to envision the origin of life events, without supporting experimentation, observation and independently replicated experiments required for science, is a significant constraint. The challenge remains how to better understand the origin of microbial life using observations and experimental methods as opposed to speculation, assumptions, scenarios, envisioning events and un-testable hypotheses. This is not an easy challenge as experimental design and plausible hypothesis testing are difficult. Since past approaches have been inconclusive in providing evidence for the origin of microbial life mechanisms and the manner in which genetic instructions was encoded into DNA/RNA, it is reasonable and logical to propose that progress will be made when testable, plausible hypotheses and methods are used in the origin of microbial life research, and the experimental observations are, or are not reproduced in independent laboratories. These perspectives will be discussed in this article as well as the possibility that a pre-biotic film preceded a microbial biofilm as a possible micro-location for the origin of microbial cells capable of growth and division. 2010 Elsevier B.V. All rights reserved.

A Microbial Oasis in the Hypersaline Atacama Subsurface Discovered by a Life Detector Chip: Implications for the Search for Life on Mars

PubMed Central

de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A.; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J.; Rivas, Luis A.; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N.; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-01-01

Abstract The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg−1) and perchlorate (41.13 μg g−1 maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g−1) or formate (76.06 μg g−1) as electron donors, and sulfate (15875 μg g−1), nitrate (13490 μg g−1), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars. Key Words: Atacama Desert—Life detection—Biosensor—Biopolymers—In situ measurement. Astrobiology 11, 969–996. PMID:22149750

Using Astrobiology case studies to bring science decision making into the classroom: Mars sample return, exobiology and SETI

NASA Astrophysics Data System (ADS)

Race, Margaret

As citizens and decision makers of the future, today's students need to understand the nature of science and the implications of scientific discoveries and activities in a broad societal context. Astrobiology provides an opportunity to introduce students to real world decision-making involving cutting edge, multidisciplinary research topics that involve Earth, the solar system and beyond. Although textbooks and curricular materials may take years to develop, teachers can easily bring the latest astrobiological discoveries and hypotheses into the classroom in the form of case studies to complement science classes. For example, using basic biological, geological and chemical information from Earth and other planets, students can discuss the same questions that experts consider when planning a Mars Sample Return mission. How would you recognize extraterrestrial life? What would be the impact of bringing martian life to Earth? How should martian samples be handled and tested to determine whether they pose hazards to Earth's biota and ecosystems? If truly martian life exists, what are the implications for future human missions or colonies on the planet? What are the ethical and societal implications of discovering extraterrestrial life, whether in the solar system or beyond? What difference world it make if the extraterrestrial life is microbial and simple vs. intelligent and advanced? By integrating basic science concepts, up-to-date research findings, and information about laws, societal concerns, and public decision making, students can experience first-hand the kind of questions and challenges we're likely to face in the years ahead.

Microbial Analysis of Australian Dry Lake Cores; Analogs For Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Nguyen, A. V.; Baldridge, A. M.; Thomson, B. J.

2014-12-01

Lake Gilmore in Western Australia is an acidic ephemeral lake that is analogous to Martian geochemical processes represented by interbedded phyllosilicates and sulfates. These areas demonstrate remnants of a global-scale change on Mars during the late Noachian era from a neutral to alkaline pH to relatively lower pH in the Hesperian era that continues to persist today. The geochemistry of these areas could possibly be caused by small-scale changes such as microbial metabolism. Two approaches were used to determine the presence of microbes in the Australian dry lake cores: DNA analysis and lipid analysis. Detecting DNA or lipids in the cores will provide evidence of living or deceased organisms since they provide distinct markers for life. Basic DNA analysis consists of extraction, amplification through PCR, plasmid cloning, and DNA sequencing. Once the sequence of unknown DNA is known, an online program, BLAST, will be used to identify the microbes for further analysis. The lipid analysis approach consists of phospholipid fatty acid analysis that is done by Microbial ID, which will provide direct identification any microbes from the presence of lipids. Identified microbes are then compared to mineralogy results from the x-ray diffraction of the core samples to determine if the types of metabolic reactions are consistent with the variation in composition in these analog deposits. If so, it provides intriguing implications for the presence of life in similar Martian deposits.

Microbial colonization of Ca-sulfate crusts in the hyperarid core of the Atacama Desert: implications for the search for life on Mars.

PubMed

Wierzchos, J; Cámara, B; de Los Ríos, A; Davila, A F; Sánchez Almazo, I M; Artieda, O; Wierzchos, K; Gómez-Silva, B; McKay, C; Ascaso, C

2011-01-01

The scarcity of liquid water in the hyperarid core of the Atacama Desert makes this region one of the most challenging environments for life on Earth. The low numbers of microbial cells in the soils suggest that within the Atacama Desert lies the dry limit for life on our planet. Here, we show that the Ca-sulfate crusts of this hyperarid core are the habitats of lithobiontic micro-organisms. This microporous, translucent substrate is colonized by epilithic lichens, as well as endolithic free-living algae, fungal hyphae, cyanobacteria and non photosynthetic bacteria. We also report a novel type of endolithic community, "hypoendoliths", colonizing the undermost layer of the crusts. The colonization of gypsum crusts within the hyperarid core appears to be controlled by the moisture regime. Our data shows that the threshold for colonization is crossed within the dry core, with abundant colonization in gypsum crusts at one study site, while crusts at a drier site are virtually devoid of life. We show that the cumulative time in 1 year of relative humidity (RH) above 60% is the best parameter to explain the difference in colonization between both sites. This is supported by controlled humidity experiments, where we show that colonies of endolithic cyanobacteria in the Ca-sulfate crust undergo imbibition process at RH >60%. Assuming that life once arose on Mars, it is conceivable that Martian micro-organisms sought refuge in similar isolated evaporite microenvironments during their last struggle for life as their planet turned arid. © 2010 Blackwell Publishing Ltd.

The composition of the gut microbiota throughout life, with an emphasis on early life

PubMed Central

Rodríguez, Juan Miguel; Murphy, Kiera; Stanton, Catherine; Ross, R. Paul; Kober, Olivia I.; Juge, Nathalie; Avershina, Ekaterina; Rudi, Knut; Narbad, Arjan; Jenmalm, Maria C.; Marchesi, Julian R.; Collado, Maria Carmen

2015-01-01

The intestinal microbiota has become a relevant aspect of human health. Microbial colonization runs in parallel with immune system maturation and plays a role in intestinal physiology and regulation. Increasing evidence on early microbial contact suggest that human intestinal microbiota is seeded before birth. Maternal microbiota forms the first microbial inoculum, and from birth, the microbial diversity increases and converges toward an adult-like microbiota by the end of the first 3–5 years of life. Perinatal factors such as mode of delivery, diet, genetics, and intestinal mucin glycosylation all contribute to influence microbial colonization. Once established, the composition of the gut microbiota is relatively stable throughout adult life, but can be altered as a result of bacterial infections, antibiotic treatment, lifestyle, surgical, and a long-term change in diet. Shifts in this complex microbial system have been reported to increase the risk of disease. Therefore, an adequate establishment of microbiota and its maintenance throughout life would reduce the risk of disease in early and late life. This review discusses recent studies on the early colonization and factors influencing this process which impact on health. PMID:25651996

The microbiome in early life: implications for health outcomes.

PubMed

Tamburini, Sabrina; Shen, Nan; Wu, Han Chih; Clemente, Jose C

2016-07-07

Recent studies have characterized how host genetics, prenatal environment and delivery mode can shape the newborn microbiome at birth. Following this, postnatal factors, such as antibiotic treatment, diet or environmental exposure, further modulate the development of the infant's microbiome and immune system, and exposure to a variety of microbial organisms during early life has long been hypothesized to exert a protective effect in the newborn. Furthermore, epidemiological studies have shown that factors that alter bacterial communities in infants during childhood increase the risk for several diseases, highlighting the importance of understanding early-life microbiome composition. In this review, we describe how prenatal and postnatal factors shape the development of both the microbiome and the immune system. We also discuss the prospects of microbiome-mediated therapeutics and the need for more effective approaches that can reconfigure bacterial communities from pathogenic to homeostatic configurations.

Long-Term Prophylactic Antibiotic Treatment: Effects on Survival, Immunocompetence and Reproduction Success of Parasemia plantaginis (Lepidoptera: Erebidae).

PubMed

Dickel, Franziska; Freitak, Dalial; Mappes, Johanna

2016-01-01

Hundreds of insect species are nowadays reared under laboratory conditions. Rearing of insects always implicates the risk of diseases, among which microbial infections are the most frequent and difficult problems. Although there are effective prophylactic treatments, the side effects of applied antibiotics are not well understood. We examined the effect of prophylactic antibiotic treatment on the overwintering success of wood tiger moth (Parasemia plantaginis) larvae, and the postdiapause effect on their life-history traits. Four weeks before hibernation larvae were treated with a widely used antibiotic (fumagillin). We monitored moths' survival and life-history traits during the following 10 mo, and compared them to those of untreated control larvae. Prophylactic antibiotic treatment had no effect on survival but we show effects on some life-history traits by decreasing the developmental time of treated larvae. However, we also revealed relevant negative effects, as antibiotic treated individuals show a decreased number of laid eggs and also furthermore a suppressed immunocompetence. These results implicate, that a prophylactic medication can also lead to negative effects on life-history traits and reproductive success, which should be seriously taken in consideration when applying a prophylactic treatment to laboratory reared insect populations. © The Author 2016. Published by Oxford University Press on behalf of the Entomological Society of America.

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Microbial Biogeochemistry of Seafloor Fluid Flow on Earth and Implications for Biological Potential on Enceladus

NASA Astrophysics Data System (ADS)

Huber, J. A.

2017-12-01

The interaction between liquid water and the rocky seafloor provides high potential for release of chemical energy, thus seafloor fluid flow is viewed an essential driver of subseafloor microbial life in Earth's oceans. Given predictions that Enceladus hosts a global-scale ocean underlain by a rocky seafloor, and new data suggesting on-going hydrothermal activity on Enceladus based on detection of hydrogen by Cassini, it is timely to investigate those subseafloor Earth analogs that may be informative when developing future missions to and interpreting mission data from Enceladus. Over the last 35 years, the breadth of seafloor fluid flow regimes that have been discovered and studied on Earth has expanded to include a wide spectrum of geological settings, geochemical characteristics, and microorganisms, including environments that were not previously known to exist, e.g. hydrogen-rich mafic systems, ridge-flank oxic systems, etc. This presentation will provide an overview of the latest and most exciting findings on the microbial biogeochemistry of seafloor fluid flow in Earth's oceans and place these findings in the context of biological potential for Enceladus.

Morphological biosignatures and the search for life on Mars.

PubMed

Cady, Sherry L; Farmer, Jack D; Grotzinger, John P; Schopf, J William; Steele, Andrew

2003-01-01

This report provides a rationale for the advances in instrumentation and understanding needed to assess claims of ancient and extraterrestrial life made on the basis of morphological biosignatures. Morphological biosignatures consist of bona fide microbial fossils as well as microbially influenced sedimentary structures. To be recognized as evidence of life, microbial fossils must contain chemical and structural attributes uniquely indicative of microbial cells or cellular or extracellular processes. When combined with various research strategies, high-resolution instruments can reveal such attributes and elucidate how morphological fossils form and become altered, thereby improving the ability to recognize them in the geological record on Earth or other planets. Also, before fossilized microbially influenced sedimentary structures can provide evidence of life, criteria to distinguish their biogenic from non-biogenic attributes must be established. This topic can be advanced by developing process-based models. A database of images and spectroscopic data that distinguish the suite of bona fide morphological biosignatures from their abiotic mimics will avoid detection of false-positives for life. The use of high-resolution imaging and spectroscopic instruments, in conjunction with an improved knowledge base of the attributes that demonstrate life, will maximize our ability to recognize and assess the biogenicity of extraterrestrial and ancient terrestrial life.

Life Support Systems Microbial Challenges

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.

2009-01-01

This viewgraph presentation reviews the current microbial challenges of environmental control and life support systems. The contents include: 1) Environmental Control and Life Support Systems (ECLSS) What is it?; 2) A Look Inside the International Space Station (ISS); 3) The Complexity of a Water Recycling System; 4) ISS Microbiology Acceptability Limits; 5) Overview of Current Microbial Challenges; 6) In a Perfect World What we Would like to Have; and 7) The Future.

Photosynthesis and early Earth.

PubMed

Shih, Patrick M

2015-10-05

Life has been built on the evolution and innovation of microbial metabolisms. Even with our scant understanding of the full diversity of microbial life, it is clear that microbes have become integral components of the biogeochemical cycles that drive our planet. The antiquity of life further suggests that various microbial metabolisms have been core and essential to global elemental cycling for a majority of Earth's history. Copyright © 2015 Elsevier Ltd. All rights reserved.

The moral status of extraterrestrial life.

PubMed

Persson, Erik

2012-10-01

If we eventually discover extraterrestrial life, do we have any moral obligations for how to treat the life-forms we find; does it matter whether they are intelligent, sentient, or just microbial-and does it matter that they are extraterrestrial? In this paper, I examine these questions by looking at two of the basic questions in moral philosophy: What does it take to be a moral object? and What has value of what kind? I will start with the first of these questions by looking at the most important attempts to answer this question on our own planet and by asking whether and how they could be applied to extraterrestrial life. The results range from a very strong protection of all extraterrestrial life and all extraterrestrial environments, whether inhabited or not, to total exclusion of extraterrestrial life. Subsequently, I also examine whether extraterrestrial life that lacks moral status can have value to human or alien life with moral status, and if that could generate any obligations for how to treat extraterrestrial life. Based on this analysis, I conclude that extraterrestrial life-forms can have both instrumental value and end value to moral objects, which has strong implications for how to treat them.

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.

PubMed

Brown, Christopher T; Sharon, Itai; Thomas, Brian C; Castelle, Cindy J; Morowitz, Michael J; Banfield, Jillian F

2013-12-17

The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored. To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences related to respiratory metabolism and motility. Genome-based analysis provided direct insight into strain-specific potential for anaerobic respiration and yielded the first genome for the genus Varibaculum. Importantly, comparison of these de novo assembled genomes with closely related isolate genomes supported the accuracy of the metagenomic methodology. Over a one-week period, the early gut microbial community transitioned to a community with a higher representation of obligate anaerobes, emphasizing both taxonomic and metabolic instability during colonization.

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

PubMed Central

2013-01-01

Background The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored. Results To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community. We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation. During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences related to respiratory metabolism and motility. Conclusions Genome-based analysis provided direct insight into strain-specific potential for anaerobic respiration and yielded the first genome for the genus Varibaculum. Importantly, comparison of these de novo assembled genomes with closely related isolate genomes supported the accuracy of the metagenomic methodology. Over a one-week period, the early gut microbial community transitioned to a community with a higher representation of obligate anaerobes, emphasizing both taxonomic and metabolic instability during colonization. PMID:24451181

Can nanotechnology deliver the promised benefits without negatively impacting soil microbial life?

PubMed

Dimkpa, Christian O

2014-09-01

Nanotechnology exploits the enhanced reactivity of materials at the atomic scale to improve various applications for humankind. In agriculture, potential nanotechnology applications include crop protection and fertilization. However, such benefits could come with risks for the environment: non-target plants, plant-beneficial soil microbes and other life forms could be impacted if nanoparticles (nanomaterials) contaminate the environment. This review evaluates the impact of the major metallic nanoparticles (Ag, ZnO, CuO, CeO2 , TiO2 , and FeO-based nanoparticles) on soil microbes involved in agricultural processes. The current literature indicate that in addition to population and organismal-scale effects on microbes, other subtle impacts of nanoparticles are seen in the nitrogen cycle, soil enzyme activities, and processes involved in iron metabolism, phytohormone, and antibiotic production. These effects are negative or positive, the outcome being dependent on specific nanoparticles. Collectively, published results suggest that nanotechnology portends considerable, many negative, implications for soil microbes and, thus, agricultural processes that are microbially driven. Nonetheless, the potential of plant and soil microbial processes to mitigate the bioreactivity of nanoparticles also are observed. Whereas the roots of most terrestrial plants are associated with microbes, studies of nanoparticle interactions with plants and microbes are generally conducted separately. The few studies in actual microbe-plant systems found effects of nanoparticles on the functioning of arbuscular mycorrhizal fungi, nitrogen fixation, as well as on the production of microbial siderophores in the plant rhizosphere. It is suggested that a better understanding of the agro-ecological ramifications of nanoparticles would require more in-depth interactive studies in combined plant-microbe-nanoparticle systems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigating Microbial Biofilm Formations on Crustal Rock Substrates

NASA Astrophysics Data System (ADS)

Weiser, M.; D'Angelo, T.; Carr, S. A.; Orcutt, B.

2017-12-01

Ocean crust hosts microbial life that, in some cases, alter the component rocks as a means of obtaining energy. Variations in crust lithology, included trace metal and mineral content, as well as the chemistry of the fluids circulating through them, provide substrates for some microbes to metabolize, leading to formation of biofilm community structures. Microbes have different parameters for the situations in which they will form biofilms, but they must have some source of energy in excess at the site of biofilm formation for them to become stationary and form the carbohydrate-rich structures connecting the cells to one another and the substrate. Generally, the requirements for microbes to form biofilms on crustal minerals are unclear. We designed two experiments to test (1) mineral preference and biofilm formation rates by natural seawater microbial communities, and (2) biofilm development as a function of phosphate availability for an organism isolated from subseafloor ocean crust. In Experiment 1, we observed that phyric basalt groundmass is preferentially colonized over aphyric basalt or metal sulfides in a shallow water and oxic seawater environment. In experiment 2, tests of the anaerobic heterotroph Thalassospira bacteria isolated from oceanic crustal fluids showed that they preferentially form biofilms, lose motility, and increase exponentially in number over time in higher-PO4 treatments (50 micromolar), including with phosphate-doped basalts, than in treatments with low phosphate concentrations (0.5 micromolar) often found in crustal fluids. These observations suggest phosphate as a main driver of biofilm formation in subsurface crust. Overall, these data suggest that the drivers of microbial biofilm formation on crustal substrates are selective to the substrate conditions, which has important implications for estimating the global biomass of life harbored in oceanic crust.

Novel approaches in function-driven single-cell genomics.

PubMed

Doud, Devin F R; Woyke, Tanja

2017-07-01

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision. © FEMS 2017.

The changing landscape of microbial biodiversity exploration and its implications for systematics.

PubMed

Hedlund, Brian P; Dodsworth, Jeremy A; Staley, James T

2015-06-01

A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life. Copyright © 2015 Elsevier GmbH. All rights reserved.

The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit.

PubMed

Kearns, Patrick J; Bowen, Jennifer L; Tlusty, Michael F

2017-05-01

Public aquaria offer numerous educational opportunities for visitors while touch-tank exhibits offer guests the ability to directly interact with marine life via physical contact. Despite the popularity of touch-tanks, there is a paucity of research about animal health in these exhibits and, in particular, there is little research on the microbial communities in these highly interactive exhibits. Microbial community structure can have implications for both host health and habitat function. To better understand the microbiome of a touch-tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as their environment in a frequently visited touch-tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (∼55%), Flavobacteriales (∼19%), and Pseudomonadales (∼12%), taxonomic groups commonly associated with other fish species. Our results provide a survey of ray-associated bacterial communities in a touch-tank environment, thereby laying the foundation for future studies examining the role of potential challenges to ray microbiota and their associated health. © 2017 Wiley Periodicals, Inc.

A microbial oasis in the hypersaline Atacama subsurface discovered by a life detector chip: implications for the search for life on Mars.

PubMed

Parro, Victor; de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J; Rivas, Luis A; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-12-01

The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg(-1)) and perchlorate (41.13 μg g(-1) maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g(-1)) or formate (76.06 μg g(-1)) as electron donors, and sulfate (15875 μg g(-1)), nitrate (13490 μg g(-1)), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars.

Community living long before man: fossil and living microbial mats and early life

NASA Technical Reports Server (NTRS)

Margulis, L.; Lopez Baluja, L.; Awramik, S. M.; Sagan, D.

1986-01-01

Microbial mats are layered communities of bacteria that form cohesive structures, some of which are preserved in sedimentary rocks as stromatolites. Certain rocks, approximately three and a half thousand million years old and representing the oldest known fossils, are interpreted to derive from microbial mats and to contain fossils of microorganisms. Modern microbial mats (such as the one described here from Matanzas, Cuba) and their fossil counterparts are of great interest in the interpretation of early life on Earth. Since examination of microbial mats and stromatolites increases our understanding of long-term stability and change, within the global environment, such structures should be protected wherever possible as natural science preserves. Furthermore, since they have existed virtually from the time of life's origin, microbial mats have developed exemplary mechanisms of local community persistence and may even play roles in the larger global environment that we do not understand.

Possibilities for the detection of microbial life on extrasolar planets.

PubMed

Knacke, Roger F

2003-01-01

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

PubMed

Trevors, J T

2011-03-01

Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

Microbial structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment

NASA Astrophysics Data System (ADS)

Dornmayr-Pfaffenhuemer, Marion; Pierson, Elisabeth; Janssen, Geert-Jan; Stan-Lotter, Helga

2010-05-01

The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their "extra-terrestrial" conditions such as darkness and mostly extreme physicochemical state they are also of astrobiological interest. The slightly radioactive thermal spring at Bad Gastein (Austria) was therefore examined for the occurrence of subsurface microbial communities. The surfaces of the submerged rocks in this warm spring were overgrown by microbial mats. Scanning electron microscopy (SEM) performed by the late Dr. Wolfgang Heinen revealed an interesting morphological diversity in biofilms found in this environment (1, 2). Molecular analysis of the community structure of the radioactive subsurface thermal spring was performed by Weidler et al. (3). The growth of these mats was simulated using sterile glass slides which were exposed to the water stream of the spring. Those mats were analysed microscopically. Staining, using fluorescent dyes such as 4',6-Diamidino-2-phenylindol (DAPI), gave an overview of the microbial diversity of these biofilms. Additional SEM samples were prepared using different fixation protocols. Scanning confocal laser microscopy (SCLM) allowed a three dimensional view of the analysed biofilms. This work presents some electron micrographs of Dr. Heinen and additionally new microscopic studies of the biofilms formed on the glass slides. The appearances of the new SEM micrographs were compared to those of Dr. Heinen that were done several years ago. The morphology and small-scale distribution in the microbial mat was analyzed by fluorescence microscopy. The examination of natural biomats and biofilms grown on glass slides using several microscopical techniques suggest that the thermal springs in the Central Alps near Bad Gastein represent a novel and unique habitat for microbial life. Results obtained during these studies revealed reproducibility of Dr. Heinen's micrographs. Hollow reticulated filaments and flat ribbons with parallel hexagonal chambers (web-structures) were found repeatedly. Given the chance that subsurface environments represent a potent opportunity to detect life on planetary bodies it is of big interest to search for representative biosignatures found on earth today. References: 1. Lauwers A. M. & Heinen W. (1985) Mikroskopie (Wien) 42, 94-101. 2. Heinen W. & Lauwers A. M. (1985) Mikroskopie (Wien) 42, 124-134. 3. Weidler G. W., Dornmayr-Pfaffenhuemer M., Gerbl F. W., Heinen W., Stan-Lotter H. (2007) AEM 73, 259-270.

The Impact of Population Bottlenecks on Microbial Adaptation

NASA Astrophysics Data System (ADS)

LeClair, Joshua S.; Wahl, Lindi M.

2018-07-01

Population bottlenecks—sudden, severe reductions in population size—are ubiquitous in nature. Because of their critical implications for conservation genetics, the effects of population bottlenecks on the loss of genetic diversity have been well studied. Bottlenecks also have important implications for adaptation, however, and these effects have been addressed more recently, typically in microbial populations. In this short review, we survey both experimental and theoretical work describing the impact of population bottlenecks on microbial adaptation. Focusing on theoretical contributions, we highlight emerging insights and conclude with several open questions of interest in the field.

Trace fossils of microbial colonization on Mars: Criteria for search and for sample return

NASA Technical Reports Server (NTRS)

Friedmann, E. I.

1988-01-01

The recent discovery of microbial trace-fossil formation in the frigid Ross Desert of Antarctica suggests that early primitive life on Mars may have left behind similar signatures. These trace fossils are apparent as chemical or physical changes in rock (or sediment) structure (or chemistry) caused by the activity of organisms. Life on Mars, if it ever existed, almost certainly did not evolve above the level of microorganisms, and this should be considered in search for fossil life. For the reasons detailed here, microbial trace fossils seem to be a better and more realistic target for search than would be true microbial fossils (remnants of cellular structures).

Mushroom speleothems: Stromatolites that formed in the absence of phototrophs

NASA Astrophysics Data System (ADS)

Bontognali, Tomaso; D'Angeli, Ilenia; Tisato, Nicola; Vasconcelos, Crisogono; Bernasconi, Stefano; Gonzales, Esteban; DeWaele, Jo

2016-04-01

Unusual speleothems resembling giant mushrooms occur in Santa Catalina Cave, Cuba. Although these mineral buildups are considered a natural heritage, their composition and formation mechanism remain poorly understood. Here we characterize their morphology and mineralogy and present a model for their genesis. We propose that the mushrooms, which are mainly comprised of calcite and aragonite, formed during four different phases within an evolving cave environment. The stipe of the mushroom is an assemblage of three well-known speleothems: a stalagmite surrounded by calcite rafts that were subsequently encrusted by cave clouds (mammilaries). More peculiar is the cap of the mushroom, which is morphologically similar to cerebroid stromatolites and thrombolites of microbial origin occurring in marine environments. Scanning electron microscopy investigations of this last unit revealed the presence of fossilized extracellular polymeric substances (EPS) - the constituents of biofilms and microbial mats. These organic microstructures are mineralized with Ca-carbonate, suggesting that the mushroom cap formed through a microbially-influenced mineralization process. The existence of cerebroid Ca-carbonate buildups forming in dark caves (i.e., in the absence of phototrophs) has interesting implications for the study of fossil microbialites preserved in ancient rocks, which are today considered as one of the earliest evidence for life on Earth.

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Treesearch

Jennifer M. Fraterrigo; Teri C. Balser; Monica g. Turner

2006-01-01

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid...

Endolithic microbial model for Martian exobiology: The road to extinction

NASA Technical Reports Server (NTRS)

Oscampo-Friedmann, R.; Friedmann, E. I.

1991-01-01

Martian exobiology is based on the assumption that on early Mars, liquid water was present and that conditions were suitable for the evolution of life. The cause for life to disappear from the surface and the recognizable fingerprints of past microbial activity preserved on Mars are addressed. The Antarctic cryptoendolithic microbial ecosystem as a model for extinction in the deteriorating Martian environment is discussed.

Purification, biochemical characterization, and implications of an alkali-tolerant catalase from the spacecraft-associated and oxidation-resistant Acinetobacter gyllenbergii 2P01AA.

PubMed

Muster, N; Derecho, I; Dallal, F; Alvarez, R; McCoy, K B; Mogul, R

2015-04-01

Herein, we report on the purification, characterization, and sequencing of catalase from Acinetobacter gyllenbergii 2P01AA, an extremely oxidation-resistant bacterium that was isolated from the Mars Phoenix spacecraft assembly facility. The Acinetobacter are dominant members of the microbial communities that inhabit spacecraft assembly facilities and consequently may serve as forward contaminants that could impact the integrity of future life-detection missions. Catalase was purified by using a 3-step chromatographic procedure, where mass spectrometry provided respective subunit and intact masses of 57.8 and 234.6 kDa, which were consistent with a small-subunit tetrameric catalase. Kinetics revealed an extreme pH stability with no loss in activity between pH 5 and 11.5 and provided respective kcat/Km and kcat values of ∼10(7) s(-1) M(-1) and 10(6) s(-1), which are among the highest reported for bacterial catalases. The amino acid sequence was deduced by in-depth peptide mapping, and structural homology suggested that the catalases from differing strains of A. gyllenbergii differ only at residues near the subunit interfaces, which may impact catalytic stability. Together, the kinetic, alkali-tolerant, and halotolerant properties of the catalase from A. gyllenbergii 2P01AA are significant, as they are consistent with molecular adaptations toward the alkaline, low-humidity, and potentially oxidizing conditions of spacecraft assembly facilities. Therefore, these results support the hypothesis that the selective pressures of the assembly facilities impact the microbial communities at the molecular level, which may have broad implications for future life-detection missions.

Lunar and Planetary Science XXXV: Astrobiology

NASA Technical Reports Server (NTRS)

2004-01-01

The presentations in this session are: 1. A Prototype Life Detection Chip 2. The Geology of Atlantis Basin, Mars, and Its Astrobiological Interest 3. Collecting Bacteria Together with Aerosols in the Martian Atmosphere by the FOELDIX Experimental Instrument Developed with a Nutrient Detector Pattern: Model Measurements of Effectivity 4. 2D and 3D X-ray Imaging of Microorganisms in Meteorites Using Complexity Analysis to Distinguish Field Images of Stromatoloids from Surrounding Rock Matrix in 3.45 Ga Strelley Pool Chert, Western Australia 4. Characterization of Two Isolates from Andean Lakes in Bolivia Short Time Scale Evolution of Microbiolites in Rapidly Receding Altiplanic Lakes: Learning How to Recognize Changing Signatures of Life 5. The Effect of Salts on Electrospray Ionization of Amino Acids in the Negative Mode 6. Determination of Aromatic Ring Number Using Multi-Channel Deep UV Native Fluorescence 7. Microbial D/H Fractionation in Extraterrestrial Materials: Application to Micrometeorites and Mars 8. Carbon Isotope Characteristics of Spring-fed Iron-precipitating Microbial Mats 9. Amino Acid Survival Under Ambient Martian Surface UV Lighting Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions 10. Laboratory Detection and Analysis of Organic Compounds in Rocks Using HPLC and XRD Methods 11. Thermal Decomposition of Siderite-Pyrite Assemblages: Implications for Sulfide Mineralogy in Martian Meteorite ALH84001 Carbonate Globules 12. Determination of the Three-Dimensional Morphology of ALH84001 and Biogenic MV-1 Magnetite: Comparison of Results from Electron Tomography and Classical Transmission Electron Microscopy 13. On the Possibility of a Crypto-Biotic Crust on Mars Based on Northern and Southern Ringed Polar Dune Spots 14. Comparative Planetology of the Terrestrial Inner Planets: Implications for Astrobiology 15. A Possible Europa Exobiology 16. A Possible Biogeochemical Model for Titan

Revisiting life strategy concepts in environmental microbial ecology.

PubMed

Ho, Adrian; Di Lonardo, D Paolo; Bodelier, Paul L E

2017-03-01

Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligotrophic strategists, and competitor-stress tolerator-ruderals framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response. We discuss the limitations and provide recommendations for future research applying microbial life strategies in environmental studies. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Analysis of the archaeal sub-seafloor community at Suiyo Seamount on the Izu-Bonin Arc.

PubMed

Hara, Kurt; Kakegawa, Takeshi; Yamashiro, Kan; Maruyama, Akihiko; Ishibashi, Jun-Ichiro; Marumo, Katsumi; Urabe, Tetsuro; Yamagishi, Akihiko

2005-01-01

A sub-surface archaeal community at the Suiyo Seamount in the Western Pacific Ocean was investigated by 16S rRNA gene sequence and whole-cell in situ hybridization analyses. In this study, we drilled and cased holes at the hydrothermal area of the seamount to minimize contamination of the hydrothermal fluid in the sub-seafloor by penetrating seawater. PCR clone analysis of the hydrothermal fluid samples collected from a cased hole indicated the presence of chemolithoautotrophic primary biomass producers of Archaeoglobales and the Methanococcales-related archaeal HTE1 group, both of which can utilize hydrogen as an electron donor. We discuss the implication of the microbial community on the early history of life and on the search for extraterrestrial life. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults.

PubMed

Yallapragada, Sushmita G; Nash, Colleen B; Robinson, Daniel T

2015-11-01

The intestinal microbiome is a complex ecosystem of microorganisms that colonize the human gastrointestinal tract. The microbiome evolves rapidly in early life with contributions from diet, genetics and immunomodulatory factors. Changes in composition of the microbiota due to antibiotics may lead to negative long-term effects including obesity and diabetes mellitus, as evidenced by both animal and large human studies. Inappropriate exposures to antibiotics occur frequently in early childhood. Therefore, an evidence-based system of antimicrobial use should be employed by all providers, especially those who care for pediatric patients. This article explores the natural evolution of the intestinal microbiome from the perinatal period into early childhood, the effect of antibiotics on the microbial ecology, and the implications for future health and disease. Copyright 2015, SLACK Incorporated.

Microbial Diversity in Surface Iron-Rich Aqueous Environments: Implications for Seeking Signs of Life on Mars

NASA Technical Reports Server (NTRS)

Brown, I. I.; Allen, C. C.; Tringe, S. G.; Klatt, C. G.; Bryant, D. A.; Sarkisova, S. A.; Garrison, D. H.; McKay, D. S.

2010-01-01

The success of selecting future landing sites on Mars to discover extinct and/or extant extraterrestrial life is dependent on the correct approximation of available knowledge about terrestrial paleogeochemistry and life evolution to Martian (paleo) geology and geochemistry. It is well known that both Earth and Mars are Fe rich. This widespread occurrence suggests that Fe may have played a key role in early life forms, where it probably served as a key constituent in early prosthetic moieties in many proteins of ancient microbes on Earth and likely Mars. The second critical idea is the premise that Life on Mars could most likely have developed when Mars experienced tectonic activity [1] which dramatically decreased around 1 bin years after Martian creation. After that Martian life could have gone extinct or hibernated in the deep subsurface, which would be expensive to reach in contrast to the successful work of Martian surface rovers. Here we analyze the diversity of microbes in several terrestrial Fe rich surface environments in conjunction with the phylogeny and molecular timing of emergence of those microbes on Earth. Anticipated results should help evaluate future landing sites on Mars in searches for biosignatures.

Ice Shelf Microbial Ecosystems in the High Arctic and Implications for Life on Snowball Earth

NASA Astrophysics Data System (ADS)

Vincent, W. F.; Gibson, J. A. E.; Pienitz, R.; Villeneuve, V.; Broady, P. A.; Hamilton, P. B.; Howard-Williams, C.

The Ward Hunt Ice Shelf (83°N, 74°W) is the largest remaining section of thick (>10m) landfast sea ice along the northern coastline of Ellesmere Island, Canada. Extensive meltwater lakes and streams occur on the surface of the ice and are colonized by photosynthetic microbial mat communities. This High Arctic cryo-ecosystem is similar in several of its physical, biological and geochemical features to the McMurdo Ice Shelf in Antarctica. The ice-mats in both polar regions are dominated by filamentous cyanobacteria but also contain diatoms, chlorophytes, flagellates, ciliates, nematodes, tardigrades and rotifers. The luxuriant Ward Hunt consortia also contain high concentrations (107-108cm-2) of viruses and heterotrophic bacteria. During periods of extensive ice cover, such as glaciations during the Proterozoic, cryotolerant mats of the type now found in these polar ice shelf ecosystems would have provided refugia for the survival, growth and evolution of a variety of organisms, including multicellular eukaryotes.

The Microbiome-Gut-Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses.

PubMed

Ntranos, Achilles; Casaccia, Patrizia

2018-01-01

Environmental and dietary stimuli have always been implicated in brain development and behavioral responses. The gut, being the major portal of communication with the external environment, has recently been brought to the forefront of this interaction with the establishment of a gut-brain axis in health and disease. Moreover, recent breakthroughs in germ-free and antibiotic-treated mice have demonstrated the significant impact of the microbiome in modulating behavioral responses in mice and have established a more specific microbiome-gut-behavior axis. One of the mechanisms by which this axis affects social behavior is by regulating myelination at the prefrontal cortex, an important site for complex cognitive behavior planning and decision-making. The prefrontal cortex exhibits late myelination of its axonal projections that could extend into the third decade of life in humans, which make it susceptible to external influences, such as microbial metabolites. Changes in the gut microbiome were shown to alter the composition of the microbial metabolome affecting highly permeable bioactive compounds, such as p-cresol, which could impair oligodendrocyte differentiation. Dysregulated myelination in the prefrontal cortex is then able to affect behavioral responses in mice, shifting them towards social isolation. The reduced social interactions could then limit microbial exchange, which could otherwise pose a threat to the survival of the existing microbial community in the host and, thus, provide an evolutionary advantage to the specific microbial community. In this review, we will analyze the microbiome-gut-behavior axis, describe the interactions between the gut microbiome and oligodendrocytes and highlight their role in the modulation of social behavior.

Geomicrobiology of basal ice in a temperate glacier: implications for primary microbial production and export, elemental cycling and soil formation

NASA Astrophysics Data System (ADS)

Toubes-Rodrigo, Mario; Potgieter-Vermaak, Sanja; Sen, Robin; Elliott, David R.; Cook, Simon J.

2017-04-01

Basal ice is a significant sub-glacial component of glaciers and ice sheets that arises from ice-bedrock/substrate interaction. As a result, basal ice of a glacier retains a distinctive physical and chemical signature characterised by a high sediment- and low bubble-content and selective ionic enrichment. Previous research concluded that sediment entrapped in the basal ice matrix originates from the bedrock/substrate, and harbours an active microbial community. However, the nature and significance of the microbial community inhabiting basal ice facies remains poorly characterised. This paper reports on an integrated chemical, mineralogical, and microbial community analysis of basal ice in the subglacial environment at Svínafellsjökull, in south-east Iceland. Basal ice sediment supported 10E7 cells g^-1 and, based on glacier velocity and sediment flux, an estimated 10E17 cells a^-1 are exported to the glacier foreland. Furthermore, 16S rRNA gene analysis highlighted a glacier basal ice bacterial community dominated by Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Sequences ascribed to chemolithotrophic-related species (Thiobacillus, Syderoxidans) were highly abundant. Minerological analyses of basal ice sediment confirmed dominant silicates and iron-containing minerals that represent susceptible substrates open to oxidation by the aforementioned chemolithotrophs. Previous studies have suggested that basal ice could constitute a good analogue for astrobiology. Svínafellsjökull and Mars geology are similar - volcanically derived rocks with a high abundance of silicates and iron-rich minerals, reinforcing this idea. Understanding where the limits of life in extreme environments, such as debris-rich basal ice, could help to unravel how life on other planets could succeed, and could help to identify which markers to use in order to find it. In dark and isolated basal ice niches, the dominating chemolithotrophic bacterial community are likely to act as primary producers, fixing carbon while weathering minerals and thus providing a plausible mechanism to explain how a basal ice microbial ecosystem can be sustained.

Metabolic activity of microorganisms in evaporites

NASA Technical Reports Server (NTRS)

Rothschild, L. J.; Giver, L. J.; White, M. R.; Mancinelli, R. L.

1994-01-01

Crystalline salt is generally considered so hostile to most forms of life that it has been used for centuries as a preservative. Here, we present evidence that prokaryotes inhabiting a natural evaporite crust of halite and gypsum are metabolically active while inside the evaporite for at least 10 months. In situ measurements demonstrated that some of these "endoevaporitic" microorganisms (probably the cyanobacterium Synechococcus Nageli) fixed carbon and nitrogen. Denitrification was not observed. Our results quantified the slow microbial activity that can occur in salt crystals. Implications of this study include the possibility that microorganisms found in ancient evaporite deposits may have been part of an evaporite community.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

PubMed

Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

2017-12-01

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease. Copyright © 2017 American Society for Microbiology.

Atmospheres and evolution. [of microbial life on earth

NASA Technical Reports Server (NTRS)

Margulis, L.; Lovelock, J. E.

1981-01-01

Studies concerning the regulation of the earth atmosphere and the relation of atmospheric changes to the evolution of microbial life are reviewed. The improbable nature of the composition of the earth atmosphere in light of the atmospheric compositions of Mars and Venus and equilibrium considerations is pointed out, and evidence for the existence of microbial (procaryotic) life on earth as far back as 3.5 billion years ago is presented. The emergence of eucaryotic life in the Phanerozoic due to evolving symbioses between different procaryotic species is discussed with examples given of present-day symbiotic relationships between bacteria and eucaryotes. The idea that atmospheric gases are kept in balance mainly by the actions of bacterial cells is then considered, and it is argued that species diversity is necessary for the maintenance and origin of life on earth in its present form.

Modern Microbial Fossilization Processes as Signatures for Interpreting Ancient Terrestrial and Extraterrestrial Microbial Forms

NASA Technical Reports Server (NTRS)

Morris, Penny A.; Wentworth, Susan J.; Nelman, Mayra; Byrne, Monica; Longazo, Teresa; Galindo, Charles; McKay, David S.; Sams, Clarence

2003-01-01

Terrestrial biotas from microbially dominated hypersaline environments will help us understand microbial fossilization processes. Hypersaline tolerant biota from Storr's Lake, San Salvador Island (Bahamas), Mono Lake (California), and the Dead Sea (Israel) represent marine and nonmarine sites for comparative studies of potential analogs for interpreting some Mars meteorites and Mars sample return rocks [1,2,3,4,5,6]. The purpose of this study is to compare microbial fossilization processes, the dominant associated minerals, and potential diagenic implications.

The perils and promises of microbial abundance: novel natures and model ecosystems, from artisanal cheese to alien seas.

PubMed

Paxson, Heather; Helmreich, Stefan

2014-04-01

Microbial life has been much in the news. From outbreaks of Escherichia coli to discussions of the benefits of raw and fermented foods to recent reports of life forms capable of living in extreme environments, the modest microbe has become a figure for thinking through the presents and possible futures of nature, writ large as well as small. Noting that dominant representations of microbial life have shifted from an idiom of peril to one of promise, we argue that microbes--especially when thriving as microbial communities--are being upheld as model ecosystems in a prescriptive sense, as tokens of how organisms and human ecological relations with them could, should, or might be. We do so in reference to two case studies: the regulatory politics of artisanal cheese and the speculative research of astrobiology. To think of and with microbial communities as model ecosystems offers a corrective to the scientific determinisms we detect in some recent calls to attend to the materiality of scientific objects.

Technical Challenges of Drilling on Mars

NASA Technical Reports Server (NTRS)

Briggs, Geoffrey; Gross, Anthony; Condon, Estelle (Technical Monitor)

2002-01-01

In the last year, NASA's Mars science advisory committee (MEPAG: Mars Exploration Payload Advisory Group) has formally recommended that deep drilling be undertaken as a priority investigation to meet astrobiology and geology goals. This proposed new dimension in Mars exploration has come about for several reasons. Firstly, geophysical models of the martian subsurface environment indicate that we may well find liquid water (in the form of brines) under ground-ice at depths of several kilometers near the equator. On Earth we invariably find life forms associated with any environmental niche that supports liquid water. New data from the Mars Global Surveyor have shown that the most recent volcanism on Mars is very young so we cannot rule out contemporary volcanism -- in which case subsurface temperatures consistent with having water in its liquid phase may be found at relatively shallow depths. Secondly, in recent decades we have learned to our surprise that the Earth's subsurface (microbial) biosphere extends to depths of many kilometers and this discovery provides the basis for planning to explore the martian subsurface in search of ancient or even extant microbial life forms. We know (from Viking measurements) that all the biogenic elements (C, H, O, N, P, S) are available on Mars. What we therefore hope to learn is whether or not the evolution of life is inevitable given the necessary ingredients and, by implication, whether the Universe may be teeming with life. The feasibility of drilling deep into the surface of Mars has been the subject of increasing attention within NASA (and more recently among some of its international partners) for several years and this led to a broad-based feasibility study carried out by the Los Alamos National Laboratory and, subsequently, to the development of several hardware prototypes. This paper is intended to provide a general survey of that activity.

Temperature profile for glacial ice at the South Pole: Implications for life in a nearby subglacial lake

PubMed Central

Price, P. Buford; Nagornov, Oleg V.; Bay, Ryan; Chirkin, Dmitry; He, Yudong; Miocinovic, Predrag; Richards, Austin; Woschnagg, Kurt; Koci, Bruce; Zagorodnov, Victor

2002-01-01

Airborne radar has detected ≈100 lakes under the Antarctic ice cap, the largest of which is Lake Vostok. International planning is underway to search in Lake Vostok for microbial life that may have evolved in isolation from surface life for millions of years. It is thought, however, that the lakes may be hydraulically interconnected. If so, unsterile drilling would contaminate not just one but many of them. Here we report measurements of temperature vs. depth down to 2,345 m in ice at the South Pole, within 10 km from a subglacial lake seen by airborne radar profiling. We infer a temperature at the 2,810-m deep base of the South Pole ice and at the lake of −9°C, which is 7°C below the pressure-induced melting temperature of freshwater ice. To produce the strong radar signal, the frozen lake must consist of a mix of sediment and ice in a flat bed, formed before permanent Antarctic glaciation. It may, like Siberian and Antarctic permafrost, be rich in microbial life. Because of its hydraulic isolation, proximity to South Pole Station infrastructure, and analog to a Martian polar cap, it is an ideal place to test a sterile drill before risking contamination of Lake Vostok. From the semiempirical expression for strain rate vs. shear stress, we estimate shear vs. depth and show that the IceCube neutrino observatory will be able to map the three-dimensional ice-flow field within a larger volume (0.5 km3) and at lower temperatures (−20°C to −35°C) than has heretofore been possible. PMID:12060731

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals.

