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Sample records for cryptoendolithic microbial environment

  1. Antarctic cryptoendolithic microbial ecosystem research, 1986-1987

    Science.gov (United States)

    Friedmann, E I; Meyer, M A

    1987-01-01

    The apparent lifelessness of the Ross Desert is in marked contrast to the diversity of cryptoendolithic microorganisms inhabiting the interstices of sandstone rocks. The endolithic habitat provides a protective niche for lichens, bacteria, algae, and fungi, enabling them to exist in an extremely dry and cold climate. Composed solely of microorganisms living under the surface of rocks and totally lacking animals and protozoa, this ecosystem is controlled by measurable physical variables and well suited for ecosystem study and modeling. The work of the antarctic cryptoendolithic microbial ecosystem research group has involved physical measurements of nanoclimate (microbial environment inside rocks) (Friedmann, McKay, and Nienow 1987), taxonomy (Darling, Friedmann, and Broady 1987; Hale 1987), microdistribution, organism-substrate interactions including the ongoing process of fossilization (Friedmann and Weed 1987), physiological ecology, and quantification of the nitrogen economy.

  2. Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats.

    Science.gov (United States)

    Omelon, Christopher R; Pollard, Wayne H; Ferris, F Grant

    2007-11-01

    Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.

  3. The Antarctic cryptoendolithic microbial ecosystem as a model for studying microbes in shale and coal

    Energy Technology Data Exchange (ETDEWEB)

    Vestal, J.R. (University of Cincinnati, Cincinnati, OH (USA). Dept. of Biological Sciences)

    1991-04-01

    In Antarctica, there exists a complete microbial ecosystem that lives hidden within the pore spaces of sandstone (cryptoendolithic). Studying microbes within this solid matrix has presented certain technical problems which have been overcome. This has allowed studies to be conducted that have shown the effects of the physical and chemical environment on growth and metabolism of the microbes in these rocks. Similar microbial communities have recently been discovered that can exist within the solid matrix of shale and coal. Even though the community and environment are different from the Antarctic microbes, many of the methods and hypotheses regarding their existence are the same. Answers to questions relating how and why these microbes exist in shale and coal may have important implications for coal desulfurization, or degradation of the shale matrix to release hydrocarbons. 40 refs., 1 fig., 1 tab.

  4. Iron isotope geochemistry in the Antarctic cryptoendolithic microbial ecosystem

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    Sun, H.

    2002-05-01

    The stable isotope composition of iron is a potentially powerful tracer of biogeochemical cycles because iron is ubiquitous, it is required by all organisms, and it is resistant to alterations during diagenesis. Here we report evidence of biological iron isotope fractionation in the weathering process of sandstone in McMurdo Dry Valleys, Antarctica, caused by the cryptoendolithic lichen-dominated microbial community that live below the rock surface. The fungi secrete oxalic acid, which under the sunlight reduces and dissolves the iron in the colonized zone. The mobilized iron diffuses to the rock surface and the rock interior below the organisms where it is re-oxidized. This leaching process is shown to prefer lighter isotopes of iron, leaving the colonized layer enriched in del 56Fe by as much 0.8 per mil. Had endolithic microorganisms occurred on Mars as commonly believed, they might have left similar iron biosignatures, well preserved in rocks because of the absence of subsequent aqueous activities.

  5. Incorporation of inorganic carbon by Antarctic cryptoendolithic fungi

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    Palmer, R. J. Jr; Friedmann, E. I.

    1988-01-01

    Fungi isolated from the cryptoendolithic community of the Ross Desert are capable of fixing inorganic carbon. Results suggest that lichen mycobionts and parasymbionts are adapted to different water regimes in the cryptoendolithic environment.

  6. Photosynthetic carbon incorporation and turnover in Antarctic cryptoendolithic microbial communities: Are they the slowest-growing communities on earth

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, C.G.; Vestal, J.R. (Univ. of Cincinnati, OH (USA))

    1991-08-01

    The main forms of terrestrial life in the cold, desolate Ross Desert of Antarctica are lichen-dominated or cyanobacterium-dominated cryptoendolithic (hidden in rock) microbial communities. Though microbial community biomass (as measured by extractable lipid phosphate) was well within the range of values determined for their microbial communities, community lipid carbon turnover times (calculated from community lipid biomass, rates of community photosynthetic carbon incorporation into lipids versus temperature, and the in situ temperature record) were among the longest on Earth (ca. 20,000 years). When the temperature is above freezing and moisture is present, moderate rates of photosynthesis can be measured. Lichen communities had a psychrophilic temperature response (maximal rate of 4.5 ng of C h{sup {minus}1}m{sup {minus}2} at 10C) while cyanobacteria communities had maximal rates at 20 to 30C(3 ng of C h{sup {minus}1} m{sup {minus}2}). These extraordinarily slowly growing communities were not nutrient limited. No significant changes in photosynthetic metabolism simple, tenacious microbial communities demonstrate strategies of survival under conditions normally considered too extreme for life.

  7. Putative cryptoendolithic life in Devonian pillow basalt, Rheinisches Schiefergebirge, Germany.

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    Peckmann, J; Bach, W; Behrens, K; Reitner, J

    2008-03-01

    Middle Devonian (Givetian) pillow basalt and inter-pillow breccia from the Rheinisches Schiefergebirge in Germany were found to contain putative biogenic filaments that indicate that life once proliferated within these volcanic rocks. Mineralized filaments are found in carbonate amygdules (vesicles filled by carbonate cement) in the volcanic rock, where they started to form on the internal surface of the once water-filled vesicles. Biogenicity of the filaments is indicated by (1) their size and shape resembling modern microorganisms including a constant diameter along the length of curved filaments, (2) their independence of crystal faces or cleavage planes, (3) branching patterns reminiscent of modern microorganisms, and (4) their spatial clustering and preferential occurrence close to the margin of pillows and in the inter-pillow breccias. A time lag between the deposition of pillow basalt and the activity of endoliths is revealed by the sequence of carbonate cements filling the amygdules. The putative filamentous microorganisms thrived after the formation of early fibrous rim cement, but before later equant calcite spar filled most of the remaining porosity. Microbial clay authigenesis analogous to the encrustation of prokaryotes in modern iron-rich environments led to the preservation of filaments. The filaments predominantly consist of the clay minerals chamosite and illite. Having dwelled in water-filled vesicles, the Devonian basalt-hosted filaments apparently represent cryptoendoliths. This finding suggests that a previously unrecognized niche for life exists within volcanic rock.

  8. Cryptoendolithic lichen and cyanobacterial communities of the Ross Desert, Antarctica

    Science.gov (United States)

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

    1988-01-01

    Cryptoendolithic microbial communities in the Ross Desert (McMurdo Dry Valleys) are characterized on the basis of photosynthetic microorganisms and fungi. Two eukaryotic communities (the lichen-dominated and Hemichloris communities) and three cyanobacterial communities (the red Gloeocapsa, Hormathonema-Gloeocapsa, and Chroococcidiopsis communities) are described. Eleven coccoid, one pleurocapsoid, and five filamentous cyanobacteria occurring in these communities are characterized and illustrated. The moisture grade of the rock substrate seems to affect pH, formation of primary iron stain, and the distribution of microbial communities.

  9. Psychrophilic and Psychrotolerant Microbial Extremophiles in Polar Environments

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    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

  10. EVALUATION OF MICROBIAL SURVIVAL IN EXTRATERRESTRIAL ENVIRONMENTS

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    Betül BULUÇ

    2012-08-01

    Full Text Available In this paper, the space environments where microbial terrestrial life could form and evolve in, were evaluted with the base of the physical and chemical properties. In addition, Earthial microbial life formation conditions in the interstellar medium and the other planets are investigated and the survival of microorganisms in the space environments are questioned. As a result, considering the aspects of terrestrial microbial life, we suggest that the space environment and other planets could not be a habitat for Earthial microorganisms.

  11. Microbial fossil record of rocks from the Ross Desert, Antarctica: implications in the search for past life on Mars

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    Wierzchos, Jacek; Ascaso, Carmen

    2002-01-01

    Cryptoendolithic microbial communities living within Antarctic rocks are an example of survival in an extremely cold and dry environment. The extinction of these micro-organisms formerly colonizing sandstone in the Mount Fleming area (Ross Desert), was probably provoked by the hostile environment. This is considered to be a good terrestrial analogue of the first stage of the disappearance of possible life on early Mars. To date, only macroscopically observed indirect biomarkers of the past activity of cryptoendoliths in Antarctic rocks have been described. The present paper confirms, for the first time, the existence of cryptoendolith microbial fossils within these sandstone rocks. The novel in situ application of scanning electron microscopy with backscattered electron imaging and simultaneous use of X-ray energy dispersive spectroscopy allowed the clear detection of microfossils left behind by Antarctic endoliths. Careful interpretation of the morphological features of cells, such as preserved cell walls in algae, fungi and bacteria, cytoplasm elements such as chloroplast membranes in algae and organic matter traces, mineral associations, and the spatial context of these structures all point to their identification as cryptoendolith microfossils. This type of investigation will prompt the development of research strategies aimed at locating and identifying the signs that Martian microbiota, probably only bacteria if they existed, may have been left for us to see.

  12. Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin - A New Type of Cryptoendolithic Fungi.

    OpenAIRE

    Magnus Ivarsson; Jörn Peckmann; Anders Tehler; Curt Broman; Wolfgang Bach; Katharina Behrens; Joachim Reitner; Böttcher, Michael E.; Lena Norbäck Ivarsson

    2015-01-01

    Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stage...

  13. Microbial survival in deep space environment.

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    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.

  14. Extreme environments and exobiology.

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    Friedmann, E I

    1993-01-01

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

  15. Probabilistic adaptation in changing microbial environments

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    Yarden Katz

    2016-12-01

    Full Text Available Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host’s behavior, diet, health and microbiota composition. Microbial cells that can anticipate environmental fluctuations by exploiting this structure would likely gain a fitness advantage (by adapting their internal state in advance. We propose that the problem of adaptive growth in structured changing environments, such as the gut, can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.

  16. Microbial consortia in meat processing environments

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    Alessandria, V.; Rantsiou, K.; Cavallero, M. C.; Riva, S.; Cocolin, L.

    2017-09-01

    Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The description of the microbial consortia in the meat processing environment is important since it is a first step in understanding possible routes of product contamination. Furthermore, it may contribute in the development of sanitation programs for effective pathogen removal. The purpose of this study was to characterize the type of microbiota in the environment of meat processing plants: the microbiota of three different meat plants was studied by both traditional and molecular methods (PCR-DGGE) in two different periods. Different levels of contamination emerged between the three plants as well as between the two sampling periods. Conventional methods of killing free-living bacteria through antimicrobial agents and disinfection are often ineffective against bacteria within a biofilm. The use of gas-discharge plasmas potentially can offer a good alternative to conventional sterilization methods. The purpose of this study was to measure the effectiveness of Atmospheric Pressure Plasma (APP) surface treatments against bacteria in biofilms. Biofilms produced by three different L. monocytogenes strains on stainless steel surface were subjected to three different conditions (power, exposure time) of APP. Our results showed how most of the culturable cells are inactivated after the Plasma exposure but the RNA analysis by qPCR highlighted the entrance of the cells in the viable-but non culturable (VBNC) state, confirming the hypothesis that cells are damaged after plasma treatment, but in a first step, still remain alive. The understanding of the effects of APP on the L. monocytogenes biofilm can improve the development of sanitation programs with the use of APP for effective pathogen removal.

  17. Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments.

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    Crits-Christoph, Alexander; Robinson, Courtney K; Ma, Bing; Ravel, Jacques; Wierzchos, Jacek; Ascaso, Carmen; Artieda, Octavio; Souza-Egipsy, Virginia; Casero, M Cristina; DiRuggiero, Jocelyne

    2016-01-01

    Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates

  18. Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in hyper-arid environments

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    Alexander eCrits-Christoph

    2016-03-01

    Full Text Available Under extreme water deficit, endolithic (inside rock microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP and polyketides (PK. Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both

  19. Deep UV Native Fluorescence Imaging of Antarctic Cryptoendolithic Communities

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    Storrie-Lombardi, M. C.; Douglas, S.; Sun, H.; McDonald, G. D.; Bhartia, R.; Nealson, K. H.; Hug, W. F.

    2001-01-01

    An interdisciplinary team at the Jet Propulsion Laboratory Center for Life Detection has embarked on a project to provide in situ chemical and morphological characterization of Antarctic cryptoendolithic microbial communities. We present here in situ deep ultraviolet (UV) native fluorescence and environmental scanning electron microscopy images transiting 8.5 mm into a sandstone sample from the Antarctic Dry Valleys. The deep ultraviolet imaging system employs 224.3, 248.6, and 325 nm lasers to elicit differential fluorescence and resonance Raman responses from biomolecules and minerals. The 224.3 and 248.6 nm lasers elicit a fluorescence response from the aromatic amino and nucleic acids. Excitation at 325 nm may elicit activity from a variety of biomolecules, but is more likely to elicit mineral fluorescence. The resultant fluorescence images provide in situ chemical and morphological maps of microorganisms and the associated organic matrix. Visible broadband reflectance images provide orientation against the mineral background. Environmental scanning electron micrographs provided detailed morphological information. The technique has made possible the construction of detailed fluorescent maps extending from the surface of an Antarctic sandstone sample to a depth of 8.5 mm. The images detect no evidence of microbial life in the superficial 0.2 mm crustal layer. The black lichen component between 0.3 and 0.5 mm deep absorbs all wavelengths of both laser and broadband illumination. Filamentous deep ultraviolet native fluorescent activity dominates in the white layer between 0.6 mm and 5.0 mm from the surface. These filamentous forms are fungi that continue into the red (iron-rich) region of the sample extending from 5.0 to 8.5 mm. Using differential image subtraction techniques it is possible to identify fungal nuclei. The ultraviolet response is markedly attenuated in this region, apparently from the absorption of ultraviolet light by iron-rich particles coating

  20. Microbially induced corrosion of carbon steel in deep groundwater environment

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    Pauliina eRajala

    2015-07-01

    Full Text Available The metallic low and intermediate level radioactive waste generally consists of carbon steel and stainless steels. The corrosion rate of carbon steel in deep groundwater is typically low, unless the water is very acidic or microbial activity in the environment is high. Therefore, the assessment of microbially induced corrosion of carbon steel in deep bedrock environment has become important for evaluating the safety of disposal of radioactive waste. Here we studied the corrosion inducing ability of indigenous microbial community from a deep bedrock aquifer. Carbon steel coupons were exposed to anoxic groundwater from repository site 100 m depth (Olkiluoto, Finland for periods of three and eight months. The experiments were conducted at both in situ temperature and room temperature to investigate the response of microbial population to elevated temperature. Our results demonstrate that microorganisms from the deep bedrock aquifer benefit from carbon steel introduced to the nutrient poor anoxic deep groundwater environment. In the groundwater incubated with carbon steel the planktonic microbial community was more diverse and 100-fold more abundant compared to the environment without carbon steel. The betaproteobacteria were the most dominant bacterial class in all samples where carbon steel was present, whereas in groundwater incubated without carbon steel the microbial community had clearly less diversity. Microorganisms induced pitting corrosion and were found to cluster inside the corrosion pits. Temperature had an effect on the species composition of microbial community and also affected the corrosion deposits layer formed on the surface of carbon steel.

  1. Soil microbial diversity patterns of a lowland spring environment

    NARCIS (Netherlands)

    Vasileiadis, S.; Puglisi, E.; Arena, M.; Cappa, F.; Van Veen, J.A.; Cocconcelli, P.S.; Trevisan, M.

    2013-01-01

    The Po river plain lowland springs represent unique paradigms of managed environments. Their current locations used to be swamps that were drained 6–7 centuries ago, and they have been in constant use ever since. Our aims were to identify the effects of land use on the microbial communities of these

  2. Microbial (per)chlorate reduction in hot subsurface environments

    NARCIS (Netherlands)

    Liebensteiner, M.