PubMed

Pothakos, Vasileios; Stellato, Giuseppina; Ercolini, Danilo; Devlieghere, Frank

2015-05-15

Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB. Pseudomonas spp., Enterobacteriaceae, Streptococcaceae, and Lactobacillus spp. constituted the most widespread operational taxonomic units (OTUs), whereas Leuconostoc gelidum was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However, L. gelidum became the most predominant microbe at the end of the shelf life. The ability of L. gelidum to outgrow notorious, spoilage-related taxa like Pseudomonas, Brochothrix, and Lactobacillus underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

PubMed Central

Stellato, Giuseppina; Devlieghere, Frank

2015-01-01

Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB. Pseudomonas spp., Enterobacteriaceae, Streptococcaceae, and Lactobacillus spp. constituted the most widespread operational taxonomic units (OTUs), whereas Leuconostoc gelidum was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However, L. gelidum became the most predominant microbe at the end of the shelf life. The ability of L. gelidum to outgrow notorious, spoilage-related taxa like Pseudomonas, Brochothrix, and Lactobacillus underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment. PMID:25769837

Intelligibility in microbial complex systems: Wittgenstein and the score of life.

PubMed

Baquero, Fernando; Moya, Andrés

2012-01-01

Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the "score of life" metaphor is more accurate to express the complexity of living systems than the classic "book of life." Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.

Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate.

PubMed

Hotaling, Scott; Hood, Eran; Hamilton, Trinity L

2017-08-01

Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation. Here, we provide a modern synthesis of the microbial ecology of mountain glacier ecosystems, and particularly those at low- to mid-latitudes. We focus on five ecological zones: the supraglacial surface, englacial interior, subglacial bedrock-ice interface, proglacial streams and glacier forefields. For each, we discuss the role of microbiota in biogeochemical cycling and outline ecological and hydrological connections among zones, underscoring the interconnected nature of these ecosystems. Collectively, we highlight the need to: better document the biodiversity and functional roles of mountain glacier microbiota; describe the ecological implications of rapid glacial retreat under climate change and resolve the relative contributions of ecological zones to broader ecosystem function. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial fuel cells applied to the metabolically based detection of extraterrestrial life.

PubMed

Abrevaya, Ximena C; Mauas, Pablo J D; Cortón, Eduardo

2010-12-01

Since the 1970s, when the Viking spacecrafts carried out experiments to detect microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that a methodology detect life independently from its composition or form and that the chosen biological signature point to a feature common to all living systems, such as the presence of metabolism. In this paper, we evaluate the use of microbial fuel cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material, releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs that use microorganism cultures or soil samples in the anode are much larger than those obtained with a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, which have been proposed as potential inhabitants of extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used for in situ detection of microbial life.

Microbial Fuel Cells Applied to the Metabolically Based Detection of Extraterrestrial Life

NASA Astrophysics Data System (ADS)

Abrevaya, Ximena C.; Mauas, Pablo J. D.; Cortón, Eduardo

2010-12-01

Since the 1970s, when the Viking spacecrafts carried out experiments to detect microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that a methodology detect life independently from its composition or form and that the chosen biological signature point to a feature common to all living systems, such as the presence of metabolism. In this paper, we evaluate the use of microbial fuel cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material, releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs that use microorganism cultures or soil samples in the anode are much larger than those obtained with a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, which have been proposed as potential inhabitants of extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used for in situ detection of microbial life.

Novel approaches in function-driven single-cell genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doud, Devin F. R.; Woyke, Tanja

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbialmore » communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.« less

Novel approaches in function-driven single-cell genomics

DOE PAGES

Doud, Devin F. R.; Woyke, Tanja

2017-06-07

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbialmore » communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.« less

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Implications of streamlining theory for microbial ecology

PubMed Central

Giovannoni, Stephen J; Cameron Thrash, J; Temperton, Ben

2014-01-01

Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, ‘simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche. PMID:24739623

New concepts of microbial treatment processes for the nitrogen removal: effect of protein and amino acids degradation.

PubMed

González-Martínez, Alejandro; Calderón, Kadiya; González-López, Jesús

2016-05-01

High concentrations of proteins and amino acids can be found in wastewater and wastewater stream produced in anaerobic digesters, having shown that amino acids could persist over different managements for nitrogen removal affecting the nitrogen removal processes. Nitrogen removal is completely necessary because of their implications and the significant adverse environmental impact of ammonium such as eutrophication and toxicity to aquatic life on the receiving bodies. In the last decade, the treatment of effluents with high ammonium concentration through anammox-based bioprocesses has been enhanced because these biotechnologies are cheaper and more environmentally friendly than conventional technologies. However, it has been shown that the presence of important amounts of proteins and amino acids in the effluents seriously affects the microbial autotrophic consortia leading to important losses in terms of ammonium oxidation efficiency. Particularly the presence of sulfur amino acids such as methionine and cysteine has been reported to drastically decrease the autotrophic denitrification processes as well as affect the microbial community structure promoting the decline of ammonium oxidizing bacteria in favor of other phylotypes. In this context we discuss that new biotechnological processes that improve the degradation of protein and amino acids must be considered as a priority to increase the performance of the autotrophic denitrification biotechnologies.

Perinatal and Early Childhood Environmental Factors Influencing Allergic Asthma Immunopathogenesis

PubMed Central

Gaffin, Jonathan M.; Kanchongkittiphon, Watcharoot; Phipatanakul, Wanda

2014-01-01

Background The prevalence of asthma has increased dramatically over the past several decades. While hereditary factors are highly important, the rapid rise outstrips the pace of genomic variation. Great emphasis has been placed on potential modifiable early life exposures leading to childhood asthma. Methods We reviewed the recent medical literature for important studies discussing the role of the perinatal and early childhood exposures and the inception of childhood asthma. Results and Discussion Early life exposure to allergens (House dust mite (HDM), furred pets, cockroach, rodent and mold)air pollution (nitrogen dioxide (NO2), ozone (O3), volatile organic compounds (VOCs), and particulate matter (PM)) and viral respiratory tract infections (Respiratory syncytial virus (RSV) and human rhinovirus (hRV)) have been implicated in the development of asthma in high risk children. Conversely, exposure to microbial diversity in the perinatal period may diminish the development of atopy and asthma symptoms. PMID:24952205

Discriminative detection and enumeration of microbial life in marine subsurface sediments.

PubMed

Morono, Yuki; Terada, Takeshi; Masui, Noriaki; Inagaki, Fumio

2009-05-01

Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

Extraterrestrial Life in the Microbial Age

NASA Astrophysics Data System (ADS)

Gronstal, Aaron L.

Humankind has long been fascinated with the potential for alien civilizations within the Solar System and beyond (e.g., Crowe and Dowd 2013; Sullivan 2013). Despite the early optimism for life beyond Earth, humankind has yet to make first contact with an alien race. Historical discourse on the topic of alien life can provide some useful input into questions about how the people of Earth today might respond to contact with alien life (e.g., Dick 2013). However, this discourse is primarily devoted to understanding humankind's response to intelligent life. We must recognize that the search for life's potential beyond Earth has dramatically changed since the dawn of the Space Age. We now know that advanced civilizations are not common on planets in our solar system. The search for life on nearby worlds is now limited to non-intelligent, microbial life. Any chance we have of contacting intelligent life lies in receiving transmissions from distant worlds, and contact with such cultures would be greatly limited by the vast expanse of space. This chapter discusses the need for more attention paid to the possible social, economic, and legal ramifications that the discovery of non-intelligent, alien microbial life might bring.

Intelligibility in microbial complex systems: Wittgenstein and the score of life

PubMed Central

Baquero, Fernando; Moya, Andrés

2012-01-01

Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the “score of life” metaphor is more accurate to express the complexity of living systems than the classic “book of life.” Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life. PMID:22919679

Glycerol enhances fungal germination at the water‐activity limit for life

PubMed Central

Stevenson, Andrew; Hamill, Philip G.; Medina, Ángel; Kminek, Gerhard; Rummel, John D.; Dijksterhuis, Jan; Timson, David J.; Magan, Naresh; Leong, Su‐Lin L.

2016-01-01

Summary For the most‐extreme fungal xerophiles, metabolic activity and cell division typically halts between 0.700 and 0.640 water activity (approximately 70.0–64.0% relative humidity). Here, we investigate whether glycerol can enhance xerophile germination under acute water‐activity regimes, using an experimental system which represents the biophysical limit of Earth's biosphere. Spores from a variety of species, including Aspergillus penicillioides, Eurotium halophilicum, Xerochrysium xerophilum (formerly Chrysosporium xerophilum) and Xeromyces bisporus, were produced by cultures growing on media supplemented with glycerol (and contained up to 189 mg glycerol g dry spores−1). The ability of these spores to germinate, and the kinetics of germination, were then determined on a range of media designed to recreate stresses experienced in microbial habitats or anthropogenic systems (with water‐activities from 0.765 to 0.575). For A. penicillioides, Eurotium amstelodami, E. halophilicum, X. xerophilum and X. bisporus, germination occurred at lower water‐activities than previously recorded (0.640, 0.685, 0.651, 0.664 and 0.637 respectively). In addition, the kinetics of germination at low water‐activities were substantially faster than those reported previously. Extrapolations indicated theoretical water‐activity minima below these values; as low as 0.570 for A. penicillioides and X. bisporus. Glycerol is present at high concentrations (up to molar levels) in many types of microbial habitat. We discuss the likely role of glycerol in expanding the water‐activity limit for microbial cell function in relation to temporal constraints and location of the microbial cell or habitat. The findings reported here have also critical implications for understanding the extremes of Earth's biosphere; for understanding the potency of disease‐causing microorganisms; and in biotechnologies that operate at the limits of microbial function. PMID:27631633

Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration

PubMed Central

Dinan, Timothy G.

2016-01-01

Abstract There is a growing realisation that the gut–brain axis and its regulation by the microbiota may play a key role in the biological and physiological basis of neurodevelopmental, age‐related and neurodegenerative disorders. The routes of communication between the microbiota and brain are being unravelled and include the vagus nerve, gut hormone signalling, the immune system, tryptophan metabolism or by way of microbial metabolites such as short chain fatty acids. The importance of early life gut microbiota in shaping future health outcomes is also emerging. Disturbances of this composition by way of antibiotic exposure, lack of breastfeeding, infection, stress and the environmental influences coupled with the influence of host genetics can result in long‐term effects on physiology and behaviour, at least in animal models. It is also worth noting that mode of delivery at birth influences microbiota composition with those born by Caesarean section having a distinctly different microbiota in early life to those born per vaginum. At the other extreme of life, ageing is associated with a narrowing in microbial diversity and healthy ageing correlates with a diverse microbiome. Recently, the gut microbiota has been implicated in a variety of conditions including depression, autism, schizophrenia and Parkinson's disease. There is still considerable debate as to whether or not the gut microbiota changes are core to the pathophysiology of such conditions or are merely epiphenomenal. It is plausible that such neuropsychiatric disorders might be treated in the future by targeting the microbiota either by microbiota transplantation, antibiotics or psychobiotics. PMID:27641441

Exploration of Subglacial Lake Ellsworth

NASA Astrophysics Data System (ADS)

Ross, N.

2012-12-01

Antarctic subglacial lakes are thought to be extreme habitats for microbial life and may contain important records of ice sheet history within their lake-floor sediments. To find if this is true, and to answer the science questions that would follow, direct measurement and sampling of these environments is required. Ever since the water depth of Vostok Subglacial Lake in East Antarctica was shown to be >500 m, attention has been given to how these unique, ancient and pristine subglacial environments may be entered without contamination and adverse disturbance. Several organizations have offered guidelines on the desirable cleanliness and sterility requirements for direct sampling experiments, including the US National Academy of Sciences and the Scientific Committee on Antarctic Research. The aims, design and implementation of subglacial lake access experiments have direct relevance for the exploration of extra-terrestrial ice-covered bodies (e.g. Europa) and the search for microbial life elsewhere in the Solar System. This presentation summarizes the scientific protocols and methods being developed for the exploration of Ellsworth Subglacial Lake in West Antarctica, and provides an up-to-date summary of the status of the project. The proposed exploration, planned for December 2012, involves accessing the lake using a hot-water drill and deploying a sampling probe and sediment corer to allow in situ measurement and sample collection. Details are presented on how this can be undertaken with minimal environmental impact that maximizes scientific return without compromising the environment for future experiments. The implications of this experiment for the search for extra-terrestrial life will be discussed.

Non-Equilibrium Thermodynamic Chemistry and the Composition of the Atmosphere of Mars

NASA Technical Reports Server (NTRS)

Levine, J. S.; Summers, M. E.

2003-01-01

A high priority objective of the Mars Exploration Program is to Determine if life exists today (MEPAG Goal I, Objective A). The measurement of gases of biogenic origin may be an approach to detect the presence of microbial life on the surface or subsurface of Mars. Chemical thermodynamic calculations indicate that on both Earth and Mars, certain gases should exist in extremely low concentrations, if at all. Microbial metabolic activity is an important non-equilibrium chemistry process on Earth, and if microbial life exists on Mars, may be an important nonequilibrium chemistry process on Mars. The non-equilibrium chemistry of the atmosphere of Mars is discussed in this paper.

A bacterial enrichment study and overview of the extractable lipids from paleosols in the Dry Valleys, Antarctica: implications for future Mars reconnaissance.

PubMed

Hart, Kris M; Szpak, Michal T; Mahaney, William C; Dohm, James M; Jordan, Sean F; Frazer, Andrew R; Allen, Christopher C R; Kelleher, Brian P

2011-05-01

The Dry Valleys of Antarctica are one of the coldest and driest environments on Earth with paleosols in selected areas that date to the emplacement of tills by warm-based ice during the Early Miocene. Cited as an analogue to the martian surface, the ability of the Antarctic environment to support microbial life-forms is a matter of special interest, particularly with the upcoming NASA/ESA 2018 ExoMars mission. Lipid biomarkers were extracted and analyzed by gas chromatography--mass spectrometry to assess sources of organic carbon and evaluate the contribution of microbial species to the organic matter of the paleosols. Paleosol samples from the ice-free Dry Valleys were also subsampled and cultivated in a growth medium from which DNA was extracted with the explicit purpose of the positive identification of bacteria. Several species of bacteria were grown in solution and the genus identified. A similar match of the data to sequenced DNA showed that Alphaproteobacteria, Gammaproteobacteria, Bacteriodetes, and Actinobacteridae species were cultivated. The results confirm the presence of bacteria within some paleosols, but no assumptions have been made with regard to in situ activity at present. These results underscore the need not only to further investigate Dry Valley cryosols but also to develop reconnaissance strategies to determine whether such likely Earth-like environments on the Red Planet also contain life.

Microbial spoilage of portuguese chouriço along shelf life period

PubMed Central

de Jesus da Silva Matos, Teresa; Bruno-Soares, Arminda; Azevedo, António Amaral

2013-01-01

Microbial flora of portuguese chouriço (Alentejano (A) and Ribatejano (R)) with abnormal sensorial characteristics along shelf life was studied. Mesophilic anaerobic bacteria, enterococci, mesophilic sporeformers, coliforms, coagulase-positive staphylococci, sulphite reducing clostridia, Clostridium perfringens, moulds and yeasts were the most representative in both types of chouriço. PMID:24159290

Increasing strawberry shelf-life with carvacrol and methyl cinnamate antimicrobial vapors released from edible films (abstract)

USDA-ARS?s Scientific Manuscript database

Shelf life of strawberries (Fragaria x ananassa) is limited by decay caused by microbial growth that negatively impacts their color, texture and weight. Plant natural volatile compounds, such as terpenoids and esters, have been reported to be effective against microbial pathogen growth. The advantag...

Microbial ecology of the cryosphere: sea ice and glacial habitats.

PubMed

Boetius, Antje; Anesio, Alexandre M; Deming, Jody W; Mikucki, Jill A; Rapp, Josephine Z

2015-11-01

The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.

Cave speleothems as repositories of microbial biosignatures

NASA Astrophysics Data System (ADS)

Miller, Ana Z.; Jurado, Valme; Pereira, Manuel F. C.; Fernández, Octavio; Calaforra, José M.; Dionísio, Amélia; Saiz-Jimenez, Cesareo

2015-04-01

The need to better understand the biodiversity, origins of life on Earth and on other planets, and the wide applications of the microbe-mineral interactions have led to a rapid expansion of interest in subsurface environments. Recently reported results indicated signs of an early wet Mars and rather recent volcanic activity which suggest that Mars's subsurface can house organic molecules or traces of microbial life, making the search for microbial life on Earth's subsurface even more compelling. Caves on Earth are windows into the subsurface that harbor a wide variety of mineral-utilizing microorganisms, which may contribute to the formation of biominerals and unusual microstructures recognized as biosignatures. These environments contain a wide variety of redox interfaces and stable physicochemical conditions, which enhance secondary mineral precipitation and microbial growth under limited organic nutrient inputs. Enigmatic microorganisms and unusual mineral features have been found associated with secondary mineral deposits or speleothems in limestone caves and lava tubes. In this study, Field Emission Scanning Electron Microscopy (FESEM) and Energy Dispersive X-ray spectroscopy (EDS) analyses were conducted on cave speleothem samples to assess microbe-mineral interactions, evaluate biogenicity, as well as to describe unusual mineral formations and microbial features. Microbial mats, extracellular polymeric substances, tubular empty sheaths, mineralized cells, filamentous fabrics, as well as "cell-sized" etch pits or microborings produced by bacterial cells were observed on minerals. These features evidence microbe-mineral interactions and may represent mineralogical signatures of life. We can thus consider that caves on Earth are plausible repositories of terrestrial biosignatures where we can look for microbial signatures. Acknowledgments: AZM acknowledges the support from the Marie Curie Intra-European Fellowship within the 7th European Community Framework Programme (PIEF-GA-2012-328689- DECAVE). The authors acknowledge the Spanish Ministry of Economy and Competitiveness (project CGL2013-41674-P) for financial support.

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia.

PubMed

Duda, Jan-Peter; Van Kranendonk, Martin J; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight-secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia

PubMed Central

Duda, Jan-Peter; Van Kranendonk, Martin J.; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight—secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation. PMID:26807732

Oxygen Profile of a Thermo-Haliophilic Community in the Badwater Salt Flat

NASA Technical Reports Server (NTRS)

Smith, H. D.; McKay, C. P.; Rainey, F.; Bebout, B.; Carpenter, S.

2004-01-01

Badwater is the lowest, saltiest, and hottest, place in North America. This extreme environment is 86 meters (282 feet) below sea level surrounded by four mountain ranges. Due to the geographical location Badwater does not receive moisture from the prevailing winds, this intern results in a hot, arid, and salty environment. Despite these extreme living conditions, microbes manage to flourish within the salt flat. The salt acts as an insulator making life just beneath the surface more comfortable In this paper, we compare the microbial population versus oxygen concentration; and the importance of and the role of oxygen in metabolic functions by these thermo-haliophiles. Furthermore a model of the oxygen profile will also provide an insight to the oxygen cycle in salty environments. This research has implications for the limits of life on Earth and Mars. Recent results from the MER rovers show that water on Mars was very salty. Measuring the oxygen profile in these salty environments on Earth provides a framework within which potential life on Mars can be evaluated. The use of an oxygen profile could also be used as a search criteria for life.

How Do I Sample the Environment and Equipment?

NASA Astrophysics Data System (ADS)

Kornacki, Jeffrey L.

Food product contamination from the post-processing environment is likely the most frequent cause of contaminated processed food product recalls and a significant source of poisoning outbreaks, and shelf life problems in North America with processed Ready-To-Eat foods. Conditions exist for the growth of microorganisms in most food processing factories. Failure to clean and effectively sanitize a microbial growth niche can lead to biofilm formation. Biofilms may be orders of magnitude more resistant to destruction by sanitizers. Cells in some biofilms have been shown to be 1,000 times more resistant to destruction than those which are freely suspended. This has implications for cleaning, sanitizing, sampling, and training. Sampling the factory environment is one means of monitoring the efficacy of microbiological control as well as a powerful tool for in-factory contamination investigation. Many sampling techniques exist and are discussed. It is important to recognize the difference between cleaning (removal of soil) and sanitization (reduction of microbial populations). Knowing where, when, and how to sample, how many samples to take, and what to test for and how to interpret test information is critical in finding and preventing contamination.

UPT scenarios: Implications for system reliability

NASA Technical Reports Server (NTRS)

Walsh, Daniel W.

1992-01-01

The objective of this project was to examine the corrosion resistance of 316L stainless steel in several urine pre-treat solutions. Four solutions were examined: untreated urine (control); urine pretreated with oxone (potassium peroxymonosulfate sulfate); urine pretreated with sodium hypochlorite (NaOCl); and urine pretreated with ozone (O3). In accordance with current procedures, all solutions but the control were acidified to a pH of 2.5 using sulfuric acid--this suppresses the generation of ammonia in the solutions and is intended to limit microbial growth. Welded and unwelded coupons were exposed to each solution. In addition, Titanium coupons (welded and unwelded) were exposed to biologically active environmental control and life support system (ECLSS) water. Microbial attachment and biofilm growth were monitored. Ozone was examined as a biocide/oxidizer/corrosion preventative (simultaneous addition) and as a remediation method (added one week after exposure). In an unrelated effort, HP 9-4-30 coupons were exposed to biologically active solutions. Corrosion rates for welded and unwelded samples were determined--results were correlated to the ongoing HP 9-4-30 weldment stress corrosion study.

Anticorrosive Microbial Polysaccharides: Structure-Function Relationships

USDA-ARS?s Scientific Manuscript database

Water-soluble microbial polysaccharides are often implicated in biofilm formation and are believed to mediate cell-cell aggregation and adhesion to surfaces. Generally, biofilm formation is considered harmful or undesirable, as it leads to increased drag, plugging of pores, dimished heat transfer, ...

Molecular Survey of Concrete Sewer Biofilm Microbial Communities

EPA Science Inventory

Although bacteria are implicated in deteriorating concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different concrete biofilms by performing sequence analysis of 16S rDNA concrete clone libraries. ...

How Will We React to the Discovery of Extraterrestrial Life?

PubMed

Kwon, Jung Yul; Bercovici, Hannah L; Cunningham, Katja; Varnum, Michael E W

2017-01-01

How will humanity react to the discovery of extraterrestrial life? Speculation on this topic abounds, but empirical research is practically non-existent. We report the results of three empirical studies assessing psychological reactions to the discovery of extraterrestrial life using the Linguistic Inquiry and Word Count (LIWC) text analysis software. We examined language use in media coverage of past discovery announcements of this nature, with a focus on extraterrestrial microbial life (Pilot Study). A large online sample ( N = 501) was asked to write about their own and humanity's reaction to a hypothetical announcement of such a discovery (Study 1), and an independent, large online sample ( N = 256) was asked to read and respond to a newspaper story about the claim that fossilized extraterrestrial microbial life had been found in a meteorite of Martian origin (Study 2). Across these studies, we found that reactions were significantly more positive than negative, and more reward vs. risk oriented. A mini-meta-analysis revealed large overall effect sizes (positive vs. negative affect language: g = 0.98; reward vs. risk language: g = 0.81). We also found that people's forecasts of their own reactions showed a greater positivity bias than their forecasts of humanity's reactions (Study 1), and that responses to reading an actual announcement of the discovery of extraterrestrial microbial life showed a greater positivity bias than responses to reading an actual announcement of the creation of man-made synthetic life (Study 2). Taken together, this work suggests that our reactions to a future confirmed discovery of microbial extraterrestrial life are likely to be fairly positive.

How Will We React to the Discovery of Extraterrestrial Life?

PubMed Central

Kwon, Jung Yul; Bercovici, Hannah L.; Cunningham, Katja; Varnum, Michael E. W.

2018-01-01

How will humanity react to the discovery of extraterrestrial life? Speculation on this topic abounds, but empirical research is practically non-existent. We report the results of three empirical studies assessing psychological reactions to the discovery of extraterrestrial life using the Linguistic Inquiry and Word Count (LIWC) text analysis software. We examined language use in media coverage of past discovery announcements of this nature, with a focus on extraterrestrial microbial life (Pilot Study). A large online sample (N = 501) was asked to write about their own and humanity’s reaction to a hypothetical announcement of such a discovery (Study 1), and an independent, large online sample (N = 256) was asked to read and respond to a newspaper story about the claim that fossilized extraterrestrial microbial life had been found in a meteorite of Martian origin (Study 2). Across these studies, we found that reactions were significantly more positive than negative, and more reward vs. risk oriented. A mini-meta-analysis revealed large overall effect sizes (positive vs. negative affect language: g = 0.98; reward vs. risk language: g = 0.81). We also found that people’s forecasts of their own reactions showed a greater positivity bias than their forecasts of humanity’s reactions (Study 1), and that responses to reading an actual announcement of the discovery of extraterrestrial microbial life showed a greater positivity bias than responses to reading an actual announcement of the creation of man-made synthetic life (Study 2). Taken together, this work suggests that our reactions to a future confirmed discovery of microbial extraterrestrial life are likely to be fairly positive. PMID:29367849

Observation to Theory in Deep Subsurface Microbiology Research: Can We Piece It Together?

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Thurber, A. R.

2016-12-01

Three decades of observations of microbes in deep environments have led to startling discoveries of life in the subsurface. Now, a few theoretical frameworks exist that help to define Stygian life. Temperature, redox gradients, productivity (e.g., in the overlying ocean), and microbial power requirements are thought to determine the distribution of microbes in the subsurface. Still, we struggle to comprehend the spatial and temporal spectra of Earth processes that define how deep microbe communities survive. Stommel diagrams, originally used to guide oceanographic sampling, may be useful in depicting the subsurface where microbial communities are impacted by co-occurring spatial and temporal phenomena that range across exponential scales. Spatially, the geological settings that influence the activity and distribution of microbes range from individual molecules or minerals all the way up to the planetary-scale where geological formations, occupying up to 105 km3, dictate the bio- and functional geography of microbial communities. Temporally, life in the subsurface may respond in time units familiar to humans (e.g., seconds to days) or to events that unfold over hundred millennial time periods. While surface community dynamics are underpinned by solar and lunar cycles, these cycles only fractionally dictate survival underground where phenomena like tectonic activity, isostatic rebound, and radioactive decay are plausible drivers of microbial life. Geological or planetary processes that occur on thousand or million year cycles could be uniquely important to microbial viability in the subsurface. Such an approach aims at a holistic comprehension of the interaction of Earth system dynamics with microbial ecology.

Towards a rapid and comprehensive microbial detection and identification system for life support and planetary protection applications

NASA Astrophysics Data System (ADS)

Lasseur, Christophe

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination. These risks concern both crew health via the metabolic consumables contamination (water, air,.) but and also the hardware degradation. In parallel to these life support issues, planetary protection experts have agreed to place clear specifications of the microbial quality of future hardware landing on extraterrestrial planets as well as elaborate the requirements of contamination for manned missions on surface. For these activities, it is necessary to have a better understanding of microbial activity, to create culture collections and to develop on-line detection tools. . In this respect, over the last 6 years , ESA has supported active scientific research on the choice of critical genes and functions, including those linked to horizontal gene pool of bacteria and its dissemination. In parallel, ESA and European industries have been developing an automated instrument for rapid microbial detection on air and surface samples. Within this paper, we first present the life support and planetary protection requirements, and the state of the art of the instrument development. Preliminary results at breadboard level, including a mock-up view of the final instrument are also presented. Finally, the remaining steps required to reach a functional instrument for planetary hardware integration and life support flight hardware are also presented.

Terrestrial Subsurface Ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Fredrickson, Jim K.

2015-10-15

The Earth’s crust is a solid cool layer that overlays the mantle, with a varying thickness of between 30-50 km on continental plates, and 5-10 km on oceanic plates. Continental crust is composed of a variety of igneous, metamorphic, and sedimentary rocks that weather and re-form over geologic cycles lasting millions to billions of years. At the crust surface, these weathered minerals and organic material combine to produce a variety of soils types that provide suitable habitats and niches for abundant microbial diversity (see Chapter 4). Beneath this soil zone is the subsurface. Once thought to be relatively free ofmore » microorganisms, recent estimates have calculated that between 1016-1017 g C biomass (2-19% of Earth’s total biomass) may be present in this environment (Whitman et al., 1998;McMahon and Parnell, 2014). Microbial life in the subsurface exists across a wide range of habitats: in pores associated with relatively shallow unconsolidated aquifer sediments to fractures in bedrock formations that are more than a kilometer deep, where extreme lithostatic pressures and temperatures are encountered. While these different environments contain varying physical and chemical conditions, the absence of light is a constant. Despite this, diverse physiologies and metabolisms enable microorganisms to harness energy and carbon for growth in water-filled pore spaces and fractures. Carbon and other element cycles are driven by microbial activity, which has implications for both natural processes and human activities in the subsurface, e.g., bacteria play key roles in both hydrocarbon formation and degradation. Hydrocarbons are a major focus for human utilization of the subsurface, via oil and gas extraction and potential geologic CO2 sequestration. The subsurface is also utilized or being considered for sequestered storage of high-level radioactive waste from nuclear power generation and residual waste from past production of weapons grade nuclear materials. While our understanding of the subsurface is continually improving, it is clear that only a small fraction of microbial habitats have been sampled and studied. In this chapter, we will discuss these studies in the context of the distribution of microbial life in the subsurface, the stresses that microorganisms must overcome to survive in these environments, and the metabolic strategies that are employed to harness energy in a region of the planet far-removed from sunlight. Finally, we will consider both beneficial and deleterious effects of microbial activity in the subsurface on human activities in this environment.« less

Implications of a 3.472-3.333 Gyr-old subaerial microbial mat from the Barberton greenstone belt, South Africa for the UV environmental conditions on the early Earth.

PubMed

Westall, Frances; de Ronde, Cornel E J; Southam, Gordon; Grassineau, Nathalie; Colas, Maggy; Cockell, Charles; Lammer, Helmut

2006-10-29

Modelling suggests that the UV radiation environment of the early Earth, with DNA weighted irradiances of about three orders of magnitude greater than those at present, was hostile to life forms at the surface, unless they lived in specific protected habitats. However, we present empirical evidence that challenges this commonly held view. We describe a well-developed microbial mat that formed on the surface of volcanic littoral sediments in an evaporitic environment in a 3.5-3.3Ga-old formation from the Barberton greenstone belt. Using a multiscale, multidisciplinary approach designed to strongly test the biogenicity of potential microbial structures, we show that the mat was constructed under flowing water by 0.25 microm filaments that produced copious quantities of extracellular polymeric substances, representing probably anoxygenic photosynthesizers. Associated with the mat is a small colony of rods-vibroids that probably represent sulphur-reducing bacteria. An embedded suite of evaporite minerals and desiccation cracks in the surface of the mat demonstrates that it was periodically exposed to the air in an evaporitic environment. We conclude that DNA-damaging UV radiation fluxes at the surface of the Earth at this period must either have been low (absorbed by CO2, H2O, a thin organic haze from photo-dissociated CH4, or SO2 from volcanic outgassing; scattered by volcanic, and periodically, meteorite dust, as well as by the upper layers of the microbial mat) and/or that the micro-organisms exhibited efficient gene repair/survival strategies.

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

PubMed Central

Bik, Holly M.; Sung, Way; De Ley, Paul; Baldwin, James G.; Sharma, Jyotsna; Rocha-Olivares, Axayácatl; Thomas, W. Kelley

2011-01-01

Summary Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and likely play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world’s largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our understanding of global biodiversity and how we perceive and mitigate the impact of environmental change and anthropogenic disturbance. Using a metagenetic approach, we present an assessment of microbial eukaryote communities across depth (shallow water to abyssal) and ocean basins (deep-sea Pacific and Atlantic). Within the 12 sites examined, our results suggest that some taxa can maintain eurybathic ranges and cosmopolitan deep-sea distributions, but the majority of species appear to be regionally restricted. For OCTUs reporting wide distributions, there appears to be a taxonomic bias towards a small subset of taxa in most phyla; such bias may be driven by specific life history traits amongst these organisms. In addition, low genetic divergence between geographically disparate deep-sea sites suggests either a shorter coalescence time between deep-sea regions or slower rates of evolution across this vast oceanic ecosystem. While high-throughput studies allow for broad assessment of genetic patterns across microbial eukaryote communities, intragenomic variation in rRNA gene copies and the patchy coverage of reference databases currently present substantial challenges for robust taxonomic interpretations of eukaryotic datasets. PMID:21985648

Probing Metabolic Activity of Deep Subseafloor Life with NanoSIMS

NASA Astrophysics Data System (ADS)

Morono, Y.; Terada, T.; Itoh, M.; Inagaki, F.

2014-12-01

There are very few natural environments where life is absent in the Earth's surface biosphere. However, uninhabitable region is expected to be exist in the deep subsurface biosphere, of which extent and constraining factor(s) have still remained largly unknown. Scientific ocean drilling have revealed that microbial communities in sediments are generally phylogenetically distinct from known spieces isolated from the Earth's surface biosphere, and hence metabolic functions of the deep subseafloor life remain unknown. In addition, activity of subseafloor microbial cells are thought to be extraordinally slow, as indicated by limited supply of neutrient and energy substrates. To understand the limits of the Earth's subseafloor biosphere and metabolic functions of microbial populations, detection and quantification of the deeply buried microbial cells in geological habitats are fundamentary important. Using newly developed cell separation techniques as well as an discriminative cell detection system, the current quantification limit of sedimentary microbial cells approaches to 102 cells/cm3. These techniques allow not only to assess very small microbial population close to the subsurface biotic fringe, but also to separate and sort the target cells using flow cytometric cell sorter. Once the deep subseafloor microbial cells are detached from mineral grains and sorted, it opens new windows to subsequent molecular ecological and element/isotopic analyses. With a combined use of nano-scale secondary ion masspectrometry (NanoSIMS) and stable isotope-probing techniques, it is possible to detect and measure activity of substrate incorporation into biomass, even for extremely slow metabolic processes such as uncharacteriszed deep subseafloor life. For example, it was evidenced by NanoSIMS that at least over 80% of microbial cells at ~200 meters-deep, 460,000-year-old sedimentary habitat are indeed live, which substrate incooporation was found to be low (10-15 gC/cell/day) even under the lab incubation condition. Also microbial activity in ultraoligotrophic biosphere samples such as the South Pacific Gyre (i.e., IODP Expeditions 329) will be shown. Our results demonstrates metabolic potential of microbes that have been survived for geological timescale in extremely starved condition.

Marine Microbial Mats and the Search for Evidence of Life in Deep Time and Space

NASA Technical Reports Server (NTRS)

Des Marais, David J.

2011-01-01

Cyanobacterial mats in extensive seawater evaporation ponds at Guerrero Negro, Baja California, Mexico, have been excellent subjects for microbial ecology research. The studies reviewed here have documented the steep and rapidly changing environmental gradients experienced by mat microorganisms and the very high rates of biogeochemical processes that they maintained. Recent genetic studies have revealed an enormous diversity of bacteria as well as the spatial distribution of Bacteria, Archaea and Eukarya. These findings, together with emerging insights into the intimate interactions between these diverse populations, have contributed substantially to our understanding of the origins, environmental impacts, and biosignatures of photosynthetic microbial mats. The biosignatures (preservable cells, sedimentary fabrics, organic compounds, minerals, stable isotope patterns, etc.) potentially can serve as indicators of past life on early Earth. They also can inform our search for evidence of any life on Mars. Mars exploration has revealed evidence of evaporite deposits and thermal spring deposits; similar deposits on Earth once hosted ancient microbial mat ecosystems.

On microbial contaminants, micropseudofossils, and the oldest records of life

USGS Publications Warehouse

Cloud, P.; Morrison, K.

1979-01-01

Microbial contaminants may be introduced on outcrop as well as en route to or in the laboratory. Micropseudofossils may be natural or man-made. It is possible to recognize such misleading objects and important that they are not allowed to dilute the growing record of authentic pre-Phanerozoic life. Filamentous microbial contaminants from minute cracks in samples of ancient carbonate rocks from Brazil (perhaps 1 Ga old) and South Africa (???2.3 Ga old) are similar to occurrences previously described as fossils. Published records of supposedly Archean microbial life also include microcontaminants and laboratory artifacts. Although microstructures from sedimentary rocks of the Swaziland system could be fossils, they are not demonstrably so. The oldest structurally preserved fossils yet known seem to be the filaments described by Lois Nagy from stromatolitic limestone in the ???2.3 Ga old Malmani Dolomite of South Africa. It will be difficult to establish unequivocal older records in the absence of definitive ultrastructural or micro-chemical evidence. ?? 1979.

Human life support during interplanetary travel and domicile. VI - Generic modular flow schematic for hybrid physical/chemical-biological life support systems

NASA Technical Reports Server (NTRS)

Ganapathi, Gani B.; Seshan, P. K.; Ferrall, Joseph; Rohatgi, Naresh

1992-01-01

An extension is proposed for the NASA Space Exploration Initiative's Generic Modular Flow Schematics for physical/chemical life support systems which involves the addition of biological processes. The new system architecture includes plant, microbial, and animal habitat, as well as the human habitat subsystem. Major Feedstock Production and Food Preparation and Packaging components have also been incorporated. Inedible plant, aquaculture, microbial, and animal solids are processed for recycling.

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

PubMed

Inagaki, F; Hinrichs, K-U; Kubo, Y; Bowles, M W; Heuer, V B; Hong, W-L; Hoshino, T; Ijiri, A; Imachi, H; Ito, M; Kaneko, M; Lever, M A; Lin, Y-S; Methé, B A; Morita, S; Morono, Y; Tanikawa, W; Bihan, M; Bowden, S A; Elvert, M; Glombitza, C; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, C-H; Murayama, M; Ohkouchi, N; Ono, S; Park, Y-S; Phillips, S C; Prieto-Mollar, X; Purkey, M; Riedinger, N; Sanada, Y; Sauvage, J; Snyder, G; Susilawati, R; Takano, Y; Tasumi, E; Terada, T; Tomaru, H; Trembath-Reichert, E; Wang, D T; Yamada, Y

2015-07-24

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed. Copyright © 2015, American Association for the Advancement of Science.

Gene expression in the deep biosphere.

PubMed

Orsi, William D; Edgcomb, Virginia P; Christman, Glenn D; Biddle, Jennifer F

2013-07-11

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

Environmental implications of herbicide resistance: soil biology and ecology

USDA-ARS?s Scientific Manuscript database

Soil microbial community structure and activity are clearly linked to plant communities established in natural and agricultural ecosystems. A limited number of studies confirm that weeds alter their soil environment and select for specific microbial communities in the rhizosphere. Such rhizosphere m...

Elucidating Adverse Nutritional Implications of Exposure to Endocrine-Disrupting Chemicals and Mycotoxins through Stable Isotope Techniques.

PubMed

Owino, Victor O; Cornelius, Carolin; Loechl, Cornelia U

2018-03-23

Multiple drivers of the double burden of malnutrition (DBM) include a rapid shift from predominantly plant-based diets to energy-dense foods based on meats, milk, animal fats and vegetable oils. The shift to overweight and obesity is driven by increased exposure to mass media, urbanization, technological advances in food processing, rising income and increased population density associated with increased access to cheap foods. At the same time, undernutrition persists mainly due to food insecurity and lack of access to safe water, sanitation and adequate health care. All known nutrition interventions result in only one third reduction in stunting. Little consideration has been given to hazardous exposure to endocrine disrupting chemicals (EDCs) and microbial toxins as major components of the malnutrition-causal framework. These hazards include microbial toxins, for example, mycotoxins, and environmental pollutants such as persistent organic pollutants (POPs), some of which are known to disrupt the endocrine system. These hazards sit at the cross road of undernutrition and overweight and obesity since the exposure cuts across the critical window of opportunity (the first 1000 days). In this review, we update on the role of food and environmental contaminants, especially EDCs and aflatoxins, in child growth and on the implications for metabolic dysfunction and disease risk in later life, and discuss potential applications of nuclear and isotopic techniques to elucidate the underlying biological mechanisms, outcome indicators, as well as occurrence levels.

The microbial environment and its influence on asthma prevention in early life.

PubMed

von Mutius, Erika

2016-03-01

There is accumulating evidence to suggest that the environmental microbiome plays a significant role in asthma development. The very low prevalence of asthma in populations highly exposed to microbial environments (farm children and Amish populations) highlights its preventive potential. This microbial diversity might be necessary to instruct a well-adapted immune response and regulated inflammatory responses to other inhaled and ingested environmental elements, such as allergens, particles, and viruses. Like the internal gut microbiome, which is increasingly recognized as an important instructor of immune maturation, the external environmental microbiome might shape immune responses on the skin, airway mucosal surfaces, and potentially also the gut early in life. The diversity of the external microbial world will ensure that of the many maladapted pathways leading to asthma development, most, if not all, will be counterbalanced. Likewise, important contributors to asthma, such as allergen sensitization and allergic manifestations early in life, are being suppressed. Thus the facets of innate immunity targeted by microbes and their compounds and metabolites might be the master switch to asthma and allergy protection, which has been found in environments rich in microbial exposures. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Early microbial contact, the breast milk microbiome and child health.

PubMed

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

The Search for Life on Mars Using Macroscopically Visible Microbial Mats (Stromatolites) in 3.5 3.3 Ga Cherts from the Pilbara in Australia and Barberton in South Africa as Analogues

NASA Astrophysics Data System (ADS)

Westall, F.; Hofmann, B.; Brack, A.

2004-03-01

Microbial mats from early terrestrial environments can be macroscopically visible and represent excellent analogues in the search for life on Mars. Tests using the Beagle 2 camera show that they can be observed by in situ instrumentation.

Ecology and exploration of the rare biosphere.

PubMed

Lynch, Michael D J; Neufeld, Josh D

2015-04-01

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

The Rise of Complexity: Do the Pavilion Lake Microbialites Suggest a Way to Build a Macroorganism?

NASA Astrophysics Data System (ADS)

Schulze-Makuch, D.; Laval, B.; Lim, D. S.; Irwin, L. N.

2005-12-01

The distinctive assemblage of freshwater calcite microbialites discovered at Pavilion Lake, BC, has been associated with organisms such as Epiphyton and Girvanella, fossils from just before the Cambrian explosion about 550 million years ago (Laval et al., 2000). The presence of the microbialite structures in a dimictic mid-latitude lake and their establishment after the last ice age about 10,000 years ago is puzzling. Their distinctive morphologies include cone-shaped seepage structures 2 m or more in height with hollow internal conduits that open at the top of the cones, and dense artichoke-like structures with calcite "leaves" greater than 1 m in height. These structures are astounding as they imply functional properties. In principle, this is not unlike the interaction of individual cells in a macroorganism, in which many different types of specialized cells interact with each other to the benefit of the whole organism (e.g. interaction of blood, integument, and organ cells within animals). Certainly, the complex interaction of these microbial cells is not equivalent to the collaboration of cells within an individual multicellular organism, where each cell has the same genetic information but differential gene expression provides well-defined cellular specializations. However, the microbialites raise the question of how much complexity and structure can be achieved by a high degree of communication within a multitude of microbial cells. Our findings indicate a complex and interacting microbial consortium associated with the structures at Pavilion Lake, and revealed biomarkers for proteobacteria, sulphur reducing bacteria, and firmicutes (possibly photosynthetic heliobacteria), among others. Types of genetic exchange among these microbial cells may include lateral gene transfer via conjugation, transformation, and transduction, or other mechanisms. This finding may have significant implications for the evolution of life on Earth and possible life on other planets. References: Laval, B., Cady, S.L., Pollack, J.C., McKay, C.P., Bird, J.S., Grotzinger, J.P., Ford, D.C., and Bohm, H.R. (2000) Modern freshwater microbialite analogues for ancient dendritic reef structures. Nature 407, 626-629.

Research and Application of Marine Microbial Enzymes: Status and Prospects

PubMed Central

Zhang, Chen; Kim, Se-Kwon

2010-01-01

Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes. PMID:20631875

Hot spring microbial community composition, morphology, and carbon fixation: implications for interpreting the ancient rock record

NASA Astrophysics Data System (ADS)

Schuler, Caleb G.; Havig, Jeff R.; Hamilton, Trinity L.

2017-11-01

Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA) of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate i) natural abundance δ13C values of biomass from these features (-11.0 to -24.3 ‰) are similar to those found in the rock record; ii) carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; iii) oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and iv) increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower. Our data highlight important differences in primary productivity between structures despite indistinguishable δ13C values of the biomass. Furthermore, low primary productivity by stromatolites compared to other structures underscores the need to consider a larger role for microbial mats and filaments in carbon fixation and O2 generation during the Archean and Proterozoic.

Garnets within geode-like serpentinite veins: Implications for element transport, hydrogen production and life-supporting environment formation

NASA Astrophysics Data System (ADS)

Plümper, Oliver; Beinlich, Andreas; Bach, Wolfgang; Janots, Emilie; Austrheim, Håkon

2014-09-01

Geochemical micro-environments within serpentinizing systems can abiotically synthesize hydrocarbons and provide the ingredients required to support life. Observations of organic matter in microgeode-like hydrogarnets found in Mid-Atlantic Ridge serpentinites suggest these garnets possibly represent unique nests for the colonization of microbial ecosystems within the oceanic lithosphere. However, little is known about the mineralogical and geochemical processes that allow such unique environments to form. Here we present work on outcrop-scale vein networks from an ultramafic massif in Norway that contain massive amounts of spherulitic garnets (andradite), which help to constrain such processes. Vein andradite spherulites are associated with polyhedral serpentine, brucite, Ni-Fe alloy (awaruite), and magnetite indicative of low temperature (<200 °C) alteration under low fO2 and low aSiO2,aq geochemical conditions. Together with the outcrop- and micro-scale analysis geochemical reaction path modeling shows that there was limited mass transport and fluid flow over a large scale. Once opened the veins remained isolated (closed system), forming non-equilibrium microenvironments that allowed, upon a threshold supersaturation, the rapid crystallization (seconds to weeks) of spherulitic andradite. The presence of polyhedral serpentine spheres indicates that veins were initially filled with a gel-like protoserpentine phase. In addition, massive Fe oxidation associated with andradite formation could have generated as much as 600 mmol H2,aq per 100 cm3 vein. Although no carboneous matter was detected, the vein networks fulfill the reported geochemical criteria required to generate abiogenic hydrocarbons and support microbial communities. Thus, systems similar to those investigated here are of prime interest when searching for life-supporting environments within the deep subsurface.

Destruction of Raman biosignatures by ionising radiation and the implications for life detection on Mars.

PubMed

Dartnell, Lewis R; Page, Kristian; Jorge-Villar, Susana E; Wright, Gary; Munshi, Tasnim; Scowen, Ian J; Ward, John M; Edwards, Howell G M

2012-04-01

Raman spectroscopy has proven to be a very effective approach for the detection of microorganisms colonising hostile environments on Earth. The ExoMars rover, due for launch in 2018, will carry a Raman laser spectrometer to analyse samples of the martian subsurface collected by the probe's 2-m drill in a search for similar biosignatures. The martian surface is unprotected from the flux of cosmic rays, an ionising radiation field that will degrade organic molecules and so diminish and distort the detectable Raman signature of potential martian microbial life. This study employs Raman spectroscopy to analyse samples of two model organisms, the cyanobacterium Synechocystis sp. PCC 6803 and the extremely radiation resistant polyextremophile Deinococcus radiodurans, that have been exposed to increasing doses of ionising radiation. The three most prominent peaks in the Raman spectra are from cellular carotenoids: deinoxanthin in D. radiodurans and β-carotene in Synechocystis. The degradative effect of ionising radiation is clearly seen, with significant diminishment of carotenoid spectral peak heights after 15 kGy and complete erasure of Raman biosignatures by 150 kGy of ionising radiation. The Raman signal of carotenoid in D. radiodurans diminishes more rapidly than that of Synechocystis, believed to be due to deinoxanthin acting as a superior scavenger of radiolytically produced reactive oxygen species, and so being destroyed more quickly than the less efficient antioxidant β-carotene. This study highlights the necessity for further experimental work on the manner and rate of degradation of Raman biosignatures by ionising radiation, as this is of prime importance for the successful detection of microbial life in the martian near subsurface.

Modeling low-temperature serpentinization reactions to estimate molecular hydrogen production with implications for potential microbial life on Saturn's moon Enceladus.

NASA Astrophysics Data System (ADS)

Zwicker, Jennifer; Smrzka, Daniel; Taubner, Ruth-Sophie; Bach, Wolfgang; Rittmann, Simon; Schleper, Christa; Peckmann, Jörn

2017-04-01

Serpentinization of ultramafic rocks attracts much interest in research on the origin of life on Earth and the search for life on extraterrestrial bodies including icy moons like Enceladus. Serpentinization on Earth occurs in peridotite-hosted systems at slow-spreading mid-ocean ridges, and produces large amounts of molecular hydrogen and methane. These reduced compounds can be utilized by diverse chemosynthetic microbial consortia as a metabolic energy source. Although many hydrothermal vents emit hot and acidic fluids today, it is more likely that life originated in the Archean at sites producing much cooler and more alkaline fluids that allowed for the synthesis and stability of essential organic molecules necessary for life. Therefore, a detailed understanding of water-rock interaction processes during low-temperature serpentinization is of crucial importance in assessing the life-sustaining potential of these environments. In the course of serpentinization, the metasomatic hydration of olivine and pyroxene produces various minerals including serpentine minerals, magnetite, brucite, and carbonates. Hydrogen production only occurs if ferrous iron within iron-bearing minerals is oxidized and incorporated as ferric iron into magnetite. The PHREEQC code was used to model the pH- and temperature-dependent dissolution of olivine and pyroxene to form serpentine, magnetite and hydrogen under pressure and temperature conditions that may exist on Saturn's icy moon Enceladus. Various model setups at 25 and 50°C were run to assess the influence of environmental parameters on hydrogen production. The results reveal that hydrogen production rates depend on the composition of the initial mineral assemblage and temperature. The current assumption is that there is a gaseous phase between Enceladus' ice sheet and subsurface ocean. To test various scenarios, model runs were conducted with and without the presence of a gas phase. The model results show that hydrogen production is further dependent on carbon dioxide partial pressure within the gas phase. Moreover, no other gases apart from hydrogen, such as methane, were produced in any of the model runs. The combined results offer a constraint on hydrogen production over time, and may aid habitability assessments of extraterrestrial bodies where serpentinization could occur.

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. In order to predict how disturbance affects belowground carbon storage, it is important to understand how the forest floor and soil microbial community respond to changes in land cover, and the consequences on SOM formation and stabilization. We are measuring microbial functional diversity and activity across a long-term successional chronosequence of secondary forests regrowing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Here we report intra- and interannual data on soil and litter microbial community composition (via phospholipid fatty acid analysis, PLFA) and microbial activity (via extracellular enzyme activity) from active pastures, secondary forests aged 20, 30, 40, 70, and 90-years, and primary forests. Microbial community composition and extracellular enzyme activity differed significantly by season in these wet subtropical ecosystems, even though differences in mean monthly precipitation between the middle of the dry season (January) and the wet season (July) is only 30mm. Despite seasonal differences, there was a persistent strong effect of land cover type and forest successional stage, or age, on overall microbial community PLFA structure. Using principal component analysis, we found differences in microbial community structure among active pastures, early, and late successional forests. The separation of soil microbes into early and late successional communities parallels the clustering of tree composition data. While the successional patterns held across seasons, the importance of different microbial groups driving these patterns differed seasonally. Biomarkers for gram-positive and actinobacteria (i15:0 and 16:0 10Me) were associated with early (20, 30 & 40 year old) secondary forests in the dry season. These younger forest communities were identified by the biomarker for anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

Metabolic Activity and Biosignatures of Microbes in the Lower Ocean Crust of Atlantis Bank, IODP Expedition 360

NASA Astrophysics Data System (ADS)

Wee, S. Y.; Edgcomb, V. P.; Burgaud, G.; Klein, F.; Schubotz, F.; Yvon-Lewis, S. A.; Sylvan, J. B.

2017-12-01

International Ocean Discovery Program (IODP) Expedition 360 represents the first leg of a multi-phase drilling program, SloMo, aimed at investigating the nature of the lower crust and Moho at slow spreading ridges. The goal of Expedition 360 was to recover a representative transect of the lower oceanic crust formed at Atlantis Bank, an oceanic core complex on the SW Indian Ridge. Recovered cores were primarily gabbro and olivine gabbro, which may potentially host serpentinization reactions and associated microbial life. Our goal was to sample this subseafloor environment and determine quantity, diversity and metabolic capabilities of any resident microbial life. Hole U1473A was drilled during Expedition 360 down to 790 m below seafloor and samples for detection of microbial communities and microbial biosignatures were collected throughout. We present here quantification of microbial biomass via fluorescence microscopy, preliminary analysis of nutrient addition experiments, data from sequencing of microbial 16S rRNA genes, analysis of microbial lipids, and data from Raman spectra of subsurface isolates. We initiated and sampled 12 nutrient addition experiments from 71-745 mbsf by adding sampled rocks to artificial seawater with no additions, added ammonium, added ammonium plus phosphate, and added organic acids. In nearly all of the experiment bottles, methane was detected when samples were collected at six months and again after one year of incubation. Phosphate in the incubations was drawn down, indicating active microbial metabolism, and archaeal lipids from in situ samples indicate the presence of methanogens, corroborating the likelihood of methanogens as the source of detected methane in the nutrient addition incubations. Altogether, the interdisciplinary approach used here provides a peek into life in the subseafloor upper ocean crust.

Life in ice: implications to astrobiology

NASA Astrophysics Data System (ADS)

Hoover, Richard B.; Pikuta, Elena V.

2009-08-01

During previous research expeditions to Siberia, Alaska and Antarctica, it was observed that glaciers and ice wedges contained bacterial cells that became motile as soon as the ice melted. This phenomenon of live bacteria in ice was first documented for microbes in ancient ice cores from Vostok, Antarctica. The first validly published species of Pleistocene bacteria alive on Earth today was Carnobacterium pleistocenium. This extremophile had remained for 32,000 years, encased in ice recently exposed in the Fox Tunnel of Alaska. These frozen bacteria began to swim as soon as the ice was thawed. Dark field microscopy studies revealed that large numbers of bacteria exhibited motility as soon as glacial ice was melted during our recent Expeditions to Alaska and Antarctica led to the conclusion that microbial life in ice was not a rare phenomenon. The ability of bacteria to remain alive while frozen in ice for long periods of time is of great significance to Astrobiology. In this paper, we describe the recent observations and advance the hypothesis that life in ice provides valuable clues to how we can more easily search for evidence of life on the Polar Caps of Mars, comets and other icy bodies of our Solar System. It is suggested that cryopanspermia may have played a far more important role in Origin of Life on Earth and the distribution of Life throughout the Cosmos and than previously thought possible.

Sub-Optimal Treatment of Bacterial Biofilms

PubMed Central

Song, Tianyan; Duperthuy, Marylise; Wai, Sun Nyunt

2016-01-01

Bacterial biofilm is an emerging clinical problem recognized in the treatment of infectious diseases within the last two decades. The appearance of microbial biofilm in clinical settings is steadily increasing due to several reasons including the increased use of quality of life-improving artificial devices. In contrast to infections caused by planktonic bacteria that respond relatively well to standard antibiotic therapy, biofilm-forming bacteria tend to cause chronic infections whereby infections persist despite seemingly adequate antibiotic therapy. This review briefly describes the responses of biofilm matrix components and biofilm-associated bacteria towards sub-lethal concentrations of antimicrobial agents, which may include the generation of genetic and phenotypic variabilities. Clinical implications of bacterial biofilms in relation to antibiotic treatments are also discussed. PMID:27338489

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment.

PubMed

Lomstein, Bente Aa; Langerhuus, Alice T; D'Hondt, Steven; Jørgensen, Bo B; Spivack, Arthur J

2012-03-18

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.

Microfossils, biomolecules and biominerals in carbonaceous meteorites: implications to the origin of life

NASA Astrophysics Data System (ADS)

Hoover, Richard B.

2012-11-01

Environmental and Field Emission Scanning Electron Microscopy (ESEM and FESEM) investigations have shown that a wide variety of carbonaceous meteorites contain the remains of large filaments embedded within freshly fractured interior surfaces of the meteorite rock matrix. The filaments occur singly or in dense assemblages and mats and are often encased within carbon-rich, electron transparent sheaths. Electron Dispersive X-ray Spectroscopy (EDS) spot analysis and 2D X-Ray maps indicate the filaments rarely have detectable nitrogen levels and exhibit elemental compositions consistent with that interpretation that of the meteorite rock matrix. Many of the meteorite filaments are exceptionally well-preserved and show evidence of cells, cell-wall constrictions and specialized cells and processes for reproduction, nitrogen fixation, attachment and motility. Morphological and morphometric analyses permit many of the filaments to be associated with morphotypes of known genera and species of known filamentous trichomic prokaryotes (cyanobacteria and sulfur bacteria). The presence in carbonaceous meteorites of diagenetic breakdown products of chlorophyll (pristane and phytane) along with indigenous and extraterrestrial chiral protein amino acids, nucleobases and other life-critical biomolecules provides strong support to the hypothesis that these filaments represent the remains of cyanobacteria and other microorganisms that grew on the meteorite parent body. The absence of other life-critical biomolecules in the meteorites and the lack of detectable levels of nitrogen indicate the filaments died long ago and can not possibly represent modern microbial contaminants that entered the stones after they arrived on Earth. This paper presents new evidence for microfossils, biomolecules and biominerals in carbonaceous meteorites and considers the implications to some of the major hypotheses for the Origin of Life.

Detection of Nitric Oxide by the Sample Analysis at Mars (SAM) Instrument Implications for the Presence of Nitrates

NASA Technical Reports Server (NTRS)

Navarro-Gonzalez, R.; Stern, J.; Freissinet, C.; Franz, H. B.; Eigenbrode, J. L..; McKay, C. P.; Coll, P.; Sutter, B.; Archer, D.; McAdam, A.;

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE PAGES

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; ...

2017-11-01

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

Robotic Astrobiology: Searching for Life with Rovers

NASA Astrophysics Data System (ADS)

Cabrol, N. A.; Wettergreen, D. S.; Team, L.

2006-05-01

The Life In The Atacama (LITA) project has developed and field tested a long-range, solar-powered, automated rover platform (Zoe) and a science payload assembled to search for microbial life in the Atacama desert. Life is hardly detectable over most of the extent of the driest desert on Earth. Its geological, climatic, and biological evolution provides a unique training ground for designing and testing exploration strategies and life detection methods for the robotic search for life on Mars. LITA opens the path to a new generation of rover missions that will transition from the current study of habitability (MER) to the upcoming search for, and study of, habitats and life on Mars. Zoe's science payload reflects this transition by combining complementary elements, some directed towards the remote sensing of the environment (geology, morphology, mineralogy, weather/climate) for the detection of conditions favorable to microbial habitats and oases along survey traverses, others directed toward the in situ detection of life' signatures (biological and physical, such as biological constructs and patterns). New exploration strategies specifically adapted to the search for microbial life were designed and successfully tested in the Atacama between 2003-2005. They required the development and implementation in the field of new technological capabilities, including navigation beyond the horizon, obstacle avoidance, and "science-on-the-fly" (automated detection of targets of science value), and that of new rover planning tools in the remote science operation center.

Carbonate mineralisation in sabkha microbial mats; a comparative study of field and laboratory systems

NASA Astrophysics Data System (ADS)

Dutton, Kirsten E.; Paul, Andreas; Lessa Andrade, Luiza; Sherry, Angela; Lokier, Stephen; Head, Ian M.; van der Land, Cees

2017-04-01

Microbial mats and their lithified counterparts are some of the earliest evidence of life on Earth. The coastal sabkha in Abu Dhabi, United Arab Emirates, is a modern setting where microbial mats flourish in a hypersaline and arid environment. These microbial communities are composed of microbes such as cyanobacteria, thermoplasmata and sulphate-reducing bacteria. The mats thrive as they are protected from predators, which are excluded by the extreme environmental conditions. Microbial mats are highly reactive to change, with their microbial communities and geochemistry varying on a millimetre scale, likely controlling mineralisation processes. Exact carbonate mineralisation rates within coastal sabkha microbial mats have not to date been quantified. Defining the mineralisation pathways and knowledge of precise mineralisation rates will help to explain how these organosedimentary structures are retained in the rock record. A fundamental understanding of the role of microbial mats in the formation of different carbonate phases is important, yet there are also other practical implications. For example, structures observed in core from the oil-bearing Arab Formation have been likened to modern microbial mats in terms of structure and mineralogy. The depositional configuration and primary mineralogy generated by microbial mats may control syndepositional lithification and later diagenesis thereby influencing reservoir porosity and permeability. In order to constrain factors effecting mineralisation and early lithification, experimentation in a controlled laboratory environment is required. Parameters for experimentation have been established during fieldwork and were applied to a tank-based laboratory simulation of sabkha microbial mats. These parameters include light, salinity and cation and anion water chemistry, gas production chemistry and vertical mat growth. Parameters were measured weekly with sampling for mineralogical and microbial community analysis on a biweekly basis. In addition to these parameter measurements already in place in current experiments, temperature and tidal cycle were monitored in the field. Over the course of the first three months, the microbial mat, which was submerged in an artificial seawater medium, grew vertically and developed a green surface at the top and sides. Thermogravimetric analysis has established that the top 1 mm surface mat biomass contains carbonate minerals, leading to an initial inferred carbonate mineralisation rate of approximately 0.5 g per 1 cm2 per year (approx. per 10 g surface mat material). This rate of mineralisation will become more accurate as more analysis is completed particularly comparing samples of mat, initially before they went in to the tank experiment and after incremental time periods, 3 months, 6 months etc. Further analysis of mat growth will establish the extent to which the precipitated carbonate minerals result from microbial activity and the types of minerals precipitated. The rate of mineralisation can be scaled-up to the km scale with the potential to isolate mineralisation rates promoted by different communities and in different types of microbial mat.

The Intestinal Microbiome in Early Life: Health and Disease

PubMed Central

Arrieta, Marie-Claire; Stiemsma, Leah T.; Amenyogbe, Nelly; Brown, Eric M.; Finlay, Brett

2014-01-01

Human microbial colonization begins at birth and continues to develop and modulate in species abundance for about 3 years, until the microbiota becomes adult-like. During the same time period, children experience significant developmental changes that influence their health status as well as their immune system. An ever-expanding number of articles associate several diseases with early-life imbalances of the gut microbiota, also referred to as gut microbial dysbiosis. Whether early-life dysbiosis precedes and plays a role in disease pathogenesis, or simply originates from the disease process itself is a question that is beginning to be answered in a few diseases, including IBD, obesity, and asthma. This review describes the gut microbiome structure and function during the formative first years of life, as well as the environmental factors that determine its composition. It also aims to discuss the recent advances in understanding the role of the early-life gut microbiota in the development of immune-mediated, metabolic, and neurological diseases. A greater understanding of how the early-life gut microbiota impacts our immune development could potentially lead to novel microbial-derived therapies that target disease prevention at an early age. PMID:25250028

Role of Waterborne Pathogens in the Food Supply Chain: Implications to Risk Management with Local and Global Perspectives

EPA Science Inventory

Microbial risk assessment (MRA) in the food industry is used to support HACCP – which largely focuses on bacterial pathogen control in processing foodstuffs Potential role of microbially-contaminated water used in food production is not as well understood Emergence...

Biofilm-induced changes in microbial quality of irrigation water: Indicator bacteria and antibiotic-resistance

USDA-ARS?s Scientific Manuscript database

Irrigation waters are implicated in the transmission of pathogens to fresh produce, and microbial release and retention from biofilms that form on inner surfaces of irrigation lines may impact the quality of delivered water. Biofilms in water distribution systems have been suggested as a reservoir ...

Microbial community-level physiological profiling based on O2 consumption as an indicator of nitrogen status of agricultural soils

USDA-ARS?s Scientific Manuscript database

Nitrogen-limited soil microbial activity has important implications for soil carbon storage and nutrient availability, but previous methods for assessing resource limitation have been restricted, due to enrichment criteria (i.e., long incubation periods, high substrate amendments) and/or logistical ...

Microbial Mats of the Tswaing Impact Crater: Results of a South African Exobiology Expedition and Implications for the Search for Biological Molecules on Mars

NASA Astrophysics Data System (ADS)

Cockell, C. S.; Brandt, D.; Hand, K.; Lee, P.

2001-03-01

We describe microbial mats from the Tswaing impact crater in South Africa. The mats provide insights into the unique biological characteristics of impact craters and can help strategies for the search for biomolecules on Mars.

Year-round metagenomes reveal remarkably stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

USDA-ARS?s Scientific Manuscript database

Insight to what underlies the seasonal dynamics of indigenous soil microbial communities in agricultural soils, especially after major activities such as nitrogen fertilization, remain elusive. More detailed understanding of population dynamics will have important implications for modeling efforts a...

Antimicrobial properties of natural substances in irradiated fresh poultry

NASA Astrophysics Data System (ADS)

Mahrour, A.; Lacroix, M.; Nketsa-Tabiri, J.; Calderon, N.; Gagnon, M.

1998-06-01

This study was undertaken to determine if a combined treatment (marinating in natural plant extracts or vacuum) with irradiation could have a synergetic effect, in order to reduce the dose required for complete elimination of Salmonella on fresh poultry. The effect of these combined treatments on the shelf-life extension was also evaluated. The fresh chicken legs were irradiated at 0, 3 and 5 kGy. The poultry underwent microbial analysis(mesophilic and Salmonella detection). For each treatment, the total microbial count decreased with increase of irradiation dose. The marinating treatment have a synergistic effect with irradiation treatment to reduce the total microbial count and controlling the proliferation during storage at 4°C. Irradiation of fresh chicken pieces with a dose of 3 kGy appears to be able to extend the microbial shelf-life by a factor of 2. When the chicken is marinating and irradiated at 3 kGy or when irradiated at 5 kGy without marinating, the microbial shelf-life is extended by a factor of 7 to 8. No Salmonella was found during all the experiment in the chicken in air and marinated. However, a presence of Salmonella was found in samples irradiated at 5 kGy under vacuum, in unirradiated samples and samples irradiated at 3kGy in air and under vacuum.

Development of an autofluorescence spectral database for the identification and classification of microbial extremophiles

NASA Astrophysics Data System (ADS)

Davis, Justin; Howard, Hillari; Hoover, Richard B.; Sabanayagam, Chandran R.

2010-09-01

Extremophiles are microorganisms that have adapted to severe conditions that were once considered devoid of life. The extreme settings in which these organisms flourish on Earth resemble many extraterrestrial environments. Identification and classification of extremophiles in situ (without the requirement for excessive handling and processing) can provide a basis for designing remotely operated instruments for extraterrestrial life exploration. An important consideration when designing such experiments is to prevent contamination of the environments. We are developing a reference spectral database of autofluorescence from microbial extremophiles using long-UV excitation (408 nm). Aromatic compounds are essential components of living systems, and biological molecules such as aromatic amino acids, nucleotides, porphyrins and vitamins can also exhibit fluorescence under long-UV excitation conditions. Autofluorescence spectra were obtained from a light microscope that additionally allowed observations of microbial geometry and motility. It was observed that all extremophiles studied displayed an autofluorescence peak at around 470 nm, followed by a long decay that was species specific. The autofluorescence database can potentially be used as a reference to identify and classify past or present microbial life in our solar system.

Development of an Autofluorescence Spectral Database for the Identification and Classification of Microbial Extremophiles

NASA Technical Reports Server (NTRS)

Sabanayagam, Chandran; Howard, Hillari; Hoover, Richard B.

2010-01-01

Extremophiles are microorganisms that have adapted to severe conditions that were once considered devoid of life. The extreme settings in which these organisms flourish on earth resemble many extraterrestrial environments. Identification and classification of extremophiles in situ (without the requirement for excessive handling and processing) can provide a basis for designing remotely operated instruments for extraterrestrial life exploration. An important consideration when designing such experiments is to prevent contamination of the environments. We are developing a reference spectral database of autofluorescence from microbial extremophiles using long-UV excitation (405 nm). Aromatic compounds are essential components of living systems, and biological molecules such as aromatic amino acids, nucleotides, porphyrins and vitamins can also exhibit fluorescence under long-UV excitation conditions. Autofluorescence spectra were obtained from a confocal microscope that additionally allowed observations of microbial geometry and motility. It was observed that all extremophiles studied displayed an autofluorescence peak at around 470 nm, followed by a long decay that was species specific. The autofluorescence database can potentially be used as a reference to identify and classify past or present microbial life in our solar system.

Manipulating rumen microbiome and fermentation through interventions during early life: a review

PubMed Central

Yáñez-Ruiz, David R.; Abecia, Leticia; Newbold, Charles J.

2015-01-01

The nutritional manipulations of the rumen microbiome to enhance productivity and health are rather limited by the resilience of the ecosystem once established in the mature rumen. Based on recent studies, it has been suggested that the microbial colonization that occurs soon after birth opens a possibility of manipulation with potential to produce lasting effects into adult life. This paper presents the state-of-the-art in relation to early life nutritional interventions by addressing three areas: the development of the rumen as an organ in regards to the nutrition of the new-born, the main factors that determine the microbial population that first colonizes and establishes in the rumen, and the key immunity players that contribute to shaping the commensal microbiota in the early stage of life to understand host-microbiome specificity. The development of the rumen epithelium and muscularization are differently affected by the nature of the diet and special care should be taken with regards to transition from liquid (milk) to solid feed. The rumen is quickly colonized by all type of microorganisms straight after birth and the colonization pattern may be influenced by several factors such as presence/absence of adult animals, the first solid diet provided, and the inclusion of compounds that prevent/facilitate the establishment of some microorganisms or the direct inoculation of specific strains. The results presented show how early life events may be related to the microbial community structure and/or the rumen activity in the animals post-weaning. This would create differences in adaptive capacity due to different early life experiences and leads to the idea of microbial programming. However, many elements need to be further studied such as: the most sensitive window of time for interventions, the best means to test long term effectiveness, the role of key microbial groups and host-immune regulations. PMID:26528276

Microbial survival in deep space environment.

NASA Technical Reports Server (NTRS)

Silverman, G. J.

1971-01-01

Review of the knowledge available on the extent to which microorganisms (mainly microbial spores, vegetative cells, and fungi) are capable of surviving the environment of deep space, based on recent simulation experiments of deep space. A description of the experimental procedures used is followed by a discussion of deep space ecology, the behavior of microorganisms in ultrahigh vacuum, and factors influencing microbial survival. It is concluded that, so far, simulation experiments have proved far less lethal to microorganisms than to other forms of life. There are, however, wide gaps in the knowledge available, and no accurate predictions can as yet be made on the degree of lethality that might be incurred by a microbial population on a given mission. Therefore, sterilization of spacecraft surfaces is deemed necessary if induced panspermia (i.e., interplanetary life propagation) is to be avoided.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust.

PubMed

Salas, Everett C; Bhartia, Rohit; Anderson, Louise; Hug, William F; Reid, Ray D; Iturrino, Gerardo; Edwards, Katrina J

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

Toward Understanding, Managing, and Protecting Microbial Ecosystems

PubMed Central

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

Subduction zone forearc serpentinites as incubators for deep microbial life

NASA Astrophysics Data System (ADS)

Plümper, Oliver; King, Helen E.; Geisler, Thorsten; Liu, Yang; Pabst, Sonja; Savov, Ivan P.; Rost, Detlef; Zack, Thomas

2017-04-01

Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine serpentinite clasts expelled from mud volcanoes above the Izu-Bonin-Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni-Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides. Although an abiotic or subduction slab-derived fluid origin cannot be excluded, the similarities between the molecular signatures identified in the clasts and those of bacteria-derived biopolymers from other serpentinizing systems hint at the possibility of deep microbial life within the forearc. To test this hypothesis, we coupled the currently known temperature limit for life, 122 °C, with a heat conduction model that predicts a potential depth limit for life within the forearc at ˜10,000 m below the seafloor. This is deeper than the 122 °C isotherm in known oceanic serpentinizing regions and an order of magnitude deeper than the downhole temperature at the serpentinized Atlantis Massif oceanic core complex, Mid-Atlantic Ridge. We suggest that the organic-rich serpentinites may be indicators for microbial life deep within or below the mud volcano. Thus, the hydrated forearc mantle may represent one of Earth’s largest hidden microbial ecosystems. These types of protected ecosystems may have allowed the deep biosphere to thrive, despite violent phases during Earth’s history such as the late heavy bombardment and global mass extinctions.

Subduction zone forearc serpentinites as incubators for deep microbial life.

PubMed

Plümper, Oliver; King, Helen E; Geisler, Thorsten; Liu, Yang; Pabst, Sonja; Savov, Ivan P; Rost, Detlef; Zack, Thomas

2017-04-25

Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine serpentinite clasts expelled from mud volcanoes above the Izu-Bonin-Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni-Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides. Although an abiotic or subduction slab-derived fluid origin cannot be excluded, the similarities between the molecular signatures identified in the clasts and those of bacteria-derived biopolymers from other serpentinizing systems hint at the possibility of deep microbial life within the forearc. To test this hypothesis, we coupled the currently known temperature limit for life, 122 °C, with a heat conduction model that predicts a potential depth limit for life within the forearc at ∼10,000 m below the seafloor. This is deeper than the 122 °C isotherm in known oceanic serpentinizing regions and an order of magnitude deeper than the downhole temperature at the serpentinized Atlantis Massif oceanic core complex, Mid-Atlantic Ridge. We suggest that the organic-rich serpentinites may be indicators for microbial life deep within or below the mud volcano. Thus, the hydrated forearc mantle may represent one of Earth's largest hidden microbial ecosystems. These types of protected ecosystems may have allowed the deep biosphere to thrive, despite violent phases during Earth's history such as the late heavy bombardment and global mass extinctions.

Subduction zone forearc serpentinites as incubators for deep microbial life

PubMed Central

Plümper, Oliver; Geisler, Thorsten; Liu, Yang; Pabst, Sonja; Savov, Ivan P.; Rost, Detlef; Zack, Thomas

2017-01-01

Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine serpentinite clasts expelled from mud volcanoes above the Izu–Bonin–Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni–Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides. Although an abiotic or subduction slab-derived fluid origin cannot be excluded, the similarities between the molecular signatures identified in the clasts and those of bacteria-derived biopolymers from other serpentinizing systems hint at the possibility of deep microbial life within the forearc. To test this hypothesis, we coupled the currently known temperature limit for life, 122 °C, with a heat conduction model that predicts a potential depth limit for life within the forearc at ∼10,000 m below the seafloor. This is deeper than the 122 °C isotherm in known oceanic serpentinizing regions and an order of magnitude deeper than the downhole temperature at the serpentinized Atlantis Massif oceanic core complex, Mid-Atlantic Ridge. We suggest that the organic-rich serpentinites may be indicators for microbial life deep within or below the mud volcano. Thus, the hydrated forearc mantle may represent one of Earth’s largest hidden microbial ecosystems. These types of protected ecosystems may have allowed the deep biosphere to thrive, despite violent phases during Earth’s history such as the late heavy bombardment and global mass extinctions. PMID:28396389

Cultivation Of Deep Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Obrzut, Natalia; Casar, Caitlin; Osburn, Magdalena R.

2018-01-01

The potential habitability of surface environments on other planets in our solar system is limited by exposure to extreme radiation and desiccation. In contrast, subsurface environments may offer protection from these stressors and are potential reservoirs for liquid water and energy that support microbial life (Michalski et al., 2013) and are thus of interest to the astrobiology community. The samples used in this project were extracted from the Deep Mine Microbial Observatory (DeMMO) in the former Homestake Mine at depths of 800 to 2000 feet underground (Osburn et al., 2014). Phylogenetic data from these sites indicates the lack of cultured representatives within the community. We used geochemical data to guide media design to cultivate and isolate organisms from the DeMMO communities. Media used for cultivation varied from heterotrophic with oxygen, nitrate or sulfate to autotrophic media with ammonia or ferrous iron. Environmental fluid was used as inoculum in batch cultivation and strains were isolated via serial transfers or dilution to extinction. These methods resulted in isolating aerobic heterotrophs, nitrate reducers, sulfate reducers, ammonia oxidizers, and ferric iron reducers. DNA sequencing of these strains is underway to confirm which species they belong to. This project is part of the NASA Astrobiology Institute Life Underground initiative to detect and characterize subsurface microbial life; by characterizing the intraterrestrials, the life living deep within Earth’s crust, we aim to understand the controls on how and where life survives in subsurface settings. Cultivation of terrestrial deep subsurface microbes will provide insight into the survival mechanisms of intraterrestrials guiding the search for these life forms on other planets.

Molecular Microbial Analyses of the Mars Exploration Rovers Assembly Facility

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; LaDuc, Myron T.; Newcombe, David; Kempf, Michael J.; Koke, John. A.; Smoot, James C.; Smoot, Laura M.; Stahl, David A.

2004-01-01

During space exploration, the control of terrestrial microbes associated with robotic space vehicles intended to land on extraterrestrial solar system bodies is necessary to prevent forward contamination and maintain scientific integrity during the search for life. Microorganisms associated with the spacecraft assembly environment can be a source of contamination for the spacecraft. In this study, we have monitored the microbial burden of air samples of the Mars Exploration Rovers' assembly facility at the Kennedy Space Center utilizing complementary diagnostic tools. To estimate the microbial burden and identify potential contaminants in the assembly facility, several microbiological techniques were used including culturing, cloning and sequencing of 16S rRNA genes, DNA microarray analysis, and ATP assays to assess viable microorganisms. Culturing severely underestimated types and amounts of contamination since many of the microbes implicated by molecular analyses were not cultivable. In addition to the cultivation of Agrobacterium, Burkholderia and Bacillus species, the cloning approach retrieved 16s rDNA sequences of oligotrophs, symbionts, and y-proteobacteria members. DNA microarray analysis based on rational probe design and dissociation curves complemented existing molecular techniques and produced a highly parallel, high resolution analysis of contaminating microbial populations. For instance, strong hybridization signals to probes targeting the Bacillus species indicated that members of this species were present in the assembly area samples; however, differences in dissociation curves between perfect-match and air sample sequences showed that these samples harbored nucleotide polymorphisms. Vegetative cells of several isolates were resistant when subjected to treatments of UVC (254 nm) and vapor H202 (4 mg/L). This study further validates the significance of non-cultivable microbes in association with spacecraft assembly facilities, as our analyses have identified several non-cultivable microbes likely to contaminate the surfaces of spacecraft hardware.

Implications of a 3.472–3.333 Gyr-old subaerial microbial mat from the Barberton greenstone belt, South Africa for the UV environmental conditions on the early Earth

PubMed Central

Westall, Frances; de Ronde, Cornel E.J; Southam, Gordon; Grassineau, Nathalie; Colas, Maggy; Cockell, Charles; Lammer, Helmut

2006-01-01

Modelling suggests that the UV radiation environment of the early Earth, with DNA weighted irradiances of about three orders of magnitude greater than those at present, was hostile to life forms at the surface, unless they lived in specific protected habitats. However, we present empirical evidence that challenges this commonly held view. We describe a well-developed microbial mat that formed on the surface of volcanic littoral sediments in an evaporitic environment in a 3.5–3.3 Ga-old formation from the Barberton greenstone belt. Using a multiscale, multidisciplinary approach designed to strongly test the biogenicity of potential microbial structures, we show that the mat was constructed under flowing water by 0.25 μm filaments that produced copious quantities of extracellular polymeric substances, representing probably anoxygenic photosynthesizers. Associated with the mat is a small colony of rods–vibroids that probably represent sulphur-reducing bacteria. An embedded suite of evaporite minerals and desiccation cracks in the surface of the mat demonstrates that it was periodically exposed to the air in an evaporitic environment. We conclude that DNA-damaging UV radiation fluxes at the surface of the Earth at this period must either have been low (absorbed by CO2, H2O, a thin organic haze from photo-dissociated CH4, or SO2 from volcanic outgassing; scattered by volcanic, and periodically, meteorite dust, as well as by the upper layers of the microbial mat) and/or that the micro-organisms exhibited efficient gene repair/survival strategies. PMID:17008224

Astrobiological implications of dim light phototrophy in deep-sea red clays

NASA Astrophysics Data System (ADS)

Das, Anindita; Singh, Tanya; LokaBharathi, P. A.; Dhakephalkar, Prashant K.; Mallik, Sweta; Kshirsagar, Pranav R.; Khadge, N. H.; Nath, B. Nagender; Bhattacharya, Satadru; Dagar, Aditya Kumar; Kaur, Prabhjot; Ray, Dwijesh; Shukla, Anil D.; Fernandes, Christabelle E. G.; Fernandes, Sheryl O.; Thomas, Tresa Remya A.; Mamatha, S. S.; Mourya, Babu Shashikant; Meena, Ram Murti

2017-02-01

Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66 W m-2, were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2 °C and 25°± 2 °C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably influence Doppler effects and consequently spectral detection techniques exo-planetary microbial life.

Detection of Biosignatures in Natural and Microbial Cultured Jarosites Using Laser- Desorption Fourier Transform Mass Spectrometry: Implications for Astrobiology

NASA Astrophysics Data System (ADS)

Kotler, J.; Hinman, N. W.; Yan, B.; Stoner, D. L.; Scott, J. R.

2006-12-01

The jarosite group minerals have received increasing attention since the discovery by the Mars Exploration Rover-Opportunity of jarosite on the Martian surface. The general chemical formula for jarosite is XFe3(SO4)2(OH)6 where the X represents both monovalent and divalent cations that can occupy the axial positions in the crystal structure. Commonly found ions include K+, Na+, H3O+, NH4+, and Pb2+ with reports of other large ions occupying this position in the literature. Modeling efforts have been performed to confirm that jarosite has the ability to incorporate a variety of "foreign" cations. The minerals unique ability to incorporate various large ions in its structure and its association with biological activity in terrestrial environments has lead to investigations regarding its use as an indicator of aqueous and/or biological activity. The use of laser desorption Fourier transform mass spectrometry (LD-FTMS) has revealed the presence of organic matter including the amino acid, glycine, in several jarosite samples from various worldwide locations. Iron precipitates derived from acidophilic microbial cultures were also analyzed. Using attenuated total reflectance infrared spectroscopy (ATR-IR), signals indicative of microbes or microbial exudates were weak and ambiguous. In contrast, LD-FTMS clearly detected bioorganic constituents in some desorption spots. However, the signals were sporadic and required the laser scanning/imaging capability of our laboratory built system to locate the microbial signatures in the heterogeneous samples. The ability to observe these bioorganic signatures in jarosite samples using the instrumental technique employed in this study furthers the goals of planetary geologists to determine whether signs of life (e.g., presence of biomolecules or biomolecule precursors) can be detected in the rock record of terrestrial and extraterrestrial samples.

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

PubMed Central

Bledsoe, Jacob W.; Peterson, Brian C.; Swanson, Kelly S.; Small, Brian C.

2016-01-01

Aquaculture recently overtook capture fisheries as the largest producer of food fish, but to continue increasing fish production the industry is in search of better methods of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high-throughput DNA sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (dph), while also characterizing the environmental microbes derived from the water supply and the administered diets. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 dph when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 dph. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the species Cetobacterium somerae and Plesiomonas shigelloides showing the highest abundance in the catfish microbiota after 3 dph. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water-supply. Although, there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Our results have implications for future research related to channel catfish biology and culture, and increase our understanding of ontogenetic effects on the microbiota of teleost fish. PMID:27846300

Abiogenic and Microbial Controls on Volatile Fatty Acids in Precambrian Crustal Fracture Waters

NASA Astrophysics Data System (ADS)

McDermott, J. M.; Heuer, V.; Tille, S.; Moran, J.; Slater, G.; Sutcliffe, C. N.; Glein, C. R.; Hinrichs, K. U.; Sherwood Lollar, B.

2015-12-01

Saline fracture waters within the Precambrian Shield rocks of Canada and South Africa have been sequestered underground over geologic timescales up to 1.1-1.8 Ga [1, 2]. These fluids are rich in H2 derived from radiolysis and hydration of mafic and ultramafic rocks [1, 2, 3] and host a low-biomass, low-diversity microbial ecosystem at some sites [2]. The abiogenic or biogenic nature of geochemical processes has important implications for bioavailable carbon sources and the role played by abiotic organic synthesis in sustaining a chemosynthetic deep biosphere. Volatile fatty acids (VFAs) are simple carboxylic acids that may support microbial communities in such environments, such as those found in terrestrial [4] and deep-sea [5] hot springs. We present abundance and δ13C analysis for VFAs in a spectrum of Canadian Shield fluids characterized by varying dissolved H2, CH4, and C2+ n-alkane compositions. Isotope mass balance indicates that microbially mediated fermentation of carbon-rich graphitic sulfides may produce the elevated levels of acetate (39-273 μM) found in Birchtree and Thompson mine. In contrast, thermodynamic considerations and isotopic signatures of the notably higher acetate (1.2-1.9 mM), as well as formate and propionate abundances (371-816 μM and 20-38 μM, respectively) found at Kidd Creek mine suggest a role for abiogenic production via reduction of dissolved inorganic carbon with H2 for formate, and oxidation of C2+ n-alkanes for acetate and propionate, along with possible microbial cycling. VFAs comprise the bulk of dissolved and total organic carbon in the mines surveyed, and as such represent a potential key substrate for life. [1] Holland et al. (2013) Nature 497: 367-360. [2] Lin et al. (2006) Science 314: 479-482. [3] Sherwood Lollar et al. (2014) Nature 516: 379-382. [4] Windman et al. (2007) Astrobiology 7(6): 873-890. [5] Lang et al. (2010) Geochim. Cosmochim. Acta 92: 82-99.

Glycerol enhances fungal germination at the water-activity limit for life.

PubMed

Stevenson, Andrew; Hamill, Philip G; Medina, Ángel; Kminek, Gerhard; Rummel, John D; Dijksterhuis, Jan; Timson, David J; Magan, Naresh; Leong, Su-Lin L; Hallsworth, John E

2017-03-01

For the most-extreme fungal xerophiles, metabolic activity and cell division typically halts between 0.700 and 0.640 water activity (approximately 70.0-64.0% relative humidity). Here, we investigate whether glycerol can enhance xerophile germination under acute water-activity regimes, using an experimental system which represents the biophysical limit of Earth's biosphere. Spores from a variety of species, including Aspergillus penicillioides, Eurotium halophilicum, Xerochrysium xerophilum (formerly Chrysosporium xerophilum) and Xeromyces bisporus, were produced by cultures growing on media supplemented with glycerol (and contained up to 189 mg glycerol g dry spores -1 ). The ability of these spores to germinate, and the kinetics of germination, were then determined on a range of media designed to recreate stresses experienced in microbial habitats or anthropogenic systems (with water-activities from 0.765 to 0.575). For A. penicillioides, Eurotium amstelodami, E. halophilicum, X. xerophilum and X. bisporus, germination occurred at lower water-activities than previously recorded (0.640, 0.685, 0.651, 0.664 and 0.637 respectively). In addition, the kinetics of germination at low water-activities were substantially faster than those reported previously. Extrapolations indicated theoretical water-activity minima below these values; as low as 0.570 for A. penicillioides and X. bisporus. Glycerol is present at high concentrations (up to molar levels) in many types of microbial habitat. We discuss the likely role of glycerol in expanding the water-activity limit for microbial cell function in relation to temporal constraints and location of the microbial cell or habitat. The findings reported here have also critical implications for understanding the extremes of Earth's biosphere; for understanding the potency of disease-causing microorganisms; and in biotechnologies that operate at the limits of microbial function. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.

PubMed

Zhang, Naili; Liu, Weixing; Yang, Haijun; Yu, Xingjun; Gutknecht, Jessica L M; Zhang, Zhe; Wan, Shiqiang; Ma, Keping

2013-11-01

A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.

Potential Research and Development Synergies between Life support and Planetary protection

NASA Astrophysics Data System (ADS)

Lasseur, Ch.; Kminek, G.; Mergeay, M.