    2014-01-01

     

    The microbial reduction of chlorate and perchlorate has been known for long as a respiratory process of mesophilic bacteria that thrive in diverse environments such as soils, marine and freshwater sediments. Chlorate and perchlorate are found in nature deriving from anthropogenic and

  3. Microbial (per)chlorate reduction in hot subsurface environments

    NARCIS (Netherlands)

    Liebensteiner, M.

    2014-01-01

     

    The microbial reduction of chlorate and perchlorate has been known for long as a respiratory process of mesophilic bacteria that thrive in diverse environments such as soils, marine and freshwater sediments. Chlorate and perchlorate are found in nature deriving from anthropogenic and

  4. Results of microbial research of environment of international space station

    Science.gov (United States)

    Novikova, N.; Poddubko, S.; Deshevaya, E.; Polikarpov, N.; Rakova, N.

    Many years of exploitation of orbital space stations have moved forward ecological problems among which microbial society of the environment plays a most important role. Qualitative and quantitative characteristics of microorganisms in the environment of a space object can change considerably under the influence of conditions of space flight. In the process of exploitation of the International Space Station (ISS) microflora of air, interior surfaces and equipment is monitored on a regular basis to keep continuous assessment of sanitary and microbiological state of the environment. Up to the present time 32 species of microorganisms have been recovered in the ISS, namely 15species f bacteria and 17 species of moldy fungi. In the composition of microbial species mainly nonpathogenic species have been found. However, a number of bacteria discovered on the ISS, particularly some representatives of human microflora, are capable of causing different diseases when human immune system is compromised. Moreover, some bacteria and a considerable number of fungi are known to be potential biodestructors of construction materials, which leads to biodeterioration of construction materials and equipment. Results of our research show that the existing set of life-supporting systems can maintain microbial contamination within regulated levels. Furthermore, constant microbial monitoring of the environment is an integral part, which provides for the safety of space missions.

  5. A review of microbial diversity in polar terrestrial environments

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    Weidong Kong

    2013-07-01

    Full Text Available Polar regions refer to the areas at high latitudes and altitudes, that are characterized by low temperature and limited nutrients, and are very vulnerable and sensitive to global climate change. They include the Antarctic, the Arctic and the Tibetan Plateau, which is recognized as “the third pole”. The harsh polar environments are inhabited by abundant microbes that shape and maintain ecosystems by driving biogeochemical cycles. This article herein reviews microbial diversity in these polar terrestrial environments, including soils, lakes and glaciers in the Antarctic, the Arctic and the Tibetan Plateau. In the three poles, five major groups of microbes have been detected, e.g. Acidobacteria, Actinobacteria, Bacteroidetes, Cynobacteria, and Firmicutes. These microbes are salt- and cold-tolerant. Research in polar microbial ecology in China is currently lagging behind developed countries. Priorities should be given to long-term observations on theTibetan Plateau, which is easily approached. This will facilitate microbial ecology research and expand our understanding of microbial processes and their ecological roles in extreme environments.

  6. Quorum Sensing in Marine Microbial Environments

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    Hmelo, Laura R.

    2017-01-01

    Quorum sensing (QS) is a form of chemical communication used by certain bacteria that regulates a wide range of biogeochemically important bacterial behaviors. Although QS was first observed in a marine bacterium nearly four decades ago, only in the past decade has there been a rise in interest in the role that QS plays in the ocean. It has become clear that QS, regulated by signals such as acylated homoserine lactones (AHLs) or furanosyl-borate diesters [autoinducer-2 (AI-2) molecules], is involved in important processes within the marine carbon cycle, in the health of coral reef ecosystems, and in trophic interactions between a range of eukaryotes and their bacterial associates. The most well-studied QS systems in the ocean occur in surface-attached (biofilm) communities and rely on AHL signaling. AHL-QS is highly sensitive to the chemical and biological makeup of the environment and may respond to anthropogenic change, including ocean acidification and rising sea surface temperatures.

  7. A cryptoendolithic community in volcanic glass.

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    Herrera, Aude; Cockell, Charles S; Self, Stephen; Blaxter, Mark; Reitner, Joachim; Thorsteinsson, Thorsteinn; Arp, Gernot; Dröse, Wolfgang; Tindle, Andrew G

    2009-05-01

    Fluorescent in situ hybridization (FISH) and 16S rDNA analysis were used to characterize the endolithic colonization of silica-rich rhyolitic glass (obsidian) in a barren terrestrial volcanic environment in Iceland. The rocks were inhabited by a diverse eubacterial assemblage. In the interior of the rock, we identified cyanobacterial and algal 16S (plastid) sequences and visualized phototrophs by FISH, which demonstrates that molecular methods can be used to characterize phototrophs at the limits of photosynthetically active radiation (PAR). Temperatures on the surface of the dark rocks can exceed 40 degrees C but are below freezing for much of the winter. The rocks effectively shield the organisms within from ultraviolet radiation. Although PAR sufficient for photosynthesis cannot penetrate more than approximately 250 mum into the solid rock, the phototrophs inhabit cavities; and we hypothesize that by weathering the rock they may contribute to the formation of cavities in a feedback process, which allows them to acquire sufficient PAR at greater depths. These observations show how pioneer phototrophs can colonize the interior of volcanic glasses and rocks, despite the opaque nature of these materials. The data show that protected microhabitats in volcanic rocky environments would have been available for phototrophs on early Earth.

  8. Soil microbial diversity patterns of a lowland spring environment.

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    Vasileiadis, Sotirios; Puglisi, Edoardo; Arena, Maria; Cappa, Fabrizio; van Veen, Johannes A; Cocconcelli, Pier S; Trevisan, Marco

    2013-11-01

    The Po river plain lowland springs represent unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and they have been in constant use ever since. Our aims were to identify the effects of land use on the microbial communities of these soils, look for associated diversity drivers, and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high-throughput sequencing of partial 16S rrRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon and pH were major diversity drivers for Bacteria, and pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights into potential roles of taxa in the organic carbon turnover. Verrucomicrobia coincided with the higher values of the recalcitrant organic carbon. Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the soils less enzymatically active and relatively poorer in nutrients, may be explained to an extent by niche-based theories such as the resource heterogeneity hypothesis and Connell's intermediate disturbance hypothesis.

  9. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry.

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  10. Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert

    Directory of Open Access Journals (Sweden)

    Jacek eWierzchos

    2015-09-01

    Full Text Available The Atacama Desert, northern Chile, is one of the driest deserts on Earth and, as such, a natural laboratory to explore the limits of life and the strategies evolved by microorganisms to adapt to extreme environments. Here we report the exceptional adaptation strategies of chlorophototrophic and eukaryotic algae, and chlorophototrophic and prokaryotic cyanobacteria to the hyperarid and extremely high solar radiation conditions occurring in this desert. Our approach combined several microscopy techniques, spectroscopic analytical methods, and molecular analyses. We found that the major adaptation strategy was to avoid the extreme environmental conditions by colonizing cryptoendolithic, as well as, hypoendolithic habitats within gypsum deposits. The cryptoendolithic colonization occurred a few millimeters beneath the gypsum surface and showed a succession of organized horizons of algae and cyanobacteria, which has never been reported for endolithic microbial communities. The presence of cyanobacteria beneath the algal layer, in close contact with sepiolite inclusions, and their hypoendolithic colonization suggest that occasional liquid water might persist within these sub-microhabitats. We also identified the presence of abundant carotenoids in the upper cryptoendolithic algal habitat and scytonemin in the cyanobacteria hypoendolithic habitat. This study illustrates that successful lithobiontic microbial colonization at the limit for microbial life is the result of a combination of adaptive strategies to avoid excess solar irradiance and extreme evapotranspiration rates, taking advantage of the complex structural and mineralogical characteristics of gypsum deposits – conceptually called rock’s habitable architecture. Additionally self-protection by synthesis and accumulation of secondary metabolites likely produces a shielding effect that prevents photoinhibition and lethal photooxidative damage to the chlorophototrophs, representing another

  11. Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert

    Science.gov (United States)

    Wierzchos, Jacek; DiRuggiero, Jocelyne; Vítek, Petr; Artieda, Octavio; Souza-Egipsy, Virginia; Škaloud, Pavel; Tisza, Michel; Davila, Alfonso F.; Vílchez, Carlos; Garbayo, Inés; Ascaso, Carmen

    2015-01-01

    The Atacama Desert, northern Chile, is one of the driest deserts on Earth and, as such, a natural laboratory to explore the limits of life and the strategies evolved by microorganisms to adapt to extreme environments. Here we report the exceptional adaptation strategies of chlorophototrophic and eukaryotic algae, and chlorophototrophic and prokaryotic cyanobacteria to the hyperarid and extremely high solar radiation conditions occurring in this desert. Our approach combined several microscopy techniques, spectroscopic analytical methods, and molecular analyses. We found that the major adaptation strategy was to avoid the extreme environmental conditions by colonizing cryptoendolithic, as well as, hypoendolithic habitats within gypsum deposits. The cryptoendolithic colonization occurred a few millimeters beneath the gypsum surface and showed a succession of organized horizons of algae and cyanobacteria, which has never been reported for endolithic microbial communities. The presence of cyanobacteria beneath the algal layer, in close contact with sepiolite inclusions, and their hypoendolithic colonization suggest that occasional liquid water might persist within these sub-microhabitats. We also identified the presence of abundant carotenoids in the upper cryptoendolithic algal habitat and scytonemin in the cyanobacteria hypoendolithic habitat. This study illustrates that successful lithobiontic microbial colonization at the limit for microbial life is the result of a combination of adaptive strategies to avoid excess solar irradiance and extreme evapotranspiration rates, taking advantage of the complex structural and mineralogical characteristics of gypsum deposits—conceptually called “rock's habitable architecture.” Additionally, self-protection by synthesis and accumulation of secondary metabolites likely produces a shielding effect that prevents photoinhibition and lethal photooxidative damage to the chlorophototrophs, representing another level of

  12. Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert.

    Science.gov (United States)

    Wierzchos, Jacek; DiRuggiero, Jocelyne; Vítek, Petr; Artieda, Octavio; Souza-Egipsy, Virginia; Škaloud, Pavel; Tisza, Michel; Davila, Alfonso F; Vílchez, Carlos; Garbayo, Inés; Ascaso, Carmen

    2015-01-01

    The Atacama Desert, northern Chile, is one of the driest deserts on Earth and, as such, a natural laboratory to explore the limits of life and the strategies evolved by microorganisms to adapt to extreme environments. Here we report the exceptional adaptation strategies of chlorophototrophic and eukaryotic algae, and chlorophototrophic and prokaryotic cyanobacteria to the hyperarid and extremely high solar radiation conditions occurring in this desert. Our approach combined several microscopy techniques, spectroscopic analytical methods, and molecular analyses. We found that the major adaptation strategy was to avoid the extreme environmental conditions by colonizing cryptoendolithic, as well as, hypoendolithic habitats within gypsum deposits. The cryptoendolithic colonization occurred a few millimeters beneath the gypsum surface and showed a succession of organized horizons of algae and cyanobacteria, which has never been reported for endolithic microbial communities. The presence of cyanobacteria beneath the algal layer, in close contact with sepiolite inclusions, and their hypoendolithic colonization suggest that occasional liquid water might persist within these sub-microhabitats. We also identified the presence of abundant carotenoids in the upper cryptoendolithic algal habitat and scytonemin in the cyanobacteria hypoendolithic habitat. This study illustrates that successful lithobiontic microbial colonization at the limit for microbial life is the result of a combination of adaptive strategies to avoid excess solar irradiance and extreme evapotranspiration rates, taking advantage of the complex structural and mineralogical characteristics of gypsum deposits-conceptually called "rock's habitable architecture." Additionally, self-protection by synthesis and accumulation of secondary metabolites likely produces a shielding effect that prevents photoinhibition and lethal photooxidative damage to the chlorophototrophs, representing another level of adaptation.

  13. Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment

    OpenAIRE

    Montoya, Lilia; Vizioli, Carlotta; Rodríguez, Nuria; Rastoll, María José; Amils, Ricardo; Marín, Irma

    2013-01-01

    Background: The aim was to study the seasonal microbial diversity variations of an athalassohaline environment with a high concentration of sulfates in Tirez lagoon (La Mancha, Spain). Despite the interest in these types of environments there is scarce information about their microbial ecology, especially on their anoxic sediments. Results: We report the seasonal microbial diversity of the water column and the sediments of a highly sulfated lagoon using both molecular and conventional microbi...

  14. Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin – A New Type of Cryptoendolithic Fungi

    Science.gov (United States)

    Ivarsson, Magnus; Peckmann, Jörn; Tehler, Anders; Broman, Curt; Bach, Wolfgang; Behrens, Katharina; Reitner, Joachim; Böttcher, Michael E.; Norbäck Ivarsson, Lena

    2015-01-01

    Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II) oxidation to form Mn(III,VI) oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies. PMID:26181773

  15. Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin--A New Type of Cryptoendolithic Fungi.

    Science.gov (United States)

    Ivarsson, Magnus; Peckmann, Jörn; Tehler, Anders; Broman, Curt; Bach, Wolfgang; Behrens, Katharina; Reitner, Joachim; Böttcher, Michael E; Norbäck Ivarsson, Lena

    2015-01-01

    Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II) oxidation to form Mn(III,VI) oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies.

  16. Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin--A New Type of Cryptoendolithic Fungi.

    Directory of Open Access Journals (Sweden)

    Magnus Ivarsson

    Full Text Available Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II oxidation to form Mn(III,VI oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies.

  17. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  18. Microbial Bioremediation of Fuel Oil Hydrocarbons in Marine Environment

    Directory of Open Access Journals (Sweden)

    Sapna Pavitran

    2006-04-01

    Full Text Available Pollution in marine environment due to heavier petroleum products such as high-speeddiesel is known to take from days to months for complete natural remediation owing to its lowvolatility. For the survival of marine flora and fauna, it is important to control pollution causedby such recalcitrant and xenobiotic substances. Several petroleum hydrocarbons found in natureare toxic and recalcitrant. Therefore, pollution due to high-speed diesel is a cause of concern.The natural dispersion of high-speed diesel, a slow process, is attributed to an overall combinedeffect of physico-chemical and biological processes which take months for complete dispersion.History of marine oil spill bioremediation indicates limited laboratory studies. But experiencesfrom various oil spill management and field trials indicate important role of bioremediation, where,biodegradation of hydrocarbons through microbial mediators plays a major role in pollutant oildispersion. These microbial mediators such as bioemulsifiers and fimbrae, help in emulsification,dispersion, allowing attachment of bacteria to oil layers, followed by substrate-specific enzymaticbiodegradation in water.

  19. Microbial Oxidation of Iron Sulfides in Anaerobic Environments

    DEFF Research Database (Denmark)

    Vaclavkova, Sarka

    . Under anaerobic conditions FeSx serves as an electron donor in nitrate (NO3-) reduction processes. In this PhD thesis, unknown controls of microbial FeSx oxidation by NO3- (MISON), as a potentially important NO3- reducing process, were investigated. The importance of understanding the NO3- removal...... environments including sandy aquifer, freshwater peatland and moderately brackish muddy marine sediment. An apparent salinity limitation of MISON was shown in heavily brackish sediment, where FeSx oxidation was inhibited while other NO3-reduction processes did not appear to be affected by the salinity levels......Abstract (shortened): Iron sulfides (FeSx), representing 0.04-10 % of Danish dry soil weight, oxidize in a presence of oxygen, releasing sulfuric acid and free iron. Environmental impact of FeSx oxidation is commonly seen on agricultural sites cultivated by drainage as acid sulfate soil formation...

  20. Amino Acids as a Source of Organic Nitrogen in Antarctic Endolithic Microbial Communities

    Science.gov (United States)

    McDonald, G. D.; Sun, H. J.