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination These risks concern both crew health via the metabolic consumables contamination water air but and also the hardware degradation Over the last six years ESA and IBMP have developed a collaboration to elaborate and document these microbial contamination issues The collaboration involved the mutual exchanges of knowledge as well as microbial samples and leads up to the microbial survey of the Russian module of the ISS Based on these results and in addition to an external expert report commissioned by ESA the agency initiated the development of a rapid and automated microbial detection and identification tool for use in future space missions In parallel to these developments and via several international meetings planetary protection experts have agreed to place clear specification of the microbial quality of future hardware landing on virgin planets as well as elaborate the preliminary requirements of contamination for manned missions on surface For these activities its is necessary to have a better understanding of microbial activity to create culture collection and to develop on-line detection tools Within this paper we present more deeply the life support activities related to microbial issues we identify some potential synergies with Planetary protection developments and we propose some pathway for collaboration between these two communities

Life cycle of soil sggregates: from root residue to microbial and physical hotspots

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2017-12-01

Soil aggregation is a physical state of soil in which clumps of primary soil particles are held together by biological and/or chemical cementing agents. Aggregations plays important role in storage and movement of water and essential gases, nutrient cycling, and ultimately supporting microbial and plant life. It is also one of the most dynamic and sensitive soil qualities, which readily responds to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

[Microbial secondary metabolites as potential reserve of pharmaceuticals].

PubMed

Orlova, T I; Bulgakova, V G; Polin, A N

2014-01-01

The major characteristics of new bioactive microbial secondary metabolites are summarized in the review. A wide range of new molecular targets are implicated in discovery of new nonantibiotic compounds with some other pharmacological activities (noninfectious diseases). Microorganisms represent fascinating resources due to their production of novel products with broad spectra of bioactivities.

Plant–microbial competition for nitrogen increases microbial activities and carbon loss in invaded soils

Treesearch

Matthew E. Craig; Jennifer M. Fraterrigo

2017-01-01

Many invasive plant species show high rates of nutrient acquisition relative to their competitors. Yet the mechanisms underlying this phenomenon, and its implications for ecosystem functioning, are poorly understood, particularly in nutrient-limited systems. Here, we test the hypothesis that an invasive plant species (Microstegium vimineum...

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

PubMed Central

Lindensmith, Christian A.; Rider, Stephanie; Bedrossian, Manuel; Wallace, J. Kent; Serabyn, Eugene; Showalter, G. Max; Deming, Jody W.; Nadeau, Jay L.

2016-01-01

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. PMID:26812683

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

PubMed

Lindensmith, Christian A; Rider, Stephanie; Bedrossian, Manuel; Wallace, J Kent; Serabyn, Eugene; Showalter, G Max; Deming, Jody W; Nadeau, Jay L

2016-01-01

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.

Endolithic microbial habitats as refuges for life in polyextreme environment of the Atacama Desert.

PubMed

Wierzchos, Jacek; Casero, M Cristina; Artieda, Octavio; Ascaso, Carmen

2018-01-22

The extremely harsh conditions of hyperarid deserts are a true challenge for microbial life. Microorganisms thriving in such polyextreme environments are fascinating as they can tell us more about life, its strategies and its boundaries than other groups of organisms. The Atacama Desert (North Chile) holds two world records of extreme environmental characteristics: the lowest rainfall and greatest surface ultraviolet radiation and total solar irradiance ever measured on Earth. Despite these limiting conditions for life, we recently identified several remarkable examples of endolithic habitats colonized by phototrophic and heterotrophic microorganisms in the hyperarid core of the Atacama Desert. Copyright © 2018 Elsevier Ltd. All rights reserved.

A trait-based approach for examining microbial community assembly

NASA Astrophysics Data System (ADS)

Prest, T. L.; Nemergut, D.

2015-12-01

Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

PubMed Central

Davis, Erin C.; Wang, Mei; Donovan, Sharon M.

2017-01-01

ABSTRACT The development of the human infant intestinal microbiota is a sequential process that begins in utero and continues during the first 2 to 3 years of life. Microbial composition and diversity are shaped by host genetics and multiple environmental factors, of which diet is a principal contributor. An understanding of this process is of clinical importance as the microbiota acquired in early life influence gastrointestinal, immune and neural development, and reduced microbial diversity or dysbiosis during infancy is associated with disorders in infancy and later childhood. The goal of this article was to review the published literature that used culture-independent methods to describe the development of the gastrointestinal microbiota in breast- and formula-fed human infants as well as the impact of prebiotic and probiotic addition to infant formula, and the addition of solid foods. PMID:28068209

TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells.

PubMed

Piersma, Sjouke; Denham, Emma L; Drulhe, Samuel; Tonk, Rudi H J; Schwikowski, Benno; van Dijl, Jan Maarten

2013-01-01

Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly 'noisy' heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological 'cell factory'. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images.

The intestinal microbiome, probiotics and prebiotics in neurogastroenterology

PubMed Central

Saulnier, Delphine M.; Ringel, Yehuda; Heyman, Melvin B.; Foster, Jane A.; Bercik, Premysl; Shulman, Robert J.; Versalovic, James; Verdu, Elena F.; Dinan, Ted G.; Hecht, Gail; Guarner, Francisco

2013-01-01

The brain-gut axis allows bidirectional communication between the central nervous system (CNS) and the enteric nervous system (ENS), linking emotional and cognitive centers of the brain with peripheral intestinal functions. Recent experimental work suggests that the gut microbiota have an impact on the brain-gut axis. A group of experts convened by the International Scientific Association for Probiotics and Prebiotics (ISAPP) discussed the role of gut bacteria on brain functions and the implications for probiotic and prebiotic science. The experts reviewed and discussed current available data on the role of gut microbiota on epithelial cell function, gastrointestinal motility, visceral sensitivity, perception and behavior. Data, mostly gathered from animal studies, suggest interactions of gut microbiota not only with the enteric nervous system but also with the central nervous system via neural, neuroendocrine, neuroimmune and humoral links. Microbial colonization impacts mammalian brain development in early life and subsequent adult behavior. These findings provide novel insights for improved understanding of the potential role of gut microbial communities on psychological disorders, most particularly in the field of psychological comorbidities associated with functional bowel disorders like irritable bowel syndrome (IBS) and should present new opportunity for interventions with pro- and prebiotics. PMID:23202796

Discovery of a hypersaline subglacial lake complex beneath Devon Ice Cap, Canadian Arctic

PubMed Central

Blankenship, Donald D.; Schroeder, Dustin M.; Dowdeswell, Julian A.

2018-01-01

Subglacial lakes are unique environments that, despite the extreme dark and cold conditions, have been shown to host microbial life. Many subglacial lakes have been discovered beneath the ice sheets of Antarctica and Greenland, but no spatially isolated water body has been documented as hypersaline. We use radio-echo sounding measurements to identify two subglacial lakes situated in bedrock troughs near the ice divide of Devon Ice Cap, Canadian Arctic. Modeled basal ice temperatures in the lake area are no higher than −10.5°C, suggesting that these lakes consist of hypersaline water. This implication of hypersalinity is in agreement with the surrounding geology, which indicates that the subglacial lakes are situated within an evaporite-rich sediment unit containing a bedded salt sequence, which likely act as the solute source for the brine. Our results reveal the first evidence for subglacial lakes in the Canadian Arctic and the first hypersaline subglacial lakes reported to date. We conclude that these previously unknown hypersaline subglacial lakes may represent significant and largely isolated microbial habitats, and are compelling analogs for potential ice-covered brine lakes and lenses on planetary bodies across the solar system. PMID:29651462

Acetylene as fast food: implications for development of life on anoxic primordial Earth and in the outer solar system.

PubMed

Oremland, Ronald S; Voytek, Mary A

2008-02-01

Acetylene occurs, by photolysis of methane, in the atmospheres of jovian planets and Titan. In contrast, acetylene is only a trace component of Earth's current atmosphere. Nonetheless, a methane-rich atmosphere has been hypothesized for early Earth; this atmosphere would also have been rich in acetylene. This poses a paradox, because acetylene is a potent inhibitor of many key anaerobic microbial processes, including methanogenesis, anaerobic methane oxidation, nitrogen fixation, and hydrogen oxidation. Fermentation of acetylene was discovered approximately 25 years ago, and Pelobacter acetylenicus was shown to grow on acetylene by virtue of acetylene hydratase, which results in the formation of acetaldehyde. Acetaldehyde subsequently dismutates to ethanol and acetate (plus some hydrogen). However, acetylene hydratase is specific for acetylene and does not react with any analogous compounds. We hypothesize that microbes with acetylene hydratase played a key role in the evolution of Earth's early biosphere by exploiting an available source of carbon from the atmosphere and in so doing formed protective niches that allowed for other microbial processes to flourish. Furthermore, the presence of acetylene in the atmosphere of a planet or planetoid could possibly represent evidence for an extraterrestrial anaerobic ecosystem.

Neutral theory, microbial practice: challenges in bacterial population genetics.

PubMed

Rocha, Eduardo P C

2018-04-19

Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.

Properties of biophotons and their theoretical implications.

PubMed

Popp, Fritz-Albert

2003-05-01

The word "biophotons" is used to denote a permanent spontaneous photon emission from all living systems. It displays a few up to some hundred photons/(s x cm2) within the spectral range from at least 260 to 800 nm. It is closely linked to delayed luminescence (DL) of biological tissues which describes the long term and ultra weak reemission of photons after exposure to light illumination. During relaxation DL turns continuously into the steady state biophoton emission, where both, DL and biophoton emission exhibit mode coupling over the entire spectrum and a Poissonian photo count distribution. DL is representing excited states of the biophoton field. The physical properties indicate that biophotons originate from fully coherent and sometimes even squeezed states. The physical analysis provides thermodynamic and quantum optical interpretation, in order to understand the biological impacts of biophotons. Biological phenomena like intracellular and intercellular communication, cell growth and differentiation, interactions among biological systems (like "Gestaltbildung" or swarming), and microbial infections can be understood in terms of biophotons. "Biophotonics", the corresponding field of applications, provide a new powerful tool for assessing the quality of food (like freshness and shelf life), microbial infections, environmental influences and for substantiating medical diagnosis and therapy.

Acetylene as fast food: Implications for development of life on anoxic primordial earth and in the outer solar system

USGS Publications Warehouse

Oremland, R.S.; Voytek, M.A.

2008-01-01

Acetylene occurs, by photolysis of methane, in the atmospheres of jovian planets and Titan. In contrast, acetylene is only a trace component of Earth's current atmosphere. Nonetheless, a methane-rich atmosphere has been hypothesized for early Earth; this atmosphere would also have been rich in acetylene. This poses a paradox, because acetylene is a potent inhibitor of many key anaerobic microbial processes, including methanogenesis, anaerobic methane oxidation, nitrogen fixation, and hydrogen oxidation. Fermentation of acetylene was discovered 25 years ago, and Pelobacter acetylenicus was shown to grow on acetylene by virtue of acetylene hydratase, which results in the formation of acetaldehyde. Acetaldehyde subsequently dismutates to ethanol and acetate (plus some hydrogen). However, acetylene hydratase is specific for acetylene and does not react with any analogous compounds. We hypothesize that microbes with acetylene hydratase played a key role in the evolution of Earth's early biosphere by exploiting an available source of carbon from the atmosphere and in so doing formed protective niches that allowed for other microbial processes to flourish. Furthermore, the presence of acetylene in the atmosphere of a planet or planetoid could possibly represent evidence for an extraterrestrial anaerobic ecosystem. ?? Mary Ann Liebert, Inc.

Parenteral Nutrition-Associated Liver Disease: The Role of the Gut Microbiota.

PubMed

Cahova, Monika; Bratova, Miriam; Wohl, Petr

2017-09-07

Parenteral nutrition (PN) provides life-saving nutritional support in situations where caloric supply via the enteral route cannot cover the necessary needs of the organism. However, it does have serious adverse effects, including parenteral nutrition-associated liver disease (PNALD). The development of liver injury associated with PN is multifactorial, including non-specific intestine inflammation, compromised intestinal permeability, and barrier function associated with increased bacterial translocation, primary and secondary cholangitis, cholelithiasis, short bowel syndrome, disturbance of hepatobiliary circulation, lack of enteral nutrition, shortage of some nutrients (proteins, essential fatty acids, choline, glycine, taurine, carnitine, etc.), and toxicity of components within the nutrition mixture itself (glucose, phytosterols, manganese, aluminium, etc.). Recently, an increasing number of studies have provided evidence that some of these factors are directly or indirectly associated with microbial dysbiosis in the intestine. In this review, we focus on PN-induced changes in the taxonomic and functional composition of the microbiome. We also discuss immune cell and microbial crosstalk during parenteral nutrition, and the implications for the onset and progression of PNALD. Finally, we provide an overview of recent advances in the therapeutic utilisation of pro- and prebiotics for the mitigation of PN-associated liver complications.

Lunar and Planetary Science XXXVI, Part 3

NASA Technical Reports Server (NTRS)

2005-01-01

Topics discussed include: Characterization of Non-Organized Soils at Gusev Crater with the Spirit Rover Data; Searching for Life with Rovers: Exploration Methods & Science Results from the 2004 Field Campaign of the "Life in the Atacama" Project and Applications to Future Mars Missions; Analysis of the Lunar Surface with Global Mineral and Mg-Number Maps ALH77005: The Magmatic History from Rehomogenized Melt Inclusions; New 70-cm Radar Mapping of the Moon; Cryptomare Deposits Revealed by 70-cm Radar; Construction of a PZT Sensor Network for Low and Hypervelocity Impact Detection; Palmer Quest: A Feasible Nuclear Fission "Vision Mission" to the Mars Polar Caps; Physical Properties of Volcanic Deposits on Venus from Radar Polarimetry; Science Alert Demonstration with a Rover Traverse Science Data Analysis System; Earth and Mars, Similar Features and Parallel Lives? Didactic Activities; Expected Constraints on Rhea s Interior from Cassini; Microbially Induced Precipitates: Examples from CO3, Si-, Mn- and Fe-rich Deposits; Li, B - Behavior in Lunar Basalts During Shock and Thermal Metamorphism: Implications for H2O in Martian Magmas; Evaluation of CO Self-Shielding as a Possible Mechanism for Anomalous Oxygen Isotopic Composition of Early Solar System Materials; Effect of Ground Ice on Apparent Thermal Inertia on Mars; Utah Marbles and Mars Blueberries: Comparative Terrestrial Analogs for Hematite Concretions on Mars; Newly Discovered Meteor Crater Metallic Impact Spherules: Report and Implications; and Evidence of Very Young Glacial Processes in Central Candor Chasma, Mars.

Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

NASA Technical Reports Server (NTRS)

Bebout, Brad M.; Bucaria, Robin

2006-01-01

Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively compact (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, we have developed curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. Our web site (http://microbes.arc.nasa.gov) includes reference materials, lesson plans, and a "Web Lab", featuring living mats maintained in a mini-aquarium. The site also provides information as to how research on microbial mats supports NASA's goals, and various NASA missions. A photo gallery contains images of mats, microscopic views of the organisms that form them, and our own research activities. An animated educational video on the web site uses computer graphic and video microscopy to take students on a journey into a microbial mat. These activities are targeted to a middle school audience and are aligned with the National Science Standards.

Basaltic glass as a habitat for microbial life: Implications for astrobiology and planetary exploration

NASA Astrophysics Data System (ADS)

Izawa, M. R. M.; Banerjee, N. R.; Flemming, R. L.; Bridge, N. J.; Schultz, C.

2010-03-01

Recent studies have demonstrated that terrestrial subaqueous basalts and hyaloclastites are suitable microbial habitats. During subaqueous basaltic volcanism, glass is produced by the quenching of basaltic magma upon contact with water. On Earth, microbes rapidly begin colonizing the glassy surfaces along fractures and cracks that have been exposed to water. Microbial colonization of basaltic glass leads to the alteration and modification of the rocks and produces characteristic granular and/or tubular bioalteration textures. Infilling of the alteration textures by minerals such as phyllosilicates, zeolites and titanite may enable their preservation through geologic time. Basaltic rocks are a major component of the Martian crust and are widespread on other solar system bodies. A variety of lines of evidence strongly suggests the long-term existence of abundant liquid water on ancient Mars. Recent orbiter, lander and rover missions have found evidence for the presence of transient liquid water on Mars, perhaps persisting to the present day. Many other solar system bodies, notably Europa, Enceladus and other icy satellites, may contain (or have once hosted) subaqueous basaltic glasses. The record of terrestrial glass bioalteration has been interpreted to extend as far back as ˜3.5 billion years ago and is widespread in oceanic crust and its metamorphic equivalents. The terrestrial record of glass bioalteration strongly suggests that glassy or formerly glassy basaltic rocks on extraterrestrial bodies that have interacted with liquid water are high-value targets for astrobiological exploration.

Experimental observations on the decay of environmental DNA from bighead and silver carps

USGS Publications Warehouse

Lance, Richard F.; Klymus, Katy E.; Richter, Cathy; Guan, Xin; Farrington, Heather L.; Carr, Matthew R.; Thompson, Nathan; Chapman, Duane C.; Baerwaldt, Kelly L.

2017-01-01

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp (Hypophthalmichthys nobilis) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp (H. molitrix), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

An astrophysical view of Earth-based metabolic biosignature gases.

PubMed

Seager, Sara; Schrenk, Matthew; Bains, William

2012-01-01

Microbial life on Earth uses a wide range of chemical and energetic resources from diverse habitats. An outcome of this microbial diversity is an extensive and varied list of metabolic byproducts. We review key points of Earth-based microbial metabolism that are useful to the astrophysical search for biosignature gases on exoplanets, including a list of primary and secondary metabolism gas byproducts. Beyond the canonical, unique-to-life biosignature gases on Earth (O(2), O(3), and N(2)O), the list of metabolic byproducts includes gases that might be associated with biosignature gases in appropriate exoplanetary environments. This review aims to serve as a starting point for future astrophysical biosignature gas research.

Biomineralization of As(V)-hydrous ferric oxyhydroxide in microbial mats of an acid-sulfate-chloride geothermal spring, Yellowstone National Park

NASA Astrophysics Data System (ADS)

Inskeep, William P.; Macur, Richard E.; Harrison, Gregory; Bostick, Benjamin C.; Fendorf, Scott

2004-08-01

Acid-sulfate-chloride (pH˜3) geothermal springs in Yellowstone National Park (YNP) often contain Fe(II), As(III), and S(-II) at discharge, providing several electron donors for chemolithotrophic metabolism. The microbial populations inhabiting these environments are inextricably linked with geochemical processes controlling the behavior of As and Fe. Consequently, the objectives of the current study were to (i) characterize Fe-rich microbial mats of an ASC thermal spring, (ii) evaluate the composition and structure of As-rich hydrous ferric oxides (HFO) associated with these mats, and (iii) identify microorganisms that are potentially responsible for mat formation via the oxidation of Fe(II) and or As(III). Aqueous and solid phase mat samples obtained from a spring in Norris Basin, YNP (YNP Thermal Inventory NHSP35) were analyzed using a complement of chemical, microscopic and spectroscopic techniques. In addition, molecular analysis (16S rDNA) was used to identify potentially dominant microbial populations within different mat locations. The biomineralization of As-rich HFO occurs in the presence of nearly equimolar aqueous As(III) and As(V) (˜12 μM), and ˜ 48 μM Fe(II), forming sheaths external to microbial cell walls. These solid phases were found to be poorly ordered nanocrystalline HFO containing mole ratios of As(V):Fe(III) of 0.62 ± 0.02. The bonding environment of As(V) and Fe(III) is consistent with adsorption of arsenate on edge and corner positions of Fe(III)-OH octahedra. Numerous archaeal and bacterial sequences were identified (with no closely related cultured relatives), along with several 16S sequences that are closely related to Acidimicrobium, Thiomonas, Metallosphaera and Marinithermus isolates. Several of these cultured relatives have been implicated in Fe(II) and or As(III) oxidation in other low pH, high Fe, and high As environments (e.g. acid-mine drainage). The unique composition and morphologies of the biomineralized phases may be useful as modern-day analogs for identifying microbial life in past Fe-As rich environments.

Non-extremophilic 'extremophiles' - Archaeal dominance in the subsurface and their implication for life

NASA Astrophysics Data System (ADS)

Reitschuler, Christoph; Lins, Philipp; Illmer, Paul

2014-05-01

Archaea - besides bacteria and eukaryota constituting the third big domain of life - were so far regarded as typical inhabitants of extreme environments, as indicated by the name (Archaeon, Greek: 'original', 'primal'). Previous research and cultivation successes were basically carried out in habitats characterized by extreme temperature, pH and salinity regimes. Such extreme conditions, as expected at the beginning of the Earth's evolution, are occasionally also prevalent on extraterrestrial planets and moons and make the Archaeal domain a key group to be studied concerning life's evolution and the most likely pioneer organisms to colonize environments that are regarded as hostile. However, in recent years it became obvious that Archaea, in particular non-extremophilic species, can be found almost ubiquitously in marine, freshwater, terrestrial and also subsurface habitats and occasionally outnumber other microbial domains and hold key positions in globally relevant energy and nutrient cycles. Besides extreme environments - the big question remains how to define a parameter as extreme - subsurface and cave environments present a window to the past, where adaptions to early life's conditions can be studied and how microbiomes may be structured in a habitat that represents a refugium on extraterrestrial celestial bodies, were surface conditions might be at first sight too extreme for life. The lower part of the alpine Hundsalm cave in Tyrol (Austria) offered a unique opportunity to study an almost pristine cave habitat, which is separated from the touristic part of the ice cave. The main focus of our research was laid on the microbial communities that were supposed to be in connection with secondary carbonate precipitations ('moonmilk'). For the ascertainment of these so far poorly evaluated structures a multiple approach assessment was chosen to generate a virtually complete picture of these subsurface microbiomes. Thereby, a combination of different cultivation strategies was applied as well as physiological analyses, comprising HPLC and GC analyses, and molecular approaches, covering end-point and quantitative PCRs, DGGE, cloning, and sequencing analyses. Outstanding in the course of this research was that assumed non-extremophilic Archaea clearly outnumbered bacteria within the different moonmilk deposits, while fungi were only of minor importance. Moreover, the Archaeal species formed a constant element within the investigated samples, while bacteria and fungi showed a much more diverse and inhomogeneous community pattern. This indicates that the Archaea might constitute the central element within the microbial communities, holding key positions in nutrient and energy-cycles. Furthermore, it was possible to cultivate the Archaeal community over a certain time period, demonstrating that so far uncultured or as 'not cultivable' regarded organisms are accessible with certain cultivation strategies. On the other hand the vast majority of bacterial and fungal representatives are in close relation to species, which are valuable concerning biotechnological or medical applications. Summing up, further research on cave microbiomes, especially Archaea, might be reasonable with regards to life's evolution, global nutrient cycles, requirements for possible refuges of extraterrestrial life forms and also concerning new technological applications.

Uniformitarianism and its Discontents: Microbial Evolution and Co-evolution of Life and Earth

NASA Astrophysics Data System (ADS)

Wing, B. A.

2016-12-01

For the first ≈4 billion years of Earth history, life was microscopic. There are ≈5x1030 bacteria and archaea on Earth today. Mean turnover times of natural microbial populations are days to millennia (10-2 to 103 years). Assuming that a similar-sized microbial biosphere has been maintained since ≈4 billion years ago, the number of microbes that have ever lived on Earth is awesome: >1037 to 1042. In broad brush, these numbers represent the individual microbial evolution experiments run by Nature. They are many, many orders of magnitude greater than the number of stars in the universe. Despite this numerical hurdle, the geological record is read with the assumption that microbes in the geological past were doing exactly what microbes do today. In this presentation, I will discuss evolutionary impacts on a critical microbial phentypic trait - sulfur isotope fractionation - that has played a critical role in our interpretations of the the evolution of the Earth system. The discussion will range from microbial evolution experiments to models of metabolic evolution, with an eye toward understanding the evolutionary weaknesses and strengths in our uniformiatrian world view.

Clinical Implications of Basic Science Discoveries: Immune Homeostasis and the Microbiome-Dietary and Therapeutic Modulation and Implications for Transplantation.

PubMed

Fishman, J A; Thomson, A W

2015-07-01

Links between the human microbiome and the innate and adaptive immune systems and their impact on autoimmune and inflammatory diseases are only beginning to be recognized. Characterization of the complex human microbial community is facilitated by culture-independent nucleic acid sequencing tools and bioinformatics systems. Specific organisms and microbial antigens are linked with initiation of innate immune responses that, depending on the context, may be associated with tolerogenic or effector immune responses. Further complexity is introduced by preclinical data that demonstrate the impacts of dietary manipulation on the prevention of genetically determined, systemic autoimmune disorders and on gastrointestinal microbiota. Investigation of interactions of complex microbial populations with the human immune system may provide new targets for clinical management in allotransplantation. © Copyright 2015 The American Society of Transplantation and the American Society of Transplant Surgeons.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust

PubMed Central

Salas, Everett C.; Bhartia, Rohit; Anderson, Louise; Hug, William F.; Reid, Ray D.; Iturrino, Gerardo; Edwards, Katrina J.

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities. PMID:26617595

Short-term degradation of terrestrial DOM in the coastal ocean: Implications for nutrient subsidies and marine microbial community structure

NASA Astrophysics Data System (ADS)

Oliver, A. A.; Tank, S. E.; Kellogg, C.

2015-12-01

The export of riverine dissolved organic matter (DOM) to the coastal ocean provides an important link between terrestrial and aquatic ecosystems. The coastal temperate rainforests of British Columbia contain extensive freshwater networks that export significant amounts of water and DOM to the ocean, representing significant cross-system hydrologic and biogeochemical linkages. To better understand the importance of these linkages and implications for ecosystem structure and function, we used an experimental approach to investigate the role of microbial and photodegradation transformations of DOM exported from small coastal catchments to the marine environment. At two time periods (August 2014, March 2015), stream water from the outlets of two coastal watersheds was filtered (<0.2 μm), and treated with microbial inoculums from across a salinity gradient (i.e., freshwater, estuarine, and marine). Treatments were incubated in the ocean under light and dark conditions for 8 days. At 0, 3 and 8 days, samples were analyzed for DOC, TDN, DIN, and DON. Changes in DOM composition were determined with optical characterization techniques such as absorbance (SUVA, S, Sr) and fluorescence (EEM). Microbial community response was measured using cell counts and DNA/RNA amplicon sequencing to determine changes in bacterial abundance and community composition. General patterns indicated that microbial communities from the high salinity treatment (i.e. most marine) were the most effective at utilizing freshwater DOM, especially under light conditions. In some treatments, DOM appeared as a potential source of inorganic nitrogen with corresponding shifts in microbial community composition. Incubations using inoculum from low and mid salinity levels demonstrated smaller changes, indicating that DOM exported from these streams may not be extensively utilized until exposed to higher salinity environments further from stream outlets. These results suggest a role for terrestrial sourced-DOM as a subsidy for microbial communities within the near shore marine environment, and emphasize that changes in DOM exports due to land development or climate change may have implications for coastal food web processes and biogeochemical cycling.

Mars' surface radiation environment measured with the Mars Science Laboratory's Curiosity rover.

PubMed

Hassler, Donald M; Zeitlin, Cary; Wimmer-Schweingruber, Robert F; Ehresmann, Bent; Rafkin, Scot; Eigenbrode, Jennifer L; Brinza, David E; Weigle, Gerald; Böttcher, Stephan; Böhm, Eckart; Burmeister, Soenke; Guo, Jingnan; Köhler, Jan; Martin, Cesar; Reitz, Guenther; Cucinotta, Francis A; Kim, Myung-Hee; Grinspoon, David; Bullock, Mark A; Posner, Arik; Gómez-Elvira, Javier; Vasavada, Ashwin; Grotzinger, John P

2014-01-24

The Radiation Assessment Detector (RAD) on the Mars Science Laboratory's Curiosity rover began making detailed measurements of the cosmic ray and energetic particle radiation environment on the surface of Mars on 7 August 2012. We report and discuss measurements of the absorbed dose and dose equivalent from galactic cosmic rays and solar energetic particles on the martian surface for ~300 days of observations during the current solar maximum. These measurements provide insight into the radiation hazards associated with a human mission to the surface of Mars and provide an anchor point with which to model the subsurface radiation environment, with implications for microbial survival times of any possible extant or past life, as well as for the preservation of potential organic biosignatures of the ancient martian environment.

Patterns and Processes of Microbial Community Assembly

PubMed Central

Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

2013-01-01

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

Proceedings of the Astrobiology Science Conference 2010. Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond

NASA Technical Reports Server (NTRS)

2010-01-01

The Program of the 2010 Astrobiology Science Conference: Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond, included sessions on: 50 Years of Exobiology and Astrobiology: Greatest Hits; Extraterrestrial Molecular Evolution and Pre-Biological Chemistry: From the Interstellar Medium to the Solar System I; Human Exploration, Astronaut Health; Diversity in Astrobiology Research and Education; Titan: Past, Present, and Future; Energy Flow in Microbial Ecosystems; Extraterrestrial Molecular Evolution and Prebiological Chemistry: From the Interstellar Medium to the Solar System II; Astrobiology in Orbit; Astrobiology and Interdisciplinary Communication; Science from Rio Tinto: An Acidic Environment; Can We Rule Out Spontaneous Generation of RNA as the Key Step in the Origin of Life?; How Hellish Was the Hadean Earth?; Results from ASTEP and Other Astrobiology Field Campaigns I; Prebiotic Evolution: From Chemistry to Life I; Adaptation of Life in Hostile Space Environments; Extrasolar Terrestrial Planets I: Formation and Composition; Collaborative Tools and Technology for Astrobiology; Results from ASTEP and Other Astrobiology Field Campaigns II; Prebiotic Evolution: From Chemistry to Life II; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Environments; Extrasolar Terrestrial Planets II: Habitability and Life; Planetary Science Decadal Survey Update; Astrobiology Research Funding; Bioessential Elements Through Space and Time I; State of the Art in Life Detection; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Psychrophiles and Polar Environments; Life in Volcanic Environments: On Earth and Beyond; Geochronology and Astrobiology On and Off the Earth; Bioessential Elements Through Space and Time II; Origins and Evolution of Genetic Systems; Evolution of Advanced Life; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Impact Events and Evolution; A Warm, Wet Mars?; Titan Versus Europa - Potential for Astrobiology; Habitability Potential of Mars; Biosignatures: Tools and Development I; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Deserts and Evaporite Basins and Associated Microbialite Systems; Ancient Life and Synthetic Biology: Crossroad of the Past and Future; Biosignatures: Tools and Development II; Free Oxygen: Proxies, Causes, and Consequences; Life in Modern Microbialite Systems - Function and Adaptation; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Where Should We Go on Mars to Seek Signs of Life?; Search for Intelligent Life I. Innovative SETI Observing Programs and Future Directions; Integrating Astrobiology Research Across and Beyond the Community; Education in Astrobiology in K-12; Search for Intelligent Life II. Global Engagement and Interstellar Message Construction; Poster sessions included: Extraterrestrial Molecular Evolution and Pre-Biological Chemistry; Prebiotic Evolution: From Chemistry to Life; RNA World; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Virology and Astrobiology; Horizontal Genetic Transfer and Properties of Ancestral Organisms; Life in Volcanic Environments: On Earth and Beyond; Impact Events and Evolution; Evolution of Advanced Life; Evolution of Intelligent Life; Education in Astrobiology in K-12; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Astrobiology and Interdisciplinary Communication; Diversity in Astrobiology Research and Education; Integrating Astrobiology Research Across and Beyond the Community; Policy and Societal Issues: Dealing with Potential Bumps in the Astrobiology Road Ahead; Results from ASTEP and Other Astrobiology Field Campaigns; Energy Flow in Microbial Ecosystems; Psychrophiles and Polar Environments; Deserts and Evaporite Basins and Associated Microbialite stems; Life in Modern Microbialite Systems - Function and Adaptation; Free Oxygen: Proxies, Causes, and Consequences; Bioessential Elements Through Space and Time; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Biosignatures: Tools and Developments; Robotics and Instrumentation for Astrobiology; State of the Art in Life Detection; Astrobiology in Orbit; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Evolution; Search for Intelligent Life; Habitability Potential of Mars; How and Where Should We Seek Signs of Life on Mars?; Titan: Past, Present, and Future; Extrasolar Terrestrial Planets: Formation, Composition, Diversity, Habitability and Life; Human Exploration, Astronaut Health; Science from Rio Tinto: An Acidic Environment and Adaptation of Life in Hostile Space Environments;

Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape.

PubMed

Lachaise, Tom; Ourry, Morgane; Lebreton, Lionel; Guillerm-Erckelboudt, Anne-Yvonne; Linglin, Juliette; Paty, Chrystelle; Chaminade, Valérie; Marnet, Nathalie; Aubert, Julie; Poinsot, Denis; Cortesero, Anne-Marie; Mougel, Christophe

2017-12-01

Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape (Brassica napus) and the cabbage root fly (Delia radicum) as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities ("high," "medium," "low") were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The "medium" modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

DOE PAGES

Xiong, Weili; Brown, Christopher T.; Morowitz, Michael J.; ...

2017-07-10

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. But, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for eachmore » of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We also identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. By applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.« less

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Weili; Brown, Christopher T.; Morowitz, Michael J.

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. But, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for eachmore » of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We also identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. By applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.« less

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

PubMed

Xiong, Weili; Brown, Christopher T; Morowitz, Michael J; Banfield, Jillian F; Hettich, Robert L

2017-07-10

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.

Microbial trace fossils in Antarctica and the search for evidence of early life on Mars

NASA Technical Reports Server (NTRS)

Friedmann, E. Imre; Friedmann, Roseli O.

1989-01-01

It is possible to hypothesize that, if microbial life evolved on early Mars, fossil remnants of these organisms may be preserved on the surface. However, the cooling and drying of Mars probably resembled a cold desert and such an environment is not suitable for the process of fossilization. The frigid Ross Desert of Antarctica is probably the closest terrestrial analog to conditions that may have prevailed on the surface of the cooling and drying Mars. In this desert, cryptoendolithic microbial communities live in the airspaces of porous rocks, the last habitable niche in a hostile outside environment. The organisms produce characteristic chemical and physical changes in the rock substrate. Environmental changes (deterioration of conditions) may result in the death of the community. Although no cellular structures are fossilized, the conspicuous changes in the rock substrate are preserved as trace fossils. Likewise, microbial trace fossils (without cellular structures) may also be preserved on Mars: Discontinuities in structure or chemistry of the rock that are independent of physical or chemical gradients may be of biological origin. Ross Desert trace fossils can be used as a model for planning search strategies and for instrument design to find evidence of past Martian life.

Preparation and Application of LDPE/ZnO Nanocomposites for Extending Shelf Life of Fresh Strawberries

PubMed Central

Mohammadizadeh, Mehri

2015-01-01

Summary Strawberries have a very short post-harvest life mostly due to their relatively high water content, intense metabolic activity and susceptibility to microbial rot. Antimicrobial low-density polyethylene nanocomposite films containing ZnO nanoparticles at different mass fractions were prepared by melt mixing and followed by compression moulding using a hot press machine. Fresh strawberries were packed in nanocomposite films and stored at 4 °C. Their microbial stability, ascorbic acid content and titratable acidity were evaluated after 0, 4, 8, 12 and 16 days of storage. Microbial growth rate was significantly reduced up to 16 days as a result of the use of nanocomposite packaging material containing ZnO nanoparticles. By increasing the ZnO nanoparticle mass fraction to 5%, the antimicrobial activity of the film increased. All packages containing the ZnO nanoparticles kept the microbial load of fresh strawberries below the level that affects shelf life (5 log CFU/g) up to 16 days. The lowest degradation of ascorbic acid content (6.55 mg per 100 g), and loss of acidity (0.68%) were observed in packages containing 3% of ZnO nanoparticles with 10% polyethylene-grafted maleic anhydride. PMID:27904384

Preparation and Application of LDPE/ZnO Nanocomposites for Extending Shelf Life of Fresh Strawberries.

PubMed

Emamifar, Aryou; Mohammadizadeh, Mehri

2015-12-01

Strawberries have a very short post-harvest life mostly due to their relatively high water content, intense metabolic activity and susceptibility to microbial rot. Antimicrobial low-density polyethylene nanocomposite films containing ZnO nanoparticles at different mass fractions were prepared by melt mixing and followed by compression moulding using a hot press machine. Fresh strawberries were packed in nanocomposite films and stored at 4 °C. Their microbial stability, ascorbic acid content and titratable acidity were evaluated after 0, 4, 8, 12 and 16 days of storage. Microbial growth rate was significantly reduced up to 16 days as a result of the use of nanocomposite packaging material containing ZnO nanoparticles. By increasing the ZnO nanoparticle mass fraction to 5%, the antimicrobial activity of the film increased. All packages containing the ZnO nanoparticles kept the microbial load of fresh strawberries below the level that affects shelf life (5 log CFU/g) up to 16 days. The lowest degradation of ascorbic acid content (6.55 mg per 100 g), and loss of acidity (0.68%) were observed in packages containing 3% of ZnO nanoparticles with 10% polyethylene-grafted maleic anhydride.

Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

PubMed

Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

2017-06-15

This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of gamma irradiation and storage time on microbial growth and physicochemical characteristics of pumpkin (Cucurbita Moschata Duchesne ex Poiret) puree.

PubMed

Gliemmo, María F; Latorre, María E; Narvaiz, Patricia; Campos, Carmen A; Gerschenson, Lía N

2014-01-01

The effect of gamma irradiation (0-2 kGy) and storage time (0-28 days) on microbial growth and physicochemical characteristics of a packed pumpkin puree was studied. For that purpose, a factorial design was applied. The puree contained potassium sorbate, glucose and vanillin was stored at 25°C . Gamma irradiation diminished and storage time increased microbial growth. A synergistic effect between both variables on microbial growth was observed. Storage time decreased pH and color of purees. Sorbate content decreased with storage time and gamma irradiation. Mathematical models of microbial growth generated by the factorial design allowed estimating that a puree absorbing 1.63 kGy would have a shelf-life of 4 days. In order to improve this time, some changes in the applied hurdles were assayed. These included a thermal treatment before irradiation, a reduction of irradiation dose to 0.75 kGy and a decrease in storage temperature at 20°C . As a result, the shelf-life of purees increased to 28 days.

Microbial biofilm formation and its consequences for the CELSS program

NASA Technical Reports Server (NTRS)

Mitchell, R.

1994-01-01

A major goal of the Controlled Ecology Life Support System (CELSS) program is to provide reliable and efficient life support systems for long-duration space flights. A principal focus of the program is on the growth of higher plants in growth chambers. These crops should be grown without the risk of damage from microbial contamination. While it is unlikely that plant pathogens will pose a risk, there are serious hazards associated with microorganisms carried in the nutrient delivery systems and in the atmosphere of the growth chamber. Our experience in surface microbiology showed that colonization of surfaces with microorganisms is extremely rapid even when the inoculum is small. After initial colonization extensive biofilms accumulate on moist surfaces. These microbial films metabolize actively and slough off continuously to the air and water. During plant growth in the CELSS program, microbial biofilms have the potential to foul sensors and to plug nutrient delivery systems. In addition both metabolic products of microbial growth and degradation products of materials being considered for use as nutrient reservoirs and for delivery are likely sources of chemicals known to adversly affect plant growth.

The dark side of the mushroom spring microbial mat: Life in the shadow of chlorophototrophs. I. Microbial diversity based on 16S rRNA gene amplicons and metagenomics

USDA-ARS?s Scientific Manuscript database

Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflex...

Microbial Life in the Deep Subsurface: Deep, Hot and Radioactive

NASA Technical Reports Server (NTRS)

DeStefano, Andrea L.; Ford, Jill C.; Winsor, Seana K.; Allen, Carlton C.; Miller, Judith; McNamara, Karen M.; Gibson, Everett K., Jr.

2000-01-01

Recent studies, motivated in part by the search for extraterrestrial life, continue to expand the recognized limits of Earth's biosphere. This work explored evidence for life a high-temperature, radioactive environment in the deep subsurface.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth.

PubMed

Grosch, Eugene G; Hazen, Robert M

2015-10-01

Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

Having older siblings is associated with gut microbiota development during early childhood.

PubMed

Laursen, Martin Frederik; Zachariassen, Gitte; Bahl, Martin Iain; Bergström, Anders; Høst, Arne; Michaelsen, Kim F; Licht, Tine Rask

2015-08-01

Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies. We investigated whether presence of older siblings, furred pets and early life infections affected gut microbial communities at 9 and 18 months of age and whether these differences were associated with the cumulative prevalence of atopic symptoms of eczema and asthmatic bronchitis at 3 years of age. Bacterial compositions and diversity indices were determined in fecal samples collected from 114 infants in the SKOT I cohort at age 9 and 18 months by 16S rRNA gene sequencing. These were compared to the presence of older siblings, furred pets and early life infections and the cumulative prevalence of diagnosed asthmatic bronchitis and self-reported eczema at 3 years of age. The number of older siblings correlated positively with bacterial diversity (p = 0.030), diversity of the phyla Firmicutes (p = 0.013) and Bacteroidetes (p = 0.004) and bacterial richness (p = 0.006) at 18 months. Further, having older siblings was associated with increased relative abundance of several bacterial taxa at both 9 and 18 months of age. Compared to the effect of having siblings, presence of household furred pets and early life infections had less pronounced effects on the gut microbiota. Gut microbiota characteristics were not significantly associated with cumulative occurrence of eczema and asthmatic bronchitis during the first 3 years of life. Presence of older siblings is associated with increased gut microbial diversity and richness during early childhood, which could contribute to the substantiation of the hygiene hypothesis. However, no associations were found between gut microbiota and atopic symptoms of eczema and asthmatic bronchitis during early childhood and thus further studies are required to elucidate whether sibling-associated gut microbial changes influence development of allergies later in childhood.

Biofilm on the tracheoesophageal voice prosthesis: considerations for oral decontamination.

PubMed

Somogyi-Ganss, Eszter; Chambers, Mark S; Lewin, Jan S; Tarrand, Jeffrey J; Hutcheson, Katherine A

2017-01-01

The tracheoesophageal puncture (TEP) restores verbal communication after total laryngectomy using a one-way valved voice prosthesis (VP). Microbial colonization can shorten VP device life. Our aims were to investigate patterns of prosthetic and oral colonization, and record changes in VP device life after targeted decontamination. We conducted a retrospective review of TEP clinic patients who underwent microbial analysis of the VP between 01/2003 and 07/2013. Two subgroups were analyzed: (1) patients with microbial analysis of the VP and the mouth were analyzed to identify patterns of common contamination, and (2) patients who were prescribed targeted oral decontamination on the basis of the microbial analysis of the VP were analyzed to evaluate effects on device life. Among 42 patients, 3 patients had only fungal, 5 only bacterial, and 33 had polyspecies fungal and bacterial colonization. In the TEP-oral microflora subgroup (n = 15), 7 had common microorganisms in the mouth and on the VP. Among the decontamination subgroup (n = 23), 6 patients received broad spectrum rinse, 16 antifungal agents and 13 antibiotics, or a combination thereof. After targeted decontamination, the median device life of prostheses improved from 7.89 to 10.82 weeks (p = 0.260). The majority of patients with a suboptimal VP device life in this pilot had polyspecies bacterial and fungal colonization. VPs rarely had fungal contamination alone (3 %), and non-albicans fungal species were more common than expected. For these reasons, we are exploring the use of targeted decontamination regimens that were associated with 1.4-fold improvement in VP duration.

Microbial exposure in infancy and subsequent appearance of type 1 diabetes mellitus-associated autoantibodies: a cohort study.

PubMed

Virtanen, Suvi M; Takkinen, Hanna-Mari; Nwaru, Bright I; Kaila, Minna; Ahonen, Suvi; Nevalainen, Jaakko; Niinistö, Sari; Siljander, Heli; Simell, Olli; Ilonen, Jorma; Hyöty, Heikki; Veijola, Riitta; Knip, Mikael

2014-08-01

The role of microbial exposure during early life in the development of type 1 diabetes mellitus is unclear. To investigate whether animal contact and other microbial exposures during infancy are associated with the development of preclinical and clinical type 1 diabetes. A birth cohort of children with HLA antigen-DQB1-conferred susceptibility to type 1 diabetes was examined. Participants included 3143 consecutively born children at 2 hospitals in Finland between 1996 and 2004. The following exposures during the first year of life were assessed: indoor and outdoor dogs and cats, farm animals, farming, visit to a stable, day care, and exposure to antibiotics during the first week of life. Clinical and preclinical type 1 diabetes were used as outcomes. The latter was defined as repeated positivity for islet-cell antibodies plus for at least 1 of 3 other diabetes-associated autoantibodies analyzed and/or clinical type 1 diabetes. The autoantibodies were analyzed at 3- to 12-month intervals since the birth of the child. Children exposed to an indoor dog, compared with otherwise similar children without an indoor dog exposure, had a reduced odds of developing preclinical type 1 diabetes (adjusted odds ratio [OR], 0.47; 95% CI, 0.28-0.80; P = .005) and clinical type 1 diabetes (adjusted OR, 0.40; 95% CI, 0.14-1.14; P = .08). All of the other microbial exposures studied were not associated with preclinical or clinical diabetes: the odds ratios ranged from 0.74 to 1.58. Among the 9 early microbial exposures studied, only the indoor dog exposure during the first year of life was inversely associated with the development of preclinical type 1 diabetes. This finding needs to be confirmed in other populations.

Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance.

PubMed

Horrocks, Nicholas P C; Hegemann, Arne; Matson, Kevin D; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B; Tinbergen, Joost M; Tieleman, B Irene

2012-01-01

Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on their slower pace of life, the trade-off hypothesis predicts relatively stronger immune defenses in desert larks compared with temperate larks. However, as predicted by the antigen exposure hypothesis, reduced microbial abundances in deserts should result in desert-living larks having relatively weaker immune defenses. We quantified host-independent and host-dependent microbial abundances of culturable microbes in ambient air and from the surfaces of birds. We measured components of immunity by quantifying concentrations of the acute-phase protein haptoglobin, natural antibody-mediated agglutination titers, complement-mediated lysis titers, and the microbicidal ability of whole blood. Desert-living larks were exposed to significantly lower concentrations of airborne microbes than temperate larks, and densities of some bird-associated microbes were also lower in desert species. Haptoglobin concentrations and lysis titers were also significantly lower in desert-living larks, but other immune indexes did not differ. Thus, contrary to the trade-off hypothesis, we found little evidence that a slow pace of life predicted increased immunological investment. In contrast, and in support of the antigen exposure hypothesis, associations between microbial exposure and some immune indexes were apparent. Measures of antigen exposure, including assessment of host-independent and host-dependent microbial assemblages, can provide novel insights into the mechanisms underlying immunological variation.

Imperfect asymmetry of life: earth microbial communities prefer D-lactate but can use L-lactate also.

PubMed

Moazeni, Faegheh; Zhang, Gaosen; Sun, Henry J

2010-05-01

Asymmetrical utilization of chiral compounds has been sought on Mars as evidence for biological activity. This method was recently validated in glucose. Earth organisms utilize D-glucose, not L-glucose, a perfect asymmetry. In this study, we tested the method in lactate and found utilization of both enantiomers. Soil-, sediment-, and lake-borne microbial communities prefer D-lactate but can consume L-lactate if given extra time to acclimate. This situation is termed imperfect asymmetry. Future life-detection mission investigators need to be aware of imperfect asymmetry so as not to miss relatively subtle signs of life.

Subsurface microbial habitats on Mars

NASA Technical Reports Server (NTRS)

Boston, P. J.; Mckay, C. P.

1991-01-01

We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

The ecology and biogeochemistry of stream biofilms.

PubMed

Battin, Tom J; Besemer, Katharina; Bengtsson, Mia M; Romani, Anna M; Packmann, Aaron I

2016-04-01

Streams and rivers form dense networks, shape the Earth's surface and, in their sediments, provide an immensely large surface area for microbial growth. Biofilms dominate microbial life in streams and rivers, drive crucial ecosystem processes and contribute substantially to global biogeochemical fluxes. In turn, water flow and related deliveries of nutrients and organic matter to biofilms constitute major constraints on microbial life. In this Review, we describe the ecology and biogeochemistry of stream biofilms and highlight the influence of physical and ecological processes on their structure and function. Recent advances in the study of biofilm ecology may pave the way towards a mechanistic understanding of the effects of climate and environmental change on stream biofilms and the biogeochemistry of stream ecosystems.

Man and his spaceships

PubMed Central

Siefert, Janet L.

2012-01-01

The resiliency and adaptive ability of microbial life in real time on Earth relies heavily upon horizontal gene transfer. Based on that knowledge, how likely is earth based microbial life to colonize extraterrestrial targets such as Mars? To address this question, we consider manned and unmanned space exploration, the resident microbiota that is likely to inhabit those vehicles, the adaptive potential of that microbiota in an extraterrestrial setting especially with regards to mobile genetic elements, and the likelihood that Mars like environments could initiate and sustain colonization. PMID:23481263

Man and his spaceships: Vehicles for extraterrestrial colonization?

PubMed

Siefert, Janet L

2012-11-01

The resiliency and adaptive ability of microbial life in real time on Earth relies heavily upon horizontal gene transfer. Based on that knowledge, how likely is earth based microbial life to colonize extraterrestrial targets such as Mars? To address this question, we consider manned and unmanned space exploration, the resident microbiota that is likely to inhabit those vehicles, the adaptive potential of that microbiota in an extraterrestrial setting especially with regards to mobile genetic elements, and the likelihood that Mars like environments could initiate and sustain colonization.

Extremes of Survival Achieved by the Radiophile Deinococcus Radiodurans: A Model for Microbial Life on Mars

NASA Technical Reports Server (NTRS)

Daly, M.; Sridhar, R.; Richmond, R.

1999-01-01

Deinococcus radiodurans is an extremophile in more than one defined way. First it is extreme in its resistance to freeze drying. Second it is probably uniquely extreme on Earth in its resistance to ionizing radiation. The polyextremophilic capacity of D. radiodurans will be considered. The selection pressures on Mars will then be considered in relation to D. radiodurans in order to support a hypothesis that if microbial life exists on Mars, then it likely includes polyextremophiles.

Microbial communities inhabiting hypersaline microbial mats from the Abu Dhabi sabkha

NASA Astrophysics Data System (ADS)

Andrade, Luiza; Dutton, Kirsten; Paul, Andreas; van der Land, Cees; Sherry, Angela; Lokier, Stephen; Head, Ian

2017-04-01

Microbial mats are organo-sedimentary structures that are typically found in areas with extreme environmental conditions. Since these ecosystems are considered to be representative of the oldest forms of life on Earth, the study of microbial mats can inform our understanding of the development of life early in the history of our planet. In this study, we used hypersaline microbial mats from the Abu Dhabi sabkha (coastal salt flats). Cores of microbial mats (ca. 90 mm depth) were collected within an intertidal region. The cores were sliced into layers 2-3 mm thick and genomic DNA was extracted from each layer. A fragment of the 16S rRNA encoding gene was amplified in all DNA extracts, using barcoded primers, and the amplicons sequenced with the Ion Torrent platform to investigate the composition of the microbial communities down the depth of the cores. Preliminary results revealed a high proportion of Archaea (15.5-40.8% abundance) in all layers, with Halobacteria appearing to be more significant in the first 40 mm (0.4-10.3% of the total microbial community). Members of the Deltaproteobacteria were dominant in almost all layers of the microbial mat (≤ 48.6% relative abundance); however this dominance was not reflected in the first 8 mm, where the abundance was less than 2%. Chloroflexi and Anaerolinea, representing 93% of bacterial abundance, dominated the first 8 mm depth and decreased at greater depth (≤ 3% relative abundance). Cyanobacteria were found only in the top 10 mm, with unexpected low abundance (≤ 3% of the total number of reads). These results show a vertical zonation of microbial communities and processes in the microbial mats. Further analyses are underway to investigate if these patterns are repeated at other sites along a transect of the sabkha, and to relate the microbial composition to the physical-chemical conditions of the sites.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

PubMed Central

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges.

PubMed

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan D W

2007-05-01

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.

Microbial life in cold, sulfur-rich environments: Investigations of an Arctic ecosystem and implications for life detection at Europa

NASA Astrophysics Data System (ADS)

Gleeson, Damhnait Fagan

2009-12-01

Exobiological investigations require a detailed understanding of life's interactions with its environment here on Earth before we can confidently recognize signs of these interactions at other worlds such as Europa. Using a cold, sulfur-based ecosystem at Borup Fiord pass in the Canadian High Arctic as a study site, I investigated how the supraglacial non-ice materials are represented across different scales in spectral data, how microbiology is influencing the mineralogy of the site, and whether the products of microbial sulfide oxidation preserve indications of their biogenic origin. A systematic scale-integrated approach was applied to query orbital (Hyperion), field, and laboratory spectra to identify sulfur-rich materials precipitated on a glacier. While sulfur, the main constituent of the deposits, is well represented in Hyperion data, minor constituents such as calcite and gypsum are partially or entirely masked. Absorption features of sulfates, where present, are shifted in wavelength due to the effects of mixing or temperature. Autonomous detection methods were successfully applied to monitor the generation and extent of the deposits, which show spectral similarities to Europa's non-ice materials. Geomicrobiological cultivation of sulfide oxidizing bacteria succeeded in demonstrating that the microbiological community present at the site has the potential to catalyze the generation of sulfur deposits. Sulfur generated in culture is present as biomineralized structures comprised of microbial filaments and sheaths along which sulfur globules are deposited. Consortia producing these structures are dominated by gamma-Proteobacteria closely related to Marinobacter, not previously known to oxidize sulfide. The sulfur structures produced by these consortia are not observed in abiotic controls and have the potential to serve as morphological biosignatures. Investigations into the biogenicity of field deposits reveal mineral assemblages with similar morphologies to those generated in culture. X-ray diffraction analyses show some evidence for rosickyite, a metastable form of biogenic sulfur. Mid-infrared laboratory spectroscopy also indicates the presence of organic functional groups diagnostic of proteins and fatty acids within the sulfur deposits. These combined investigations suggest that sulfur minerals extruded onto Europa's near surface, analogous to those of Borup Fiord pass, have the potential to contain identifiable biosignatures which low-temperature conditions could help stabilize and preserve.

Following a New Path Along the Search for Life in the Solar System

NASA Astrophysics Data System (ADS)

Colonna, Thomas E.; Thomas, Desencia E.

2000-05-01

Imagined by several generations of science fiction authors as smooth-talking aliens envious of our blue-water world, extraterrestrial life on Earth's planetary siblings may take the form of bacteria or other microbial life.

Cultural Resources and Cognitive Frames: Keys to an Anthropological Approach to Prediction

NASA Astrophysics Data System (ADS)

Lowrie, Ian

In this chapter, I suggest a methodological and theoretical framework for preliminary investigations designed to gauge the potential societal response to the discovery of either microbial or intelligent extraterrestrial life. The uncritical use of analogies to the ethnographic record of contact between societies and the discovery of extraterrestrial life has been, rightfully, the target of sharp criticism since the earliest days of the scientific search for this life. However, I argue that by approaching this record with different epistemological premises, and shifting the focus from the material to the symbolic and cognitive dimensions of this contact, one can avoid many of the pitfalls of the analogical mode of argumentation, and provide a solid conceptual basis for the development of an adequate heuristic. Specifically, I draw upon the germinal debate between Sahlins and Obeyesekere over the nature of human meaning-making in the face of radically other societies and their meanings to treat the discovery of an intelligent civilization. In parallel, I draw upon Sharp's discussion of the relationship between the changes in the symbolic order and the material organization of society to suggest that much of this analysis also applies to the discovery of extraterrestrial microbial life. In both cases, I do not argue for a one-to-one correspondence between the historical and the contemporary, but rather use these arguments as illustrations of what I see as particularly profitable modes of conceptualizing the universal human processes of making sense out of novel objects and phenomena. Finally, this chapter argues for a mixed-methods quantitative-qualitative investigation into the character and distribution of societal resources for understanding life and intelligence, rather than the extraterrestrial as such. The qualitative is advanced as a necessary adjunct to the quantitative, as the best method for gaining access to the repertoire of cultural frames upon which people more or less unconsciously draw in forming their understandings of the world. The focus on life and intelligence is justified both insofar as they are the categories which will be brought to bear on the extraterrestrial in terms of integrating it into people's worldviews, and insofar as these categories are substantially more implicated in both societal and personal stability than that of the extraterrestrial as such.

Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

PubMed Central

Gonzalez, David J.; Haste, Nina M.; Hollands, Andrew; Fleming, Tinya C.; Hamby, Matthew; Pogliano, Kit; Nizet, Victor

2011-01-01

Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery. PMID:21719540

Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

2017-12-01

Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the tree of life. In contrast, genes related to nitrogen fixation display much more consistent rates of horizontal gene transfer throughout Earth's history. Studies that couple genomics approaches with geochemistry have the potential to reveal insights into the co-evolution of life and Earth both in the recent and distant past.

Unconventional food regeneration in space - Opportunities for microbial food production

NASA Technical Reports Server (NTRS)

Petersen, Gene R.; Schubert, Wayne W.; Seshan, P. K.; Dunlop, Eric H.

1987-01-01

The possible role of microbial species in regenerating food is considered, and three areas where microbial systems can be used in controlled ecological life support systems are discussed. Microbial species can serve as the biological portion of hybrid chemical/biological schemes for primary food products, as a means more fully to utilize waste materials from agronomical food production, and as a source of nutritional supplements to conventional plant foods. Work accomplished in each of these areas is described. The role of microgravity fermenters in this technology is addressed.

A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Gangsheng; Post, Wilfred M

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other twomore » models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.« less

Impact of mechanical shear on Listeria monocytogenes survival on surfaces

USDA-ARS?s Scientific Manuscript database

Microbial inactivation using high temperatures is well known process and has contributed significantly toward food safety and shelf life extension for the food industry. Mechanical high pressure (hydrostatic) treatment is also gaining interest in food processing applications for achieving microbial...

The relative importance of exogenous and substrate-derived nitrogen for microbial growth during leaf decomposition

Treesearch

B.M. Cheever; J. R. Webster; E. E. Bilger; S. A. Thomas

2013-01-01

Heterotrophic microbes colonizing detritus obtain nitrogen (N) for growth by assimilating N from their substrate or immobilizing exogenous inorganic N. Microbial use of these two pools has different implications for N cycling and organic matter decomposition in the face of the global increase in biologically available N. We used sugar maple leaves labeled with

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

PubMed Central

2013-01-01

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome. PMID:24267946

Buried treasure: evolutionary perspectives on microbial iron piracy

PubMed Central

Barber, Matthew F.; Elde, Nels C.

2015-01-01

Host-pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a critical innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of `iron piracy' to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host-pathogen evolution, but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. PMID:26431675

Diversity of the gut microbiota and eczema in early life.

PubMed

Forno, Erick; Onderdonk, Andrew B; McCracken, John; Litonjua, Augusto A; Laskey, Daniel; Delaney, Mary L; Dubois, Andrea M; Gold, Diane R; Ryan, Louise M; Weiss, Scott T; Celedón, Juan C

2008-09-22

A modest number of prospective studies of the composition of the intestinal microbiota and eczema in early life have yielded conflicting results. To examine the relationship between the bacterial diversity of the gut and the development of eczema in early life by methods other than stool culture. Fecal samples were collected from 21 infants at 1 and 4 months of life. Nine infants were diagnosed with eczema by the age of 6 months (cases) and 12 infants were not (controls). After conducting denaturating gradient gel electrophoresis (DGGE) of stool samples, we compared the microbial diversity of cases and controls using the number of electrophoretic bands and the Shannon index of diversity (H') as indicators. Control subjects had significantly greater fecal microbial diversity than children with eczema at ages 1 (mean H' for controls = 0.75 vs. 0.53 for cases, P = 0.01) and 4 months (mean H' for controls = 0.92 vs. 0.59 for cases, P = 0.02). The increase in diversity from 1 to 4 months of age was significant in controls (P = 0.04) but not in children who developed eczema by 6 months of age (P = 0.32). Our findings suggest that reduced microbial diversity is associated with the development of eczema in early life.

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds.

PubMed

Trembath-Reichert, Elizabeth; Morono, Yuki; Ijiri, Akira; Hoshino, Tatsuhiko; Dawson, Katherine S; Inagaki, Fumio; Orphan, Victoria J

2017-10-31

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be "hot spots" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of 13 C- or 15 N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50-2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell-targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

Microbial astronauts: assembling microbial communities for advanced life support systems.

PubMed

Roberts, M S; Garland, J L; Mills, A L

2004-02-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag

Microbial exposure early in life regulates airway inflammation in mice after infection with Streptococcus pneumoniae with enhancement of local resistance.

PubMed

Yasuda, Yasuki; Matsumura, Yoko; Kasahara, Kazuki; Ouji, Noriko; Sugiura, Shigeki; Mikasa, Keiichi; Kita, Eiji

2010-01-01

The immunological explanation for the "hygiene hypothesis" has been proposed to be induction of T helper 1 (Th1) responses by microbial products. However, the protective results of hygiene hypothesis-linked microbial exposures are currently shown to be unlikely to result from a Th1-skewed response. Until now, effect of microbial exposure early in life on airway innate resistance remained unclear. We examined the role of early life exposure to microbes in airway innate resistance to a respiratory pathogen. Specific pathogen-free weanling mice were nasally exposed to the mixture of microbial extracts or PBS (control) every other day for 28 days and intratracheally infected with Streptococcus pneumoniae 10 days after the last exposure. Exposure to microbial extracts facilitated colonization of aerobic gram-positive bacteria, anaerobic microorganisms, and Lactobacillus in the airway, compared with control exposure. In pneumococcal pneumonia, the exposure prolonged mouse survival days by suppressing bacterial growth and by retarding pneumococcal blood invasion, despite significantly low levels of leukocyte recruitment in the lung. Enhancement of airway resistance was associated with a significant decrease in production of leukocyte chemokine (KC) and TNFalpha, and suppression of matrix metalloproteinase (MMP-9) expression/activation with enhancement of tissue inhibitor of MMP (TIMP-3) activation. The exposure increased production of IFN-gamma, IL-4, and monocyte chemoattractant-1 following infection. Furthermore, expression of Toll-like receptor 2, 4, and 9 was promoted by the exposure but no longer upregulated upon pneumococcal infection. Thus, we suggest that hygiene hypothesis is more important in regulating the PMN-dominant inflammatory response than in inducing a Th1-dominant response.

Microbial astronauts: assembling microbial communities for advanced life support systems

NASA Technical Reports Server (NTRS)

Roberts, M. S.; Garland, J. L.; Mills, A. L.

2004-01-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag.

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

PubMed Central

Trembath-Reichert, Elizabeth; Morono, Yuki; Ijiri, Akira; Hoshino, Tatsuhiko; Dawson, Katherine S.; Inagaki, Fumio

2017-01-01

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of 13C- or 15N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates. PMID:29078310

Evidence for Microbial Activity in ~3.5 Ga Pillow Basalts From the Barberton Greenstone Belt, South Africa

NASA Astrophysics Data System (ADS)

Muehlenbachs, K.; Banerjee, N. R.; Furnes, H.; Staudigel, H.; de Wit, M.

2004-05-01

We have discovered biosignatures in the formerly glassy rims of pillow lavas from the Mesoarchean Barberton Greenstone Belt (BGB) in South Africa. Over the last decade, bioalteration of basaltic glass in pillow lavas and volcaniclastic rocks has been well documented from in-situ oceanic crust and well-preserved Phanerozoic ophiolites. Much of the debate regarding the biogenicity of purported microfossils of early life centers on the interpretation of the host rocks' protoliths. To date, most protoliths have been interpreted to be of sedimentary origin. Some workers have proposed alternate origins for these substrates, including hydrothermal and even volcanic derivation, to cast doubt on their putative biogenicity. Hence studies documenting evidence for early life have proven to be controversial. Here we document evidence for microbial activity in ~3.5 Ga subaqueous volcanic rocks that represent a new, unambiguous geological setting in the search for early life on Earth. The BGB magmatic sequence is dominated by mafic to ultramafic pillow lavas, sheet flows, and intrusions interpreted to represent 3480- to 3220-million-year-old oceanic crust and island arc assemblages. The BGB pillow lavas are exceptionally well-preserved and represent unequivocal evidence that these rocks were erupted in a subaqueous environment. The formerly glassy rims of the BGB pillow lavas contain micron-sized, microbially generated, tubular structures consisting of titanite. These structures are interpreted to have formed during microbial etching of the originally glassy pillow rims and were subsequently mineralized by titanite during greenschist facies seafloor hydrothermal alteration. Overlapping metamorphic and magmatic dates from the pillow lavas suggest this process occurred soon after eruption of the pillow lavas on the seafloor. X-ray mapping has revealed the presence of carbon along the margins of the tubular structures. Disseminated carbonates within the microbially altered BGB pillow rims have C-isotope values depleted by as much as -16 per mil, which is consistent with microbial oxidation of organic matter. In contrast, the crystalline pillow interiors exhibit C-isotope values bracketed between Archean marine carbonate (~0 per mil) and mantle CO2 (-5 to -7 per mil). On the basis of the observed textural and geochemical signatures we propose that the glassy rims of the BGB pillow lavas hosted microbial life almost 3.5 billion years ago. Remnants of Archean oceanic crust may therefore be one of the most promising places to search for vestiges of early life on Earth.

The Cuatro Ciénegas Basin in Coahuila, Mexico: An Astrobiological Precambrian Park

PubMed Central

Siefert, Janet L.; Escalante, Ana E.; Elser, James J.; Eguiarte, Luis E.

2012-01-01

Abstract The Cuatro Ciénegas Basin (CCB) is a rare oasis in the Chihuahuan Desert in the state of Coahuila, Mexico. It has a biological endemism similar to that of the Galapagos Islands, and its spring-fed ecosystems have very low nutrient content (nitrogen or phosphorous) and are dominated by diverse microbialites. Thus, it has proven to be a distinctive opportunity for the field of astrobiology, as the CCB can be seen as a proxy for an earlier time in Earth's history, in particular the late Precambrian, the biological frontier when prokaryotic life yielded at least partial dominance to eukaryotes and multicellular life. It is a kind of ecological time machine that provides abundant opportunities for collaborative investigations by geochemists, geologists, ecologists, and population biologists in the study of the evolutionary processes that structured Earth-based life, especially in the microbial realm. The CCB is an object of investigation for the identification of biosignatures of past and present biota that can be used in our search for extraterrestrial life. In this review, we summarize CCB research efforts that began with microbial ecology and population biology projects and have since been expanded into broader efforts that involve biogeochemistry, comparative genomics, and assessments of biosignatures. We also propose that, in the future, the CCB is sanctioned as a “Precambrian Park” for astrobiology. Key Words: Microbial mats—Stromatolites—Early Earth—Extremophilic microorganisms—Microbial ecology. Astrobiology 12, 641–647. PMID:22920514

Distribution of Gull Specific Molecular Marker in Coastal Areas of Lake Ontario

EPA Science Inventory

Gulls have been implicated as primary sources of fecal contamination in the Great Lakes, a fact that may have health implications due to the potential spread of microbial pathogens by waterfowl. To better understand the spatial variability of gull fecal contamination, a gull-spe...

Forum on Microbial Threats

DTIC Science & Technology

2012-01-01

extreme environments such as the human gut , deep sea hydrothermal vents, and the windswept terrain of Antarctica – teem with microbial life that interact......Recent studies on the human microbiome have begun to reveal the complexity of these interactions within the human body and the effects of the

Life in Oligotropic Desert Environments: Contrasting Taxonomic and Functional Diversity of Two Microbial Mats with Metagenomics

NASA Astrophysics Data System (ADS)

Bonilla-Rosso, G.; Peimbert, M.; Olmedo, G.; Alcaraz, L. D.; Eguiarte, L. E.; Souza, V.

2010-04-01

The metagenomic analysis of two microbial mats from the oligotrophic waters in the Cuatrociéngas basin reveals large differences both at taxonomic and functional level. These are explained in terms of environmental stability and nutrient availability.

Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex

PubMed Central

Kubo, Yusuke; Hoshino, Tatsuhiko; Sakai, Sanae; Arnold, Gail L.; Case, David H.; Lever, Mark A.; Morita, Sumito; Nakamura, Ko-ichi

2018-01-01

Microbial life inhabiting subseafloor sediments plays an important role in Earth’s carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm−3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated. PMID:29928689

Ecohydrological Impacts of Groundwater Drawdown : Effects on Microbial Activity in the Hyporheic Zone

NASA Astrophysics Data System (ADS)

Auhl, A.; Rutlidge, H.; Andersen, M. S.; Eberhard, S. M.; Baker, A.; Holley, C.

2016-12-01

Our current understanding of ecohydrological processes in the ecotone between surface water and groundwater - the hyporheic zone - is limited. Groundwater drawdown is a key stressor for many groundwater dependent ecosystems, as groundwater levels are declining globally. It is caused by different perturbations, including agriculture, mine dewatering and climate change. Therefore, there is a pressing need to examine how different ecohydrological systems work under different types of stress. This research aims to investigate the impacts of groundwater drawdown on hyporheic zone microbial activity. For two six week sampling campaigns (winter and summer) at Maules Creek, Namoi, New South Wales, Australia, microbial activity was measured using the cotton strip degradation method. Unprimed cotton canvas was affixed to rulers which were then placed for six weeks in different habitats (dry bar, hyporheic zone and surface waters) at three different water regimes found at different sections of the creek (perennial, ephemeral, and losing). The microbial activity was related to the loss of cotton strip tensile strength. The water regimes were used as proxies for different stages of groundwater drawdown. Key physico-chemical variables were also measured. The preliminary results show that there is a positive correlation between moisture status (i.e. the degree of habitat saturation over six weeks) and microbial activity.This suggests that groundwater drawdown and desaturation of streambed sediments may lead to a decrease in microbial activity and therefore, the recycling of organic carbon and nutrients. This research has local implications for environmental impact assessments and global implications for the assessment and management of ecological impacts of declining shallow groundwater levels.

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation.

PubMed

Lee, Keehoon; Pletcher, Steven D; Lynch, Susan V; Goldberg, Andrew N; Cope, Emily K

2018-01-01

Recent studies leveraging next-generation sequencing and functional approaches to understand the human microbiota have demonstrated the presence of diverse, niche-specific microbial communities at nearly every mucosal surface. These microbes contribute to the development and function of physiologic and immunological features that are key to host health status. Not surprisingly, several chronic inflammatory diseases have been attributed to dysbiosis of microbiota composition or function, including chronic rhinosinusitis (CRS). CRS is a heterogeneous disease characterized by inflammation of the sinonasal cavity and mucosal microbiota dysbiosis. Inflammatory phenotypes and bacterial community compositions vary considerably across individuals with CRS, complicating current studies that seek to address causality of a dysbiotic microbiome as a driver or initiator of persistent sinonasal inflammation. Murine models have provided some experimental evidence that alterations in local microbial communities and microbially-produced metabolites influence health status. In this perspective, we will discuss the clinical implications of distinct microbial compositions and community-level functions in CRS and how mucosal microbiota relate to the diverse inflammatory endotypes that are frequently observed. We will also describe specific microbial interactions that can deterministically shape the pattern of co-colonizers and the resulting metabolic products that drive or exacerbate host inflammation. These findings are discussed in the context of CRS-associated inflammation and in other chronic inflammatory diseases that share features observed in CRS. An improved understanding of CRS patient stratification offers the opportunity to personalize therapeutic regimens and to design novel treatments aimed at manipulation of the disease-associated microbiota to restore sinus health.

A critical assessment of the "sterile womb" and "in utero colonization" hypotheses: implications for research on the pioneer infant microbiome.

PubMed

Perez-Muñoz, Maria Elisa; Arrieta, Marie-Claire; Ramer-Tait, Amanda E; Walter, Jens

2017-04-28

After more than a century of active research, the notion that the human fetal environment is sterile and that the neonate's microbiome is acquired during and after birth was an accepted dogma. However, recent studies using molecular techniques suggest bacterial communities in the placenta, amniotic fluid, and meconium from healthy pregnancies. These findings have led many scientists to challenge the "sterile womb paradigm" and propose that microbiome acquisition instead begins in utero, an idea that would fundamentally change our understanding of gut microbiota acquisition and its role in human development. In this review, we provide a critical assessment of the evidence supporting these two opposing hypotheses, specifically as it relates to (i) anatomical, immunological, and physiological characteristics of the placenta and fetus; (ii) the research methods currently used to study microbial populations in the intrauterine environment; (iii) the fecal microbiome during the first days of life; and (iv) the generation of axenic animals and humans. Based on this analysis, we argue that the evidence in support of the "in utero colonization hypothesis" is extremely weak as it is founded almost entirely on studies that (i) used molecular approaches with an insufficient detection limit to study "low-biomass" microbial populations, (ii) lacked appropriate controls for contamination, and (iii) failed to provide evidence of bacterial viability. Most importantly, the ability to reliably derive axenic animals via cesarean sections strongly supports sterility of the fetal environment in mammals. We conclude that current scientific evidence does not support the existence of microbiomes within the healthy fetal milieu, which has implications for the development of clinical practices that prevent microbiome perturbations after birth and the establishment of future research priorities.

Controlling Brochothrix thermosphacta as a spoilage risk using in-package atmospheric cold plasma.

PubMed

Patange, Apurva; Boehm, Daniela; Bueno-Ferrer, Carmen; Cullen, P J; Bourke, Paula

2017-09-01

Brochothrix thermosphacta is the predominant spoilage microorganism in meat and its control in processing environments is important to maintain meat product quality. Atmospheric cold plasma is of interest for control of pathogenic and spoilage microorganisms in foods. This study ascertained the potential of dielectric barrier discharge atmospheric cold plasma (DBD-ACP) for control of B. thermosphacta, taking microbial and food environment factors into consideration, and investigated the shelf-life of lamb chop after in-package plasma treatment in modified atmosphere. Community profiling was used to assess the treatment effects on the lamb microflora. ACP treatment (80 kV) for 30s inactivated B. thermosphacta populations below detection levels in PBS, while 5 min treatment achieved a 2 Log cycle reduction using a complex meat model medium and attached cells. The antimicrobial efficacy of plasma was reduced but still apparent on lamb chop surface-inoculated with high concentrations of B. thermosphacta. Lamb chop treated under modified atmosphere exhibited reduced microbial growth over the product shelf-life and community profiling showed no evident changes to the microbial populations after the treatment. The overall results indicated potential of ACP to enhance microbial control leading to meat storage life extension through adjusting the modality of treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Gut microbiota: Description, role and pathophysiologic implications].

PubMed

Landman, C; Quévrain, E

2016-06-01

The human gut contains 10(14) bacteria and many other micro-organisms such as Archaea, viruses and fungi. Studying the gut microbiota showed how this entity participates to gut physiology and beyond this to human health, as a real "hidden organ". In this review, we aimed to bring information about gut microbiota, its structure, its roles and its implication in human pathology. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to four major phyla. The use of culture independent methods and more recently the development of high throughput sequencing allowed to depict precisely gut microbiota structure and diversity as well as its alteration in diseases. Gut microbiota is implicated in the maturation of the host immune system and in many fundamental metabolic pathways including sugars and proteins fermentation and metabolism of bile acids and xenobiotics. Imbalance of gut microbial populations or dysbiosis has important functional consequences and is implicated in many digestive diseases (inflammatory bowel diseases, colorectal cancer, etc.) but also in obesity and autism. These observations have led to a surge of studies exploring therapeutics which aims to restore gut microbiota equilibrium such as probiotics or fecal microbiota transplantation. But recent research also investigates biological activity of microbial products which could lead to interesting therapeutics leads. Copyright © 2015 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

A compendium of multi-omic sequence information from the Saanich Inlet water column

DOE PAGES

Hawley, Alyse K.; Torres-Beltran, Monica; Zaikova, Elena; ...

2017-10-31

Microbial communities play vital roles in earth’s geochemical cycles. Within marine oxygen minimum zones (OMZs) gradients of oxygen, nitrate and sulfide create redox gradients that drive biogeochemical cycling of carbon, nitrogen and sulphur. Climate-change induced expansion and intensification of OMZs and associated biogeochemical activities has significant implications for green house gas production i.e. nitrous oxide and methane. Next generation sequencing technologies have enabled observations of changes in microbial community structure and expression of RNA and protein along these redox gradients within OMZs. Here, we present a multi-omic time series dataset from Saanich Inlet spanning six years, including high spatial resolutionmore » small subunit ribosomal RNA tags, metagenomes, metatranscriptomes, and metaproteomes. As a result, this compendium provides paired multi-omic datasets over multiple time points providing a basis for exploring shifts in microbial community interactions and regulation of metabolic activities both along redox gradients and over time with implications for global climate models.« less

A compendium of multi-omic sequence information from the Saanich Inlet water column

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawley, Alyse K.; Torres-Beltran, Monica; Zaikova, Elena

Microbial communities play vital roles in earth’s geochemical cycles. Within marine oxygen minimum zones (OMZs) gradients of oxygen, nitrate and sulfide create redox gradients that drive biogeochemical cycling of carbon, nitrogen and sulphur. Climate-change induced expansion and intensification of OMZs and associated biogeochemical activities has significant implications for green house gas production i.e. nitrous oxide and methane. Next generation sequencing technologies have enabled observations of changes in microbial community structure and expression of RNA and protein along these redox gradients within OMZs. Here, we present a multi-omic time series dataset from Saanich Inlet spanning six years, including high spatial resolutionmore » small subunit ribosomal RNA tags, metagenomes, metatranscriptomes, and metaproteomes. As a result, this compendium provides paired multi-omic datasets over multiple time points providing a basis for exploring shifts in microbial community interactions and regulation of metabolic activities both along redox gradients and over time with implications for global climate models.« less

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

PubMed

Ascaso, C; Wierzchos, J

2002-12-01

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.

Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions.

PubMed

Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik; Mastroleo, Felice; Morin, Nicolas; Wilmotte, Annick; Janssen, Paul; Mergeay, Max

2006-01-01

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model--still in full development--that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration.

The role of the commensal microbiota in adaptive and maladaptive stressor-induced immunomodulation

PubMed Central

Mackos, Amy R.; Maltz, Ross; Bailey, Michael T.

2016-01-01

Over the past decade, it has become increasingly evident that there are extensive bidirectional interactions between the body and its microbiota. These interactions are evident during stressful periods, where it is recognized that commensal microbiota community structure is significantly changed. Many different stressors, ranging from early life stressors to stressors administered during adulthood, lead to significant, community-wide differences in the microbiota. The mechanisms through which this occurs are not yet known, but it is known that commensal microbes can recognize, and respond to, mammalian hormones and neurotransmitters, including those that are involved with the physiological response to stressful stimuli. In addition, the physiological stress response also changes many aspects of gastrointestinal physiology that can impact microbial community composition. Thus, there are many routes through which microbial community composition might be disrupted during stressful periods. The implications of these disruptions in commensal microbial communities for host health are still not well understood, but the commensal microbiota have been linked to stressor-induced immunopotentiation. The role of the microbiota in stressor-induced immunopotentiation can be adaptive, such as when these microbes stimulate innate defenses against bacterial infection. However, the commensal microbiota can also lead to maladaptive immune responses during stressor-exposure. This is evident in animal models of colonic inflammation where stressor exposure increases the inflammation through mechanisms involving the microbiota. It is likely that during stressor exposure, immune cell functioning is regulated by combined effects of both neurotransmitters/hormones and commensal microbes. Defining this regulation should be a focus of future studies. PMID:27760302

The role of the commensal microbiota in adaptive and maladaptive stressor-induced immunomodulation.

PubMed

Mackos, Amy R; Maltz, Ross; Bailey, Michael T

2017-02-01

Over the past decade, it has become increasingly evident that there are extensive bidirectional interactions between the body and its microbiota. These interactions are evident during stressful periods, where it is recognized that commensal microbiota community structure is significantly changed. Many different stressors, ranging from early life stressors to stressors administered during adulthood, lead to significant, community-wide differences in the microbiota. The mechanisms through which this occurs are not yet known, but it is known that commensal microbes can recognize, and respond to, mammalian hormones and neurotransmitters, including those that are involved with the physiological response to stressful stimuli. In addition, the physiological stress response also changes many aspects of gastrointestinal physiology that can impact microbial community composition. Thus, there are many routes through which microbial community composition might be disrupted during stressful periods. The implications of these disruptions in commensal microbial communities for host health are still not well understood, but the commensal microbiota have been linked to stressor-induced immunopotentiation. The role of the microbiota in stressor-induced immunopotentiation can be adaptive, such as when these microbes stimulate innate defenses against bacterial infection. However, the commensal microbiota can also lead to maladaptive immune responses during stressor-exposure. This is evident in animal models of colonic inflammation where stressor exposure increases the inflammation through mechanisms involving the microbiota. It is likely that during stressor exposure, immune cell functioning is regulated by combined effects of both neurotransmitters/hormones and commensal microbes. Defining this regulation should be a focus of future studies. Copyright © 2016 Elsevier Inc. All rights reserved.

Epistemological issues in the study of microbial life: alternative terran biospheres?

PubMed

Cleland, Carol E

2007-12-01

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

PubMed Central

2013-01-01

Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology. PMID:24238386

Gut microbes in correlation with mood: case study in a closed experimental human life support system.

PubMed

Li, L; Su, Q; Xie, B; Duan, L; Zhao, W; Hu, D; Wu, R; Liu, H

2016-08-01

Gut microbial community, which may influence our mood, can be shaped by modulating the gut ecosystem through dietary strategies. Understanding the gut-brain correlationship in healthy people is important for maintenance of mental health and prevention of mental illnesses. A case study on the correlation between gut microbial alternation and mood swing of healthy adults was conducted in a closed human life support system during a 105-day experiment. Gut microbial community structures were analyzed using high-throughput sequencing every 2 weeks. A profile of mood states questionnaire was used to record the mood swings. Correlation between gut microbes and mood were identified with partial least squares discrimination analysis. Microbial community structures in the three healthy adults were strongly correlated with mood states. Bacterial genera Roseburia, Phascolarctobacterium, Lachnospira, and Prevotella had potential positive correlation with positive mood, while genera Faecalibacterium, Bifidobacterium, Bacteroides, Parabacteroides, and Anaerostipes were correlated with negative mood. Among which, Faecalibacterium spp. had the highest abundance, and showed a significant negative correlation with mood. Our results indicated that the composition of microbial community could play a role in emotional change in mentally physically healthy adults. © 2016 John Wiley & Sons Ltd.

Life in the "plastisphere": microbial communities on plastic marine debris.

PubMed

Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

2013-07-02

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

Microbial Dysbiosis Is Associated with Human Breast Cancer

PubMed Central

Xuan, Caiyun; Shamonki, Jaime M.; Chung, Alice; DiNome, Maggie L.; Chung, Maureen; Sieling, Peter A.; Lee, Delphine J.

2014-01-01

Breast cancer affects one in eight women in their lifetime. Though diet, age and genetic predisposition are established risk factors, the majority of breast cancers have unknown etiology. The human microbiota refers to the collection of microbes inhabiting the human body. Imbalance in microbial communities, or microbial dysbiosis, has been implicated in various human diseases including obesity, diabetes, and colon cancer. Therefore, we investigated the potential role of microbiota in breast cancer by next-generation sequencing using breast tumor tissue and paired normal adjacent tissue from the same patient. In a qualitative survey of the breast microbiota DNA, we found that the bacterium Methylobacterium radiotolerans is relatively enriched in tumor tissue, while the bacterium Sphingomonas yanoikuyae is relatively enriched in paired normal tissue. The relative abundances of these two bacterial species were inversely correlated in paired normal breast tissue but not in tumor tissue, indicating that dysbiosis is associated with breast cancer. Furthermore, the total bacterial DNA load was reduced in tumor versus paired normal and healthy breast tissue as determined by quantitative PCR. Interestingly, bacterial DNA load correlated inversely with advanced disease, a finding that could have broad implications in diagnosis and staging of breast cancer. Lastly, we observed lower basal levels of antibacterial response gene expression in tumor versus healthy breast tissue. Taken together, these data indicate that microbial DNA is present in the breast and that bacteria or their components may influence the local immune microenvironment. Our findings suggest a previously unrecognized link between dysbiosis and breast cancer which has potential diagnostic and therapeutic implications. PMID:24421902

Workshop to develop deep-life continental scientific drilling projects

DOE PAGES

Kieft, T. L.; Onstott, T. C.; Ahonen, L.; ...

2015-05-29

The International Continental Scientific Drilling Program (ICDP) has long espoused studies of deep subsurface life, and has targeted fundamental questions regarding subsurface life, including the following: "(1) What is the extent and diversity of deep microbial life and what are the factors limiting it? (2) What are the types of metabolism/carbon/energy sources and the rates of subsurface activity? (3) How is deep microbial life adapted to subsurface conditions? (4) How do subsurface microbial communities affect energy resources? And (5) how does the deep biosphere interact with the geosphere and atmosphere?" (Horsfield et al., 2014) Many ICDP-sponsored drilling projects have includedmore » a deep-life component; however, to date, not one project has been driven by deep-life goals, in part because geomicrobiologists have been slow to initiate deep biosphere-driven ICDP projects. Therefore, the Deep Carbon Observatory (DCO) recently partnered with the ICDP to sponsor a workshop with the specific aim of gathering potential proponents for deep-life-driven ICDP projects and ideas for candidate drilling sites. Twenty-two participants from nine countries proposed projects and sites that included compressional and extensional tectonic environments, evaporites, hydrocarbon-rich shales, flood basalts, Precambrian shield rocks, subglacial and subpermafrost environments, active volcano–tectonic systems, megafan deltas, and serpentinizing ultramafic environments. The criteria and requirements for successful ICDP applications were presented. Deep-life-specific technical requirements were discussed and it was concluded that, while these procedures require adequate planning, they are entirely compatible with the sampling needs of other disciplines. As a result of this workshop, one drilling workshop proposal on the Basin and Range Physiographic Province (BRPP) has been submitted to the ICDP, and several other drilling project proponents plan to submit proposals for ICDP-sponsored drilling workshops in 2016.« less

The limits of extremophilic life expanded under extraterrestrial environment-simulated experiments

NASA Astrophysics Data System (ADS)

Lage, C.; Dalmaso, G.; Teixeira, L.; Bendia, A.; Rosado, A.

2012-09-01

Astrobiology is a brand new area of science that seeks to understand the origin and dynamics of life in the universe. Several hypotheses to explain life in the cosmic context have been developed throughout human history, but only now technology has allowed many of them to be tested. Laboratory experiments have been able to show how chemical elements essential to life, carbon, nitrogen, oxygen and hydrogen combine in biologically important compounds. Interestingly, these compounds are found universally. As these compounds were combined to the point of originating cells and complex organisms is still a challenge to be unveiled by science. However, our 4.5 billion years-old solar system was born within a 10-billion years-old universe. Thus, simple cells like microorganisms may have had time to form in planets older than ours or other suitable molecular places in the universe. One hypothesis to explain the origin of life on Earth is called panspermia, which predicts that microbial life could have been formed in the universe billions of years ago, traveling between planets, and inseminating units of life that could have become more complex in habitable planets like ours. A project designed to test the viability of extremophile microorganisms exposed to simulated extraterrestrial environments is ongoing at the Carlos Chagas Filho Institute of Biophysics to test whether microbial life could withstand those inhospitable environments. Ultra-resistant (known or novel ones) microorganisms collected from terrestrial extreme environments, extremophiles, have been exposed to intense radiation sources simulating solar radiation (at synchrotron accelerators), capable of emitting in a few hours radiation equivalent of million years accumulated doses. The results obtained in these experiments reveal the interesting possibility of the existence of microbial life beyond Earth.

Mini-Review: Probing the limits of extremophilic life in extraterrestrial environment-simulated experiments

NASA Astrophysics Data System (ADS)

Lage, Claudia A. S.; Dalmaso, Gabriel Z. L.; Teixeira, Lia C. R. S.; Bendia, Amanda G.; Paulino-Lima, Ivan G.; Galante, Douglas; Janot-Pacheco, Eduardo; Abrevaya, Ximena C.; Azúa-Bustos, Armando; Pelizzari, Vivian H.; Rosado, Alexandre S.

2012-10-01

Astrobiology is a relatively recent scientific field that seeks to understand the origin and dynamics of life in the Universe. Several hypotheses have been proposed to explain life in the cosmic context throughout human history, but only now, technology has allowed many of them to be tested. Laboratory experiments have been able to show how chemical elements essential to life, such as carbon, nitrogen, oxygen and hydrogen combine in biologically important compounds. Interestingly, these compounds are ubiquitous. How these compounds were combined to the point of originating cells and complex organisms is still to be unveiled by science. However, our 4.5 billion years old Solar system appeared in a 10 billion years old Universe. Thus, simple cells such as micro-organisms may have had time to form in planets older than ours or in other suitable places in the Universe. One hypothesis related to the appearance of life on Earth is called panspermia, which predicts that microbial life could have been formed in the Universe billions of years ago, travelling between planets, and inseminating units of life that could have become more complex in habitable planets such as Earth. A project designed to test the viability of extremophile micro-organisms exposed to simulated extraterrestrial environments is in progress at the Carlos Chagas Filho Institute of Biophysics (UFRJ, Brazil) to test whether microbial life could withstand inhospitable environments. Radiation-resistant (known or novel ones) micro-organisms collected from extreme terrestrial environments have been exposed (at synchrotron accelerators) to intense radiation sources simulating Solar radiation, capable of emitting radiation in a few hours equivalent to many years of accumulated doses. The results obtained in these experiments reveal an interesting possibility of the existence of microbial life beyond Earth.