    2002-12-01

    In the Antarctic Dry Valleys, cryptoendolithic microbial communities occur within porous sandstone rocks. Current understanding of the mechanisms of physiological adaptation of these communities to the harsh Antarctic environment is limited, because traditional methods of studying microbial physiology are very difficult to apply to organisms with extremely low levels of metabolic activity. In order to fully understand carbon and nitrogen cycling and nutrient uptake in cryptoendolithic communities, and the metabolic costs that the organisms incur in order to survive, it is necessary to employ molecular geochemical techniques such as amino acid analysis in addition to physiological methods. Low-molecular-weight biomolecules such as amino acids can be used as tracers of carbon and nitrogen uptake and loss by microbial communities living in solid-state matrices such as rock or sediment. We have measured the concentrations and D/L ratios for several amino acids as a function of depth in a large sandstone boulder. Concentrations of both free and bound amino acids decrease by more than two orders of magnitude from the surface to the visible base of the community (approximately 1.2 cm depth), while the D/L ratios of the amino acids increase from near zero to 0.2 or greater over the same depth interval. We interpret these data as an indication that one or more community members are selectively scavenging L-amino acids as the amino acids are transported through the rock by intermittently percolating meltwater. This is consistent with the known preference of lichens for amino acids as nitrogen sources rather than inorganic nitrogen under conditions of nutrient limitation. It is not yet clear whether there is also a contribution to amino acid uptake from heterotropic bacteria associated with the cryptoendolithic community. The increase in D/L ratios with depth observed in the rock is too great to be attributable solely to the natural occurrence of D-amino acids in bacteria

  1. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity.

    Science.gov (United States)

    Mulder, Imke E; Schmidt, Bettina; Lewis, Marie; Delday, Margaret; Stokes, Christopher R; Bailey, Mick; Aminov, Rustam I; Gill, Bhupinder P; Pluske, John R; Mayer, Claus-Dieter; Kelly, Denise

    2011-01-01

    Acquisition of the intestinal microbiota in early life corresponds with the development of the mucosal immune system. Recent work on caesarean-delivered infants revealed that early microbial composition is influenced by birthing method and environment. Furthermore, we have confirmed that early-life environment strongly influences both the adult gut microbiota and development of the gut immune system. Here, we address the impact of limiting microbial exposure after initial colonization on the development of adult gut immunity. Piglets were born in indoor or outdoor rearing units, allowing natural colonization in the immediate period after birth, prior to transfer to high-health status isolators. Strikingly, gut closure and morphological development were strongly affected by isolator-rearing, independent of indoor or outdoor origins of piglets. Isolator-reared animals showed extensive vacuolation and disorganization of the gut epithelium, inferring that normal gut closure requires maturation factors present in maternal milk. Although morphological maturation and gut closure were delayed in isolator-reared animals, these hard-wired events occurred later in development. Type I IFN, IL-22, IL-23 and Th17 pathways were increased in indoor-isolator compared to outdoor-isolator animals during early life, indicating greater immune activation in pigs originating from indoor environments reflecting differences in the early microbiota. This difference was less apparent later in development due to enhanced immune activation and convergence of the microbiota in all isolator-reared animals. This correlated with elevation of Type I IFN pathways in both groups, although T cell pathways were still more affected in indoor-reared animals. Environmental factors, in particular microbial exposure, influence expression of a large number of immune-related genes. However, the homeostatic effects of microbial colonization in outdoor environments require sustained microbial exposure

  2. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity.

    Directory of Open Access Journals (Sweden)

    Imke E Mulder

    Full Text Available BACKGROUND: Acquisition of the intestinal microbiota in early life corresponds with the development of the mucosal immune system. Recent work on caesarean-delivered infants revealed that early microbial composition is influenced by birthing method and environment. Furthermore, we have confirmed that early-life environment strongly influences both the adult gut microbiota and development of the gut immune system. Here, we address the impact of limiting microbial exposure after initial colonization on the development of adult gut immunity. METHODOLOGY/PRINCIPAL FINDINGS: Piglets were born in indoor or outdoor rearing units, allowing natural colonization in the immediate period after birth, prior to transfer to high-health status isolators. Strikingly, gut closure and morphological development were strongly affected by isolator-rearing, independent of indoor or outdoor origins of piglets. Isolator-reared animals showed extensive vacuolation and disorganization of the gut epithelium, inferring that normal gut closure requires maturation factors present in maternal milk. Although morphological maturation and gut closure were delayed in isolator-reared animals, these hard-wired events occurred later in development. Type I IFN, IL-22, IL-23 and Th17 pathways were increased in indoor-isolator compared to outdoor-isolator animals during early life, indicating greater immune activation in pigs originating from indoor environments reflecting differences in the early microbiota. This difference was less apparent later in development due to enhanced immune activation and convergence of the microbiota in all isolator-reared animals. This correlated with elevation of Type I IFN pathways in both groups, although T cell pathways were still more affected in indoor-reared animals. CONCLUSIONS/SIGNIFICANCE: Environmental factors, in particular microbial exposure, influence expression of a large number of immune-related genes. However, the homeostatic effects of

  3. A Miniaturized Sensor for Microbial Monitoring of Spacecraft Water Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Accurate real-time microbial monitoring of water environment is of paramount importance to crew health as well as to ensure proper functioning and control of the...

  4. A Miniaturized Sensor for Microbial Monitoring of Spacecraft Water Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Accurate real-time microbial monitoring of water environment is of paramount importance to crew health as well as to ensure proper functioning and control of the...

  5. Resistance of Antarctic black fungi and cryptoendolithic communities to simulated space and Martian conditions

    OpenAIRE

    S. Onofri; Barreca, D.; Selbmann, L.; D. Isola; E. Rabbow; Horneck, G.; de Vera, J.P.P.; J. Hatton; L. Zucconi

    2008-01-01

    Dried colonies of the Antarctic rock-inhabiting meristematic fungi Cryomyces antarcticus CCFEE 515, CCFEE 534 and C. minteri CCFEE 5187, as well as fragments of rocks colonized by the Antarctic cryptoendolithic community, were exposed to a set of ground-based experiment verification tests (EVTs) at the German Aerospace Center (DLR, Köln, Germany). These were carried out to test the tolerance of these organisms in view of their possible exposure to space conditions outside of the International...

  6. Microbial formation of labile organic carbon in Antarctic glacial environments

    Science.gov (United States)

    Smith, H. J.; Foster, R. A.; McKnight, D. M.; Lisle, J. T.; Littmann, S.; Kuypers, M. M. M.; Foreman, C. M.

    2017-04-01

    Roughly six petagrams of organic carbon are stored within ice worldwide. This organic carbon is thought to be of old age and highly bioavailable. Along with storage of ancient and new atmospherically deposited organic carbon, microorganisms may contribute substantially to the glacial organic carbon pool. Models of glacial microbial carbon cycling vary from net respiration to net carbon fixation. Supraglacial streams have not been considered in models although they are amongst the largest ecosystems on most glaciers and are inhabited by diverse microbial communities. Here we investigate the biogeochemical sequence of organic carbon production and uptake in an Antarctic supraglacial stream in the McMurdo Dry Valleys using nanometre-scale secondary ion mass spectrometry, fluorescence spectroscopy, stable isotope analysis and incubation experiments. We find that heterotrophic production relies on highly labile organic carbon freshly derived from photosynthetic bacteria rather than legacy organic carbon. Exudates from primary production were utilized by heterotrophs within 24 h, and supported bacterial growth demands. The tight coupling of microbially released organic carbon and rapid uptake by heterotrophs suggests a dynamic local carbon cycle. Moreover, as temperatures increase there is the potential for positive feedback between glacial melt and microbial transformations of organic carbon.

  7. Novel long-chain anteiso-alkanes and anteiso-alkanoic acids in Antarctic rocks colonized by living and fossil cryptoendolithic microorganisms

    Science.gov (United States)

    Matsumoto, G. I.; Friedmann, E. I.; Watanuki, K.; Ocampo-Friedmann, R.

    1992-01-01

    Saponified extracts of rock samples colonized by cryptoendolithic microbial communities from the McMurdo Dry Valleys of Southern Victoria Land, Antarctica, were separated into hydrocarbon and fatty acid fractions by silica gel column chromatography. Hydrocarbons and methyl esters of fatty acids were analyzed by capillary gas chromatography-mass spectrometry. Unusually, a suite of long-chain anteiso-alkanes (a-C20 to a-C30) and anteiso-alkanoic acids (a-C20 to a-C30) were detected in many samples, together with straight-chain, branched and/or cyclic and acyclic isoprenoid compounds. These novel compounds are probably derived from unidentified heterotrophic bacteria or symbiotic processes in a unique microbial community in the Antarctic cold desert and suggest the occurrence of a special biosynthetic pathway. Long-chain anteiso-alkanes are probably formed through microbial decarboxylation of corresponding anteiso-alkanoic acids. They may serve as new biomarkers in environmental and geochemical studies.

  8. New Abundant Microbial Groups in Aquatic Hypersaline Environments

    OpenAIRE

    Ghai, Rohit; Pašić, Lejla; Fernández González, Ana Beatriz; Martín Cuadrado, Ana Belén; Megumi Mizuno, Carolina; McMahon, Katherine D.; Papke, R Thane; Stepanauskas, Ramunas; Rodríguez Brito, Beltrán; Rohwer, Forest; Sánchez-Porro Álvarez, Cristina; Ventosa Ucero, Antonio; Rodríguez Valera, Francisco

    2011-01-01

    We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. M...

  9. Electrical potential source mechanisms in microbial induced sulfate reducing environments

    Science.gov (United States)

    Zhang, C.; Slater, L.; Ntarlagiannis, D.; Singh, K.; Doherty, R.

    2007-12-01

    In order to compare self-potential (SP) signals resulting from possible 'geobattery' effects with electrodic potential signals based on a known galvanic cell (GC) effect in the presence of sulfide, we designed a column experiment using dual sensor Ag-AgCl electrodes. Water from the Langan River (Belfast, UK), known to contain a sulfate reducing microbial community, was obtained. Two experimental columns were packed with fine-grained glass beads. One column continuously circulated (closed loop) with autoclaved river water as a control, while the other retained biologically active natural river water. Six Ag-AgCl electrodes equally spaced along one side of each column, and three Ag-AgCl self potential electrodes (where the metal is in electrolytic contact with the column via a sterilized 1M KCl agar gel), were placed on the other side of each column. Electrical potential signals were continuously recorded with both sensor types. Induced polarization, electrical resistivity, temperature and aqueous geochemistry measurements (pH, Eh, and conductivity) were taken once daily. Over the 20 day experiment duration, darkening of the circulating fluid, biofilm formation and a sulfurous smell were observed in the biologically active column whereas no such color change (or smell) was observed for the control column. In the active column electrodic potential readings approached 570 mV whereas stable and small electrodic potential values (~8 mV) were detected in the control column.. Self potential signals were consistently only 1-8 mV in both columns. The experiment shows although electrodic potentials (at the electrode) are diagnostic of microbial driven sulfate reduction there is no measurable self potential (geobattery) effect associated with this microbial process.

  10. The genomics of microbial domestication in the fermented food environment.

    Science.gov (United States)

    Gibbons, John G; Rinker, David C

    2015-12-01

    Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.

  11. Quantitative phylogenetic assessment of microbial communities indiverse environments

    Energy Technology Data Exchange (ETDEWEB)

    von Mering, C.; Hugenholtz, P.; Raes, J.; Tringe, S.G.; Doerks,T.; Jensen, L.J.; Ward, N.; Bork, P.

    2007-01-01

    The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.

  12. Biologically active substances produced by antarctic cryptoendolithic fungi.

    Science.gov (United States)

    Ocampo-Friedmann, R; Friedmann, E I

    1993-01-01

    Researchers report results of laboratory studies of over 200 microbial strains of fungi, algae, cyanobacteria, and heterotrophic bacteria collected in the Ross Desert region of Antarctica. All of the 35 fungal strains produced substances that inhibited the growth of cyanobacteria and algae. The inhibitory effect of the biologically active substance was evident in crushed cell extract but less in spent broth.

  13. Coupling of fog and marine microbial content in the near-shore coastal environment

    Directory of Open Access Journals (Sweden)

    M. E. Dueker

    2012-02-01

    Full Text Available Microbes in the atmosphere (microbial aerosols play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (<2 m s−1 the near-shore deposition of microbial aerosols (microbial fallout decreased with increasing wind speeds, whereas microbial fallout rates under clear conditions and comparable low wind speeds showed no wind speed dependence. Mean aerosol particle size also increased with onshore wind speed when fog was present, indicating increased shoreward transport of larger aerosol particles. 16S rRNA sequencing of culturable ocean surface bacteria and microbial aerosols deposited onshore resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium making up 66 % of all sequences. The sequence library from microbial aerosol isolates, as with libraries found in other coastal/marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the culturable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97 % similarity cut-off, sequence libraries from ocean surface and fog isolates shared eight operational taxonomic units (OTU's in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28

  14. Coupling of fog and marine microbial content in the near-shore coastal environment

    Directory of Open Access Journals (Sweden)

    M. E. Dueker

    2011-09-01

    Full Text Available Microbes in the atmosphere (microbial aerosols play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (< 2 m s−1 the near-shore deposition of microbial aerosols (microbial fallout decreased with increasing wind speeds, whereas microbial fallout rates under clear conditions and comparable low wind speeds showed no wind speed dependence. Mean aerosol particle size also increased with onshore wind speed when fog was present, indicating increased shoreward transport of larger aerosol particles. 16S rRNA sequencing of culturable ocean surface bacteria and microbial aerosols deposited onshore resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium making up 66% of all sequences. The microbial aerosol sequence library, as with libraries found in other coastal/marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the viable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97% similarity cut-off, ocean surface and fog sequence libraries shared eight operational taxonomic units (OTU's in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28% and fog (21% libraries. The fog and

  15. Microbial dehalogenation of organohalides in marine and estuarine environments.

    Science.gov (United States)

    Zanaroli, Giulio; Negroni, Andrea; Häggblom, Max M; Fava, Fabio

    2015-06-01

    Marine sediments are the ultimate sink and a major entry way into the food chain for many highly halogenated and strongly hydrophobic organic pollutants, such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), polybrominated diphenylethers (PBDEs) and 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT). Microbial reductive dehalogenation in anaerobic sediments can transform these contaminants into less toxic and more easily biodegradable products. Although little is still known about the diversity of respiratory dehalogenating bacteria and their catabolic genes in marine habitats, the occurrence of dehalogenation under actual site conditions has been reported. This suggests that the activity of dehalogenating microbes may contribute, if properly stimulated, to the in situ bioremediation of marine and estuarine contaminated sediments.

  16. Microbial Fossils from Terrestrial Subsurface Hydrothermal Environments: Examples and Implications for Mars

    Science.gov (United States)

    Hofmann, Beda A.; Farmer, Jack; Chang, Sherwood (Technical Monitor)

    1997-01-01

    The recognition of biological signatures in ancient epithermal deposits has special relevance for studies of early blaspheme evolution and in exploring for past life on Mars. Recently, proposals for the existence of an extensive subsurface blaspheme on Earth, dominated by chemoautotrophic microbial life, has gained prominence. However, reports of fossilized microbial remains, or biosedimentary structures (e.g. stromatolites) from the deposits of ancient subsurface systems, are rare. Microbial preservation is favoured where high population densities co-exist with rapid mineral precipitation. Near-surface epithetical systems with strong gradients in temperature and redox are good candidates for the abundant growth and fossilization of microorganisms, and are also favorable environments for the precipitation of ore minerals. Therefore, we might expect microbial remain, to be particularly well preserved in various kinds of hydrothermal and diagenetic mineral precipitates that formed below the upper temperature limit for life (approx. 120 C).

  17. Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

    Directory of Open Access Journals (Sweden)

    Nishat Tasnim

    2017-10-01

    Full Text Available Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies. Since the immune system development is influenced by microbial components, early microbial colonization may be a key factor in determining disease susceptibility patterns later in life. Evidence indicates that the gut microbiota is vertically transmitted from the mother and this affects offspring immunity. However, the role of the external environment in gut microbiome and immune development is poorly understood. Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. These health-effects may be ablated due to changes in the human lifestyle, diet, living environment and environmental biodiversity as a result of urbanization. Importantly, if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be a public health threat. Here, we summarize key questions in environmental health research and discuss some of the challenges that have hindered progress toward a better understanding of the role of the environment on gut microbiome development.

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

    Science.gov (United States)

    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.

  19. Coupling of fog and marine microbial content in the near-shore coastal environment

    Science.gov (United States)

    Dueker, M. E.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

    2012-02-01

    Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA) and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the culturable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97 % similarity cut-off, sequence libraries from ocean surface and fog isolates shared eight operational taxonomic units (OTU's) in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28 %) and fog (21 %) libraries. The fog and ocean surface libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries, according to both Jaccard and Sorenson indices. These findings provide the first evidence of a difference in community composition and microbial culturability of aerosols associated with fog compared to clear conditions. The data support a dual role for fog in enhancing the fallout of viable microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms, which may include relief from UV inactivation, desiccation, and oligotrophic microconditions. This study provides a strong case for ocean to terrestrial transport of microbes and a potential connection

  20. Preliminary report on radiocarbon dating of cryptoendolithic microorganisms

    Science.gov (United States)

    Bonani, G.; Friedmann, E. I.; Ocampo-Friedmann, R.; McKay, C. P.; Woelfli, W.

    1988-01-01

    The existence of microbial communities living inside desert rocks has been reported by FRIEDMANN et al. (1967, 1976), first in rocks collected from the hot and dry Negev desert and later in rocks in the frigid Ross Desert of Southern Victoria Land, Antarctica. The extremely inhospitable climatic conditions in both places has led to the suggestion that these organisms have very low rates of metabolism and may, in addition, be very old (FRIEDMANN 1982). Our preliminary measurements showed a 14C deficiency indicating a carbon age in the order of magnitude of 10(3) years.

  1. Connectivity of microbial populations in coral reef environments: microbiomes of sediment, fish and water

    Science.gov (United States)

    Biddle, J.; Leon, Z. R.; McCargar, M.; Drew, J.

    2016-12-01

    The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared between the ecosystem of sediments, seagrasses and reef fish, however it is unknown to what degree. We investigated the potential connections between the microbiomes of sediments, seagrass blades and roots (Syringodium isoetifolium), Surgeonfish (A. nigricauda, Acanthurinae sp. unknown, C. striatus) and Parrotfish (C. spinidens) guts in reef areas of Fiji. We contrasted these with sediment samples from the Florida Keys and ocean water microbiomes from the Atlantic, Pacific and Indian Oceans. In general, we see a higher diversity of sediment microbial communities in Fiji compared to the Florida Keys. However, many of the same taxa are shared in these chemically similar environments, whereas the ocean water environments are completely distinct with few overlapping groups. We were able to show connectivity of a core microbiome between seagrass, fish and sediments in Fiji, including identifying a potential environmental reservoir of a surgeonfish symbiont, Epulopiscum. Finally, we show that fish guts have different microbial populations from crop to hindgut, and that microbial populations differ based on food source. The connection of these ecosystems suggest that the total microbiome of these environments may vary as their animal inhabitants shift in a changing ocean.

  2. Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

    Science.gov (United States)

    Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

    2016-12-01

    There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.

  3. Carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review

    Directory of Open Access Journals (Sweden)

    Tingting eZhu

    2016-01-01

    Full Text Available Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation (MCP, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnology such as metal remediation, carbon sequestration, enhanced oil recovery and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.

  4. Emergence of microbial networks as response to hostile environments

    Directory of Open Access Journals (Sweden)

    Dario eMadeo

    2014-08-01

    Full Text Available The majority of microorganisms live in complex communities under varying conditions. One pivotal question in evolutionary biology is the emergence of cooperative traits and their sustainment in altered environments or in the presence of free-riders. Co-occurrence patterns in the spatial distribution of biofilms can help define species' identities, and systems biology tools are revealing networks of interacting microorganisms. However, networks of inter-dependencies involving micro-organisms in the planktonic phase may be just as important, with the added complexity that they are not bounded in space. An integrated approach linking imaging, ``Omics'' and modeling has the potential to enable new hypothesis and working models. In order to understand how cooperation can emerge and be maintained without abilities like memory or recognition we use evolutionary game theory as the natural framework to model cell-cell interactions arising from evolutive decisions. We consider a finite population distributed in a spatial domain (biofilm, and divided into two interacting classes with different traits. This interaction can be weighted by distance, and produces physical connections between two elements allowing them to exchange finite amounts of energy and matter. Available strategies to each individual of one class in the population are the propensities or ``willingness'' to connect any individual of the other class. Following evolutionary game theory, we propose a mathematical model which explains the patterns of connections which emerge when individuals are able to find connection strategies that asymptotically optimize their fitness. The process explains the formation of a network for efficiently exchanging energy and matter among individuals and thus ensuring their survival in hostile environments.

  5. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

    Science.gov (United States)

    Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

    2013-01-01

    Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

  6. The evaluation of microbial contamination in the working environment of tanneries

    Directory of Open Access Journals (Sweden)

    Justyna Skóra

    2014-02-01

    Full Text Available Background: Due to their animal material processing, tannery workers may be exposed to biological agents. The aim of the study was the microbial contamination assessment of tanneries with different production specifications. Health risk was estimated based on particle size distribution. Moreover, indicators of microbial contamination of tanneries were selected. Materials and Methods: The studies were conducted in 2 types of tanneries - processing raw hides and producing chrome-tanned leather. Air was sampled with MAS-100 Eco Air Sampler, leathers using RODAC Envirocheck® contact plates and swab method, microbial numbers were determined by a culture method. For the bioaerosols size distribution analysis, a six-stage Andersen sampler was used; identification was performed using microscopy and biochemical methods. Microbial contamination was identified by 16S RNA and ITS1/2 rDNA analysis for bacteria and fungi respectively. Results: The microbial number in the air ranged between 1.2×103 and 3.7×103 CFU/m3. While on the leather, it ranged between 7.6×101 and 5.5×105 CFU/100 cm2. Bacteria dominated in the tanneries (air: 51-92%, leathers: 60-100%. Results indicate that potential health risks arise from the fungal small bioaerosol particles presence (0.65-2.1 μm. Eleven indicator microorganisms were determined: B. pumilus, B. subtilis, B. cereus, C. lubricantis, C. cladosporioides, P. commune, P. echinulatum, P. chrysogenum, P. crustosum, C. parapsilosis and C. albidus. Conclusions: Microbial contamination evaluation in the tanneries showed the increased bacteria and fungi number in the air in relation to the outdoor air, which indicates an occupational inhalation risk to workers. The designated indicators of microbial contamination in the tanneries are associated with their specific and potentially pathogenic working environment. Med Pr 2014;65(1:15–32

  7. Evolution of soil microbial biomass in restoration process of Robinia pseudoacacia plantations in an eroded environment

    Institute of Scientific and Technical Information of China (English)

    Sha XUE; Guobin LIU; Quanhou DAI; Chao ZHANG; Na YU

    2008-01-01

    Vegetation recovery is a key measure to improve ecosystems in the Loess Plateau in China. To understand the evolution of soil microorganisms in forest plantations in the hilly areas of the Loess Plateau, the soil microbial biomass, microbial respiration and physical and chemical properties of the soil of Robinia pseudoacacia plantations were studied. In this study, eight forest soils of different age classes were used to study the evolution of soil microbial biomass, while a farmland and a native forest community of Platycladus orientalis L. were chosen as controls. By measuring soil microbial biomass, meta-bolic quotient, and physical and chemical properties, it can be concluded that soil quality was improved steadily after planting. Soil microbial biomass of C, N and P (SMBC, SMBN and SMBP) increased significantly after 10 to 15 years of afforestation and vegetation recovery. A relatively stable state of soil microbial biomass was main-tained in near-mature or mature plantations. There was an increase of soil microbial biomass appearing at the end of the mature stage. After 50 years of afforestation and vegetation recovery, compared with those in farmland, the soil microbial biomass of C, N and P increased by 213%, 201% and 83% respectively, but only accounting for 51%, 55% and 61% of the increase in P. orientalis forest. Microbial soil respiration was enhanced in the early stages, and then weakened in the later stage after restoration, which was different from the change of soil organic carbon. The metabolic quotient (qCO2) was sig-nificantly higher in the soils of the P. orientalis forest than that in farmland at the early restoration stage and then decreased rapidly. After 25 years of afforestation and vegetation recovery, qCO2 in soils of the R. pseudoacacia forest was lower than that in the farmland soil, and reached a minimum after 50 years, which was close to that of the P. orientalis forest. A significant relationship was found among soil microbial

  8. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

    Science.gov (United States)

    Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys; Mele, Pauline M; Reith, Frank; Dennis, Paul G; Breed, Martin F; Brown, Belinda; Brown, Mark V; Brugger, Joel; Byrne, Margaret; Caddy-Retalic, Stefan; Carmody, Bernie; Coates, David J; Correa, Carolina; Ferrari, Belinda C; Gupta, Vadakattu V S R; Hamonts, Kelly; Haslem, Asha; Hugenholtz, Philip; Karan, Mirko; Koval, Jason; Lowe, Andrew J; Macdonald, Stuart; McGrath, Leanne; Martin, David; Morgan, Matt; North, Kristin I; Paungfoo-Lonhienne, Chanyarat; Pendall, Elise; Phillips, Lori; Pirzl, Rebecca; Powell, Jeff R; Ragan, Mark A; Schmidt, Susanne; Seymour, Nicole; Snape, Ian; Stephen, John R; Stevens, Matthew; Tinning, Matt; Williams, Kristen; Yeoh, Yun Kit; Zammit, Carla M; Young, Andrew

    2016-01-01

    Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

  9. Microbial biosynthesis of wax esters during desiccation: an adaptation for colonization of the earliest terrestrial environments?

    Science.gov (United States)

    Finkelstein, D. B.; Brassell, S. C.; Pratt, L. M.

    2008-12-01

    Biosynthesis of wax esters (WE) by prokaryotes in natural systems, notably bacteria from hot springs and marine phytoplankton, is poorly documented, primarily because saponification is a routine step in the analysis of microbial mat lipids. Use of this preparative procedure, critical for characterization of the diagnostic distributions of carboxylic acids in phospholipids, precludes recovery of intact WE. Examination of non-saponified lipids in emergent and desiccated mats with comparable microbial communities from the Warner Lake region, Oregon, reveals increases in the relative abundance (18.6 to 59.9μg/g Corg) and average chain length (C38 to C46) of WE in the latter, combined with assimilation of phytol and tocopherol moieties. Prokaryotes can accumulate WE as storage lipids in vitro, notably at elevated temperature or under nitrogen limiting conditions, but we propose that biosynthesis of long-chain WE that have a low solubility and are resistant to degradation/oxidation may represent an evolutionary strategy to survive desiccation in evaporative environments. Moreover, aeolian transport of desiccated mat-rip-ups between lake flats allows for migration of microbial communities within and between lake flats and basins during arid conditions. Subsequent rehydration within an alkaline environment would naturally saponify WE, and thereby regenerate alcohol and acid moieties that could serve as membrane lipids for the next viable microbial generation. The evolutionary cradle of WE was likely abiotic generation under hydrothermal conditions, which is consistent with the antiquity of the ester linkage necessitated by its integral role in the membranes of Eubacteria (though not Archaea) and in bacteriochlorophyll. The subsequent capability of microbes to biosynthesize WE may have facilitated their survival when nutrients were limiting, and production of long-chain WE (>C40) may represent a further critical evolutionary threshold that enabled their persistence through

  10. A New Strategy for Heavy Metal Polluted Environments: A Review of Microbial Biosorbents

    Directory of Open Access Journals (Sweden)

    Ayansina Segun Ayangbenro

    2017-01-01

    Full Text Available Persistent heavy metal pollution poses a major threat to all life forms in the environment due to its toxic effects. These metals are very reactive at low concentrations and can accumulate in the food web, causing severe public health concerns. Remediation using conventional physical and chemical methods is uneconomical and generates large volumes of chemical waste. Bioremediation of hazardous metals has received considerable and growing interest over the years. The use of microbial biosorbents is eco-friendly and cost effective; hence, it is an efficient alternative for the remediation of heavy metal contaminated environments. Microbes have various mechanisms of metal sequestration that hold greater metal biosorption capacities. The goal of microbial biosorption is to remove and/or recover metals and metalloids from solutions, using living or dead biomass and their components. This review discusses the sources of toxic heavy metals and describes the groups of microorganisms with biosorbent potential for heavy metal removal.

  11. A New Strategy for Heavy Metal Polluted Environments: A Review of Microbial Biosorbents

    Science.gov (United States)

    Ayangbenro, Ayansina Segun; Babalola, Olubukola Oluranti

    2017-01-01

    Persistent heavy metal pollution poses a major threat to all life forms in the environment due to its toxic effects. These metals are very reactive at low concentrations and can accumulate in the food web, causing severe public health concerns. Remediation using conventional physical and chemical methods is uneconomical and generates large volumes of chemical waste. Bioremediation of hazardous metals has received considerable and growing interest over the years. The use of microbial biosorbents is eco-friendly and cost effective; hence, it is an efficient alternative for the remediation of heavy metal contaminated environments. Microbes have various mechanisms of metal sequestration that hold greater metal biosorption capacities. The goal of microbial biosorption is to remove and/or recover metals and metalloids from solutions, using living or dead biomass and their components. This review discusses the sources of toxic heavy metals and describes the groups of microorganisms with biosorbent potential for heavy metal removal. PMID:28106848

  12. Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

    Science.gov (United States)

    Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

    2015-04-01

    Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5

  13. Modeling the microbial growth of two Escherichia coli strains in a multi-substrate environment

    OpenAIRE

    Poccia,M. E.; Beccaria, A. J.; R. G. Dondo

    2014-01-01

    The microbial growth in multi-substrate environments may be viewed as an optimal resources allocation problem. The optimization aims at maximizing some biological objective like the biomass growth. The models developed using this hypothesis are called “cybernetic” and they represent the complex cell structure as an optimizing function that regulates the intracellular enzymatic machinery. In this work, a cybernetic model was developed to represent the growth of two E. coli strains (JM 109 and ...