One Step Closer to Mars with Aquaponics: Cultivating Citizen Science in K12 Schools

NASA Technical Reports Server (NTRS)

Kolattukudy, Maria; Puranik, Niyati; Sane, Nishant; Bisht, Kritika; Saffat, Nabeeha; Gupta, Anika; McHugh, Anne; Detweiler, Angela; Bebout, Brad; Everroad, R. Craig

2017-01-01

The Microbial Ecology and Biogeochemistry Research Laboratory at NASA Ames Research Center focuses primarily on the nutrient cycling and diversity of complex microbial communities. NASA is interested in the composition and functioning of microbial mat communities as these processes fundamentally shape the form and function of these analogs for the earliest forms of life on Earth (3.6 billion years ago), and likely will on other planets as well. Aquaponics systems are supported by microbial communities who perform many complex ecosystem services, including cycling nitrogen. Microbes are integral to the stability and productivity of aquaponics systems, which are analogous to microbial communities in food production systems that are essential for building efficient life support systems for long-distance space travel. Students at Meadow Park Middle School created 10 parallel aquaponics systems and took temporal microbial samples to characterize whether any macro-ecology variables impacted or changed the microbial diversity of these systems. Students additionally created a website so that other classrooms can pursue similar projects in their own schools (https://go.nasa.gov/2uJhxmF). Our lab at NASA Ames has sequenced water samples from each of the 10 tanks at 3 timepoints using a MinION sequencer. MPMS students will be involved in the analysis of the bioinformatics data generated through this collaboration. Our ongoing collaboration aims to collect and analyze data in the classroom setting that has utility for research scientists, while involving students as collaborators in the research process.

Final Report: The Human Microbiome as a Multipurpose Biomarker

DTIC Science & Technology

2015-11-23

Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 microbiome, biomarker, microbial forensics, microbial ecology , identifiability REPORT...temporal variation in the ecology of the human microbiome, this work demonstrated the feasibility of microbiome-based identifiability for the first time...a result with important ethical implications for microbiome study design. In order to construct metagenomic codes that are stable over time, we

Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: implications for life detection and planetary protection.

PubMed

Tauscher, Courtney; Schuerger, Andrew C; Nicholson, Wayne L

2006-08-01

Bacterial spores have been considered as microbial life that could survive interplanetary transport by natural impact processes or human spaceflight activity. Deposition of terrestrial microbes or their biosignature molecules onto the surface of Mars could negatively impact life detection experiments and planetary protection measures. Simulated Mars solar radiation, particularly the ultraviolet component, has been shown to reduce spore viability, but its effect on spore germination and resulting production of biosignature molecules has not been explored. We examined the survival and germinability of Bacillus subtilis spores exposed to simulated martian conditions that include solar radiation. Spores of B. subtilis that contain luciferase resulting from expression of an sspB-luxAB gene fusion were deposited on aluminum coupons to simulate deposition on spacecraft surfaces and exposed to simulated Mars atmosphere and solar radiation. The equivalent of 42 min of simulated Mars solar radiation exposure reduced spore viability by nearly 3 logs, while germination-induced bioluminescence, a measure of germination metabolism, was reduced by less than 1 log. The data indicate that spores can retain the potential to initiate germination-associated metabolic processes and produce biological signature molecules after being rendered nonviable by exposure to Mars solar radiation.

Survival of microbial life under shock compression: implications for Panspermia

NASA Astrophysics Data System (ADS)

Burchell, M.

2007-09-01

An analysis is carried out of the survival fraction of micro-organisms exposed to extreme shock pressures. A variety of data sources are used in this analysis. The key findings are that survival depends on the behaviour of the cell wall. Below a critical shock pressure there is a relatively slow fall in survival fraction as shock pressures increase. Above the critical threshold survival starts to fall rapidly as shock pressure increases further. The critical shock pressures found here are in the range 2.4 to 20 GPa, and vary not only from organism to organism, but also depend on the growth stage of given organisms, with starved (i.e., no growth) states favoured for survival. At the shock pressures typical of those involved in interplanetary transfer of rocky materials, the survival fractions are found to be small but finite. This lends credence to the idea of Panspermia, i.e. life may naturally migrate through space. Thus for example, Martian meteorites should not a prior be considered as sterile due to the shock processes they have undergone, but their lack of viable micro-organisms either reflects no such life being present at the source at the time of departure or the influence of other hazardous processes such as radiation in space or heating of surfaces during entry into a planetary atmosphere.

TLM-Quant: An Open-Source Pipeline for Visualization and Quantification of Gene Expression Heterogeneity in Growing Microbial Cells

PubMed Central

Piersma, Sjouke; Denham, Emma L.; Drulhe, Samuel; Tonk, Rudi H. J.; Schwikowski, Benno; van Dijl, Jan Maarten

2013-01-01

Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly ‘noisy’ heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological ‘cell factory’. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images. PMID:23874729

Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition.

PubMed

Javan, Gulnaz T; Finley, Sheree J; Smith, Tasia; Miller, Joselyn; Wilkinson, Jeremy E

2017-01-01

Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, Clostridium spp. These microorganisms have been implicated as etiological agents in potentially life-threatening infections; notwithstanding, the scale and trajectory of these microbes after death have not been elucidated. We performed phylogenetic surveys of thanatomicrobiome signatures of cadavers' internal organs to compare the microbial diversity between the 16S rRNA gene V4 hypervariable region and V3-4 conjoined regions from livers and spleens of 45 cadavers undergoing forensic microbiological studies. Phylogenetic analyses of 16S rRNA gene sequences revealed that the V4 region had a significantly higher mean Chao1 richness within the total microbiome data. Permutational multivariate analysis of variance statistical tests, based on unweighted UniFrac distances, demonstrated that taxa compositions were significantly different between V4 and V3-4 hypervariable regions ( p < 0.001). Of note, we present the first study, using the largest cohort of criminal cases to date, that two hypervariable regions show discriminatory power for human postmortem microbial diversity. In conclusion, here we propose the impact of hypervariable region selection for the 16S rRNA gene in differentiating thanatomicrobiomic profiles to provide empirical data to explain a unique concept, the Postmortem Clostridium Effect.

Proceedings of the NASA Microbiology Workshop

NASA Technical Reports Server (NTRS)

Roman, M. C.; Jan, D. L.

2012-01-01

Long-term spaceflight is characterized by extraordinary challenges to maintain the life-supporting instrumentation free from microbial contamination and the crew healthy. The methodology currently employed for microbial monitoring in space stations or short spaceflights within the orbit of Earth have been instrumental in safeguarding the success of the missions, but suffers certain shortcomings that are critical for long spaceflights. This workshop addressed current practices and methodologies for microbial monitoring in space systems, and identified and discussed promising alternative methodologies and cutting-edge technologies for pursuit in the microbial monitoring that hold promise for supporting future NASA long-duration space missions.

Microbial endocrinology: Why the intersection of microbiology and neurobiology matters to poultry health.

PubMed

Villageliu, Daniel N; Lyte, Mark

2017-08-01

The union of microbiology and neurobiology has led to a revolution in the way we view the microbiome. Now recognized as important symbionts, the microorganisms which inhabit multiple niches in mammalian and avian (chicken) hosts, such as the intestinal tract and skin, serve and influence many important physiological functions. The realization that the gut microbiome serves as a kind of "microbial organ" has important implications for many areas of biology. In this paper advances in the field of microbial endocrinology which may hold relevance for the poultry industry are examined. © 2017 Poultry Science Association Inc.

Synthetic networks in microbial communities

NASA Astrophysics Data System (ADS)

Suel, Gurol

2015-03-01

While bacteria are single celled organisms, they predominantly reside in structured communities known as biofilms. Cells in biofilms are encapsulated and protected by the extracellular matrix (ECM), which also confines cells in space. During biofilm development, microbial cells are organized in space and over time. Little is known regarding the processes that drive the spatio-temporal organization of microbial communities. Here I will present our latest efforts that utilize synthetic biology approaches to uncover the organizational principles that drive biofilm development. I will also discuss the possible implications of our recent findings in terms of the cost and benefit to biofilm cells.

Long-Term Effects of Irrigation with Waste Water on Soil AM Fungi Diversity and Microbial Activities: The Implications for Agro-Ecosystem Resilience

PubMed Central

del Mar Alguacil, Maria; Torrecillas, Emma; Torres, Pilar; García-Orenes, Fuensanta; Roldán, Antonio

2012-01-01

The effects of irrigation with treated urban wastewater (WW) on the arbuscular mycorrhizal fungi (AMF) diversity and soil microbial activities were assayed on a long-term basis in a semiarid orange-tree orchard. After 43 years, the soil irrigated with fresh water (FW) had higher AMF diversity than soils irrigated with WW. Microbial activities were significantly higher in the soils irrigated with WW than in those irrigated with FW. Therefore, as no negative effects were observed on crop vitality and productivity, it seems that the ecosystem resilience gave rise to the selection of AMF species better able to thrive in soils with higher microbial activity and, thus, to higher soil fertility. PMID:23094075

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

PubMed

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Microbial consortia in Oman oil fields: a possible use in enhanced oil recovery.

PubMed

Al-Bahry, Saif N; Elshafie, Abdulkader E; Al-Wahaibi, Yahya M; Al-Bemani, Ali S; Joshi, Sanket J; Al-Maaini, Ratiba A; Al-Alawi, Wafa J; Sugai, Yuichi; Al-Mandhari, Mussalam

2013-01-01

Microbial enhanced oil recovery (MEOR) is one of the most economical and efficient methods for extending the life of production wells in a declining reservoir. Microbial consortia from Wafra oil wells and Suwaihat production water, Al-Wusta region, Oman were screened. Microbial consortia in brine samples were identified using denaturing gradient gel electrophoresis and 16S rRNA gene sequences. The detected microbial consortia of Wafra oil wells were completely different from microbial consortia of Suwaihat formation water. A total of 33 genera and 58 species were identified in Wafra oil wells and Suwaihat production water. All of the identified microbial genera were first reported in Oman, with Caminicella sporogenes for the first time reported from oil fields. Most of the identified microorganisms were found to be anaerobic, thermophilic, and halophilic, and produced biogases, biosolvants, and biosurfactants as by-products, which may be good candidates for MEOR.

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

DesMarais, David J.

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

Psychrophilic and Psychrotolerant Microbial Extremophiles in Polar Environments

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.

2010-01-01

The microbial extremophiles that inhabit the polar regions of our planet are of tremendous significance. The psychrophilic and psychrotolerant microorganisms, which inhabit all of the cold environments on Earth have important applications to Bioremediation, Medicine, Pharmaceuticals, and many other areas of Biotechnology. Until recently, most of the research on polar microorganisms was confined to studies of polar diatoms, yeast, fungi and cyanobacteria. However, within the past three decades, extensive studies have been conducted to understand the bacteria and archaea that inhabit the Arctic and Antarctic sea-ice, glaciers, ice sheets, permafrost and the cryptoendolithic, cryoconite and ice-bubble environments. These investigations have resulted in the discovery of many new genera and species of anaerobic and aerobic microbial extremophiles. Exotic enzymes, cold-shock proteins and pigments produced by some of the extremophiles from polar environments have the potential to be of great benefit to Mankind. Knowledge about microbial life in the polar regions is crucial to understanding the limitations and biodiversity of life on Earth and may provide valuable clues to the Origin of Life on Earth. The discovery of viable microorganisms in ancient ice from the Fox Tunnel, Alaska and the deep Vostok Ice has shown that microorganisms can remain alive while cryopreserved in ancient ice. The psychrophilic lithoautotrophic homoacetogen isolated from the deep anoxic trough of Lake Untersee is an ideal candidate for life that might inhabit comets or the polar caps of Mars. The spontaneous release of gas from within the Anuchin Glacier above Lake Untersee may provide clues to the ice geysers that erupt from the tiger stripe regions of Saturn s moon Enceladus. The methane productivity in the lower regimes of Lake Untersee may also provide insights into possible mechanisms for the recently discovered methane releases on Mars. Since most of the other water bearing bodies of our Solar system are frozen worlds, microbial extremophiles from the Polar Regions of Earth are of great importance to Astrobiology in understanding where and how to search for evidence of life elsewhere in the Cosmos.

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

PubMed

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management

PubMed Central

Head, Ian M.; Gray, Neil D.; Larter, Stephen R.

2014-01-01

Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80–90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures. PMID:25426105

The contamination impact of human exploration to a subterranean environment and the implications for further crewed space exploration

NASA Astrophysics Data System (ADS)

Leuko, Stefan; Rettberg, Petra; De Waele, Jo; Sanna, Laura; Koskinen, Kaisa

2016-07-01

The quest of exploring and looking for life in new places is a human desire since centuries. Nowadays, we are not only looking on planet Earth any more, but our endeavours focus on nearby planets in our solar system. It is therefore of great importance to preserve the extra-terrestrial environment and not to contaminate it with terrestrial / human associated bacteria. At this point in time we are not able to send crewed missions to other planets; however, analysing the impact of human exploration on environments is of great planetary protection concern. This can be achieved by obtaining samples from a subterranean environment, where only expert speleologists have access and the human impact is considered very low. For this study, astronauts participating in the 2014 ESA CAVES (Cooperative Adventure for Valuing and Exercising human behaviour and performance Skills) training course, obtained samples from deep within a subterranean environment and returned them to the laboratory for molecular microbial analysis. The diversity of the returned soil samples was analysed by molecular means such as clone library and next-generation sequencing (NGS). It was found that humans have an immense impact on the microbial diversity in the environment. Although the cave system is sparsely entered by humans, a high relative abundance of Staphylococcus spp. and Propionibacteria spp., organisms that are characteristic for human skin, have been recovered. Some samples even showed the presence of human gut associated methanogenic archaea, Methanomassiliicoccus spp. The obtained data from this investigation indicate that human exploration is strongly polluting an environment and may lead to false-positive sign of life on other planets. It is therefore imperative to increase our awareness to this problem as well as work towards new protocols to protect a pristine extraterrestrial environment during exploration.

Astrobiological implications of dim light phototrophy in deep-sea red clays.

PubMed

Das, Anindita; Singh, Tanya; LokaBharathi, P A; Dhakephalkar, Prashant K; Mallik, Sweta; Kshirsagar, Pranav R; Khadge, N H; Nath, B Nagender; Bhattacharya, Satadru; Dagar, Aditya Kumar; Kaur, Prabhjot; Ray, Dwijesh; Shukla, Anil D; Fernandes, Christabelle E G; Fernandes, Sheryl O; Thomas, Tresa Remya A; S S, Mamatha; Mourya, Babu Shashikant; Meena, Ram Murti

2017-02-01

Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66Wm -2 , were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2°C and 25°± 2°C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably influence Doppler effects and consequently spectral detection techniques exo-planetary microbial life. Copyright © 2017 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Light-Dependant Biostabilisation of Sediments by Stromatolite Assemblages

PubMed Central

Paterson, David M.; Aspden, Rebecca J.; Visscher, Pieter T.; Consalvey, Mireille; Andres, Miriam S.; Decho, Alan W.; Stolz, John; Reid, R. Pamela

2008-01-01

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas). It was shown that the most effective assemblages could produce a rapid (12–24 h) and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h). Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the mat forming process. The evolution of photosynthesis may have provided an important advance for the niche construction activity of microbial systems and the formation and persistence of the stromatolites which came to dominate shallow coastal environments for 80% of the biotic history of the earth. PMID:18781202

Light-dependant biostabilisation of sediments by stromatolite assemblages.

PubMed

Paterson, David M; Aspden, Rebecca J; Visscher, Pieter T; Consalvey, Mireille; Andres, Miriam S; Decho, Alan W; Stolz, John; Reid, R Pamela

2008-09-10

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas). It was shown that the most effective assemblages could produce a rapid (12-24 h) and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h). Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the mat forming process. The evolution of photosynthesis may have provided an important advance for the niche construction activity of microbial systems and the formation and persistence of the stromatolites which came to dominate shallow coastal environments for 80% of the biotic history of the earth.

Genome-Based Microbial Taxonomy Coming of Age.

PubMed

Hugenholtz, Philip; Skarshewski, Adam; Parks, Donovan H

2016-06-01

Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Astrobiology and Microbial Diversity Websites at MBL

NASA Astrophysics Data System (ADS)

Bahr, M.; Bordenstein, S. R.

2006-12-01

The NASA Astrobiology Institute (NAI) mission is to study the origin, evolution and future of life in the Universe. The MBL Astrobiology team explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology over evolutionary time scales. Communication about our research includes the personal contact of teacher workshops, and the development of web-based resources. Microbial Life Educational Resources (MLER) provides an expanding internet resource about the ecology, diversity and evolution for students, K-12 teachers, university faculty, and the general public. MLER includes websites, PowerPoint presentations, teaching activities, data sets, and other useful materials for creating or enhancing courses related to astrobiology. Our second site, micro*scope (http://microscope.mbl.edu), has images of microbes, classification schemes, descriptions of organisms, talks and other educational resources to improve awareness of the biodiversity of our microbial partners.

Biomarkers in Carbonate Thermal Springs: Implications for Mars

NASA Technical Reports Server (NTRS)

Allen, C. C.; Kivett, S. J.; McKay, D. S.

1998-01-01

Evidence of possible relict biogenic activity has been reported in carbonate inclusions within martian meteorite ALH 84001. The initial evidence included ovoid and elongated forms 50 - 500 nanometers in length, morphologically similar to but significantly smaller than many terrestrial microbes. More recently, thin structures resembling the remains of organic biofilms have been reported in the same meteorite. Carbonates have also been discussed in the context of Mars sample return missions. Thermal spring deposits have often been cited as prime locations for exobiological exploration. By analogy to Earth, specialized microbes may have existed in the heated, mineralized waters, and precipitates of carbonate and/or silica from these waters may have trapped and preserved evidence of life. Since the geological interactions that produce thermal springs can be recognized in orbital imagery, directed searches for microfossils in such deposits are deemed possible. We are engaged in a study of the signatures produced by contemporary biogenic activity (biomarkers) in carbonate thermal springs. We are examining the microbes that live in such environments and the preservation of microbial forms, biofilms, and petrographic fabrics indicative of life in thermal spring mineral deposits. This work is part of a much more extensive study to refine the appropriate tools, techniques, and approaches to seek evidence of life in a range of planetary samples. A deeper understanding of biological signatures will prepare us for the detailed search for life on Mars and eventually on other planets. Overall. the study of biomarkers in rocks and soils will provide insight into the evolution of life because such signatures are a record of how life interacts with its environment, how it adapts to changing conditions, and how life can influence geology and climate.

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco).

PubMed

Bruneel, Odile; Mghazli, N; Hakkou, R; Dahmani, I; Filali Maltouf, A; Sbabou, L

2017-07-01

In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.

The Changing Seasonality of Tundra Nutrient Cycling: Implications for Arctic Ecosystem Function

NASA Astrophysics Data System (ADS)

Weintraub, M. N.; Steltzer, H.; Sullivan, P.; Schimel, J.; Wallenstein, M. D.; Darrouzet-Nardi, A.; Segal, A. D.

2011-12-01

Arctic soils contain large stores of carbon (C) and may act as a significant CO2 source with warming. However, the key to understanding tundra soil processes is nitrogen (N), as both plant growth and decomposition are N limited. However, current models of tundra ecosystems assume that while N limits plant growth, C limits decomposition. In addition, N availability is strongly seasonal with relatively high concentrations early in the growing season followed by a pronounced crash. We need to understand the controls on this seasonality to predict responses to climate change, but there are multiple questions that need answers: 1) What causes the seasonality in N? 2) Does microbial activity switch seasonally between C and N limitation? 3) How will a lengthening of the growing season alter overall ecosystem C and N dynamics, as a result of differential extension of the periods before and after the nutrient crash? We hypothesized that microbial activity is C limited early in the growing season, when N availability is higher and root exudate C is unavailable, and that microbial activity becomes N limited in response to plant N uptake and immobilization stimulated by root C. To address these questions we are conducting an accelerated snow-melt X warming field experiment in an Alaskan moist acidic arctic tundra community, and following plant and soil dynamics. Changes in the timing of C and N interactions in the different treatments will enable us to develop an enhanced mechanistic understanding of why the nutrient crash occurs and what the implications are for a lengthening of the arctic growing season. In 2010 we successfully accelerated snowmelt by 4 days. Both earlier snowmelt and warming accelerated early season plant life history events, with a few exceptions. However, responses to the combined treatment could not always be predicted from single factor effects. End of season life history events occurred later in response to the treatments, again with a few exceptions. Continuous measurements of plant community NDVI suggest that the peak of the plant growing season (i.e. maximum greenness) ended 4 days earlier in response to earlier snowmelt and climate warming, due to earlier senescence by birch. Root growth was significantly delayed in the early snowmelt plots and accelerated in the combined treatment. Despite the changes in root growth, though, we did not observe significant treatment effects on soil N availability, which tended to decline in July in all treatments. In 2011 we achieved a snowmelt acceleration of 15 days while control plots were snowfree on almost the same date as in 2010. This relatively large treatment effect should enable us to more conclusively determine the extent to which the timing of plant growth regulates soil N availability, but final results from the 2011 are currently pending.

Solving the problems with chirality as a biomarker for alien life

NASA Astrophysics Data System (ADS)

Levin, Gilbert V.

2010-09-01

The basis for chiral biomarkers that have been increasingly proposed to obtain evidence for life is reviewed. Specific problems in accepting them and other biomarkers as proof of life are cited. A new chiral method is offered to overcome these difficulties, a method that can make an unambiguous determination of extant microbial life.

The deep, hot biosphere.

PubMed

Gold, T

1992-07-01

There are strong indications that microbial life is widespread at depth in the crust of the Earth, just as such life has been identified in numerous ocean vents. This life is not dependent on solar energy and photosynthesis for its primary energy supply, and it is essentially independent of the surface circumstances. Its energy supply comes from chemical sources, due to fluids that migrate upward from deeper levels in the Earth. In mass and volume it may be comparable with all surface life. Such microbial life may account for the presence of biological molecules in all carbonaceous materials in the outer crust, and the inference that these materials must have derived from biological deposits accumulated at the surface is therefore not necessarily valid. Subsurface life may be widespread among the planetary bodies of our solar system, since many of them have equally suitable conditions below, while having totally inhospitable surfaces. One may even speculate that such life may be widely disseminated in the universe, since planetary type bodies with similar subsurface conditions may be common as solitary objects in space, as well as in other solar-type systems.

Under the sea: microbial life in volcanic oceanic crust.

PubMed

Edwards, Katrina J; Wheat, C Geoffrey; Sylvan, Jason B

2011-09-06

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.

Improvement in shelf life of minimally processed cilantro leaves through integration of kinetin pretreatment and packaging interventions: Studies on microbial population dynamics, biochemical characteristics and flavour retention.

PubMed

Ranjitha, K; Shivashankara, K S; Sudhakar Rao, D V; Oberoi, Harinder Singh; Roy, T K; Bharathamma, H

2017-04-15

Effect of integrating optimized combination of pretreatment with packaging on shelf life of minimally processed cilantro leaves (MPCL) was appraised through analysis of their sensory attributes, biochemical characteristics, microbial population and flavour profile during storage. Minimally pretreated cilantro leaves pretreated with 50ppm kinetin and packed in 25μ polypropylene bags showed a shelf life of 21days. Optimized combination helped in efficiently maintaining sensory parameters, flavour profile, and retention of antioxidants in MPCL until 21days. Studies conducted on the effect of optimized combination on microbial population and flavour profile revealed that among different microorganisms, pectinolysers had a significant effect on spoilage of MPCL and their population of ⩽3.59logcfu/g was found to be acceptable. Principal component analysis of headspace volatiles revealed that (E)-2-undecenal, (E)-2-hexadecenal, (E)-2-tetradecenal & (E)-2-tetradecen-1-ol in stored samples clustered with fresh samples and therefore, could be considered as freshness indicators for MPCL. Copyright © 2016 Elsevier Ltd. All rights reserved.

Shelf-life extension of semi-dried buckwheat noodles by the combination of aqueous ozone treatment and modified atmosphere packaging.

PubMed

Bai, Yi-Peng; Guo, Xiao-Nao; Zhu, Ke-Xue; Zhou, Hui-Ming

2017-12-15

The present study investigated the combined effects of aqueous ozone treatment and modified atmosphere packaging (MAP) on prolonging the shelf-life of semi-dried buckwheat noodles [SBWN; moisture content (22.5±0.5%)] at 25°C. Firstly, the different concentrations of ozonated water were used to make SBWN. Subsequently, SBWN prepared with ozonated water were packaged under six different conditions and stored for 11days. Changes in microbial, chemical-physical, textural properties and sensorial qualities of SWBN were monitored during storage. Microbiological results indicated that adopting 2.21mg/L of ozonated water resulted in a 1.8 log 10 CFU/g reduction of the initial microbial loads in SBWN. In addition, MAP suppressed the microbial growth with a concomitant reduction in the rates of acidification and quality deteriorations of SBWN. Finally, the shelf-life of sample packed under N 2 :CO 2 =30:70 was extended to 9days, meanwhile textural and sensorial characteristics were maintained during the whole storage period. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial ecology and host-microbiota interactions during early life stages

PubMed Central

Collado, Maria Carmen; Cernada, Maria; Baüerl, Christine; Vento, Máximo; Pérez-Martínez, Gaspar

2012-01-01

The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life. PMID:22743759

Deep and Ultra-deep Underground Observatory for In Situ Stress, Fluids, and Life

NASA Astrophysics Data System (ADS)

Boutt, D. F.; Wang, H.; Kieft, T. L.

2008-12-01

The question 'How deeply does life extend into the Earth?' forms a single, compelling vision for multidisciplinary science opportunities associated with physical and biological processes occurring naturally or in response to construction in the deep and ultra-deep subsurface environment of the Deep Underground Science and Engineering Laboratory (DUSEL) in the former Homestake mine. The scientific opportunity is to understand the interaction between the physical environment and microbial life, specifically, the coupling among (1) stress state and deformation; (2) flow and transport and origin of fluids; and (3) energy and nutrient sources for microbial life; and (4) microbial identity, diversity and activities. DUSEL-Homestake offers the environment in which these questions can be addressed unencumbered by competing human activities. Associated with the interaction among these variables are a number of questions that will be addressed at variety of depths and scales in the facility: What factors control the distribution of life as a function of depth and temperature? What patterns in microbial diversity, microbial activity and nutrients are found along this gradient? How do state variables (stress, strain, temperature, and pore pressure) and constitutive properties (permeability, porosity, modulus, etc.) vary with scale (space, depth, time) in a large 4D heterogeneous system: core - borehole - drift - whole mine - regional? How are fluid flow and stress coupled in a low-permeability, crystalline environment dominated by preferential flow paths? How does this interaction influence the distribution of fluids, solutes, gases, colloids, and biological resources (e.g. energy and nutritive substrates) in the deep continental subsurface? What is the interaction between geomechanics/geohydrology and microbiology (microbial abundance, diversity, distribution, and activities)? Can relationships elucidated within the mechanically and hydrologically altered subsurface habitat of the Homestake DUSEL be extrapolated to the pristine subsurface biosphere? In the absence of extensive intrusive investigations (drifts, mines, etc), can we characterize hydrogeologic and geomechanical processes in the subsurface? To what depth can we effectively characterize such processes, and what is the confidence in our interpretations? In addition to addressing these question in the 10-km3 of mine volume, the Homestake facility offers the deepest drilling platform in North America. The extant depth of 8000 feet can be doubled by drilling. An array of three or more 8,200 ft. boreholes, wire-line drilled from the 8,000 ft. level at Homestake will probe to at least 16,200 ft. below land surface, a depth at this location approaching the expected lower biosphere limit (e.g. the 120°C isotherm). Cores will be collected aseptically and then fracture patterns (e.g., orientation, aperture, etc.) will be determined and fracture fluids will be intensively sampled over time. Cores and fracture fluids will be analyzed for indigenous microbial communities, including their genetic elements, metabolic processes, and biosignatures.

Microbial biodiversity, quality and shelf life of microfiltered and pasteurized extended shelf life (ESL) milk from Germany, Austria and Switzerland.

PubMed

Schmidt, Verena S J; Kaufmann, Veronika; Kulozik, Ulrich; Scherer, Siegfried; Wenning, Mareike

2012-03-01

Information on factors limiting the shelf life of extended shelf life (ESL) milk produced by microfiltration and subsequent pasteurization is very limited. In this study, three different batches of ESL milk were analyzed at different stages of the production process and during storage at 4 °C, 8 °C and 10 °C in order to evaluate the changes in bacterial cell counts, microbial diversity and enzymatic quality. Additionally, detailed biodiversity analyses of 250 retail ESL milk packages produced by five manufacturers in Germany, Austria and Switzerland were performed at the end of shelf life. It was observed that microfiltration decreased the microbial loads by 5-6 log₁₀ units to lower than 1 CFU/mL. However, bacterial counts at the end of shelf life were extremely variable and ranged between <1 and 8 log₁₀ CFU/mL. 8% of all samples showed spoilage indicated by cell counts higher than 6 log₁₀ CFU/mL. The main spoilage groups of bacteria were Gram-negative post-process recontaminants (Acinetobacter, Chryseobacterium, Psychrobacter, Sphingomonas) and the spore formers Paenibacillus and Bacillus cereus, while other spore formers and Microbacterium spp. did not reach spoilage levels. Paenibacillus spp. and B. cereus apparently influenced enzymatic spoilage, as indicated by increased free fatty acid production, pH 4.6 soluble peptide fractions and off-flavors. In some cases, enzymatic spoilage was observed although microbial counts were well below 6 log₁₀ CFU/mL. Thirteen B. cereus isolates were characterized for their toxin profiles and psychrotolerance. Hbl, nhe, and cytK toxin genes were detected in ten, thirteen, and four isolates, respectively, whereas the ces gene was always absent. Interestingly, only three of the thirteen isolates could be allocated to psychrotolerant genotypes, as indicated by the major cold shock cspA gene signature. Generally, large discrepancies in microbial loads and biodiversity were observed at the end of shelf life, even among packages of the same production batch. We suggest that such unexpected differences may be due to very low cell counts after ESL treatment, causing stochastic variations of initial species distributions in individual packages. This would result in the development of significantly different bacterial populations during cold storage, including the occasional development of high numbers of pathogenic species such as B. cereus or Acinetobacter. Copyright © 2011 Elsevier B.V. All rights reserved.

Microbial biotechnology addressing the plastic waste disaster.

PubMed

Narancic, Tanja; O'Connor, Kevin E

2017-09-01

Oceans are a major source of biodiversity, they provide livelihood, and regulate the global ecosystem by absorbing heat and CO 2 . However, they are highly polluted with plastic waste. We are discussing here microbial biotechnology advances with the view to improve the start and the end of life of biodegradable polymers, which could contribute to the sustainable use of marine and coastal ecosystems (UN Sustainability development goal 14). © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Ecogenomics: Ensemble Analysis of Gene Expression in Microbial Communities

NASA Technical Reports Server (NTRS)

Sogin, Mitchell; DesMarais, David J.; Stahl, D. A.; Pace, Norman R.

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

DART Employees at Work

NASA Image and Video Library

2014-10-31

The Dust Atmospheric Recovery Technology, or DART, spacecraft is being assembled in a laboratory inside the Space Life Sciences Lab at NASA’s Kennedy Space Center in Florida. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces.

DART Employees at Work

NASA Image and Video Library

2014-10-31

A researcher at NASA’s Kennedy Space Center in Florida checks a reading on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces.

DART Employees at Work

NASA Image and Video Library

2014-10-31

Researchers at NASA’s Kennedy Space Center in Florida check readings on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces.

Microbial Quality and Shelf Life of Blueberry Purée Developed Using Cavitation Technology.

PubMed

Fan, Lihua; Martynenko, Alex; Doucette, Craig; Hughes, Timothy; Fillmore, Sherry

2018-03-01

Blueberry purée was developed using hydrodynamic cavitation technology. The product was made from entire blueberries without adding any food additives. In this study, microbial reduction following each processing stage (at the industry setting) and after product pasteurization at 86, 88, 90, 92, 94, and 96 °C was investigated. Microbial quality including total plate counts, yeast and molds, and heat-resistant molds counts was determined. Shelf life of pasteurized products stored for up to 24 weeks at room temperature were assessed for microbial quality, soluble solids (°Brix), titratable acidity (citric acid %), pH, viscosity (cP) and flow rate (cm/30 s). Our results indicated that heat-resistant molds, initially present in frozen blueberries with counts at 2.03 log CFU/200g, were totally inactivated at 94 to 96 °C with 1 to 2 min holding time. Shelf life study showed that no product spoilage was caused by bacteria, yeasts and heat-resistant molds along with non-significant changes of textural characteristics. This study provided useful information for the food industry to develop variety of fruit purée products with no wastes of fruit materials. This study provides useful information for the food industry to develop safe liquid food products using cavitation technology without wasting any raw materials. © 2018 Institute of Food Technologists®.

Gut microbial functional maturation and succession during human early life.

PubMed

Cerdó, Tomás; Ruiz, Alicia; Acuña, Inmaculada; Jáuregui, Ruy; Jehmlich, Nico; Haange, Sven-Bastian; von Bergen, Martin; Suárez, Antonio; Campoy, Cristina

2018-04-24

The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin.

PubMed

Santos-Júnior, Célio Dias; Kishi, Luciano Takeshi; Toyama, Danyelle; Soares-Costa, Andrea; Oliveira, Tereza Cristina Souza; de Miranda, Fernando Pellon; Henrique-Silva, Flávio

2017-01-12

Tropical freshwater environments, like rivers, are important reservoirs of microbial life. This study employed metagenomic sequencing to survey prokaryotic microbiota in the Solimões, Purus, and Urucu Rivers of the Amazon Basin in Brazil. We report a rich and diverse microbial community. Copyright © 2017 Santos-Júnior et al.

Phylogenetic perspective and the search for life on earth and elsewhere

NASA Technical Reports Server (NTRS)

Pace, Norman R.

1989-01-01

Any search for microbial life on Mars cannot rely upon cultivation of indigenous organisms. Only a minority of even terrestrial organisms that are observed in mixed, naturally-occurring microbial populations can be cultivated in the laboratory. Consequently, methods are being developed for analyzing the phylogenetic affiliations of the constituents of natural microbial populations without the need for their cultivation. This is more than an exercise in taxonomy, for the extent of phylogenetic relatedness between unknown and known organisms is some measure of the extent of their biochemical commonalities. In one approach, total DNA is isolated from natural microbial populations and 16S rRNA genes are shotgun cloned for rapid sequence determinations and phylogenetic analyses. A second approach employs oligodeoxynucleotide hybridization probes that bind to phylogenetic group-specific sequences in 16S rRNA. Since each actively growing cell contains about 104 ribosomes, the binding of the diagnostic probes to single cells can be visualized by radioactivity or fluorescence. The application of these methods and the use of in situ cultivation techniques is illustrated using submarine hydrothermal vent communities. Recommendations are made regarding planning toward future Mars missions.

Microbial Pre-exposure and Vectorial Competence of Anopheles Mosquitoes

PubMed Central

Dieme, Constentin; Rotureau, Brice; Mitri, Christian

2017-01-01

Anopheles female mosquitoes can transmit Plasmodium, the malaria parasite. During their aquatic life, wild Anopheles mosquito larvae are exposed to a huge diversity of microbes present in their breeding sites. Later, adult females often take successive blood meals that might also carry different micro-organisms, including parasites, bacteria, and viruses. Therefore, prior to Plasmodium ingestion, the mosquito biology could be modulated at different life stages by a suite of microbes present in larval breeding sites, as well as in the adult environment. In this article, we highlight several naturally relevant scenarios of Anopheles microbial pre-exposure that we assume might impact mosquito vectorial competence for the malaria parasite: (i) larval microbial exposures; (ii) protist co-infections; (iii) virus co-infections; and (iv) pathogenic bacteria co-infections. In addition, significant behavioral changes in African Anopheles vectors have been associated with increasing insecticide resistance. We discuss how these ethological modifications may also increase the repertoire of microbes to which mosquitoes could be exposed, and that might also influence their vectorial competence. Studying Plasmodium–Anopheles interactions in natural microbial environments would efficiently contribute to refining the transmission risks. PMID:29376030

Microbial Safety and Shelf Life of UV-C Treated Freshly Squeezed White Grape Juice.

PubMed

Unluturk, Sevcan; Atilgan, Mehmet R

2015-08-01

The effects of UV-C irradiation on the inactivation of Escherichia coli K-12 (ATCC 25253), a surrogate of E. coli O157:H7, and on the shelf life of freshly squeezed turbid white grape juice (FSWGJ) were investigated. FSWGJ samples were processed at 0.90 mL/s for 32 min by circulating 8 times in an annular flow UV system. The UV exposure time was 244 s per cycle. The population of E. coli K-12 was reduced by 5.34 log cycles after exposure to a total UV dosage of 9.92 J/cm(2) (1.24 J/cm(2) per cycle) at 0.90 mL/s flow rate. The microbial shelf life of UV-C treated FSWGJ was extended up to 14 d at 4 °C. UV exposure was not found to alter pH, total soluble solid, and titratable acidity of juice. There was a significant effect (P < 0.05) on turbidity, absorbance coefficient, color, and ascorbic acid content. Furthermore, all physicochemical properties were altered during refrigerated storage. The microbial shelf life of FSWGJ was doubled after UV-C treatment, whereas the quality of juice was adversely affected similarly observed in the control samples. © 2015 Institute of Food Technologists®

Application of Sequence-based Methods in Human MicrobialEcology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weng, Li; Rubin, Edward M.; Bristow, James

2005-08-29

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning tomore » apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE PAGES

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick; ...

2015-06-19

The mission of the United States Culture Collection Network (USCCN;http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Here, representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

PubMed Central

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A.; Inderbitzin, Patrik; Sitepu, Irnayuli R.; Torok, Tamas; Brown, Daniel R.; Cho, Juliana; Wertz, John E.; Mukherjee, Supratim; Cady, Sherry L.

2015-01-01

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. PMID:26092453

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick

The mission of the United States Culture Collection Network (USCCN;http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Here, representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boundy-Mills, K.; Hess, Matthias; Bennett, A. R.

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

Central role of the cell in microbial ecology.

PubMed

Zengler, Karsten

2009-12-01

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

Implications of altered rainfall and exotic plants on soil microbial communities and carbon biomass

NASA Astrophysics Data System (ADS)

Castro, S.; Lipson, D.; Cleland, E. E.

2016-12-01

Climate and exotic plant disturbances are among the most significant threats to Mediterranean-type ecosystems, compromising their renowned biodiversity and role in the global carbon cycle. Predicted shifts in rainfall patterns have become a particular concern, especially when interactions with other stressors and effects on biogeochemical processes remain poorly understood. To understand the impacts of altered rainfall on belowground dynamics as well as the role of inter- and intra-annual variation and plant community composition, we monitored soil microbial communities under native and exotic plant dominated plots with rainfall manipulation treatments in a semi-arid Mediterranean-type ecosystem. We measured microbial biomass, respiration rates, and community structure across treatments and vegetation types. Soil moisture and dissolved organic carbon were also measured to characterize abiotic soil properties. The soil moisture gradient established by the rainfall treatments had a positive correlation with microbial biomass carbon under native- and exotic-dominated plots but had no effect on respiration rates. A significant reduction in microbial biomass under exotic plants was found in 2013 but not in 2014 and 2015. Substrate-induced respiration values were higher in the exotic-dominated plots during the spring seasons, resulting in a significant interaction between plant community type and season. Bacterial communities showed little variation except in the Proteobacteria phyla, which was lower in exotic plants-dominated plots. Dissolved organic carbon was significantly reduced in exotic-dominated plots by approximately 26% based on average values of all plots throughout. Our results illustrate that rainfall quantity and exotic plants can cause changes in microbial biomass, community composition and respiration rates jeopardizing soil carbon storage. They also reinforce the importance of temporal variability and the need for repeated sampling to correctly interpret environmental changes in semi-arid ecosystems. We conclude that to improve predictions of the implications of global stressors on biogeochemical cycles in semi-arid ecosystems, there is a need to incorporate microbial data with the understanding that it is highly dependent on temporal dynamics and plant community.

Physico-chemical parameters, bioactive compounds and microbial quality of thermo-sonicated carrot juice during storage.

PubMed

Martínez-Flores, Héctor E; Garnica-Romo, Ma Guadalupe; Bermúdez-Aguirre, Daniela; Pokhrel, Prashant Raj; Barbosa-Cánovas, Gustavo V

2015-04-01

Thermosonication has been successfully tested in food for microbial inactivation; however, changes in bioactive compounds and shelf-life of treated products have not been thoroughly investigated. Carrot juice was thermo-sonicated (24 kHz, 120 μm amplitude) at 50 °C, 54 °C and 58 °C for 10 min (acoustic power 2204.40, 2155.72, 2181.68 mW/mL, respectively). Quality parameters and microbial growth were evaluated after processing and during storage at 4 °C. Control and sonicated treatments at 50 °C and 54 °C had 10, 12 and 14 d of shelf-life, respectively. Samples sonicated at 58 °C had the best quality; microbial growth remained low at around 3-log for mesophiles, 4.5-log for yeasts and molds and 2-log for enterobacteria after 20 d of storage. Furthermore, thermo-sonicated juice at 58 °C retained >98% of carotenoids and 100% of ascorbic acid. Phenolic compounds increased in all stored, treated juices. Thermo-sonication is therefore a promising technology for preserving the quality of carrot juice by minimising the physicochemical changes during storage, retarding microbial growth and retaining the bioactive compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits

PubMed Central

Djokic, Tara; Van Kranendonk, Martin J.; Campbell, Kathleen A.; Walter, Malcolm R.; Ward, Colin R.

2017-01-01

The ca. 3.48 Ga Dresser Formation, Pilbara Craton, Western Australia, is well known for hosting some of Earth’s earliest convincing evidence of life (stromatolites, fractionated sulfur/carbon isotopes, microfossils) within a dynamic, low-eruptive volcanic caldera affected by voluminous hydrothermal fluid circulation. However, missing from the caldera model were surface manifestations of the volcanic-hydrothermal system (hot springs, geysers) and their unequivocal link with life. Here we present new discoveries of hot spring deposits including geyserite, sinter terracettes and mineralized remnants of hot spring pools/vents, all of which preserve a suite of microbial biosignatures indicative of the earliest life on land. These include stromatolites, newly observed microbial palisade fabric and gas bubbles preserved in inferred mineralized, exopolymeric substance. These findings extend the known geological record of inhabited terrestrial hot springs on Earth by ∼3 billion years and offer an analogue in the search for potential fossil life in ancient Martian hot springs. PMID:28486437

Astrobiology Investigations at a Martian Hematite Site

NASA Technical Reports Server (NTRS)

Allen, Carlton, C.; Westall, Frances; Schelble, Rachel T.

2001-01-01

Christensen et al, using data from the Mars Global Surveyor Thermal Emission Spectrometer (TES), have identified gray crystalline hematite in a 350 km by 750 km region near Sinus Meridiani. The deposit corresponds closely to the low-albedo highlands unit 'sm', mapped as a wind-eroded, ancient, subaqueous sedimentary deposit. Christensen et al interpreted the Sinus Meridiani deposit to be 'an in-place, rock-stratigraphic sedimentary unit characterized by smooth, friable layers composed primarily of basaltic sediments with approximately 10 to 15 % crystalline gray hematite.' Christensen et al discussed five possible mechanisms for the formation of this deposit: direct precipitation from standing, oxygenated, Fe-rich water; precipitation from Fe-rich hydrothermal fluids; low-temperature dissolution and precipitation through mobile groundwater leaching; surface weathering and coatings; thermal oxidation of magnetite-rich lavas. Four of these mechanisms involve the interactions of rock with water, and thus have implications in the search for evidence of microbial life.