  14. Flood management: prediction of microbial contamination in large-scale floods in urban environments.

    Science.gov (United States)

    Taylor, Jonathon; Lai, Ka Man; Davies, Mike; Clifton, David; Ridley, Ian; Biddulph, Phillip

    2011-07-01

    With a changing climate and increased urbanisation, the occurrence and the impact of flooding is expected to increase significantly. Floods can bring pathogens into homes and cause lingering damp and microbial growth in buildings, with the level of growth and persistence dependent on the volume and chemical and biological content of the flood water, the properties of the contaminating microbes, and the surrounding environmental conditions, including the restoration time and methods, the heat and moisture transport properties of the envelope design, and the ability of the construction material to sustain the microbial growth. The public health risk will depend on the interaction of these complex processes and the vulnerability and susceptibility of occupants in the affected areas. After the 2007 floods in the UK, the Pitt review noted that there is lack of relevant scientific evidence and consistency with regard to the management and treatment of flooded homes, which not only put the local population at risk but also caused unnecessary delays in the restoration effort. Understanding the drying behaviour of flooded buildings in the UK building stock under different scenarios, and the ability of microbial contaminants to grow, persist, and produce toxins within these buildings can help inform recovery efforts. To contribute to future flood management, this paper proposes the use of building simulations and biological models to predict the risk of microbial contamination in typical UK buildings. We review the state of the art with regard to biological contamination following flooding, relevant building simulation, simulation-linked microbial modelling, and current practical considerations in flood remediation. Using the city of London as an example, a methodology is proposed that uses GIS as a platform to integrate drying models and microbial risk models with the local building stock and flood models. The integrated tool will help local governments, health authorities

  15. Microbiome interplay: plants alter microbial abundance and diversity within the built environment.

    Science.gov (United States)

    Mahnert, Alexander; Moissl-Eichinger, Christine; Berg, Gabriele

    2015-01-01

    The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria, and Eukaryota (fungi) increased on surrounding floor and wall surfaces within 6 months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g., Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  16. Microbiome interplay: plants alter microbial abundance and diversity within the built environment

    Directory of Open Access Journals (Sweden)

    Alexander eMahnert

    2015-08-01

    Full Text Available The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria and Eukaryota (fungi increased on surrounding floor and wall surfaces within six months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g. Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  17. Tracking microbial colonization patterns associated with micro-environments of rice

    Science.gov (United States)

    Schmidt, Hannes; Eickhorst, Thilo

    2015-04-01

    The interface between soil and roots (i.e. the rhizosphere) represents a highly dynamic micro-environment for microbial populations. Root-derived compounds are released into the rhizosphere and may attract, stimulate, or inhibit native soil microorganisms. Microbes associated with the rhizosphere, in turn, may have deleterious, neutral, or promoting effects on the plant. Such influences of microbial populations on the plant and vice versa are likely to be greatest in close vicinity to the root surface. It is therefore essential to detect and visualize preferential micro-sites of microbial root colonization to identify potential areas of microbe-plant interaction. We present a single-cell based approach allowing for the localization, quantification, and visualization of native microbial populations in the rhizosphere and on the rhizoplane of soil-grown roots in situ. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with confocal laser scanning microscopy was applied to observe colonization densities and patterns of microbial populations associated with wetland rice. Hybridizations with domain- and phylum-specific oligonucleotide probes showed that the growth stage of the rice plant as well as the distance to the root surface had a strong influence on microbial colonization patterns. Three-dimensional visualizations of root-associated microbes revealed micro-sites of preferential colonization. Highest cell numbers of archaea and bacteria were found at flowering stage of rice plant development. Irregular distribution patterns of microbiota observed at early growth stages shifted towards more uniform colonization with plant age. Accordingly, the highest colonization densities shifted from the tip to more mature regions of rice roots. Methanogenic archaea and methanotrophic bacteria were found to be co-localized at basal regions of lateral roots. Beneficial effects of a close association with root surfaces were indicated by

  18. Microbial deterioration of artistic tiles from the façade of the Grande Albergo Ausonia & Hungaria (Venice, Italy).

    Science.gov (United States)

    Giacomucci, Lucia; Bertoncello, Renzo; Salvadori, Ornella; Martini, Ilaria; Favaro, Monica; Villa, Federica; Sorlini, Claudia; Cappitelli, Francesca

    2011-08-01

    The Grande Albergo Ausonia & Hungaria (Venice Lido, Italy) has an Art Nouveau polychrome ceramic coating on its façade, which was restored in 2007. Soon after the conservation treatment, many tiles of the façade decoration showed coloured alterations putatively attributed to the presence of microbial communities. To confirm the presence of the biological deposit and the stratigraphy of the Hungaria tiles, stereomicroscope, optical and environmental scanning electron microscope observations were made. The characterisation of the microbial community was performed using a PCR-DGGE approach. This study reported the first use of a culture-independent approach to identify the total community present in biodeteriorated artistic tiles. The case study examined here reveals that the coloured alterations on the tiles were mainly due to the presence of cryptoendolithic cyanobacteria. In addition, we proved that the microflora present on the tiles was generally greatly influenced by the environment of the Hungaria hotel. We found several microorganisms related to the alkaline environment, which is in the range of the tile pH, and related to the aquatic environment, the presence of the acrylic resin Paraloid B72® used during the 2007 treatment and the pollutants of the Venice lagoon.

  19. Optimization of microbial detoxification for an aquatic mercury-contaminated environment.

    Science.gov (United States)

    Figueiredo, Neusa L; Canário, João; Serralheiro, Maria Luísa; Carvalho, Cristina

    2017-08-29

    Mercury (Hg) reduction performed by microorganisms is well recognized as a biological means for remediation of contaminated environment. Recently, studies demonstrated that Hg-resistant microorganisms of Tagus Estuary are involved in metal reduction processes. In the present study, aerobic microbial community isolated from a highly Hg-contaminated area of Tagus Estuary was used to determine the optimization of the reduction process in conditions such as the contaminated ecosystem. Factorial design methodology was employed to examine the influence of glucose, sulfate, iron, and chloride on Hg reduction. In the presence of several concentrations of these elements, microbial community reduced Hg in a range of 37-61% of the initial 0.1 mg/ml Hg(2+) levels. The response prediction through central composite design showed that the increase of sulfate concentration led to an optimal response in Hg reduction by microbial community, while the rise in chloride levels markedly decreased metal reduction. Iron may exert antagonistic effects depending upon the media composition. These results are useful in understanding the persistence of Hg contamination in Tagus Estuary after inactivation of critical industrial units, as well as data might also be beneficial for development of new bioremediation strategies either in Tagus Estuary and/or in other Hg-contaminated aquatic environments.

  20. PRELIMINARY BIOGEOCHEMICAL DATA ON MICROBIAL CARBONATOGENESIS IN ANCIENT EXTREME ENVIRONMENTS (KESS-KESS MOUNDS, MOROCCO

    Directory of Open Access Journals (Sweden)

    ADRIANO GUIDO

    2013-03-01

    Full Text Available The Devonian Kess-Kess mounds, cropping out in the Hamar Laghdad Ridge (SE Morocco, provide a useful case-study for understanding the relationships between the microbial metabolic activities and micrite precipitation in an extreme environment. Very fine dark and white wrinkled laminae record microbial activity and the geochemistry of the organic matter allows the  characterization of the source organisms. The biogeochemical characterization of extracted organic matter was performed through the functional group analyses by FT-IR Spectroscopy. FT-IR parameters indicate a marine origin and low thermal evolution for the organic material. The organic matter is characterized by the presence of stretching ?C=C vibrations attributable to alkene and/or unsaturated carboxylic acids. Preliminary analysis with GC-MS provides evidence for an autochthonous (microbial carbonate precipitation in an ancient extreme environment may have implications in astrobiological research considering the recent discovery of carbonate deposits on Mars. 

  1. Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

    Science.gov (United States)

    Musat, N.; Kuypers, M. M. M.

    2009-04-01

    Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

  2. Anticipating Changing in Environments: Adaptation in Fluctuating Environments in A Heterogeneous Microbial Communites

    Science.gov (United States)

    Belete, Merzu; Bálazsi, Gábor

    2015-03-01

    The environments in which micro-organisms grow often fluctuate. To survive in temporally changing environments, cells have evolved mechanisms to survive environmental changes. One survival mechanism is generating phenotypic differences among identical cells in a given environment, with cells randomly switching between phenotypes. Such cells form subpopulations that proliferate at different rates. Optimal population fitness was attributed before to matching cellular and environmental switching rates. However, the conditions for this optimum are not well understood. In particular, it is unknown how the growth rates of the phenotypes affect the optimum. We use mathematical models to address this question. We find that the existence of the predicted optimum depends on cell growth rates in each phenotype. The predicted optimum exists for wider parameter regimes if the environmental durations are long. In addition, we study how mutants arising among such phenotypically heterogeneous cells spread in the population.

  3. Microbial hitchhikers on marine plastic debris: Human exposure risks at bathing waters and beach environments.

    Science.gov (United States)

    Keswani, Anisha; Oliver, David M; Gutierrez, Tony; Quilliam, Richard S

    2016-07-01

    Marine plastic debris is well characterized in terms of its ability to negatively impact terrestrial and marine environments, endanger coastal wildlife, and interfere with navigation, tourism and commercial fisheries. However, the impacts of potentially harmful microorganisms and pathogens colonising plastic litter are not well understood. The hard surface of plastics provides an ideal environment for opportunistic microbial colonisers to form biofilms and might offer a protective niche capable of supporting a diversity of different microorganisms, known as the "Plastisphere". This biotope could act as an important vector for the persistence and spread of pathogens, faecal indicator organisms (FIOs) and harmful algal bloom species (HABs) across beach and bathing environments. This review will focus on the existent knowledge and research gaps, and identify the possible consequences of plastic-associated microbes on human health, the spread of infectious diseases and bathing water quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Long-term tracking of microbial survivability and growth in a controlled environment

    Science.gov (United States)

    Sutandar, Andiyanto; Abdiel Foo, Jong Yong; Lim, Chu Sing; Hsu, Li-Yang

    2008-04-01

    The ecological and histological study of a microbial population in a given environment provides important information leading to its survivability and growth. Current standard laboratory practices adopt culture on a medium housed in an incubated environment. However, large numbers of cultures are usually required to investigate the effects of variations in parametric conditions on the microbes. This can result in a high use of resources such as consumables and man-hours. Automated systems that are able to replenish fresh nutrients and extract metabolic waste for long-term monitoring are also limited. In this study, a system capable of real-time monitoring of microbe survival and providing a suitable environment for their growth is presented. Housed within its structure is a customized chamber with temperature control, pH regulation, nutrient providence and metabolic waste removal functions. To assess the reliability of the system, five sets of Staphylococcus aureus ATCC 29213 strains are cultured and monitored continuously for 96 consecutive hours. The survival and growth of the pathogens are verified by standard laboratory techniques such as viable plate count after each successive 24 h of monitoring. The findings herein suggest that the system is able to monitor the microbial population with minimal human intervention and can be a valuable long-term tracking tool.

  5. Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

    Science.gov (United States)

    Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

    2015-07-01

    Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

  6. LIFE experiment: isolation of cryptoendolithic organisms from Antarctic colonized sandstone exposed to space and simulated Mars conditions on the international space station.

    Science.gov (United States)

    Scalzi, Giuliano; Selbmann, Laura; Zucconi, Laura; Rabbow, Elke; Horneck, Gerda; Albertano, Patrizia; Onofri, Silvano

    2012-06-01

    Desiccated Antarctic rocks colonized by cryptoendolithic communities were exposed on the International Space Station (ISS) to space and simulated Mars conditions (LiFE-Lichens and Fungi Experiment). After 1.5 years in space samples were retrieved, rehydrated and spread on different culture media. Colonies of a green alga and a pink-coloured fungus developed on Malt-Agar medium; they were isolated from a sample exposed to simulated Mars conditions beneath a 0.1 % T Suprasil neutral density filter and from a sample exposed to space vacuum without solar radiation exposure, respectively. None of the other flight samples showed any growth after incubation. The two organisms able to grow were identified at genus level by Small SubUnit (SSU) and Internal Transcribed Spacer (ITS) rDNA sequencing as Stichococcus sp. (green alga) and Acarospora sp. (lichenized fungal genus) respectively. The data in the present study provide experimental information on the possibility of eukaryotic life transfer from one planet to another by means of rocks and of survival in Mars environment.

  7. LIFE Experiment: Isolation of Cryptoendolithic Organisms from Antarctic Colonized Sandstone Exposed to Space and Simulated Mars Conditions on the International Space Station

    Science.gov (United States)

    Scalzi, Giuliano; Selbmann, Laura; Zucconi, Laura; Rabbow, Elke; Horneck, Gerda; Albertano, Patrizia; Onofri, Silvano

    2012-06-01

    Desiccated Antarctic rocks colonized by cryptoendolithic communities were exposed on the International Space Station (ISS) to space and simulated Mars conditions (LiFE— Lichens and Fungi Experiment). After 1.5 years in space samples were retrieved, rehydrated and spread on different culture media. Colonies of a green alga and a pink-coloured fungus developed on Malt-Agar medium; they were isolated from a sample exposed to simulated Mars conditions beneath a 0.1 % T Suprasil neutral density filter and from a sample exposed to space vacuum without solar radiation exposure, respectively. None of the other flight samples showed any growth after incubation. The two organisms able to grow were identified at genus level by Small SubUnit (SSU) and Internal Transcribed Spacer (ITS) rDNA sequencing as Stichococcus sp. (green alga) and Acarospora sp. (lichenized fungal genus) respectively. The data in the present study provide experimental information on the possibility of eukaryotic life transfer from one planet to another by means of rocks and of survival in Mars environment.

  8. Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources.

    Science.gov (United States)

    Resat, Haluk; Bailey, Vanessa; McCue, Lee Ann; Konopka, Allan

    2012-05-01

    We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the

  9. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings.

    Science.gov (United States)

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng; Huang, Li-Nan

    2014-06-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

  10. Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

    Science.gov (United States)

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

  11. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  12. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  13. Biodegradation of phenanthrene using adapted microbial consortium isolated from petrochemical contaminated environment.

    Science.gov (United States)

    Janbandhu, Anjali; Fulekar, M H

    2011-03-15

    In developing countries like India, there are many industrial areas discharging effluent containing large amount of polyaromatic hydrocarbon (PAH) which causes hazardous effect on the soil-water environment. The objective of this study was to isolate and characterize high-efficiency PAH-degrading microbial consortium from 3 decade old petrochemical refinery field located in Nagpur, Maharashtra with history of PAH disposal. Based on biochemical tests and 16S rDNA gene sequence analysis the consortium was identified as Sphingobacterium sp., Bacillus cereus and a novel bacterium Achromobacter insolitus MHF ENV IV with effective phenanthrene-degrading ability. The biodegradation data of phenanthrene indicates about 100%, 56.9% and 25.8% degradation at the concentration of 100mg/l, 250 mg/l and 500 mg/l respectively within 14 days. The consortium and its monoculture isolates also utilized variety of other hydrocarbons for growth. To best of our knowledge this is the first time that Achromobacter insolitus has been reported to mineralize phenanthrene effectively. GC-MS analysis of phenanthrene degradation confirmed biodegradation by detection of intermediates like salicylaldehyde, salicylic acid and catechol. All the results indicated that the microbial consortium have a promising application in bioremediation of petrochemical contaminated environments and could be potentially useful for the study of PAH degradation and for bioremediation purposes.

  14. Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments.

    Science.gov (United States)

    Ertekin, Emine; Hatt, Janet K; Konstantinidis, Konstantinos T; Tezel, Ulas

    2016-04-19

    Benzalkonium chlorides (BACs) are emerging pollutants. Identification of microorganisms and the genes involved in the biodegradation of BACs is crucial for better understanding the fate of BACs in the environment and developing treatment strategies. Four microbial communities degrading BACs were developed from sewage (SEW), activated sludge (AS), soil (SOIL) and sea sediment (SEA) samples. According to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundant species represented uncharacterized members of the Pseudomonas and Achromobacter genera. BAC biotransformation rates of the enriched microbial communities were 2.8, 3.2, 17.8, and 24.3 μM hr(-1) for SEA, AS, SOIL, and SEW, respectively, and were positively correlated with the relative abundance of a particular Pseudomonas sp. strain, BIOMIG1. The strain BIOMIG1 mineralizes BACs at a rate up to 2.40 μmol hr(-1) 10(-11) cells. Genomes of four BAC degrading and nondegrading BIOMIG1 phenotypes were sequenced and differentially compared with each other. As a result, a gene cluster encoding for transporters, an integrase and a dioxygenase were involved in BAC biotransformation. Our results suggest that BIOMIG1 plays a key role on the fate of BACs in the environment and genes, other than those reported to date, are involved in BAC biotransformation in various habitats.

  15. Microbial redox processes in deep subsurface environments and the potential application of (perchlorate in oil reservoirs

    Directory of Open Access Journals (Sweden)

    Martin G Liebensteiner

    2014-09-01

    Full Text Available The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese- and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (perchlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (perchlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (perchlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (metagenome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (perchlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (perchlorate for bioremediation, souring control and microbial enhanced oil recovery are addressed.

  16. Who's coming to dinner? Microbial phylogenetic analyses of various subsurface petroleum well environments for MEOR applications

    Energy Technology Data Exchange (ETDEWEB)

    Keeler, Sharon J.; Fallon, Robert; Jackson, Scott; Zhang, Shiping; Tomb, Jean-Francois; Miller, Mark A.; Rees, Bethany [Central Research and Development (Canada)

    2011-07-01

    This paper discussed the microbial phylogenetic analyses of various subsurface petroleum well environments for microbial-enhanced oil recovery (MEOR) applications. The objective is to add nutrients and microbes to injection water. Close to 47,000 compounds are present in petroleum and most of them are polyaromatic hydrocarbons (PAHs). Microbes that can predominate the biomass produced and the over all bioactivity are needed. Changing the electron acceptor modifies the microbial community. Characterization of microbial diversity in production water with two independent molecular methods is shown. The geology of well systems in North America was analyzed; the analyses and the results are given. Summarizing the North Slope reservoir system phylogenetics, it can be said that many genera found in association with other petroleum environments suggest they are autocthonous and transiently very high levels of acetate signify a mutual metabolic codependency on the amount of acetate present in the system.

  17. Resistance of Antarctic black fungi and cryptoendolithic communities to simulated space and Martian conditions.

    Science.gov (United States)

    Onofri, S; Barreca, D; Selbmann, L; Isola, D; Rabbow, E; Horneck, G; de Vera, J P P; Hatton, J; Zucconi, L

    2008-01-01

    Dried colonies of the Antarctic rock-inhabiting meristematic fungi Cryomyces antarcticus CCFEE 515, CCFEE 534 and C. minteri CCFEE 5187, as well as fragments of rocks colonized by the Antarctic cryptoendolithic community, were exposed to a set of ground-based experiment verification tests (EVTs) at the German Aerospace Center (DLR, Köln, Germany). These were carried out to test the tolerance of these organisms in view of their possible exposure to space conditions outside of the International Space Station (ISS). Tests included single or combined simulated space and Martian conditions. Responses were analysed both by cultural and microscopic methods. Thereby, colony formation capacities were measured and the cellular viability was assessed using live/dead dyes FUN 1 and SYTOX Green. The results clearly suggest a general good resistance of all the samples investigated. C. minteri CCFEE 5187, C. antarcticus CCFEE 515 and colonized rocks were selected as suitable candidates to withstand space flight and long-term permanence in space on the ISS in the framework of the LIchens and Fungi Experiments (LIFE programme, European Space Agency).

  18. Survival of Antarctic Cryptoendolithic Fungi in Simulated Martian Conditions On Board the International Space Station.

    Science.gov (United States)

    Onofri, Silvano; de Vera, Jean-Pierre; Zucconi, Laura; Selbmann, Laura; Scalzi, Giuliano; Venkateswaran, Kasthuri J; Rabbow, Elke; de la Torre, Rosa; Horneck, Gerda

    2015-12-01

    Dehydrated Antarctic cryptoendolithic communities and colonies of the rock inhabitant black fungi Cryomyces antarcticus (CCFEE 515) and Cryomyces minteri (CCFEE 5187) were exposed as part of the Lichens and Fungi Experiment (LIFE) for 18 months in the European Space Agency's EXPOSE-E facility to simulated martian conditions aboard the International Space Station (ISS). Upon sample retrieval, survival was proved by testing colony-forming ability, and viability of cells (as integrity of cell membrane) was determined by the propidium monoazide (PMA) assay coupled with quantitative PCR tests. Although less than 10% of the samples exposed to simulated martian conditions were able to proliferate and form colonies, the PMA assay indicated that more than 60% of the cells and rock communities had remained intact after the "Mars exposure." Furthermore, a high stability of the DNA in the cells was demonstrated. The results contribute to assessing the stability of resistant microorganisms and biosignatures on the surface of Mars, data that are valuable information for further search-for-life experiments on Mars. Endoliths-Eukaryotes-Extremophilic microorganisms-Mars-Radiation resistance.

  19. Optimal resting-growth strategies of microbial populations in fluctuating environments.

    Directory of Open Access Journals (Sweden)

    Nico Geisel

    Full Text Available Bacteria spend most of their lifetime in non-growing states which allow them to survive extended periods of stress and starvation. When environments improve, they must quickly resume growth to maximize their share of limited nutrients. Cells with higher stress resistance often survive longer stress durations at the cost of needing more time to resume growth, a strong disadvantage in competitive environments. Here we analyze the basis of optimal strategies that microorganisms can use to cope with this tradeoff. We explicitly show that the prototypical inverse relation between stress resistance and growth rate can explain much of the different types of behavior observed in stressed microbial populations. Using analytical mathematical methods, we determine the environmental parameters that decide whether cells should remain vegetative upon stress exposure, downregulate their metabolism to an intermediate optimum level, or become dormant. We find that cell-cell variability, or intercellular noise, is consistently beneficial in the presence of extreme environmental fluctuations, and that it provides an efficient population-level mechanism for adaption in a deteriorating environment. Our results reveal key novel aspects of responsive phenotype switching and its role as an adaptive strategy in changing environments.

  20. Optimal resting-growth strategies of microbial populations in fluctuating environments.

    Science.gov (United States)

    Geisel, Nico; Vilar, Jose M G; Rubi, J Miguel

    2011-04-15

    Bacteria spend most of their lifetime in non-growing states which allow them to survive extended periods of stress and starvation. When environments improve, they must quickly resume growth to maximize their share of limited nutrients. Cells with higher stress resistance often survive longer stress durations at the cost of needing more time to resume growth, a strong disadvantage in competitive environments. Here we analyze the basis of optimal strategies that microorganisms can use to cope with this tradeoff. We explicitly show that the prototypical inverse relation between stress resistance and growth rate can explain much of the different types of behavior observed in stressed microbial populations. Using analytical mathematical methods, we determine the environmental parameters that decide whether cells should remain vegetative upon stress exposure, downregulate their metabolism to an intermediate optimum level, or become dormant. We find that cell-cell variability, or intercellular noise, is consistently beneficial in the presence of extreme environmental fluctuations, and that it provides an efficient population-level mechanism for adaption in a deteriorating environment. Our results reveal key novel aspects of responsive phenotype switching and its role as an adaptive strategy in changing environments.

  1. The microbial diversity of Polar environments is a fertile ground for bioprospecting.

    Science.gov (United States)

    de Pascale, Donatella; De Santi, Concetta; Fu, Juan; Landfald, Bjarne

    2012-12-01

    The term bioprospecting has been adopted for systematic searches in nature for new bioactive compounds, genes, proteins, microorganisms and other products with potential for commercial use. Much effort has been focused on microorganisms able to thrive under harsh conditions, including the Polar environments. Both the lipid and protein cellular building blocks of Polar microorganisms are shaped by their adaptation to the permanently low temperatures. In addition, strongly differing environments, such as permafrost, glaciers and sea ice, have contributed to additional functional diversity. Emerging massive-parallel sequencing technologies have revealed the existence of a huge, hitherto unseen diversity of low-abundance phylotypes--the rare biosphere--even in the Polar environments. This realization has further strengthened the need to employ cultivation-independent approaches, including metagenomics and single-cell genomic sequencing, to get comprehensive access to the genetic diversity of microbial communities for bioprospecting purposes. In this review, we present an updated snapshot of recent findings on the molecular basis for adaptation to the cold and the phylogenetic diversities of different Polar environments. Novel approaches in bioprospecting are presented and we conclude by showing recent bioprospecting outcomes in terms of new molecules patented or applied by some biotech companies.

  2. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

    Science.gov (United States)

    Edwards, K J; Gihring, T M; Banfield, J F

    1999-08-01

    Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at higher temperatures and lower pHs ( approximately 40 degrees C; pH approximately 0.5) than T. ferrooxidans.

  3. Linking microbial ultrastructure and physiology to iron depositional processes in deep sea hydrothermal environments

    Science.gov (United States)

    Chan, C. S.; Fleming, E. J.; Emerson, D.; Edwards, K. J.

    2008-12-01

    Clara S. Chan, Emily Fleming, David Emerson, Katrina J. Edwards Iron microbial mats have been discovered in a variety of deep-sea hydrothermal environments and are increasingly being recognized as more seafloor is explored. The predominant structures found in many of these mats are iron oxyhydroxide-rich filaments. One of the most common structures is a helical stalk bearing a resemblance to the twisted stalk of the terrestrial iron-oxidizing microbe, Gallionella ferruginea. While Gallionella has not been detected in, or isolated from, these mats microaerophilic iron-oxidizing, a stalk- forming bacterium, Mariprofundus ferrooxydans (PV-1 and related strains) has been isolated from mats at the Loihi seamount in Hawaii (Emerson et al. 2007, PLoS One 2(8): e667). Fossilized aggregates of iron filaments have been observed in the rock record (e.g. Little et al. 2004, Geomicrobiol. J. 21:415), and may represent ancient versions of these microbial mats. If this is shown to be true, such filaments would represent one of the few microfossil morphologies that can be linked to a specific microbial metabolism. We have used a combination of test tube culturing, microslide culturing, time lapse microscopy, and electron microscopy to study Mariprofundus stalk morphology and genesis and link these details to physiological responses to environmental chemistry. The goals include determining specific attributes of stalk morphology that can be used to determine the biogenicity of putative iron microfossils, and interpret the conditions of the depositional environment. Light microscopic observation of microslide cultures over the course of several days allowed for determination of bacterial response to developing oxygen and Fe(II) gradients. Once gradients have been established, given an abundant supply of oxygen, cells congregate in a band perpendicular to the gradient and stalks are formed, growing in the direction of increasing oxygen (and decreasing Fe) concentration. This

  4. New perspectives on viable microbial communities in low-biomass cleanroom environments.

    Science.gov (United States)

    Vaishampayan, Parag; Probst, Alexander J; La Duc, Myron T; Bargoma, Emilee; Benardini, James N; Andersen, Gary L; Venkateswaran, Kasthuri

    2013-02-01

    The advent of phylogenetic DNA microarrays and high-throughput pyrosequencing technologies has dramatically increased the resolution and accuracy of detection of distinct microbial lineages in mixed microbial assemblages. Despite an expanding array of approaches for detecting microbes in a given sample, rapid and robust means of assessing the differential viability of these cells, as a function of phylogenetic lineage, remain elusive. In this study, pre-PCR propidium monoazide (PMA) treatment was coupled with downstream pyrosequencing and PhyloChip DNA microarray analyses to better understand the frequency, diversity and distribution of viable bacteria in spacecraft assembly cleanrooms. Sample fractions not treated with PMA, which were indicative of the presence of both live and dead cells, yielded a great abundance of highly diverse bacterial pyrosequences. In contrast, only 1% to 10% of all of the pyrosequencing reads, arising from a few robust bacterial lineages, originated from sample fractions that had been pre-treated with PMA. The results of PhyloChip analyses of PMA-treated and -untreated sample fractions were in agreement with those of pyrosequencing. The viable bacterial population detected in cleanrooms devoid of spacecraft hardware was far more diverse than that observed in cleanrooms that housed mission-critical spacecraft hardware. The latter was dominated by hardy, robust organisms previously reported to survive in oligotrophic cleanroom environments. Presented here are the findings of the first ever comprehensive effort to assess the viability of cells in low-biomass environmental samples, and correlate differential viability with phylogenetic affiliation.

  5. Microbial pathways for the mobilization of mercury as Hg(O) in anoxic subsurface environments

    Energy Technology Data Exchange (ETDEWEB)

    Barkay, Tamar

    2005-06-01

    The goal of our project which was initiated in June 2005 is focused on the presence of merA in microbial communities of anoxic environments and the effect of anaerobic respiratory pathways on MR expression and activities. The following progress has been made to date: PCR primers were designed to span the known phylogenetic range of merA genes of Gram-negative bacteria. In control experiments, these primers successfully amplified a 288 bp region at the 3? end of previously characterized merA genes from Shewanella putrefaciens pMERPH, Acidithiobacillus ferrooxidans, Pseudomonas stutzeri pPB, Tn5041, Pseudomonas sp. K-62, and Serratia marcescens pDU1358.

  6. Targeted isolation of proteins from natural microbial communities living in an extreme environment.

    Science.gov (United States)

    Singer, Steven W

    2012-01-01

    Microorganisms from extreme environments are often very difficult to cultivate, precluding detailed study by biochemical and physiological techniques. Recent advances in genomic sequencing and proteomic measurements of samples obtained from natural communities have allowed new access to these uncultivated extremophiles and identified abundant proteins that can be isolated directly from natural samples. Here we report the isolation of two abundant heme proteins from low-diversity biofilm microbial communities that thrive in very acidic (pH ~ 1), metal-rich water in a subsurface mine. Purification and detailed characterization of these proteins has afforded new insight into the possible mechanism of Fe(II) oxidation by Leptospirillum Group II, the dominant population in most of these biofilms, and demonstrated that the abundance and posttranslational modifications of one of these proteins is dependent on the lifecycle of the biofilm.

  7. Microbial pathways for the mobilization of mercury as Hg(O) in anoxic subsurface environments

    Energy Technology Data Exchange (ETDEWEB)

    Barkay, Tamar

    2005-06-01

    The goal of our project which was initiated in June 2005 is focused on the presence of merA in microbial communities of anoxic environments and the effect of anaerobic respiratory pathways on MR expression and activities. The following progress has been made to date: PCR primers were designed to span the known phylogenetic range of merA genes of Gram-negative bacteria. In control experiments, these primers successfully amplified a 288 bp region at the 3? end of previously characterized merA genes from Shewanella putrefaciens pMERPH, Acidithiobacillus ferrooxidans, Pseudomonas stutzeri pPB, Tn5041, Pseudomonas sp. K-62, and Serratia marcescens pDU1358.

  8. Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments.

    Science.gov (United States)

    Mejias Carpio, Isis E; Franco, Diego Castillo; Zanoli Sato, Maria Inês; Sakata, Solange; Pellizari, Vivian H; Seckler Ferreira Filho, Sidney; Frigi Rodrigues, Debora

    2016-04-15

    Understanding the diversity and metal removal ability of microorganisms associated to contaminated aquatic environments is essential to develop metal remediation technologies in engineered environments. This study investigates through 16S rRNA deep sequencing the composition of a biostimulated microbial consortium obtained from the polluted Tietê River in São Paulo, Brazil. The bacterial diversity of the biostimulated consortium obtained from the contaminated water and sediment was compared to the original sample. The results of the comparative sequencing analyses showed that the biostimulated consortium and the natural environment had γ-Proteobacteria, Firmicutes, and uncultured bacteria as the major classes of microorganisms. The consortium optimum zinc removal capacity, evaluated in batch experiments, was achieved at pH=5 with equilibrium contact time of 120min, and a higher Zn-biomass affinity (KF=1.81) than most pure cultures previously investigated. Analysis of the functional groups found in the consortium demonstrated that amine, carboxyl, hydroxyl, and phosphate groups present in the consortium cells were responsible for zinc uptake. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

    KAUST Repository

    Lee, O.O.

    2014-01-08

    Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.