Nitrogen and Oxygen Isotopic Studies of the Marine Nitrogen Cycle

NASA Astrophysics Data System (ADS)

Casciotti, Karen L.

2016-01-01

The marine nitrogen cycle is a complex web of microbially mediated reactions that control the inventory, distribution, and speciation of nitrogen in the marine environment. Because nitrogen is a major nutrient that is required by all life, its availability can control biological productivity and ecosystem structure in both surface and deep-ocean communities. Stable isotopes of nitrogen and oxygen in nitrate and nitrite have provided new insights into the rates and distributions of marine nitrogen cycle processes, especially when analyzed in combination with numerical simulations of ocean circulation and biogeochemistry. This review highlights the insights gained from dual-isotope studies applied at regional to global scales and their incorporation into oceanic biogeochemical models. These studies represent significant new advances in the use of isotopic measurements to understand the modern nitrogen cycle, with implications for the study of past ocean productivity, oxygenation, and nutrient status.

Evidence for methane in Martian meteorites

PubMed Central

Blamey, Nigel J. F.; Parnell, John; McMahon, Sean; Mark, Darren F.; Tomkinson, Tim; Lee, Martin; Shivak, Jared; Izawa, Matthew R. M.; Banerjee, Neil R.; Flemming, Roberta L.

2015-01-01

The putative occurrence of methane in the Martian atmosphere has had a major influence on the exploration of Mars, especially by the implication of active biology. The occurrence has not been borne out by measurements of atmosphere by the MSL rover Curiosity but, as on Earth, methane on Mars is most likely in the subsurface of the crust. Serpentinization of olivine-bearing rocks, to yield hydrogen that may further react with carbon-bearing species, has been widely invoked as a source of methane on Mars, but this possibility has not hitherto been tested. Here we show that some Martian meteorites, representing basic igneous rocks, liberate a methane-rich volatile component on crushing. The occurrence of methane in Martian rock samples adds strong weight to models whereby any life on Mars is/was likely to be resident in a subsurface habitat, where methane could be a source of energy and carbon for microbial activity. PMID:26079798

Evidence for methane in Martian meteorites.

PubMed

Blamey, Nigel J F; Parnell, John; McMahon, Sean; Mark, Darren F; Tomkinson, Tim; Lee, Martin; Shivak, Jared; Izawa, Matthew R M; Banerjee, Neil R; Flemming, Roberta L

2015-06-16

The putative occurrence of methane in the Martian atmosphere has had a major influence on the exploration of Mars, especially by the implication of active biology. The occurrence has not been borne out by measurements of atmosphere by the MSL rover Curiosity but, as on Earth, methane on Mars is most likely in the subsurface of the crust. Serpentinization of olivine-bearing rocks, to yield hydrogen that may further react with carbon-bearing species, has been widely invoked as a source of methane on Mars, but this possibility has not hitherto been tested. Here we show that some Martian meteorites, representing basic igneous rocks, liberate a methane-rich volatile component on crushing. The occurrence of methane in Martian rock samples adds strong weight to models whereby any life on Mars is/was likely to be resident in a subsurface habitat, where methane could be a source of energy and carbon for microbial activity.

Microbial and Chemical Shelf-Life of Vacuum Steam-Pasteurized Whole Flaxseed and Milled Flaxseed.

PubMed

Shah, Manoj; Eklund, Bridget; Conde Lima, Luiz Gustavo; Bergholz, Teresa; Hall, Clifford

2018-02-01

Flaxseed is an oilseed with many health benefits. Flaxseed may be consumed raw or in processed form. In the raw form, there is a potential for microbial contamination. Several pasteurization methods have been used to reduce microbial contamination. However, such treatments may affect chemical properties of foods. In this study, vacuum steam-pasteurization was conducted on whole flaxseed and milled flaxseed using 4 different conditions (3 min at 75 °C, 3 min at 90 °C, 9 min at 90 °C, and 3 min at 105 °C). Microbial and chemical shelf-life was monitored for 28 wk (36 wk for aerobic plate counts). Significant reduction (P < 0.05) in microbial counts (total aerobic plate counts, and yeast and mold counts) occurred after pasteurization and during storage of both whole flaxseed and milled flaxseed. Although both the moisture content and a w increased after pasteurization, they were similar to the unpasteurized samples during storage. Peroxide value, free fatty acid, headspace volatiles, fatty acid profiles, oil content, and secoisolariciresinol diglucoside (SDG) content were chemical indices measured. Only small changes were observed in the chemical indices after vacuum steam-pasteurization for both pasteurized whole flaxseed and milled flaxseed as compared to the unpasteurized flaxseed at most instances. Vacuum steam-pasteurization can be used as a safe alternative for the microbial reduction of low-moisture products, such as flaxseed, without significantly affecting chemical stability. Vacuum steam-pasteurization can be effectively used for the treatment of whole flaxseed and milled flaxseed to reduce spoilage microorganisms, such as total aerobes and yeasts and molds. In addition, this pasteurization method had minimal effects on several chemical shelf-life parameters with positive impact on SDG of the processed flaxseed. © 2018 Institute of Food Technologists®.

Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

PubMed

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J; Crean, StJohn; Singhrao, Sim K

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer's disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis , a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host's inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual's diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

PubMed Central

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J.; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD. PMID:29249963

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

PubMed Central

Mitchell, Jeffrey; Scow, Kate

2018-01-01

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0–5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals–organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change. PMID:29447262

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman.

PubMed

Rempfert, Kaitlin R; Miller, Hannah M; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite ("gabbro," "alkaline peridotite," "hyperalkaline peridotite," and "gabbro/peridotite contact") that vary strongly in pH and the concentrations of H 2 , CH 4 , Ca 2+ , Mg 2+ , [Formula: see text], [Formula: see text], trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus , candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira , Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman

PubMed Central

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M.; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S.

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H2, CH4, Ca2+, Mg2+, NO3-, SO42-, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites. PMID:28223966

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE PAGES

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; ...

2017-02-07

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

Microbial imbalance and intestinal pathologies: connections and contributions

PubMed Central

Yang, Ye; Jobin, Christian

2014-01-01

Microbiome analysis has identified a state of microbial imbalance (dysbiosis) in patients with chronic intestinal inflammation and colorectal cancer. The bacterial phylum Proteobacteria is often overrepresented in these individuals, with Escherichia coli being the most prevalent species. It is clear that a complex interplay between the host, bacteria and bacterial genes is implicated in the development of these intestinal diseases. Understanding the basic elements of these interactions could have important implications for disease detection and management. Recent studies have revealed that E. coli utilizes a complex arsenal of virulence factors to colonize and persist in the intestine. Some of these virulence factors, such as the genotoxin colibactin, were found to promote colorectal cancer in experimental models. In this Review, we summarize key features of the dysbiotic states associated with chronic intestinal inflammation and colorectal cancer, and discuss how the dysregulated interplay between host and bacteria could favor the emergence of E. coli with pathological traits implicated in these pathologies. PMID:25256712

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions.

PubMed

Iozzo, Patricia; Sanguinetti, Elena

2018-01-01

Early nutrition and growth in the initial years of life are important determinants of later body weight and metabolic health in humans, and the current epidemic of obesity involving children requires a better understanding of causal and protective mechanisms and components in infant foods. This review focuses on recent evidence implicating feeding modes (e.g., breast milk and formula milk) and dietary transitions toward complementary foods in the progression of microbiota maturation in children. The literature exploring body weight outcomes of microbiota changes induced by diet in early life is limited. Representative studies addressing the use of probiotics in pregnant women and infants are also examined. Methodological and geo-cultural variations make it difficult to avoid (apparently) controversial findings. Most studies indicate differences in the microbiota of formula versus breastfed infants, but some do not. Duration of breastfeeding delays the maturation of the microbiota toward an adult-like profile. However, the effect size of the early feeding pattern on microbial function was found to be very small, and absent after the third year of life. There are several interesting mediators whereby milk composition can affect infants' microbiota and their optimization is a desirable strategy for prevention. But prevention of what? Although there are few correlative evaluations relating microbiota and body weight in early life, studies demonstrating a cause-effect relationship between diet-induced changes in early microbiota development and subsequent metabolic health outcomes in humans are still missing.

Putting the Deep Biosphere on the Map for Oceanography Courses: Gas Hydrates As a Case Study for the Deep Biosphere

NASA Astrophysics Data System (ADS)

Sikorski, J. J.; Briggs, B. R.

2014-12-01

The ocean is essential for life on our planet. It covers 71% of the Earth's surface, is the source of the water we drink, the air we breathe, and the food we eat. Yet, the exponential growth in human population is putting the ocean and thus life on our planet at risk. However, based on student evaluations from our introductory oceanography course it is clear that our students have deficiencies in ocean literacy that impact their ability to recognize that the ocean and humans are inextricably connected. Furthermore, life present in deep subsurface marine environments is also interconnected to the study of the ocean, yet the deep biosphere is not typically covered in undergraduate oceanography courses. In an effort to improve student ocean literacy we developed an instructional module on the deep biosphere focused on gas hydrate deposits. Specifically, our module utilizes Google Earth and cutting edge research about microbial life in the ocean to support three inquiry-based activities that each explore different facets of gas hydrates (i.e. environmental controls, biologic controls, and societal implications). The relevant nature of the proposed module also makes it possible for instructors of introductory geology courses to modify module components to discuss related topics, such as climate, energy, and geologic hazards. This work, which will be available online as a free download, is a solid contribution toward increasing the available teaching resources focused on the deep biosphere for geoscience educators.

Microbial Substrate Use at Sites of Continental Serpentinization: The Tablelands, NL, CAD and the Cedars, CA, USA

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Rietze, A.; Kohl, L.; Miles, S.; Kavanagh, H.; Cox, A.; Brazelton, W. J.; Ishii, S.; Sherwood Lollar, B.; Schrenk, M. O.; Nealson, K. H.; Ziegler, S. E.; Ono, S.; Wang, D. T.; Lang, S. Q.; Cumming, E.

2014-12-01

Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface ultramafic environment rich in hydrogen and methane gases. Field data and results from substrate addition microcosm experiments will be presented from two contrasting continental sites of serpentinization: the Tablelands, NL, CAN and The Cedars, CA, USA both Phanerozoic in age. These continental sites share geochemical characteristics that make these environments challenging for life, such as high pH, low Eh, scarce electron acceptors, and limited dissolved inorganic carbon for autotrophic growth. However, microbiological analyses have demonstrated that life does indeed exist in these environments. While environmental genomic studies indicated the potential metabolic capabilities of microorganisms in the sites, actual microbial metabolic activities in these environments remain unknown. To expand the understanding of biogeochemistry of the sites, we are conducting studies focusing on chemical and isotopic measurements, carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms. Thus far, in situ geochemical data suggests that the methane from the Tablelands is primarily non-microbial, while the methane from The Cedars likely has some microbial contributions. To date, substrate addition microcosm experiments show no microbial production of methane from Tablelands' water and sediments. However, microbial carbon monoxide utilization has been observed in Tableland microcosms, but not in The Cedars microcosms. These results demonstrate how geochemistry and substrate addition experiments can be complementary for the determination of the processes favored at these continental sites of serpentinization.

Methanethiol abundance in high-temperature hydrothermal fluids from the Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Reeves, E.; Seewald, J. S.; Saccocia, P.; van der Meer, M.

2008-12-01

The formation of aqueous organic sulfur compounds in hydrothermal systems remains poorly constrained, despite their potential significance in 'prebiotic' chemistry and the origin of life. The simplest - methanethiol (CH3SH) - has been implicated as a critical abiogenic precursor to the establishment of primitive microbial metabolism in early Earth hydrothermal settings. It also represents a readily-utilized substrate for microbial sulfate-reducing communities and a potential intermediate species in abiotic CH4 formation. To assess the abundance of CH3SH and factors regulating its stability under hydrothermal conditions we measured CH3SH concentrations in a suite of hydrothermal fluids collected from the Rainbow, Lucky Strike, TAG and Lost City hydrothermal sites located on the Mid-Atlantic Ridge. Fluids were collected using isobaric gas-tight samplers and analyzed for CH3SH by shipboard purge-and-trap gas chromatography. Measured concentrations at Rainbow (1.2 -- 223nM), Lucky Strike (1.1 -- 26nM), TAG (8.5 -- 11nM) and Lost City (1.6 -- 3.0nM) are all substantially lower than predicted for thermodynamic equilibrium with CO2, H2 and H2S at measured vent conditions. The highest concentrations (91 -- 223nM), however, were observed at Rainbow in intermediate temperature (128 -- 175°C) H2-rich fluids that may have undergone conductive cooling. Increased concentrations with decreasing temperature is consistent with the thermodynamic drive for the formation from CO2, suggesting a possible abiotic origin for CH3SH in some fluids. Substantially lower concentrations in the low temperature fluids at Lost City are consistent with the extremely low levels of CO2 and H2S in these fluids. Other possible sources of CH3SH to vent fluids must be considered, however, and include thermal alteration of biomass present in low-temperature environments and microbial consortia that produce CH3SH as a byproduct of anaerobic methane oxidation. Current models for the emergence of primordial metabolism in highly-reducing alkaline hydrothermal environments invoke CH3SH as a key reactant leading to Acetyl CoA-based (Wood-Ljungdahl) carbon fixation pathways. Results of this study challenge the notion that high-pH, reducing fluids emanating from serpentinite-hosted hydrothermal systems like Lost City were favorable for the production of CH3SH, the establishment of a primitive metabolic cycle and the emergence of microbial life on Earth.

Where Should Search Traces of Life, Which Could Appear on Mars in the First 300 Million Years

NASA Astrophysics Data System (ADS)

Vidmachenko, A. P.

2017-10-01

In its early years, Mars was like the ancient Earth. If life on Mars today there is, then, certainly, it is microbial. The proof of the presence of liquid water on Mars does not mean that there is life on Mars. But this gives some hope.

Lytic to temperate switching of viral communities

NASA Astrophysics Data System (ADS)

Knowles, B.; Silveira, C. B.; Bailey, B. A.; Barott, K.; Cantu, V. A.; Cobián-Güemes, A. G.; Coutinho, F. H.; Dinsdale, E. A.; Felts, B.; Furby, K. A.; George, E. E.; Green, K. T.; Gregoracci, G. B.; Haas, A. F.; Haggerty, J. M.; Hester, E. R.; Hisakawa, N.; Kelly, L. W.; Lim, Y. W.; Little, M.; Luque, A.; McDole-Somera, T.; McNair, K.; de Oliveira, L. S.; Quistad, S. D.; Robinett, N. L.; Sala, E.; Salamon, P.; Sanchez, S. E.; Sandin, S.; Silva, G. G. Z.; Smith, J.; Sullivan, C.; Thompson, C.; Vermeij, M. J. A.; Youle, M.; Young, C.; Zgliczynski, B.; Brainard, R.; Edwards, R. A.; Nulton, J.; Thompson, F.; Rohwer, F.

2016-03-01

Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus ‘more microbes, fewer viruses’.

Comparison of microbially enhanced compost extracts produced from composted cattle rumen content material and from commercially available inocula.

PubMed

Shrestha, Karuna; Adetutu, Eric M; Shrestha, Pramod; Walsh, Kerry B; Harrower, Keith M; Ball, Andrew S; Midmore, David J

2011-09-01

A comparative study was performed on compost extracts prepared from cattle rumen content composted for three and nine months, nine month old compost inoculated with a Nutri-Life 4/20™ inoculum, and two commercial preparations (LivingSoil™ and Nutri-Life 4/20™), all incubated for 48h. Nutri-Life 4/20™ had the highest concentrations of NO(3)(-)-N and K(+)-K, while rumen compost extract had higher humic and fulvic acids concentration. The bacterial and fungal community level functional diversity of three month old compost extract and of LivingSoil™, assessed with Biolog™, were higher than that of nine month old rumen compost extract, with or without Nutri-Life 4/20™ inoculum, or Nutri-Life 4/20™. No difference in fungal diversity was observed between treatments, as indicated by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, however, bacterial diversity was higher in all compost extracts and LivingSoil™ compared to the Nutri-Life 4/20™. Criteria for judging the quality of a microbially enhanced extract are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study.

PubMed

Losasso, Carmen; Eckert, Ester M; Mastrorilli, Eleonora; Villiger, Jorg; Mancin, Marzia; Patuzzi, Ilaria; Di Cesare, Andrea; Cibin, Veronica; Barrucci, Federica; Pernthaler, Jakob; Corno, Gianluca; Ricci, Antonia

2018-01-01

Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant's dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified.

Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study

PubMed Central

Losasso, Carmen; Eckert, Ester M.; Mastrorilli, Eleonora; Villiger, Jorg; Mancin, Marzia; Patuzzi, Ilaria; Di Cesare, Andrea; Cibin, Veronica; Barrucci, Federica; Pernthaler, Jakob; Corno, Gianluca; Ricci, Antonia

2018-01-01

Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant’s dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified. PMID:29556222

Study to determine the aquatic biological effects on the Solid Rocket Booster (SRB). [technique for monitoring marine microbial fouling

NASA Technical Reports Server (NTRS)

Colwell, R. R.; Zachary, A.

1979-01-01

The surface of the reusable solid rocket boosters (SRB), which are jettisoned from the Shuttle Orbiter to parachute in the sea, are studied for colonization by marine life. Techniques for monitoring the marine microbial fouling of SRB materials are presented. An assessment of the nature and degree of the biofouling expected on the SRB materials in the recovery zone is reported. A determination of the degree and the effects of seasonal variation occurring on microbial fouling in the retrieval zone waters is made. The susceptibility of the SRB parachute recovery system to microbial fouling and biodeterioration is investigated. The development of scanning electron microscopy and epifluorescence microscopic observation techniques for rapid assessment of microbial fouling is discussed.

Lithobiontic life: "Atacama rocks are well and alive".

PubMed

Gómez-Silva, Benito

2018-02-01

Our knowledge on the Microbiology of the Atacama Desert has increased steadily and substantially during the last two decades. This information now supports a paradigmatic change on the Atacama Desert from a sterile, uninhabitable territory to a hyperarid region colonized by a rich microbiota that includes extremophiles and extreme-tolerant microorganisms. Also, extensive reports are available on the prevalent physical and chemical environmental conditions, ecological niches and, the abundance, diversity and organization of the microbial life in the Atacama Desert. This territory is a highly desiccated environment due to the absence of regular rain events. Liquid water scarcity is the most serious environmental factor affecting the Atacama Desert microorganisms. The intense solar irradiation in this region contributes, in a synergistic fashion with desiccation, to limit the survival and growth of the microbial life. In order to overcome these two extreme conditions, successful microorganisms, organized as microbial consortia, take advantage of (a) the physical characteristics of lithic habitats, which provide sites for colonization on, within or below the rock substrate, the attenuation and filtration of the intense solar irradiation and, the collection of liquid water from incoming fog formations and by water vapour condensation and deliquescence on or within their surfaces, and (b) the biological adaptations of members of the microbial communities that allow them to synthesize hydrophilic macromolecules, antioxidants and UV-light absorbents. Lithic habitats have been considered specialized shelters where life forms can reach protection at environments subjected to extremes of desiccation and solar irradiation, here on Earth or elsewhere. This review is an overview of part of the scientific information collected on lithobionts from the Atacama Desert, their rock substrates and their strategies to cope with extremes of desiccation and intense photosynthetic active radiation and UV irradiations.

The ECLSS Advanced Automation Project Evolution and Technology Assessment

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, James R.; Lukefahr, Brenda D.; Rogers, John S.; Rochowiak, Daniel M.; Mckee, James W.; Benson, Brian L.

1990-01-01

Viewgraphs on Environmental Control and Life Support System (ECLSS) advanced automation project evolution and technology assessment are presented. Topics covered include: the ECLSS advanced automation project; automatic fault diagnosis of ECLSS subsystems descriptions; in-line, real-time chemical and microbial fluid analysis; and object-oriented, distributed chemical and microbial modeling of regenerative environmental control systems description.

Planetary biology and microbial ecology. Biochemistry of carbon and early life

NASA Technical Reports Server (NTRS)

Margulis, L. (Editor); Nealson, K. H. (Editor); Taylor, I. (Editor)

1983-01-01

Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described.

Effects of Land Use Change on C-N cycling: Microbes Matter.

NASA Astrophysics Data System (ADS)

Hofmockel, K.

2012-12-01

Large swaths of the terrestrial landscape have been altered by human actions on Earth's biophysical systems, resulting in the homogenization of Earth's biota, while simultaneously increasing greenhouse gases and reactive nitrogen (N). This is especially poignant in grasslands that have been largely replaced by managed agricultural systems with substantial N inputs, or by unmanaged grasslands that are dominated by exotic species. Impacted ecosystems may be important for global C models, because they comprise a major portion of the global land area, terrestrial NPP and the world's soil C stocks. This research investigates how anthropogenic changes in plant community composition and agricultural management systems influence the composition and function of microbial communities that mediate key aspects of belowground C and N cycling and storage. Data from agroecology and grassland climate change experiments are used to illustrate how microbial responses can have important implications for large scale coupling of C and N cycles. In this study exotic plant species significantly decreased root inputs, causing shifts in microbial community composition, including both specific taxa and functional guilds of bacteria. By contrast, climate change (precipitation manipulation) caused functional responses (increased carbon and phosphorus cycling) that were not detected in the microbial community composition. Mycorrhizal fungi in managed systems were responsive to both root biomass and nitrogen inputs, significantly altering hydrolytic enzyme activity and aggregate turnover. Collectively small-scale processes can alter the ecosystem biogeochemical cycles. Together theses results suggest that linking microbial communities to coupled C-N cycles may have important implications for terrestrial C cycling feedbacks that are an integral part of the anthropocene era.

Rain Basin Design Implications for Soil Microbial Activity and N-mineralization in a Semi-arid Environment

NASA Astrophysics Data System (ADS)

Stern, C.; Pavao-Zuckerman, M.

2014-12-01

Rain basins have been an increasingly popular Green Infrastructure (GI) solution to the redistribution of water flow caused by urbanization. This study was conducted to examine how different approaches to basin design, specifically mulching (gravel vs. compost and gravel), influence the water availability of rain basins and the effects this has on the soil microbial activity of the basins. Soil microbes are a driving force of biogeochemical process and may impact the carbon and nitrogen dynamics of rain basin GI. In this study we sampled 12 different residential-scale rain basins, differing in design established at Biosphere 2, Arizona in 2013. Soil samples and measurements were collected before and after the onset of the monsoon season in 2014 to determine how the design of basins mediates the transition from dry to wet conditions. Soil abiotic factors were measured, such as moisture content, soil organic matter (SOM) content, texture and pH, and were related to the microbial biomass size within the basins. Field and lab potential N-mineralization and soil respiration were measured to determine how basin design influences microbial activity and N dynamics. We found that pre-monsoon basins with compost had higher moisture contents and that there was a positive correlation between the moisture content and the soil microbial biomass size of the basins. Pre-monsoon data also suggests that N-mineralization rates for basins with compost were higher than those with only gravel. These design influences on basin-scale biogeochemical dynamics and nitrogen retention may have important implications for urban biogeochemistry at neighborhood and watershed scales.

Electrodic voltages in the presence of dissolved sulfide: Implications for monitoring natural microbial activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slater, L.; Ntarlagiannis, D.; Yee, N.

2008-10-01

There is growing interest in the development of new monitoring strategies for obtaining spatially extensive data diagnostic of microbial processes occurring in the earth. Open-circuit potentials arising from variable redox conditions in the fluid local-to-electrode surfaces (electrodic potentials) were recorded for a pair of silver-silver chloride electrodes in a column experiment, whereby a natural wetland soil containing a known community of sulfate reducers was continuously fed with a sulfate-rich nutrient medium. Measurements were made between five electrodes equally spaced along the column and a reference electrode placed on the column inflow. The presence of a sulfate reducing microbial population, coupledmore » with observations of decreasing sulfate levels, formation of black precipitate (likely iron sulfide),elevated solid phase sulfide, and a characteristic sulfurous smell, suggest microbial-driven sulfate reduction (sulfide generation) in our column. Based on the known sensitivity of a silver electrode to dissolved sulfide concentration, we interpret the electrodic potentials approaching 700 mV recorded in this experiment as an indicator of the bisulfide (HS-) concentration gradients in the column. The measurement of the spatial and temporal variation in these electrodic potentials provides a simple and rapid method for monitoring patterns of relative HS- concentration that are indicative of the activity of sulfate-reducing bacteria. Our measurements have implications both for the autonomous monitoring of anaerobic microbial processes in the subsurface and the performance of self-potential electrodes, where it is critical to isolate, and perhaps quantify, electrochemical interfaces contributing to observed potentials.« less

Opportunities and challenges in studies of deep life (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.

2010-12-01

Over the past two decades, there has been an increasing awareness within the geological, microbiological, and oceanographic communities of the potentially vast microbial biosphere that is harbored beneath the surface of the Earth. With this awareness has come a mounting effort to study this potential biome - to better quantify biomass abundance, activity, and biogeochemical activity. In the Earth system, the largest deep subsurface biome is also the least accessible - the deep ocean subsurface biosphere. The oceanic deep biosphere also has greatest potential for influencing global scale biogeochemical processes -the carbon and energy cycles for example, and other elemental cycles. To address these topics and mount interdisciplinary efforts to study the deep subsurface marine biosphere, we have recently formed a center in support integrative, collaborative investigations. The national science foundation Center for Dark Biosphere Investigations (C-DEBI), has been initiated for the explicit purpose of resolving the extent, function, dynamics and implications of the subseafloor biosphere. This talk will discuss C-DEBI science, with focus on some of the opportunities and challenges in the study of deep life in the ocean, and the role that C-DEBI will play in meeting them

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Microbial shaping of sedimentary wrinkle structures

NASA Astrophysics Data System (ADS)

Mariotti, G.; Pruss, S. B.; Perron, J. T.; Bosak, T.

2014-10-01

Wrinkle structures on sandy bed surfaces were present in some of the earliest sedimentary environments, but are rare in modern environments. These enigmatic millimetre- to centimetre-scale ridges or pits are particularly common in sediments that harbour trace fossils and imprints of early animals, and appeared in the aftermath of some large mass extinctions. Wrinkle structures have been interpreted as possible remnants of microbial mats, but the formation mechanism and associated palaeoenvironmental and palaeoecological implications of these structures remain debated. Here we show that microbial aggregates can form wrinkle structures on a bed of bare sand in wave tank experiments. Waves with a small orbital amplitude at the bed surface do not move sand grains directly. However, they move millimetre-size, light microbial fragments and thereby produce linear sand ridges and rounded scour pits at the wavelengths observed in nature within hours. We conclude that wrinkle structures are morphological biosignatures that form at the sediment-water interface in wave-dominated environments, and not beneath microbial mats as previously thought. During early animal evolution, grazing by eukaryotic organisms may have temporarily increased the abundance of microbial fragments and thus the production of wrinkle structures.

Metaproteomics Reveals Functional Shifts in Microbial and Human Proteins During Infant Gut Colonization Case

DOE PAGES

Young, Jacque C.; Pan, Chongle; Adams, Rachel M.; ...

2015-01-01

The microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. Thus, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity and functions increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data indicating three distinct colonization phases. Overall microbial community functions were established relatively early in development andmore » remained stable. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Moreover, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. Our study provides the first snapshot of coordinated human and microbial protein expression in the infant gut during early development.« less

[Habitability and life support systems].

PubMed

Nefedov, Iu G; Adamovich, B A

1988-01-01

This paper discusses various aspects of space vehicle habitability and life support systems. It describes variations in the chemical and microbial composition of an enclosed atmosphere during prolonged real and simulated flights. The paper gives a detailed description of life support systems and environmental investigations onboard the Mir station. It also outlines the development of space vehicle habitability and life support systems as related to future flights.

Integrated metagenomics and network analysis of soil microbial community of the forest timberline

PubMed Central

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3−-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Application of Chemical Kinetics to Deterioration of Foods.

ERIC Educational Resources Information Center

Labuza, T. P.

1984-01-01

Possible modes of food deterioration (such as microbial decay, nonenzymatic browning, senescence, lipid oxidation) are reviewed. A basic mathematical approach to the kinetics of food deterioration, kinetic approach to accelerating shelf-life deterioration, and shelf-life predictions are discussed. (JN)

Cosmetics Safety Q&A: Shelf Life

MedlinePlus

... of cosmetics? The shelf life for eye-area cosmetics is more limited than for other products. Because of repeated microbial exposure during use by the consumer and the risk of eye infections, some industry experts recommend replacing mascara 3 months after purchase. ...

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections.

PubMed

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A Rick; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A; Inderbitzin, Patrik; Sitepu, Irnayuli R; Torok, Tamas; Brown, Daniel R; Cho, Juliana; Wertz, John E; Mukherjee, Supratim; Cady, Sherry L; McCluskey, Kevin

2015-09-01

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Microbial trace-fossil formation, biogenous, and abiotic weathering in the Antarctic cold desert

NASA Technical Reports Server (NTRS)

Friedmann, E. Imre; Weed, Rebecca

1987-01-01

In the Antarctic cold desert (Ross Desert), the survival of the cryptoendolithic microorganisms that colonize the near-surface layer of porous sandstone rocks depends on a precarious equilibrium of biological and geological factors. An unfavorable shift of this equilibrium results in death, and this may be followed by formation of trace fossils that preserve the characteristic iron-leaching pattern caused by microbial activity. Similar microbial trace fossils may exist in the geological record. If life ever arose on early Mars, similar processes may have occurred there and left recognizable traces.

Research progress of microbial corrosion of reinforced concrete structure

NASA Astrophysics Data System (ADS)

Li, Shengli; Li, Dawang; Jiang, Nan; Wang, Dongwei

2011-04-01

Microbial corrosion of reinforce concrete structure is a new branch of learning. This branch deals with civil engineering , environment engineering, biology, chemistry, materials science and so on and is a interdisciplinary area. Research progress of the causes, research methods and contents of microbial corrosion of reinforced concrete structure is described. The research in the field is just beginning and concerted effort is needed to go further into the mechanism of reinforce concrete structure and assess the security and natural life of reinforce concrete structure under the special condition and put forward the protective methods.

KSC-2014-4900

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – A researcher at NASA’s Kennedy Space Center in Florida checks a reading on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

KSC-2014-4901

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – A researcher at NASA’s Kennedy Space Center in Florida checks a reading on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

KSC-2014-4903

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – Researchers at NASA’s Kennedy Space Center in Florida check readings on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

KSC-2014-4902

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – Researchers at NASA’s Kennedy Space Center in Florida check readings on the Dust Atmospheric Recovery Technology, or DART, spacecraft inside a laboratory at the Space Life Sciences Lab. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

KSC-2014-4899

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – The Dust Atmospheric Recovery Technology, or DART, spacecraft is being assembled in a laboratory inside the Space Life Sciences Lab at NASA’s Kennedy Space Center in Florida. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

KSC-2014-4898

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – The Dust Atmospheric Recovery Technology, or DART, spacecraft is being assembled in a laboratory inside the Space Life Sciences Lab at NASA’s Kennedy Space Center in Florida. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

DART Employees at Work

NASA Image and Video Library

2014-10-31

A researcher from the University of Florida in Gainesville, checks the Dust Atmospheric Recovery Technology, or DART, spacecraft in a laboratory inside the Space Life Sciences Lab at NASA’s Kennedy Space Center in Florida. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

PubMed Central

Kinsela, Andrew S.; Bligh, Mark W.; Harrison, Jennifer J.; Payne, Timothy E.

2017-01-01

ABSTRACT During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. PMID:28667104

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.

PubMed

Vázquez-Campos, Xabier; Kinsela, Andrew S; Bligh, Mark W; Harrison, Jennifer J; Payne, Timothy E; Waite, T David

2017-09-01

During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. Copyright © 2017 Vázquez-Campos et al.

Dynamic temperature fields under Mars landing sites and implications for supporting microbial life.

PubMed

Ulrich, Richard; Kral, Tim; Chevrier, Vincent; Pilgrim, Robert; Roe, Larry

2010-01-01

While average temperatures on Mars may be too low to support terrestrial life-forms or aqueous liquids, diurnal peak temperatures over most of the planet can be high enough to provide for both, down to a few centimeters beneath the surface for some fraction of the time. A thermal model was applied to the Viking 1, Viking 2, Pathfinder, Spirit, and Opportunity landing sites to demonstrate the dynamic temperature fields under the surface at these well-characterized locations. A benchmark temperature of 253 K was used as a lower limit for possible metabolic activity, which corresponds to the minimum found for specific terrestrial microorganisms. Aqueous solutions of salts known to exist on Mars can provide liquid solutions well below this temperature. Thermal modeling has shown that 253 K is reached beneath the surface at diurnal peak heating for at least some parts of the year at each of these landing sites. Within 40 degrees of the equator, 253 K beneath the surface should occur for at least some fraction of the year; and, within 20 degrees , it will be seen for most of the year. However, any life-form that requires this temperature to thrive must also endure daily excursions to far colder temperatures as well as periods of the year where 253 K is never reached at all.

The microbiome in early life: self-completion and microbiota protection as health priorities.

PubMed

Dietert, Rodney R

2014-08-01

This minireview considers the benefits of refocusing attention away from treating the patient as a mammalian human to managing the complete patient: a majority microbial superorganism. Under the "completed self" model for formation of the human-microbial superorganism, the single, most pivotal sign in distinguishing a life course of health versus that filled with disease is self-completion (i.e., seeding of the minority mammalian human by the majority microbial portion of the symbiont). From a disease prevention perspective, microbial seeding at birth and subsequent nurturing of the microbiota are significant steps to reduce the risk of both noncommunicable diseases (e.g., type 1 diabetes) and certain infectious diseases. Management of the microbiome during pregnancy, birth, and shortly thereafter appears to be the most significant critical window for healthy superorganism formation. However, the bolus for microbiota seeding at birth and the nurturing process are subject to environmental influences and disruption, such as exposure to toxic chemicals and drugs, infections, and other physical and psychological stressors. Additionally, childhood and adult corrective measures, such as fecal transplantation and administration of prebiotics and probiotics, while potentially useful, may have limitations that are yet to be fully defined. This minireview considers (1) basic features of management of the microbiome to facilitate self-completion, (2) protection of the microbiota from environmental hazards, and (3) the benefits of using a superorganism focus for health management beginning with pregnancy and extending throughout childhood and adult life. © 2014 Wiley Periodicals, Inc.

Quantitative proteomics in the field of microbiology.

PubMed

Otto, Andreas; Becher, Dörte; Schmidt, Frank

2014-03-01

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

PubMed Central

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection. PMID:25338024

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

DOE PAGES

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; ...

2014-10-22

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems.

PubMed

Kokko, Marika; Epple, Stefanie; Gescher, Johannes; Kerzenmacher, Sven

2018-06-01

Over the last decade, there has been an ever-growing interest in bioelectrochemical systems (BES) as a sustainable technology enabling simultaneous wastewater treatment and biological production of, e.g. electricity, hydrogen, and further commodities. A key component of any BES degrading organic matter is the anode where electric current is biologically generated from the oxidation of organic compounds. The performance of BES depends on the interactions of the anodic microbial communities. To optimize the operational parameters and process design of BES a better comprehension of the microbial community dynamics and interactions at the anode is required. This paper reviews the abundance of different microorganisms in anodic biofilms and discusses their roles and possible side reactions with respect to their implications on the performance of BES utilizing wastewaters. The most important operational parameters affecting anodic microbial communities grown with wastewaters are highlighted and guidelines for controlling the composition of microbial communities are given. Copyright © 2018 Elsevier Ltd. All rights reserved.

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

PubMed

Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

The role of microbial flora on the ocular surface.

PubMed

Miller, Darlene; Iovieno, Alfonso

2009-10-01

Presence and interplay of microbial flora at the ocular surface reveal dynamic and evolving interactions with implications for both ocular surface health and disease. Data in this area are scarce or non-existent. The purpose of this review is to provide a snapshot of new and emerging developments in this area over the last 12 months. Recent findings signal potential roles for ocular surface microbial flora in both the preservation and extension of ocular surface health and in the initiation of new or escalation of common surface disorders. Contributions range from priming surface epithelial immune cells to regulating mucin composition and production. Other findings explore the emergent role of ocular microbial flora cross talk with pattern recognition receptors to protect and strengthen local and adaptive mucosal immunity while preserving vision. Deciphering the functional role of microbial communities at the ocular surface could bring new insights into and clarify the epidemiology and pathology of ocular surface dynamics in health and disease.

Truffles decontamination treatment by ionizing radiation

NASA Astrophysics Data System (ADS)

Adamo, M.; Capitani, D.; Mannina, L.; Cristinzio, M.; Ragni, P.; Tata, A.; Coppola, R.

2004-09-01

A research project, funded by the Italian Ministry of Research and the European Union, is in progress aimed to develop processes to enhance, by irradiation, the safety and the wholesomeness of fresh products relevant for Italian food industry. Irradiation was performed on truffles, since the bacterial contamination impairs their trade in foreign countries. The microbial population and the shelf life under refrigeration were studied either on samples untreated or on samples submitted to γ-rays in a 1-2.5 kGy dose range. The effect of the treatment was monitored by UV and NMR techniques. Total microbial population and the shelf life prolongation were investigated. The synergistic effect of the dose, the packaging under vacuum and the storage/irradiation temperature resulted in a direct effect on the microbial load, spoilage and shelf life. After the irradiation, small variations in the intensity of some NMR resonances due to aromatic compounds and other unassigned compounds were observed. As confirmed by UV spectrophotometric data, these phenomena seemed to originate from a small degradation of polyphenols; the induced growth of soluble phenols suggested that the 1.5 kGy dose can be considered as the radiation dose threshold beyond which clear chemical modifications on truffles appear.

Metamorphosis of a butterfly-associated bacterial community.

PubMed

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a Butterfly-Associated Bacterial Community

PubMed Central

Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies. PMID:24466308

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Modeling microbial spoilage and quality of gilthead seabream fillets: combined effect of osmotic pretreatment, modified atmosphere packaging, and nisin on shelf life.

PubMed

Tsironi, Theofania N; Taoukis, Petros S

2010-05-01

The objective of the study was the kinetic modeling of the effect of storage temperature on the quality and shelf life of chilled fish, modified atmosphere-packed (MAP), and osmotically pretreated with the addition of nisin as antimicrobial agent. Fresh gilthead seabream (Sparus aurata) fillets were osmotically treated with 50% high dextrose equivalent maltodextrin (DE 47) plus 5% NaCl. Water loss, solid gain, salt content, and water activity were monitored throughout treatment and treatment conditions were selected for the shelf life study. Untreated and osmotically pretreated slices with and without nisin (2 x 10(4) IU/100 g osmotic solution), packed in air or modified atmosphere (50% CO(2)-50% air), and stored at controlled isothermal conditions (0, 5, 10, and 15 degrees C) were studied. Quality assessment and modeling were based on growth of several microbial indices, total volatile nitrogen, trimethylamine nitrogen, lipid oxidation (TBARS), and sensory scoring. Temperature dependence of quality loss rates was modeled by the Arrhenius equation, validated under dynamic conditions. Pretreated samples showed improved quality stability during subsequent refrigerated storage, in terms of microbial growth, chemical changes, and organoleptic degradation. Osmotic pretreatment with the addition of nisin in combination with MAP was the most effective treatment resulting in significant shelf life extension of gilthead seabream fillets (48 days compared to 10 days for the control at 0 degrees C).

Breastfeeding increases microbial community resilience.

PubMed

Carvalho-Ramos, Isabel I; Duarte, Rubens T D; Brandt, Katia G; Martinez, Marina B; Taddei, Carla R

2017-09-05

Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to denaturing gradient gel electrophoresis analysis. The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the denaturing gradient gel electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5 th month of life. These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6 th month of life. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Effect of filtered wood smoke treatment on chemical and microbial changes in mahi mahi fillets.

PubMed

Kristinsson, Hordur G; Danyali, Nineveh; Ua-Angkoon, Siriporn

2007-01-01

A study was performed to investigate the effect of filtered wood smoke processing on quality and safety of mahi mahi compared to no treatment. Skinless mahi mahi fillet portions were either treated with filtered smoke (FS) or left untreated for 24 h, followed by either (a) aerobic storage at 4 degrees C for 8 d or (b) freezing for 30 d (-25 degrees C) followed by thawing and aerobic storage at 4 degrees C for 8 d. Results show that treating mahi mahi fillets with FS increased (P < 0.05) a* values (redness) of the muscle and stabilized it during frozen storage. The redness did, however, decay (P < 0.05) rapidly on cold storage for both defrosted and fresh filtered-smoke-treated products, and reached initial (presmoking) redness levels in 2 d. The FS process overall significantly (P < 0.05) improved microbial stability of the product. Stability toward lipid oxidation was also significantly (P < 0.05) increased for the FS products compared to untreated products, particularly after defrosting. Sensory studies supported the microbial and lipid oxidation findings, showing that products treated with FS were better accepted and had increased (P < 0.05) shelf life over the untreated products. The shelf life was, however, compromised when microbial levels increased; that is, the process did not mask microbial spoilage; the spoilage did become evident in the sensory trials.

Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research.

PubMed

Grote, Mathias; O'Malley, Maureen A

2011-11-01

The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A Hot Spring Origin of Life and Early Adaptive Pathway from Woese Progenotes to Marine Stromatolites

NASA Astrophysics Data System (ADS)

Norkus, R.; Damer, B. F.; Deamer, D. W.

2017-07-01

An origin of life on land is visualized as: organic compounds accumulating in hydrothermal pools, wet-dry cycling of protocells encapsulating synthesized polymers, arising of a Woese progenote and its evolution into living microbial communities.

Water Quality Criteria for Human Health and Aquatic Life

EPA Science Inventory

Collaborative effort with the Office of Water to provide science in support of the development and implementation of new or revised ambient water quality criteria for microbial and chemical contaminants for human health and aquatic life. The research also addresses implementation...

Paleobiological Perspectives on Early Microbial Evolution

PubMed Central

Knoll, Andrew H.

2015-01-01

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles. PMID:26134315

Microfluidics expanding the frontiers of microbial ecology.

PubMed

Rusconi, Roberto; Garren, Melissa; Stocker, Roman

2014-01-01

Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08628 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08616 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Relevance of antarctic microbial ecosystems to exobiology

NASA Technical Reports Server (NTRS)

Mckay, Christopher P.

1993-01-01

Antarctic microbial ecosystems which provide biological and physical analogs that can be used in exobiology are studied. Since the access to extraterrestrial habitats is extremely difficult, terrestrial analogs represent the best opportunity for both formulation and preliminary testing of hypothesis about life. Antarctica, as one of few suitable environments on earth is considered to be a major locus of progress in exobiology.

Post-Viking microbiology: new approaches, new data, new insights

NASA Technical Reports Server (NTRS)

Nealson, K. H.

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Post-Viking microbiology: new approaches, new data, new insights.

PubMed

Nealson, K H

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Survival of a microbial soil community under Martian conditions

NASA Astrophysics Data System (ADS)

Hansen, A. A.; Noernberg, P.; Merrison, J.; Lomstein, B. Aa.; Finster, K. W.

2003-04-01

Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system at University of Aarhus, Denmark allows microbiological experiments under Mars analogue conditions. Thus detailed studies on the effect of Mars environmental conditions on the survival and the activity of a natural microbial soil community were carried out. Changes in the soil community were determined with a suite of different approaches: 1) total microbial respiration activity was investigated with 14C-glucose, 2) the physiological profile was investigated by the EcoLog-system, 3) colony forming units were determined by plate counts and 4) the microbial diversity on the molecular level was accessed with Denaturing Gradient Gel Electrophoresis. The simulation experiments showed that a part of the bacterial community survived Martian conditions corresponding to 9 Sol. These and future simulation experiments will contribute to our understanding of the possibility for extraterrestrial and terrestrial life on Mars.

Coupling plant growth and waste recycling systems in a controlled life support system (CELSS)

NASA Technical Reports Server (NTRS)

Garland, Jay L.

1992-01-01

The development of bioregenerative systems as part of the Controlled Ecological Life Support System (CELSS) program depends, in large part, on the ability to recycle inorganic nutrients, contained in waste material, into plant growth systems. One significant waste (resource) stream is inedible plant material. This research compared wheat growth in hydroponic solutions based on inorganic salts (modified Hoagland's) with solutions based on the soluble fraction of inedible wheat biomass (leachate). Recycled nutrients in leachate solutions provided the majority of mineral nutrients for plant growth, although additions of inorganic nutrients to leachate solutions were necessary. Results indicate that plant growth and waste recyling systems can be effectively coupled within CELSS based on equivalent wheat yield in leachate and Hoagland solutions, and the rapid mineralization of waste organic material in the hydroponic systems. Selective enrichment for microbial communities able to mineralize organic material within the leachate was necessary to prevent accumulation of dissolved organic matter in leachate-based solutions. Extensive analysis of microbial abundance, growth, and activity in the hydroponic systems indicated that addition of soluble organic material from plants does not cause excessive microbial growth or 'biofouling', and helped define the microbially-mediated flux of carbon in hydroponic solutions.