  10. Seasonal distribution of microbial activity in bioaerosols in the outdoor environment of the Qingdao coastal region

    Science.gov (United States)

    Zhong, Xi; Qi, Jianhua; Li, Hongtao; Dong, Lijie; Gao, Dongmei

    2016-09-01

    Microbial activities in the atmosphere can indicate the physiological processes of microorganisms and can indirectly affect cloud formation and environmental health. In this study, the microbial activity in bioaerosols collected in the Qingdao coastal region was investigated using the fluorescein diacetate (FDA) hydrolysis method to detect the enzyme activity of microorganisms. The results showed that the microbial activity ranged from 5.49 to 102 ng/m3 sodium fluorescein from March 2013 to February 2014; the average value was 34.4 ng/m3. Microbial activity has no statistical correlation with total microbial quantity. Multiple linear regression analysis showed that meteorological factors such as atmospheric temperature, relative humidity and wind speed accounted for approximately 35.7% of the variation of the microbial activity, although their individual impacts on microbial activity varied. According to the correlation analysis, atmospheric temperature and wind speed had a significant positive and negative influence on microbial activity, respectively, whereas relative humidity and wind direction had no significant influence. The seasonal distribution of microbial activity in bioaerosols was in the order of summer > autumn > winter > spring, with high fluctuations in the summer and autumn. Microbial activity in bioaerosols differed in different weather conditions such as the sunny, foggy, and hazy days of different seasons. Further in situ observations in different weather conditions at different times and places are needed to understand the seasonal distribution characteristics of microbial activity in bioaerosols and the influence factors of microbial activity.

  11. Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment.

    Science.gov (United States)

    Ponce-Soto, Gabriel Y; Aguirre-von-Wobeser, Eneas; Eguiarte, Luis E; Elser, James J; Lee, Zarraz M-P; Souza, Valeria

    2015-01-01

    The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.

  12. Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment

    Directory of Open Access Journals (Sweden)

    Gabriel Yaxal Ponce-Soto

    2015-04-01

    Full Text Available The increase of nutrients in water bodies, in particular nitrogen (N and phosphorus (P due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios, suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after three weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.

  13. Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland.

    Science.gov (United States)

    Kalwasińska, Agnieszka; Felföldi, Tamás; Szabó, Attila; Deja-Sikora, Edyta; Kosobucki, Przemysław; Walczak, Maciej

    2017-07-01

    Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and ECe up to 423 dS m(-1)) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus.

  14. Resistance to UV-B induced DNA damage in extreme-tolerant cryptoendolithic Antarctic fungi: detection by PCR assays.

    Science.gov (United States)

    Selbmann, Laura; Isola, Daniela; Zucconi, Laura; Onofri, Silvano

    2011-10-01

    Cryptoendolithic Antarctic black fungi are adapted to the harshest terrestrial conditions as in the ice-free area of the McMurdo Dry Valleys. Recently, surviving space simulated conditions proves their bewildering extremotolerance. In order to investigate the potential DNA damage and their response after UV-B exposition, two strains of Antarctic cryptoendolithic black fungi, Cryomyces antarcticus CCFEE 534 and Cryomyces minteri CCFEE 5187, were irradiated at different UV-B doses. Since conventional methods cannot be applied to these organisms, the effect on the genome was assessed by RAPD and rDNA amplification PCR based assays; the results were compared with the responses of Saccharomyces pastorianus DBVPG 6283 treated with the same conditions. Results showed that template activity was drastically inhibited in S. pastorianus after irradiation. Dramatic changes in the RAPD profiles showed after 30 min of exposure while the rDNA amplification of SSU, LSU, and ITS portions failed after 30, 60, and 90 min of exposure respectively. No alteration was detected in the templates of the Antarctic strains where both RAPD profiles and rDNA PCR amplifications were unaffected even after 240 min of exposure. The electroferograms of the rDNA portions of Cryomyces strains were perfectly readable and conserved whilst the analyses revealed a marked alteration in S. pastorianus confirming the high resistance of the Antarctic strains to UV-B exposure.

  15. Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

    Science.gov (United States)

    Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

    2001-12-01

    Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

  16. Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments

    Directory of Open Access Journals (Sweden)

    Babu Zhereppa Fathepure

    2014-04-01

    Full Text Available Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.

  17. 16S rRNA gene sequencing as a tool to study microbial populations in foods and process environments

    DEFF Research Database (Denmark)

    Buschhardt, Tasja; Hansen, Tina Beck; Bahl, Martin Iain

    2015-01-01

    and their role in food safety. During method optimization, we have identified several factors which distort the characterization of microbial populations, including DNA extraction methods, DNA polymerases, and most importantly the analyzed fragment of the 16S rRNA gene. Methods: This study investigated microbial...... reference. Results: Taxonomic assignments and abundances of sequences in the total community and in the Enterobacteriaceae subpopulation were affected by the 16S rRNA gene variable region, DNA extraction methods, and polymerases chosen. However, community compositions were very reproducible when the same......Introduction: Methodological constraints during culturing and biochemical testing have left the true microbiological diversity of foods and process environments unexplored. Culture-independent molecular methods, such as 16S rRNA gene sequencing, may provide deeper insight into microbial communities...

  18. Relating Microbial Community Structure to a Dominant Environmental Variable in a Complex Environment; An Example from a Chromium Contaminated Site

    Energy Technology Data Exchange (ETDEWEB)

    Palumbo, Anthony Vito [ORNL; Schryver, Jack C [ORNL; Pfiffner, Susan M. [University of Tennessee, Knoxville (UTK); Marsh, Terence [Michigan State University, East Lansing; Brandt, Craig C [ORNL

    2008-01-01

    In a complex environment, it can be difficult to assess the degree to which a continuous variable influences microbial community structure. We propose a method that involves using the community data to "predict" the value of the presumed dominant variable. The assumption is that in order to "predict" the variable the community composition must be sensitive to or affected by the variable in question. The concentration range over which the prediction is accurate should thus provide information on the concentrations that influence community structure. We explored this approach using T-RLFP data on at a site polluted by tannery wastes. We were able to use the microbial community structure measures to predict Cr concentration over a surprisingly wide range of concentration. Although, it appears from this work that this approach can give useful information about the relationships between microbial community structure and specific environmental conditions much further testing is required.

  19. Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain.

    Science.gov (United States)

    López-Archilla, A.I.; Marin, I.; Amils, R.

    2001-01-01

    We studied the correlation between physicochemical and biological characteristics of an acidic river, the Tinto River, in Southwestern Spain. The Tinto River is an extreme environment characterized by its low pH (mean of 2.2) and high concentrations of heavy metals (Fe 2.3 g/L, Zn 0.22 g/L, Cu 0.11 g/L). These extreme conditions are the product of the metabolic activity of chemolithotrophic microorganisms, including iron- and sulfur-oxidizing bacteria, that can be found in high concentrations in its waters. The food chain in the river is very constrained and exclusively microbial. Primary productivity in the Tinto River is the sum of photosynthetic and chemolithotrophic activity. Heterotrophic bacteria and fungi are the major decomposers and protists are the major predators. A correlation analysis including the physicochemical and biological variables suggested a close relationship between the acidic pH values and abundance of both chemolithotrophic bacteria and filamentous fungi. Chemolithotrophic bacteria correlated with the heavy metals found in the river. A principal component analysis of the biotic and abiotic variables suggested that the Tinto River ecosystem can be described as a function of three main groups of variables: pH values, metal concentrations, and biological productivity.

  20. Microbial degradation of fluorinated drugs: biochemical pathways, impacts on the environment and potential applications.

    Science.gov (United States)

    Murphy, Cormac D

    2016-03-01

    Since the discovery over 60 years ago of fluorocortisone's biological properties (9-α-Fluoro derivatives of cortisone and hydrocortisone; Fried J and Sabo EF, J Am Chem Soc 76: 1455-1456, 1954), the number of fluorinated drugs has steadily increased. With the improvement in synthetic methodologies, this trend is likely to continue and will lead to the introduction of new fluorinated substituents into pharmaceutical compounds. Although the biotransformation of organofluorine compounds by microorganisms has been well studied, specific investigations on fluorinated drugs are relatively few, despite the increase in the number and variety of fluorinated drugs that are available. The strength of the carbon-fluorine bond conveys stability to fluorinated drugs; thus, they are likely to be recalcitrant in the environment or may be partially metabolized to a more toxic metabolite. This review examines the research done on microbial biotransformation and biodegradation of fluorinated drugs and highlights the importance of understanding how microorganisms interact with this class of compound from environmental, clinical and biotechnological perspectives.

  1. Microbial degradation of the herbicide molinate by defined cultures and in the environment.

    Science.gov (United States)

    Nunes, Olga C; Lopes, Ana R; Manaia, Célia M

    2013-12-01

    Molinate is a thiocarbamate herbicide used worldwide in rice crop protection. As with other pesticides, molinate is a recognized environmental pollutant, detected in soils, irrigation water, or rivers and bio-accumulated by some wildlife forms. For this reason, and in spite of its low toxicity to humans, environmental protection measures, which include reduction of use and/or remediation processes, are recommended. Due to its physic-chemical properties, molinate can easily disperse and react in the environment, originating diverse transformation products, some with increased toxicity. In spite of being a xenobiotic compound, molinate can also suffer microbial transformation by bacteria or fungi, sometimes serving as nutrient and energy source. In an attempt to isolate microorganisms to be used in the bioremediation of molinate-contaminated sites, a mixed culture, dominated by the actinobacterium Gulosibacter molinativorax ON4(T), was recovered from the runoff of a molinate-producing plant. Beyond a promising tool to decontaminate molinate-polluted sites, this culture also brought interesting insights into the biology of the degradation of this herbicide. In this review, an overview of the distribution and properties of molinate as environmental contaminant, the capability of microorganisms to transform this herbicide, and some reflections about possible bioremediation approaches are made.

  2. Soil microbial activities in Mediterranean environment as desertification indicators along a pluviometric gradient.

    Science.gov (United States)

    Novosadova, I.; Zahora, J.; Ruiz Sinoga, J. D.

    2009-04-01

    In the Mediterranean areas of Southern Spain, unsuitable agricultural practices with adverse environmental conditions (López Bermúdez and Albaladejo, 1990), have led to a permanent degradation and loss of soil fertility. This includes deterioration of the natural plant cover, which protects against erosion by contributing organic matter, the main prerequisite of ecosystem sustainability (Grace et al., 1994). Physico-chemical, microbiological and biochemical soil properties are very responsive and provide immediate and precise information on small changes occurring in soil (Dick and Tabatabai, 1993). There is increasing evidence that such parameters are also sensitive indicators of ecology stress suffered by a soil and its recovery, since microbial activity has a direct influence on the stability and fertility of ecosystems (Smith and Papendick, 1993). One method for recovering degraded soils of such semiarid regions, with their low organic matter content, is to enhance primary productivity and carbon sequestration without any additional nitrogen fertilization and preferably without incorporation of leguminous plants (Martinez Mena et al., 2008). Carbon rich materials can sustain microbial activity and growth, thus enhancing biogeochemical nutrient cycles (Pascual et al., 1997). The present study is focused in the role of physico-chemical and microbial soil properties in Mediterranean environment, in terms of in situ and ex situ microbial transformation of soil carbon and nitrogen, in order to characterise the key soil microbial activities which could strongly affect carbon and nitrogen turnover in soil and hereby soil fertility and soil organic matter "quality". These microbial activities could at unsuitable agricultural practices with adverse environmental conditions induce unfavourable hydrologycal tempo-spatial response. The final results shown modifications in the soil properties studied with the increasing of the aridity. Such changes suppose the soil

  3. Microbial Impacts to the Near-Field Environment Geochemistry: a model for estimating microbial communities in repository drifts at Yucca Mountain

    Science.gov (United States)

    Jolley, Darren M.; Ehrhorn, Thomas F.; Horn, Joanne

    2003-05-01

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned 1 million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 °C and above relative humidities of 90% in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley et al. [FEMS Microbiol. Rev. 20 (1997) 545] by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift to perform two separate mass balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C 160(H 280O 80)N 30P 2S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature and pH at that time. This optimization maximizes those reactions that produce >15 kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated and

  4. Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley; T.F. Ehrhorn; J. Horn

    2002-03-19

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C{sub 160}(H{sub 280}O{sub 80})N{sub 30}P{sub 2}S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated

  5. N2O and N2 emissions from contrasting soil environments - interactive effects of soil nitrogen, hydrology and microbial communities

    Science.gov (United States)

    Christiansen, Jesper; Elberling, Bo; Ribbons, Relena; Hedo, Javier; José Fernández Alonso, Maria; Krych, Lukasz; Sandris Nielsen, Dennis; Kitzler, Barbara

    2016-04-01

    Reactive nitrogen (N) in the environment has doubled relative to the natural global N cycle with consequences for biogeochemical cycling of soil N. Also, climate change is expected to alter precipitation patterns and increase soil temperatures which in Arctic environments may accelerate permafrost thawing. The combination of changes in the soil N cycle and hydrological regimes may alter microbial transformations of soil N with unknown impacts on N2O and N2 emissions from temperate and Arctic soils. We present the first results of soil N2O and N2 emissions, chemistry and microbial communities over soil hydrological gradients (upslope, intermediate and wet) across a global N deposition gradient. The global gradient covered an N-limited high Arctic tundra (Zackenberg-ZA), a pacific temperate rain forest (Vancouver Island-VI) and an N saturated forest in Austria (Klausenleopoldsdorf-KL). The N2O and N2 emissions were measured from intact cores at field moisture in a He-atmosphere system. Extractable NH4+ and NO3-, organic and microbial C and N and potential enzyme-activities were determined on soil samples. Soil genomic DNA was subjected to MiSeq-based tag-encoded 16S rRNA and ITS gene amplicon sequencing for the bacterial and fungal community structure. Similar soil moisture levels were observed for the upslope, intermediate and wet locations at ZA, VI and KL, respectively. Extractable NO3- was highest at the N rich KL and lowest at ZA and showed no trend with soil moisture similar to NH4+. At ZA and VI soil NH4+ was higher than NO3- indicating a tighter N cycling. N2O emissions increased with soil moisture at all sites. The N2O emissions for the wet locations ranked similarly to NO3- with the largest response to soil moisture at KL. N2 emissions were remarkably similar across the sites and increased with soil wetness. Microbial C and N also increased with soil moisture and were overall lowest at the N rich KL site. The potential activity of protease enzyme was site

  6. Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment.

    Science.gov (United States)

    Rabus, Ralf; Boll, Matthias; Heider, Johann; Meckenstock, Rainer U; Buckel, Wolfgang; Einsle, Oliver; Ermler, Ulrich; Golding, Bernard T; Gunsalus, Robert P; Kroneck, Peter M H; Krüger, Martin; Lueders, Tillmann; Martins, Berta M; Musat, Florin; Richnow, Hans H; Schink, Bernhard; Seifert, Jana; Szaleniec, Maciej; Treude, Tina; Ullmann, G Matthias; Vogt, Carsten; von Bergen, Martin; Wilkes, Heinz

    2016-01-01

    Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations funded by the Deutsche Forschungsgemeinschaft on the anaerobic microbial degradation of hydrocarbons ranged from isolation and enrichment of hitherto unknown hydrocarbon-degrading anaerobic microorganisms, discovery of novel reactions, detailed studies of enzyme mechanisms and structures to process-oriented in situ studies. Selected highlights from this program are collected in this synopsis, with more detailed information provided by theme-focused reviews of the special topic issue on 'Anaerobic biodegradation of hydrocarbons' [this issue, pp. 1-244]. The interdisciplinary character of the program, involving microbiologists, biochemists, organic chemists and environmental scientists, is best exemplified by the studies on alkyl-/arylalkylsuccinate synthases. Here, research topics ranged from in-depth mechanistic studies of archetypical toluene-activating benzylsuccinate synthase, substrate-specific phylogenetic clustering of alkyl-/arylalkylsuccinate synthases (toluene plus xylenes, p-cymene, p-cresol, 2-methylnaphthalene, n-alkanes), stereochemical and co-metabolic insights into n-alkane-activating (methylalkyl)succinate synthases to the discovery of bacterial groups previously unknown to possess alkyl-/arylalkylsuccinate synthases by means of functional gene markers and in situ field studies enabled by state-of-the-art stable isotope probing and fractionation approaches. Other topics are Mo-cofactor-dependent dehydrogenases performing O2-independent hydroxylation of hydrocarbons and alkyl side chains (ethylbenzene, p-cymene, cholesterol, n-hexadecane), degradation of p-alkylated benzoates and toluenes, glycyl radical-bearing 4-hydroxyphenylacetate decarboxylase, novel types of carboxylation reactions (for acetophenone, acetone, and potentially also benzene and

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

    Science.gov (United States)

    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.