The MASSE Project: Applications of Biotechnology for Planetary Exploration

NASA Technical Reports Server (NTRS)

Lynch, Kennda; Steele, Andrew; Hedgecock, Jud; Wainwright, Norm; McKay, David S.; Maule, Jake; Schweitzer, Mary

2003-01-01

Automated life-detection experiments for solar system exploration have been previously. proposed and used onboard the. Viking, Mars lander,s, although. with ambiguous results. The recent advances in biotechnology such as biosensors, protein microarrays, and microfluidics alongside increased. knowledge in biomarker science have led to vastly improved sophistication and sensitivity for a new approach in life detection. The MASSE project has taken the challenge of integrating all of this knowledge into a new generation of interplanetary flight instrumentation for the main purpose.ot combining several mutually. confirming tests for life, organic/microbial contamination, prebiotic and abiotic chemicals into a small low powered instrument. Although the primary goal is interplanetary exploration, several terrestrial applications have become apparent specifically in point-of-care medical technology, bio-warfare, environmental sensing and microbial monitoring of manned space-flight vehicles.

Measurement of microbial activity in soil by colorimetric observation of in situ dye reduction: an approach to detection of extraterrestrial life

PubMed Central

Crawford, Ronald L; Paszczynski, Andrzej; Lang, Qingyong; Erwin, Daniel P; Allenbach, Lisa; Corti, Giancarlo; Anderson, Tony J; Cheng, I Francis; Wai, Chien; Barnes, Bruce; Wells, Richard; Assefi, Touraj; Mojarradi, Mohammad

2002-01-01

Background Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa. Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain). We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life. The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry. Results Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature. We measured the ability of soil microbial communities to reduce artificial electron acceptors. Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP) and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT). Uninoculated or sterilized controls did not reduce the dyes. A soil from Antarctica that was determined by chemical signature and DNA analysis to be sterile also did not reduce the dyes. Conclusion Observation of dye reduction, supplemented with extraction and identification of only a few specific signature redox-active biochemicals such as porphyrins or quinones, provides a simplified means to detect a signature of life in the soils of other planets or their moons. PMID:12150716

Modeling central metabolism and energy biosynthesis across microbial life

DOE PAGES

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal; ...

2016-08-08

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Modeling central metabolism and energy biosynthesis across microbial life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Modeling central metabolism and energy biosynthesis across microbial life.

PubMed

Edirisinghe, Janaka N; Weisenhorn, Pamela; Conrad, Neal; Xia, Fangfang; Overbeek, Ross; Stevens, Rick L; Henry, Christopher S

2016-08-08

Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. To overcome this challenge, we developed methods and tools ( http://coremodels.mcs.anl.gov ) to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of model organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. We predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.

Effect of methionine supplementation in chicken feed on the quality and shelf life of fresh poultry meat.

PubMed

Albrecht, Antonia; Herbert, Ulrike; Miskel, Dennis; Heinemann, Celine; Braun, Carina; Dohlen, Sophia; Zeitz, Johanna O; Eder, Klaus; Saremi, Behnam; Kreyenschmidt, Judith

2017-08-01

The aim of this study was to investigate the influence of different methionine sources and concentrations on the quality and spoilage process of broiler meat. The trial was comprised of 7 treatment groups: one basal group (suboptimal in Methionine+Cysteine; i.e., 0.89, 0.74, 0.69% in DM SID Met+Cys in starter, grower, and finisher diets, respectively) and 3 doses (0.10, 0.25, and 0.40%) of either DL-Methionine (DLM) or DL-2-hydroxy-4-methylthio butanoic acid (DL-HMTBA) on an equimolar basis of the DLM-supplemented groups. The broilers were fed the diets for 35 d, then slaughtered and processed. The filets were aerobically packed and stored under temperature controlled conditions at 4°C. Meat quality investigations were comprised of microbial investigations (total viable count and Pseudomonas spp.), pH and drip loss measurements of the filets. The shelf life of the meat samples was determined based on sensory parameters. After slaughtering, all supplemented meat samples showed a high quality, whereby no differences between the 2 methionine sources could be detected for the microbial load, pH, and drip loss. In comparison to the control group, the supplemented samples showed a higher sensory quality, characterized by a fresh smell and fresh red color. Methionine supplementation had a significant influence on meat quality parameters during storage. The microbial load, pH and drip loss of the chicken filets were positively correlated to the methionine concentration. Additionally, the microbial load at the end of storage was positively correlated to pH and drip loss values. Nevertheless, the microbial parameters were in a normal range and the positive correlation to methionine concentration did not affect the sensory shelf life. The mean sensory shelf life of the broiler filets varied between 7 to 9 d. During storage, no difference in the development of sensory parameters was observed between the supplemented groups, while the spoilage process of the basal group occurred slightly faster. In conclusion, methionine concentration, but not methionine source, effected meat quality parameters in breast muscles of broilers. © 2017 Poultry Science Association Inc.

Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

NASA Astrophysics Data System (ADS)

Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

2017-12-01

Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

PubMed Central

Lahr, Daniel J. G.; Parfrey, Laura Wegener; Mitchell, Edward A. D.; Katz, Laura A.; Lara, Enrique

2011-01-01

Amoebae are generally assumed to be asexual. We argue that this view is a relict of early classification schemes that lumped all amoebae together inside the ‘lower’ protozoa, separated from the ‘higher’ plants, animals and fungi. This artificial classification allowed microbial eukaryotes, including amoebae, to be dismissed as primitive, and implied that the biological rules and theories developed for macro-organisms need not apply to microbes. Eukaryotic diversity is made up of 70+ lineages, most of which are microbial. Plants, animals and fungi are nested among these microbial lineages. Thus, theories on the prevalence and maintenance of sex developed for macro-organisms should in fact apply to microbial eukaryotes, though the theories may need to be refined and generalized (e.g. to account for the variation in sexual strategies and prevalence of facultative sex in natural populations of many microbial eukaryotes). We use a revised phylogenetic framework to assess evidence for sex in several amoeboid lineages that are traditionally considered asexual, and we interpret this evidence in light of theories on the evolution of sex developed for macro-organisms. We emphasize that the limited data available for many lineages coupled with natural variation in microbial life cycles overestimate the extent of asexuality. Mapping sexuality onto the eukaryotic tree of life demonstrates that the majority of amoeboid lineages are, contrary to popular belief, anciently sexual, and that most asexual groups have probably arisen recently and independently. Additionally, several unusual genomic traits are prevalent in amoeboid lineages, including cyclic polyploidy, which may serve as alternative mechanisms to minimize the deleterious effects of asexuality. PMID:21429931

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

PubMed

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.

A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life

PubMed Central

Kim, Kyung Mo; Caetano-Anollés, Gustavo

2014-01-01

The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent. PMID:25249790

Searching for Life with Rovers: Exploration Methods & Science Results from the 2004 Field Campaign of the "Life in the Atacama" Project and Applications to Future Mars Missions

NASA Technical Reports Server (NTRS)

Cabrol, N. A.a; Wettergreen, D. S.; Whittaker, R.; Grin, E. A.; Moersch, J.; Diaz, G. Chong; Cockell, C.; Coppin, P.; Dohm, J. M.; Fisher, G.

2005-01-01

The Life In The Atacama (LITA) project develops and field tests a long-range, solarpowered, automated rover platform (Zo ) and a science payload assembled to search for microbial life in the Atacama desert. Life is barely detectable over most of the driest desert on Earth. Its unique geological, climatic, and biological evolution have created a unique training site for designing and testing exploration strategies and life detection methods for the robotic search for life on Mars.

Gene transfers can date the tree of life.

PubMed

Davín, Adrián A; Tannier, Eric; Williams, Tom A; Boussau, Bastien; Daubin, Vincent; Szöllősi, Gergely J

2018-05-01

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Space life sciences: search for signatures of life, and space flight environmental effects on the nervous system.

PubMed

2004-01-01

This volume contains selected papers of the Joint COSPAR-IAC event "Search for signatures of life in the solar system, terrestrial analogues and simulation experiments" held during the World Space Congress 2002 in Houston, Texas, USA. The first section of the volume reports on the rich variety of terrestrial microbial communities adapted to extreme environments, such as microbial life at very low temperatures in permafrost and ice layers, at high salt concentrations, as inhabitants of rocks and the microbial recolonization of impact-shocked rocks. These communities are suggested to serve as analogues for extraterrestrial habitats, which are also described in this section. The second section deals with the detection of biomarkers and signatures from extinct life on Earth, which might provide clues for detection of potential extraterrestrial biomarkers. This section is followed by reports of experiments in space and in the laboratory simulating space conditions, such as the prebiotic organic chemistry, the chemistry of dust particles to be detected during the Cassini mission to Saturn, as well as the photochemistry of biological systems exposed to space or planetary surface conditions. The second part of the issue contains papers from the session "The nervous system: space flight environmental factors effects--present results and new perspectives." The presentations in this session explored various aspects of the effects of exposure to protons and heavy particles on central nervous system function and on behavior. The second series of papers examines the effects of exposure to heavy particles and protons on neurochemistry and on behavior.

Piezophilic Bacteria Isolated from Sediment of the Shimokita Coalbed, Japan

NASA Astrophysics Data System (ADS)

Fang, J.; Kato, C.; Hori, T.; Morono, Y.; Inagaki, F.

2013-12-01

The Earth is a cold planet as well as pressured planet, hosting both the surface biosphere and the deep biosphere. Pressure ranges over four-orders of magnitude in the surface biosphere and probably more in the deep biosphere. Pressure is an important thermodynamic property of the deep biosphere that affects microbial physiology and biochemistry. Bacteria that require high-pressure conditions for optimal growth are called piezophilic bacteria. Subseafloor marine sediments are one of the most extensive microbial habitats on Earth. Marine sediments cover more than two-thirds of the Earth's surface, and represent a major part of the deep biosphere. Owing to its vast size and intimate connection with the surface biosphere, particularly the oceans, the deep biosphere has enormous potential for influencing global-scale biogeochemical processes, including energy, climate, carbon and nutrient cycles. Therefore, studying piezophilic bacteria of the deep biosphere has important implications in increasing our understanding of global biogeochemical cycles, the interactions between the biosphere and the geosphere, and the evolution of life. Sediment samples were obtained during IODP Expedition 337, from 1498 meters below sea floor (mbsf) (Sample 6R-3), 1951~1999 mbsf (19R-1~25R-3; coalbed mix), and 2406 mbsf (29R-7). The samples were mixed with MB2216 growth medium and cultivated under anaerobic conditions at 35 MPa (megapascal) pressure. Growth temperatures were adjusted to in situ environmental conditions, 35°C for 6R-3, 45°C for 19R-1~25R-3, and 55°C for 29R-7. The cultivation was performed three times, for 30 days each time. Microbial cells were obtained and the total DNA was extracted. At the same time, isolation of microbes was also performed under anaerobic conditions. Microbial communities in the coalbed sediment were analyzed by cloning, sequencing, and terminal restriction fragment length polymorphism (t-RFLP) of 16S ribosomal RNA genes. From the partial 16S rRNA gene sequences, we have identified abundant Alkalibacterium sp. in 6R-3 and 29R-7 at the first HP cultivation. We also identified Haloactibacillus sp. in 6R-3 and Anoxybacillus related sp. in 19R-1~25R-3 at the third HP cultivation. These microorganisms are likely piezophiles and play an important role in degradation of sedimentary organic matter and production of microbial metabolites sustaining the deep microbial ecosystem in the Shimokita Coalbed. The complete 16S sequencing and isolation of piezophiles are now ongoing.

Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Wallace, Sarah; Mehta, Satish; Pierson, Duane

2016-01-01

Numerous spaceflight experiments have been conducted to investigate alterations in microbial responses resulting from culture during spaceflight and spaceflight-analogs. However, recent studies investigating spaceflight-associated alterations in microbial virulence have initiated the review and production of evidence to better understand the impact these alterations would have on the incidence of infectious disease during a spaceflight exploration mission. The preponderance of evidence indicates that alterations in microbial gene expression and phenotype (including virulence) are occurring; however, the clinical implications of such changes are still unclear. Greater knowledge is required including a better understanding of the mechanism behind unique spaceflight-associated microbial responses to determine how this environmental stimulus impacts various microorganisms, their diversity and concentration in the spacecraft and crew microbiome, their impact on the vehicle and crew, and their resistance to current mitigation and antibiotic regimens. This knowledge will enable us to determine requirements, guidelines, and processes for design and monitoring of the next generation vehicles.

Magnetic core/shell nanoparticle thin films deposited by MAPLE: Investigation by chemical, morphological and in vitro biological assays

NASA Astrophysics Data System (ADS)

Cristescu, R.; Popescu, C.; Socol, G.; Iordache, I.; Mihailescu, I. N.; Mihaiescu, D. E.; Grumezescu, A. M.; Balan, A.; Stamatin, I.; Chifiriuc, C.; Bleotu, C.; Saviuc, C.; Popa, M.; Chrisey, D. B.

2012-09-01

We report on thin film deposition of nanostructured Fe3O4/oleic acid/ceftriaxone and Fe3O4/oleic acid/cefepime nanoparticles (core/shell/adsorption-shell) were fabricated by matrix assisted pulsed laser evaporation (MAPLE) onto inert substrates. The thin films were characterized by profilometry, Fourier transform infrared spectroscopy, atomic force microscopy, and investigated by in vitro biological assays. The biological properties tested included the investigation of the microbial viability and the microbial adherence to the glass coverslip nanoparticle film, using Gram-negative and Gram-positive bacterial strains with known antibiotic susceptibility behavior, the microbial adherence to the HeLa cells monolayer grown on the nanoparticle pellicle, and the cytotoxicity on eukaryotic cells. The proposed system, based on MAPLE, could be used for the development of novel anti-microbial materials or strategies for fighting pathogenic biofilms frequently implicated in the etiology of biofilm associated chronic infections.

Hydrogen production from switchgrass via a hybrid pyrolysis-microbial electrolysis process

DOE PAGES

Lewis, Alex J.; Ren, Shoujie; Ye, Philip; ...

2015-06-30

A new approach to hydrogen production using a hybrid pyrolysis-microbial electrolysis process is described. The aqueous stream generated during pyrolysis of switchgrass was used as a substrate for hydrogen production in a microbial electrolysis cell, achieving a maximum hydrogen production rate of 4.3 L H2/L-day at a loading of 10 g COD/L-anode-day. Hydrogen yields ranged from 50 3.2% to76 0.5% while anode coulombic efficiency ranged from 54 6.5% to 96 0.21%, respectively. Significant conversion of furfural, organic acids and phenolic molecules was observed under both batch and continuous conditions. The electrical and overall energy efficiency ranged from 149-175% and 48-63%,more » respectively. The results demonstrate the potential of the pyrolysis-microbial electrolysis process as a sustainable and efficient route for production of renewable hydrogen with significant implications for hydrocarbon production from biomass.« less

Microbial Life Under Extreme Energy Limitation

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Jorgensen, Bo Barker

2013-01-01

A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

Methodological approaches for studying the microbial ecology of drinking water distribution systems.

PubMed

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Possibilities for extremophilic microorganisms in microbial electrochemical systems

PubMed Central

Dopson, Mark; Ni, Gaofeng; Sleutels, Tom HJA

2015-01-01

Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems. PMID:26474966

Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

2010-12-01

The aqueous alteration of ultramafic rocks (serpentinization) has been suggested to be a favorable process for the habitability of astrobodies in our solar system including subsurface environments of Mars and Europa. Serpentinization produces copious quantities of hydrogen and small organic molecules, and leads to highly reducing, highly alkaline conditions (up to pH 12) and a lack of dissolved inorganic carbon, which both stimulates and challenges microbial activities. Several environments on Earth provide insight into the relationships between serpentinization and microbial life including slow-spreading mid-ocean ridges, subduction zones, and ophiolite materials emplaced along continental margins. The Tablelands, an ophiolite in western Newfoundland, Canada provides an opportunity to carefully document and map the relationships between geochemical energy, microbial growth, and physiology. Alkaline fluids at the Tablelands originate from 500-million year old oceanic crust and accumulate in shallow pools or seep from beneath serpentinized talus. Fluids, rocks, and gases were collected from the Tablelands during a series of field excursions in 2009 and 2010, and geochemical, microscopic, molecular, and cultivation-based approaches were used to study the serpentinite microbial ecosystem. These samples provide an opportunity to generate a comprehensive map of microbial communities and their activities in space and time. Data indicate that a low but detectable stock of microorganisms inhabit high pH pools associated with end-member serpentinite fluids. Enrichment cultures yielded brightly pigmented colonies related to Alphaproteobacteria, presumably carrying out anoxygenic photosynthesis, and Firmicutes, presumably catalyzing the fermentation of organic matter. Culture-independent analyses of SSU rRNA using T-RFLP indicated low diversity communities of Firmicutes and Archaea in standing alkaline pools, communities of Beta- and Gammaproteobacteria at high pH seeps, and assemblages consisting of diverse taxa at neutral pH background sites. Terrestrial serpentinite-hosted microbial ecosystems with their accessibility, their low phylogenetic diversity, and limited range of energetic resources provide an excellent opportunity to explore the interplay between geochemical energy and life and to elucidate the native serpentinite subsurface biosphere. From the perspective of Mars exploration, studies of serpentinite ecosystems provide the opportunity to pinpoint the organisms and physiological adaptations specifically associated with serpentinization and to directly measure their geochemical impacts. Both of these results will inform modeling and life detection efforts of the Martian subsurface environment.

Microbial profiles of commercial, vacuum-packaged, fresh pork of normal or short storage life.

PubMed

Holley, Richard A; Peirson, Michael D; Lam, Jocelyn; Tan, Kit Bee

2004-12-01

The microbial ecology of fresh vacuum-packed pork cuts during storage at -1.5 degrees C for up to 45 days was examined to characterize rates of microbial growth and pH changes in commercially prepared products of normal storage quality. Pork loins in commercial distribution with odour defects were also studied to determine a possible cause of the defects and avoid future problems. In addition, microbial profiles of pork cuts from two plants were compared, after storage for 25 days at -1.5 degrees C, to identify possible reasons for differences in the storage life of product from the plants. The effects of a change in sanitation procedures on the microbial populations of products stored for 25 days were also studied. With normal product, microbial growth in different packages progressed at different rates, reflecting differences in initial levels of bacterial contamination. All samples in the study reached 8 weeks without apparent organoleptic change and samples carried 5.8+/-1.2 log bacteria cm(-2) (mean+/-S.D.). The flora of loins with the odour defect were predominately lactic acid bacteria (LAB) and carnobacteria, but they contained large fractions of Enterobacteriaceae <35 days after packaging. Aeromonas spp. and Shewanella spp. were likely responsible for the sulfide-putrid smell of these spoiled products, but species of Enterobacteriaceae and lactic acid bacteria could have contributed to spoilage. Comparison of microbial groups present in 16 other cuts, half from each of two commercial plants, which were stored for 25 days at -1.5 degrees C, showed that larger fractions of Enterobacteriaceae were present in samples from the plant having difficulty achieving the desired storage life. Additional bacterial samples from 12 cuts supplied by the latter plant obtained after adoption of an acid sanitizer step in the plant cleaning regimen, and also stored for 25 days at -1.5 degrees C, yielded few Enterobacteriaceae, Aeromonas or Shewanella. Use of an acid sanitizer in plant cleaning may be a means of controlling alkali-tolerant bacteria such as Aeromonas or Shewanella which can contaminate pork cuts and spoil vacuum-packaged product. The fraction of Enterobacteriaceae in bacteria populations on fresh pork stored for 25 days at -1.5 degrees C may be a useful indicator of the effectiveness of plant sanitation.

Microbial ecology and biogeochemistry of continental Antarctic soils.

PubMed

Cowan, Don A; Makhalanyane, Thulani P; Dennis, Paul G; Hopkins, David W

2014-01-01

The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

Microbiota of little penguins and short-tailed shearwaters during development

PubMed Central

Arnould, John P. Y.; Allnutt, Theo R.; Crowley, Tamsyn; Krause, Lutz; Reynolds, John; Dann, Peter; Smith, Stuart C.

2017-01-01

The establishment and early colonisation of the gastrointestinal (GI) tract has been recognised as a crucial stage in chick development, with pioneering microbial species responsible for influencing the development of the GI tract and influencing host health, fitness and disease status throughout life. Development of the microbiota in long lived seabirds is poorly understood. This study characterised the microbial composition of little penguin and short-tailed shearwater chicks throughout development, using Quantitative Real Time PCR (qPCR) and 16S rRNA sequencing. The results indicated that microbial development differed between the two seabird species with the short-tailed shearwater microbiota being relatively stable throughout development whilst significant fluctuations in the microbial composition and an upward trend in the abundance of Firmicutes and Bacteroidetes were observed in the little penguin. When the microbial composition of adults and chicks was compared, both species showed low similarity in microbial composition, indicating that the adult microbiota may have a negligible influence over the chick’s microbiota. PMID:28806408

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica.

PubMed

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-07-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature -23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica

PubMed Central

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-01-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature −23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival. PMID:27323892

Deep microbial life in the Altmark natural gas reservoir: baseline characterization prior CO2 injection

NASA Astrophysics Data System (ADS)

Morozova, Daria; Shaheed, Mina; Vieth, Andrea; Krüger, Martin; Kock, Dagmar; Würdemann, Hilke

2010-05-01

Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of about 3500m, is characterised by high salinity fluid and temperatures up to 127° C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery) the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism) and DGGE (Denaturing Gradient Gel Electrophoresis). First results of the baseline survey indicate the presence of microorganisms similar to representatives from other saline, hot, anoxic, deep environments. However, due to the hypersaline and hyperthermophilic reservoir conditions, cell numbers are low, so that the quantification of those microorganisms as well as the determination of microbial activity was not yet possible. Microbial monitoring methods have to be further developed to study microbial activities under these extreme conditions to access their influence on the EGR technique and on enhancing the long term safety of the process by fixation of carbon dioxide by precipitation of carbonates. We would like to thank GDF SUEZ for providing the data for the Rotliegend reservoir, sample material and enabling sampling campaigns. The CLEAN project is funded by the German Federal Ministry of Education and Research (BMBF) in the frame of the Geotechnologien Program.

Interactions in the Geo-Biosphere: Processes of Carbonate Precipitation in Microbial Mats

NASA Astrophysics Data System (ADS)

Dupraz, C.; Visscher, P. T.

2009-12-01

Microbial communities are situated at the interface between the biosphere, the lithosphere and the hydrosphere. These microbes are key players in the global carbon cycle, where they influence the balance between the organic and inorganic carbon reservoirs. Microbial populations can be organized in microbial mats, which can be defined as organosedimentary biofilms that are dominated by cyanobacteria, and exhibit tight coupling of element cycles. Complex interactions between mat microbes and their surrounding environment can result in the precipitation of carbonate minerals. This process refers as ‘organomineralization sensu lato' (Dupraz et al. in press), which differs from ‘biomineralization’ (e.g., in shells and bones) by lacking genetic control on the mineral product. Organomineralization can be: (1) active, when microbial metabolic reactions are responsible for the precipitation (“biologically-induced” mineralization) or (2) passive, when mineralization within a microbial organic matrix is environmentally driven (e.g., through degassing or desiccation) (“biologically-influenced” mineralization). Studying microbe-mineral interactions is essential to many emerging fields of the biogeoscience, such as the study of life in extreme environments (e.g, deep biosphere), the origin of life, the search for traces of extraterrestrial life or the seek of new carbon sink. This research approach combines sedimentology, biogeochemistry and microbiology. Two tightly coupled components that control carbonate organomineralization s.l.: (1) the alkalinity engine and (2) the extracellular organic matter (EOM), which is ultimately the location of mineral nucleation. Carbonate alkalinity can be altered both by microbial metabolism and environmental factors. In microbial mats, the net accumulation of carbonate minerals often reflect the balance between metabolic activities that consume/produce CO2 and/or organic acids. For example, photosynthesis and sulfate reduction will increase carbonate alkalinity and the potential of precipitation, whereas aerobic respiration and sulfide oxidation will promote carbonate dissolution. The EOM is composed of two main carbon pools: the high molecular weight extracellular polymeric substances (EPS) and the low molecular weight organic carbon compounds (LMW-OC). Both pools play a critical role in carbonate precipitation by providing Ca2+ and CO32- as well as a nucleation template for mineral growth. EOM contains several negatively charged functional groups, which, depending on the pH, can be deprotonated (each group has unique pK value(s)) and, thus, bind cations. This binding capacity can deplete the surrounding environment of cations (e.g., Ca2+, Mg2+) and, thus, inhibits carbonate precipitation. Therefore, organomineralization is only possible if the inhibition potential is reduced through (1) oversaturation of the EOM binding capacity or (2) EOM degradation.

Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

NASA Astrophysics Data System (ADS)

Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

2015-12-01

Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weng, Li; Rubin, Edward M.; Bristow, James

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Becausemore » these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent.

PubMed

Pawlett, Mark; Ritz, Karl; Dorey, Robert A; Rocks, Sophie; Ramsden, Jeremy; Harris, Jim A

2013-02-01

Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.

KSC-2014-4904

NASA Image and Video Library

2014-10-31

CAPE CANAVERAL, Fla. – A researcher from the University of Florida in Gainesville, checks the Dust Atmospheric Recovery Technology, or DART, spacecraft in a laboratory inside the Space Life Sciences Lab at NASA’s Kennedy Space Center in Florida. DART will characterize the dust loading and microbial diversity in the atmosphere over Florida during summer months with a special emphasis on their interactions during an African dust storm. DART will be used to collect atmospheric aerosols and suspended microbial cells over Florida and Kennedy. Results will help predict the risks of excessive microbial contamination adhering to spacecraft surfaces. Photo credit: NASA/Dimitri Gerondidakis

Customizing laboratory mice by modifying gut microbiota and host immunity in an early "window of opportunity".

PubMed

Hansen, Camilla H F; Metzdorff, Stine B; Hansen, Axel K

2013-01-01

We recently investigated how post-natal microbial gut colonization is important for the development of the immune system, especially in the systemic compartments. This addendum presents additional data which in accordance with our previous findings show that early life microbial colonization is critical for a fine-tuned immune homeostasis to develop also in the intestinal environment. A generalized reduction in the expression of immune signaling related genes in the small intestine may explain previously shown increased systemic adaptive immune reactivity, if the regulatory cross-talk between intra- and extra-intestinal immune cells is immature following a neonatal germ-free period. These findings are furthermore discussed in the context of recently published results on how lack of microbial exposure in the neonatal life modifies disease expression in rodents used as models mimicking human inflammatory diseases. In particular, with a focus on how these interesting findings could be used to optimize the use of rodent models.

Synthetic Ecology of Microbes: Mathematical Models and Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zomorrodi, Ali R.; Segre, Daniel

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems andmore » synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.« less

Biofilm community succession: a neutral perspective.

PubMed

Woodcock, Stephen; Sloan, William T

2017-05-22

Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

A communal catalogue reveals Earth's multiscale microbial diversity.

PubMed

Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

2017-11-23

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Synthetic Ecology of Microbes: Mathematical Models and Applications

DOE PAGES

Zomorrodi, Ali R.; Segre, Daniel

2015-11-11

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems andmore » synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.« less

Earth's Earliest Ecosystems in the Classroom: The Use of Microbial Mats to Teach General Principles in Microbial Ecology, and Scientific Inquiry

NASA Technical Reports Server (NTRS)

Beboutl, Brad M.; Bucaria, Robin

2004-01-01

Microbial mats are living examples of the most ancient biological communities on earth, and may also be useful models for the search for life elsewhere. They are centrally important to Astrobiology. In this lecture, we will present an introduction to microbial mats, as well as an introduction to our web-based educational module on the subject of microbial ecology, featuring living mats maintained in a mini "Web Lab" complete with remotely-operable instrumentation. We have partnered with a number of outreach specialists in order to produce an informative and educational web-based presentation, aspects of which will be exported to museum exhibits reaching a wide audience. On our web site, we will conduct regularly scheduled experimental manipulations, linking the experiments to our research activities, and demonstrating fundamental principles of scientific research.

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives

PubMed Central

Yamaguchi, Nobuyasu; Roberts, Michael; Castro, Sarah; Oubre, Cherie; Makimura, Koichi; Leys, Natalie; Grohmann, Elisabeth; Sugita, Takashi; Ichijo, Tomoaki; Nasu, Masao

2014-01-01

Previous space research conducted during short-term flight experiments and long-term environmental monitoring on board orbiting space stations suggests that the relationship between humans and microbes is altered in the crewed habitat in space. Both human physiology and microbial communities adapt to spaceflight. Microbial monitoring is critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space transit vehicles, space stations, and surface habitats. To address this critical need, space agencies including NASA (National Aeronautics and Space Administration), ESA (European Space Agency), and JAXA (Japan Aerospace Exploration Agency) are working together to develop and implement specific measures to monitor, control, and counteract biological contamination in closed-environment systems. In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed. PMID:25130885

Microbial contributions to the Precambrian Earth

NASA Technical Reports Server (NTRS)

Margulis, L.; Bermudes, D.; Obar, R.

1986-01-01

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

A hydrogen-based subsurface microbial community dominated by methanogens

USGS Publications Warehouse

Chapelle, F.H.; O'Neil, Kyle; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

2002-01-01

The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

Microbial mats and the early evolution of life

NASA Technical Reports Server (NTRS)

Des Marais, D. J.

1990-01-01

Microbial mats have descended from perhaps the oldest and most widespread biological communities known. Mats harbor microbes that are crucial for studies of bacterial phylogeny and physiology. They illustrate how several oxygen-sensitive biochemical processes have adapted to oxygen, and they show how life adapted to dry land long before the rise of plants. The search for the earliest grazing protists and metazoa in stromatolites is aided by observations of mats: in them, organic compounds characteristic of ancient photosynthetic protists can be identified. Recent mat studies suggest that the 13C/12C increase observed over geological time in stromatolitic organic matter was driven at least in part by a long-term decline in atmospheric carbon dioxide levels.

Reproducible analyses of microbial food for advanced life support systems

NASA Technical Reports Server (NTRS)

Petersen, Gene R.

1988-01-01

The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Molecular Insights on Dissolved Organic Matter Transformation by Supraglacial Microbial Communities.

PubMed

Antony, Runa; Willoughby, Amanda S; Grannas, Amanda M; Catanzano, Victoria; Sleighter, Rachel L; Thamban, Meloth; Hatcher, Patrick G; Nair, Shanta

2017-04-18

Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bioavailable and is transformed by resident microbial communities through parallel processes of degradation and synthesis. DOM thought to be of a more refractory nature, such as dissolved black carbon and carboxylic-rich alicyclic molecules, was also rapidly and extensively reworked. Microbially reworked DOM exhibits an increase in the number and magnitude of N-, S-, and P-containing formulas, is less oxygenated, and more aromatic when compared to the initial DOM. Shifts in the heteroatom composition suggest that microbial processes may be important in the cycling of not only C, but other elements such as N, S, and P. Microbial reworking also produces photoreactive compounds, with potential implications for DOM photochemistry. Refined measurements of supraglacial DOM and their cycling by microbes is critical for improving our understanding of supraglacial DOM cycling and the biogeochemical and ecological impacts of DOM export to downstream environments.

Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance.

PubMed

Tandukar, Madan; Oh, Seungdae; Tezel, Ulas; Konstantinidis, Konstantinos T; Pavlostathis, Spyros G

2013-09-03

The effect of benzalkonium chlorides (BACs), a widely used class of quaternary ammonium disinfectants, on microbial community structure and antimicrobial resistance was investigated using three aerobic microbial communities: BACs-unexposed (DP, fed a mixture of dextrin/peptone), BACs-exposed (DPB, fed a mixture of dextrin/peptone and BACs), and BACs-enriched (B, fed only BACs). Long-term exposure to BACs reduced community diversity and resulted in the enrichment of BAC-resistant species, predominantly Pseudomonas species. Exposure of the two microbial communities to BACs significantly decreased their susceptibility to BACs as well as three clinically relevant antibiotics (penicillin G, tetracycline, ciprofloxacin). Increased resistance to BACs and penicillin G of the two BACs-exposed communities is predominantly attributed to degradation or transformation of these compounds, whereas resistance to tetracycline and ciprofloxacin is largely due to the activity of efflux pumps. Quantification of several key multidrug resistance genes showed a much higher number of copies of these genes in the DPB and B microbial communities compared to the DP community. Collectively, our findings indicate that exposure of a microbial community to BACs results in increased antibiotic resistance, which has important implications for both human and environmental health.

Optimization of biomass composition explains microbial growth-stoichiometry relationships

USGS Publications Warehouse

Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

2011-01-01

Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

Life in Ice: Implications to Astrobiology

NASA Technical Reports Server (NTRS)

Hoover, Richard B.

2009-01-01

During the 2008 Tawani International Expedition Schirmacher Oasis/Lake Untersee Antarctica Expedition, living and instantly motile bacteria were found in freshly thawed meltwater from ice of the Schirmacher Oasis Lakes, the Anuchin Glacier ice and samples of the that perennial ice sheet above Lake Untersee. This phenomenon of living bacteria encased in ice had previously been observed in the 32,000 year old ice of the Fox Tunnel. The bacteria found in this ice included the strain FTR1T which was isolated and published as valid new species (Carnobacterium pleistocenium) the first validly published living Pleistocene organism still alive today. Living bacteria were also extracted from ancient ice cores from Vostok, Antarctica. The discovery that many strains of bacteria are able to survive and remain alive while frozen in ice sheets for long periods of time may have direct relevance to Astrobiology. The abundance of viable bacteria in the ice sheets of Antarctica suggests that the presence of live bacteria in ice is common, rather than an isolated phenomenon. This paper will discuss the results of recent studies at NSSTC of bacteria cryopreserved in ice. This paper advances the hypothesis that cryopreserved cells, and perhaps even viable bacterial cells, may exist today--frozen in the water-ice of lunar craters, the Polar Caps or craters of Mars; or in the permafrost of Mars; ice and rocks of comets or water bearing asteroids; or in the frozen crusts of the icy moons of Jupiter and Saturn. The existence of bacterial life in ice suggests that it may not be necessary to drill through a thick ice crust to reach liquid water seas deep beneath the icy crusts of Europa, Ganymede and Enceladus. The presence of viable bacteria in the ice of the Earth s Polar Caps suggests that the possibility that cryo-panspermia (i.e., the trans-planetary transfer of microbial life by impact ejection/spallation of bacteria-rich polar ice masses) deserves serious consideration and study as a possible natural phenomenon of the solar system that may have played a profoundly important role in the Origin of Life on Earth and the Distribution of Life in the Cosmos. The paper concludes with a consideration of the protective properties of ice by absorption of UV-B, UV-C, h-rays, gamma-rays and the high energy proton environment of the Jupiter Radiation Belt. A proposed instrument that may provide additional data on the potential survivability of microbial extremophiles encased in ice and subjected to the simulated space environment will be briefly described.

Microbial response to space environment, part B

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Chassay, C. E.; Ellis, W. L.; Foster, B. G.; Volz, P. A.; Spizizen, J.; Buecker, H.; Wrenn, R. T.; Simmonds, R. C.; Long, R. A.

1972-01-01

The performance of the microbial response to space environment experiment is considered excellent by all investigators. For most microbial systems, only preliminary survival data are available at this time. None of the available data indicate space flight-mediated changes in cell viability or recovery. One quite important observation has been made at this early date, however. The eggs produced after mice had been infected with N. dubius larvae demonstrated a significant decrease in hatchability when compared to identical ground controls. Except for the fact that the Apollo 16 flight larvae had been on board the command module, treatment of the flown larvae and ground control larvae was the same; neither had been exposed to UV irradiation. The significance and implications of this finding are currently being studied.

Biochemical capacitance of Geobacter sulfurreducens biofilms.

PubMed

Bueno, Paulo R; Schrott, Germán D; Bonanni, Pablo S; Simison, Silvia N; Busalmen, Juan P

2015-08-10

An electrical model able to decouple the electron pathway from microbial cell machinery impedance terms is introduced. In this context, capacitance characteristics of the biofilm are clearly resolved. In other words, the model allows separating, according to the advantage of frequency and spectroscopic response approach, the different terms controlling the performance of the microbial biofilm respiratory process and thus the directly related electricity production process. The model can be accurately fitted to voltammetry measurements obtained under steady-state conditions and also to biofilm discharge amperometric measurements. The implications of biological aspects of the electrochemical or redox capacitance are discussed theoretically in the context of current knowledge with regard to structure and physiological activity of microbial Geobacter biofilms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial threat lists: obstacles in the quest for biosecurity?

PubMed

Casadevall, Arturo; Relman, David A

2010-02-01

Anxiety about threats from the microbial world and about the deliberate misuse of microorganisms has led to efforts to define and control these dangers using lists and regulations. One list with tremendous legal implications and a potentially huge impact on research is the Select Agents and Toxins List, which was created by the US Government to limit the possession of and access to particular microorganisms and toxins. In this article, in addition to highlighting general problems with taxonomy-based, microorganism-centric lists, we discuss our view that such lists may have the paradoxical effect of increasing the societal vulnerability to biological attack and natural epidemics by interfering with the sharing of microbial samples and hindering research on vaccines and therapeutics.

Rooting Theories of Plant Community Ecology in Microbial Interactions

PubMed Central

Bever, James D.; Dickie, Ian A.; Facelli, Evelina; Facelli, Jose M.; Klironomos, John; Moora, Mari; Rillig, Matthias C.; Stock, William D.; Tibbett, Mark; Zobel, Martin

2010-01-01

Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant-soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and suggest these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance, and invasion ecology. PMID:20557974

Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits.

PubMed

Smith, David Roy; Keeling, Patrick J

2016-09-08

The DNA double helix has been called one of life's most elegant structures, largely because of its universality, simplicity, and symmetry. The expression of information encoded within DNA, however, can be far from simple or symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukaryotes). The nuclear and organelle genomes of protists are subject to the most tangled forms of gene expression yet identified. The complicated and extravagant picture of the underlying genetics of eukaryotic microbial life changes how we think about the flow of genetic information and the evolutionary processes shaping it. Here, we discuss the origins, diversity, and growing interest in noncanonical protist gene expression and its relationship to genomic architecture.

Fungal colonization of an Ordovician impact-induced hydrothermal system

PubMed Central

Ivarsson, Magnus; Broman, Curt; Sturkell, Erik; Ormö, Jens; Siljeström, Sandra; van Zuilen, Mark; Bengtson, Stefan

2013-01-01

Impacts are common geologic features on the terrestrial planets throughout the solar system, and on at least Earth and Mars impacts have induced hydrothermal convection. Impact-generated hydrothermal systems have been suggested to possess the same life supporting capability as hydrothermal systems associated with volcanic activity. However, evidence of fossil microbial colonization in impact-generated hydrothermal systems is scarce in the literature. Here we report of fossilized microorganisms in association with cavity-grown hydrothermal minerals from the 458 Ma Lockne impact structure, Sweden. Based on morphological characteristics the fossilized microorganisms are interpreted as fungi. We further infer the kerogenization of the microfossils, and thus the life span of the fungi, to be contemporaneous with the hydrothermal activity and migration of hydrocarbons in the system. Our results from the Lockne impact structure show that hydrothermal systems associated with impact structures can support colonization by microbial life. PMID:24336641

Fungal colonization of an Ordovician impact-induced hydrothermal system

NASA Astrophysics Data System (ADS)

Ivarsson, Magnus; Broman, Curt; Sturkell, Erik; Ormö, Jens; Siljeström, Sandra; van Zuilen, Mark; Bengtson, Stefan

2013-12-01

Impacts are common geologic features on the terrestrial planets throughout the solar system, and on at least Earth and Mars impacts have induced hydrothermal convection. Impact-generated hydrothermal systems have been suggested to possess the same life supporting capability as hydrothermal systems associated with volcanic activity. However, evidence of fossil microbial colonization in impact-generated hydrothermal systems is scarce in the literature. Here we report of fossilized microorganisms in association with cavity-grown hydrothermal minerals from the 458 Ma Lockne impact structure, Sweden. Based on morphological characteristics the fossilized microorganisms are interpreted as fungi. We further infer the kerogenization of the microfossils, and thus the life span of the fungi, to be contemporaneous with the hydrothermal activity and migration of hydrocarbons in the system. Our results from the Lockne impact structure show that hydrothermal systems associated with impact structures can support colonization by microbial life.

Fungal colonization of an Ordovician impact-induced hydrothermal system.

PubMed

Ivarsson, Magnus; Broman, Curt; Sturkell, Erik; Ormö, Jens; Siljeström, Sandra; van Zuilen, Mark; Bengtson, Stefan

2013-12-16

Impacts are common geologic features on the terrestrial planets throughout the solar system, and on at least Earth and Mars impacts have induced hydrothermal convection. Impact-generated hydrothermal systems have been suggested to possess the same life supporting capability as hydrothermal systems associated with volcanic activity. However, evidence of fossil microbial colonization in impact-generated hydrothermal systems is scarce in the literature. Here we report of fossilized microorganisms in association with cavity-grown hydrothermal minerals from the 458 Ma Lockne impact structure, Sweden. Based on morphological characteristics the fossilized microorganisms are interpreted as fungi. We further infer the kerogenization of the microfossils, and thus the life span of the fungi, to be contemporaneous with the hydrothermal activity and migration of hydrocarbons in the system. Our results from the Lockne impact structure show that hydrothermal systems associated with impact structures can support colonization by microbial life.

The biogeography of the atlantic salmon (Salmo salar) gut microbiome.

PubMed

Llewellyn, Martin S; McGinnity, Philip; Dionne, Melanie; Letourneau, Justine; Thonier, Florian; Carvalho, Gary R; Creer, Simon; Derome, Nicolas

2016-05-01

Although understood in many vertebrate systems, the natural diversity of host-associated microbiota has been little studied in teleosts. For migratory fishes, successful exploitation of multiple habitats may affect and be affected by the composition of the intestinal microbiome. We collected 96 Salmo salar from across the Atlantic encompassing both freshwater and marine phases. Dramatic differences between environmental and gut bacterial communities were observed. Furthermore, community composition was not significantly impacted by geography. Instead life-cycle stage strongly defined both the diversity and identity of microbial assemblages in the gut, with evidence for community destabilisation in migratory phases. Mycoplasmataceae phylotypes were abundantly recovered in all life-cycle stages. Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.

The biogeography of the atlantic salmon (Salmo salar) gut microbiome

PubMed Central

Llewellyn, Martin S; McGinnity, Philip; Dionne, Melanie; Letourneau, Justine; Thonier, Florian; Carvalho, Gary R; Creer, Simon; Derome, Nicolas

2016-01-01

Although understood in many vertebrate systems, the natural diversity of host-associated microbiota has been little studied in teleosts. For migratory fishes, successful exploitation of multiple habitats may affect and be affected by the composition of the intestinal microbiome. We collected 96 Salmo salar from across the Atlantic encompassing both freshwater and marine phases. Dramatic differences between environmental and gut bacterial communities were observed. Furthermore, community composition was not significantly impacted by geography. Instead life-cycle stage strongly defined both the diversity and identity of microbial assemblages in the gut, with evidence for community destabilisation in migratory phases. Mycoplasmataceae phylotypes were abundantly recovered in all life-cycle stages. Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome. PMID:26517698

Polar Lakes and Springs as Analogs for Mars

NASA Technical Reports Server (NTRS)

McKay, C. P.

1995-01-01

If we accept the fluvial features as evidence of liquid water on Mars we conclude that early in Martian history there was an extensive period during which liquid water was prevalent and stable. The duration of this epoch and the environmental conditions that allowed for water flow are uncertain but because liquid water is the most critical environmental requirement for life on Earth, the observation that there was liquid water on Mars during on early epoch is a strong motivation for considering the possibility of past life. Microbial ecosystems can thrive in polar lakes and springs on Earth, such as those in the Antarctic dry valleys, even when the mean temperatures are well below freezing. Mars need not have ever been above freezing for life to persist. These microbial ecosystems provide specific models for possible past martian ecosystems and can be used in the development of methods to locate and identify analogous Martian fossil forms, if they exist.