  8. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

    Science.gov (United States)

    Imhoff, Johannes F.

    2016-01-01

    During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

  9. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

    Directory of Open Access Journals (Sweden)

    Johannes F. Imhoff

    2016-05-01

    Full Text Available During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA as target for the green sulfur bacteria and of two reaction center proteins (pufLM for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS reductase (aprA, sulfate thioesterase (soxB and dissimilatory sulfite reductase (dsrAB for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK for denitrifying bacteria and with genes

  10. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

    Science.gov (United States)

    Imhoff, Johannes F

    2016-05-24

    During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

  11. Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Eric [Scripps and UCSD

    2013-03-01

    Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

    Science.gov (United States)

    Lee, On On; Wang, Yong; Tian, Renmao; Zhang, Weipeng; Shek, Chun Shum; Bougouffa, Salim; Al-Suwailem, Abdulaziz; Batang, Zenon B.; Xu, Wei; Wang, Guang Chao; Zhang, Xixiang; Lafi, Feras F.; Bajic, Vladmir B.; Qian, Pei-Yuan

    2014-01-01

    Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development. PMID:24399144

  13. Measurement of microbial growth in the low nutrient conditions of a simulated subsurface environment

    Science.gov (United States)

    Hand, V. L.; Boult, S.; Vaughan, D. J.; Beadle, I. R.; Humphreys, P.; Wogelius, R. A.

    2003-04-01

    The growth of bacteria in natural porous media may alter porosity and permeability, and therefore hydraulic conductivity. Changes are due both to pore clogging caused by the production of bacterial extracellular polysaccharides (EPS) and the formation of secondary mineral precipitates. Pore clogging has implications not only for fluid flow, but also for contaminant transport. Most biofilm research has been conducted under nutrient rich conditions, quite different from the actual subsurface environment. There is therefore a general need for studies under environmentally relevant conditions. The main objectives were to determine growth under environmental conditions and to produce reproducible homogeneously coated columns of porous media for further experiments on metal transport. Six short columns (length 25mm; diameter 20mm) instrumented with pressure, pH and dissolved oxygen sensors were used. Growth and reproducibility of the biofilm are related to the flow rate, the concentration of the nutrients and the grain size of the porous medium substrate. Two types of porous media were used; a single mineral quartz media with a constant grain size and a natural mixed mineral assemblage of non-uniform grain size. Nutrient used was a landfill derived carbon source present in synthetic trench leachate (STL) diluted with synthetic groundwater (SGW) by a factor of 100. The STL was pumped through each column at a constant, environmentally relevant flow rate of 0.109 ml/min. Experiments were performed under both aerobic and anaerobic conditions contained in a temperature-controlled room at 10^oC. Measurement of the pressure increase within the column apparatus was made, as an increase in pressure is relative to the resistance of the media to flow and indicates biofilm formation and pore clogging within the column. Monitoring of dissolved oxygen shows the metabolic conditions of the bacteria and also the biological oxygen demand. Column effluent was analysed for changes in

  14. Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

    Science.gov (United States)

    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

  15. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  16. Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments

    NARCIS (Netherlands)

    Bengtson, P.; Bastviken, D.; De Boer, W.; Öberg, G.

    2009-01-01

    Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extra

  17. Food Safety in the Domestic Environment: An Interdisciplinary Investigation of Microbial Hazards During Food Preparation

    NARCIS (Netherlands)

    Fischer, A.R.H.; Jong, de A.E.I.; Asselt, van E.D.; Jonge, de R.; Frewer, L.J.; Nauta, M.J.

    2007-01-01

    It has been established that, to a considerable extent, the domestic hygiene practices adopted by consumers can result in a greater or lesser microbial load in prepared meals. In the research presented here, an interdisciplinary study is reported in which interviews, observations of consumers prepar

  18. Spatial distribution of microbial populations and carbon cycle in the subsurface environment of the Horonobe area, Hokkaido, Japan

    Science.gov (United States)

    Amano, Y.; Ise, K.; Terashima, M.; Sasaki, Y.; Amamiya, H.; Yoshikawa, H.

    2014-12-01

    Microorganisms are widely distributed in the subsurface environments. However, the distribution, role and rate of metabolisms, and the source of their activity are not well known. In this study, we investigated deep groundwater samples from sedimentary rocks, containing saturated methane and CO2, using boreholes at the Horonobe Underground Research Laboratory (URL), northern Hokkaido, Japan. The hydrochemical conditions of groundwaters, such as in-situ water pressure, temperature, electric conductivity, pH, redox potential, were monitored without degassing at multiple intervals along the borehole. Groundwater samples were taken periodically and chemical composition was analyzed using ICP-MS, etc. Cell counts were in the range of 103 to 105 cells ml-1. Molecular analyses revealed the spatial distribution and heterogeneity of the microbial population. Abundant methanogens were detected in the groundwater, and 80% of them were related to either Methanoregula boonei or Methanobacterium flexile that can utilize H2/CO2 by methanogenesis. Phylotypes clustered within the phylum Firmicutes, beta-Proteobacteria, delta-Proteobacteria and candidate division TM7 were dominant in the groundwater samples. Laboratory experiments using a culture technique showed that humic substances purified from the groundwater at Horonobe area appear to be degraded by microorganisms. Our results suggest that microbial spatial distributions in the subsurface environment were correlated closely with geochemical conditions, such as redox condition and carbon sources. In addition, it is inferred that humic substances are one of the important carbon sources for the subsurface microbial redox processes in the environment. This study was partly funded by the Ministry of Economy, Trade and Industry of Japan.

  19. Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

    Science.gov (United States)

    Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

    2015-03-01

    Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.

  20. Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments.

    Science.gov (United States)

    Moissl-Eichinger, Christine; Auerbach, Anna K; Probst, Alexander J; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

    2015-03-17

    Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.

  1. Comparison of the Microbial Community Composition at Yucca Mountain and Laboratory Test Nuclear Repository Environments

    Energy Technology Data Exchange (ETDEWEB)

    Horn, J; Carrillo, C; Dias, V

    2002-10-09

    The microbiological community structure within a proposed nuclear waste repository at Yucca Mountain (YM), NV was determined. Microbial growth from collected rock was detected using simulated ground water as a growth medium, with or without amendment of a carbon source. Grown isolates were identified by 16s ribosomal DNA (rDNA) sequence analysis. A more complete compositional analysis of the microbial community located at the proposed nuclear waste repository site was performed using environmental DNA isolation and subsequent identification of amplified 16s rDNA genes. Concurrently, a series of corrosion testing tanks that simulate the evolution of anticipated environmental conditions within the proposed repository have been subjected to the same type of analyses.

  2. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

    DEFF Research Database (Denmark)

    Klatt, Christian G.; Inskeep, William P.; Herrgard, Markus;

    2013-01-01

    Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across...... the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average 53Mbp/site) were...

  3. Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments.

    Science.gov (United States)

    Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

    2014-06-01

    Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.

  4. Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Kuchi, N.; Kale, D.; Anil, A.C.

    processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J. 1, 19-27. 15 Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., Oakley, B.B., 2005. Ubiquity and diversity of ammonia... and the processes occurring and the communities present in the surface sediments have a profound effect on the local and global cycling of elements (Arrigo, 2005). Recently, Singh et al. (2010) reported the Archaeal community distribution through phylogenetic...

  5. Microbial activity in the subterranean environment of Dârninii Cave, Bihor Mountains

    Directory of Open Access Journals (Sweden)

    Rahela Carpa

    2009-11-01

    Full Text Available Six cave material samples from Dârninii Cave, Bihor Mountains, were microbiologically andenzymologically analyzed. The microbiological analyses consisted in determining the presence ofoligotrophs, aerobic heterotrophs, ammonifiers, nitrate and nitrite bacteria, denitrifiers and determining thepresence of micromycetes. In order to form a complete image on the microbial processes from this habitat,the bacteriological analyses were completed with quantitative and qualitative enzymological analyses. At allthe six samples of cave material the next quantitative enzymatic activities were performed: actual andpotential dehydrogenase, catalase and phosphatase. Only regarding the intensity of the processesdifferences were noticed. The qualitative enzymatic activities: amylase, dextranase, saccharase, maltaseand levanase, were not present at studied samples.

  6. Microbial Diversity of Carbonate Chimneys at the Lost City Hydrothermal Field: Implications for Life-Sustaining Systems in Peridotite Seafloor Environments

    Science.gov (United States)

    Schrenk, M. O.; Cimino, P.; Kelley, D. S.; Baross, J. A.

    2002-12-01

    The Lost City Hydrothermal Field (LCHF) is a novel peridotite-hosted vent environment discovered in Dec. 2000 at 30 N near the Mid-Atlantic Ridge. This field contains multiple large (up to 60 m), carbonate chimneys venting high pH (9-10), moderate temperature (45-75 C) fluids. The LCHF is unusual in that it is located on 1.5 my-old oceanic crust, 15 km from the nearest spreading axis. Hydrothermal flow in this system is believed to be driven by exothermic serpentinization reactions involving iron-bearing minerals in the underlying seafloor. The conditions created by such reactions, which include significant quantities of dissolved methane and hydrogen, create habitats for microbial communities specifically adapted to this unusual vent environment. Ultramafic, reducing hydrothermal environments like the LCHF may be analogous to geologic settings present on the early Earth, which have been suggested to be important for the emergence of life. Additionally, the existence of hydrothermal environments far away from an active spreading center expands the range of potential life-supporting environments elsewhere in the solar system. To study the abundance and diversity of microbial communities inhabiting the environments that characterize the LCHF, carbonate chimney samples were analyzed by microscopic and molecular methods. Cell densities of between 105 and 107 cells/g were observed within various samples collected from the chimneys. Interestingly, 4-11% of the microbial population in direct contact with vent fluids fluoresced with Flavin-420, a key coenzyme involved in methanogenesis. Enrichment culturing from chimney material under aerobic and anaerobic conditions yielded microorganisms in the thermophilic and mesophilic temperature regimes in media designed for methanogenesis, methane-oxidation, and heterotrophy. PCR analysis of chimney material indicated the presence of both Archaea and Eubacteria in the carbonate samples. SSU rDNA clone libraries constructed from the

  7. Optimal resting-growth strategies of microbial populations in fluctuating environments

    OpenAIRE

    Nico Geisel; Vilar, Jose M. G.; J. Miguel Rubi

    2011-01-01

    11 p. Bacteria spend most of their lifetime in non-growing states which allow them to survive extended periods of stress and starvation. When environments improve, they must quickly resume growth to maximize their share of limited nutrients. Cells with higher stress resistance often survive longer stress durations at the cost of needing more time to resume growth, a strong disadvantage in competitive environments. Here we analyze the basis of optimal strategies that microorganisms can use ...

  8. Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.

    Science.gov (United States)

    Hamamura, N; Macur, R E; Korf, S; Ackerman, G; Taylor, W P; Kozubal, M; Reysenbach, A-L; Inskeep, W P

    2009-02-01

    The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA-like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA-like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6-3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2-8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and beta-Proteobacteria. Modified primers designed around previously characterized and newly identified aroA-like genes successfully amplified new lineages of aroA-like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA-like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences

  9. Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment

    Science.gov (United States)

    Carré, Claire; Cellamare, Maria; Duval, Charlotte; Intertaglia, Laurent; Lavergne, Céline; Roques, Cécile

    2017-01-01

    This study describes, for the first time, the water chemistry and microbial diversity in Dziani Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6–14.5 g L-1 eq. CO32-, i.e. 160–220 mM compare to around 2–2.5 in seawater), with salinity up to 52 psu, 1.5 higher than seawater. Hierarchical clustering discriminated Dziani Dzaha water from other alkaline, saline lakes, highlighting its thalassohaline nature. The phytoplankton biomass was very high, with a total chlorophyll a concentration of 524 to 875 μg chl a L-1 depending on the survey, homogeneously distributed from surface to bottom (4 m). Throughout the whole water column the photosynthetic biomass was dominated (>97% of total biovolume) by the filamentous cyanobacteria Arthrospira sp. with a straight morphotype. In situ daily photosynthetic oxygen production ranged from 17.3 to 22.2 g O2 m-2 d-1, consistent with experimental production / irradiance measurements and modeling. Heterotrophic bacterioplankton was extremely abundant, with cell densities up to 1.5 108 cells mL-1 in the whole water column. Isolation and culture of 59 Eubacteria strains revealed the prevalence of alkaliphilic and halophilic organisms together with taxa unknown to date, based on 16S rRNA gene analysis. A single cloning-sequencing approach using archaeal 16S rDNA gene primers unveiled the presence of diverse extremophilic Euryarchaeota. The water chemistry of Dziani Dzaha Lake supports the hypothesis that it was derived from seawater and strongly modified by geological conditions and microbial activities that increased the alkalinity. Dziani Dzaha has a unique consortium of cyanobacteria, phytoplankton, heterotrophic Eubacteria and Archaea, with very few unicellular protozoa, that will deserve further deep analysis to unravel its uncommon diversity. A single taxon, belonging to the genus Arthrospira, was

  10. Microbial colonization affects the efficiency of photovoltaic panels in a tropical environment.

    Science.gov (United States)

    Shirakawa, Marcia A; Zilles, Roberto; Mocelin, Andre; Gaylarde, Christine C; Gorbushina, Anna; Heidrich, Gabriele; Giudice, Mauro C; Del Negro, Gilda M B; John, Vanderley M

    2015-07-01

    Sub-aerial biofilm (SAB) development on solar panels was studied in São Paulo. After 6, 12 and 18 months' exposure, photovoltaic panels were covered by increasing proportions of organic matter (42%, 53% and 58%, respectively). Fungi were an important component of these biofilms; very few phototrophs were found. Major microorganisms detected were melanised meristematic ascomycetes and pigmented bacterial genera Arthrobacter and Tetracoccus. While diverse algae, cyanobacteria and bacteria were identified in biofilms at 6 and 12 months, diversity at a later stage was reduced to that typical for SAB: the only fungal group detected in 18 month biofilm was the meristematic Dothideomycetes and the only phototrophs Ulothrix and Chlorella. Photovoltaic modules showed significant power reductions after 6, 12 (both 7%) and 18 (11%) months. The lack of difference in power reduction between 6 and 12 months reflects the dual nature of soiling, which can result from the deposition of particulates as well as from SAB fouling. Although 12-month old SAB demonstrated an almost 10-fold increase in fungal colonization and a higher organic content, the larger non-microbial particles (above 10 μm), which were important for efficiency reduction of lightly-biofilmed panels, were removed by high rainfall just before the 12-month sampling.

  11. Isolation of PCR quality microbial community DNA from heavily contaminated environments.

    Science.gov (United States)

    Gunawardana, Manjula; Chang, Simon; Jimenez, Abraham; Holland-Moritz, Daniel; Holland-Moritz, Hannah; La Val, Taylor P; Lund, Craig; Mullen, Madeline; Olsen, John; Sztain, Terra A; Yoo, Jennifer; Moss, John A; Baum, Marc M

    2014-07-01

    Asphalts, biochemically degraded oil, contain persistent, water-soluble compounds that pose a significant challenge to the isolation of PCR quality DNA. The adaptation of existing DNA purification protocols and commercial kits proved unsuccessful at overcoming this hurdle. Treatment of aqueous asphalt extracts with a polyamide resin afforded genomic microbial DNA templates that could readily be amplified by PCR. Physicochemically distinct asphalt samples from five natural oil seeps successfully generated the expected 291 bp amplicons targeting a region of the 16S rRNA gene, illustrating the robustness of the method. DNA recovery yields were in the 50-80% range depending on how the asphalt sample was seeded with exogenous DNA. The scope of the new method was expanded to include soil with high humic acid content. DNA from soil samples spiked with a range of humic acid concentrations was extracted with a commercial kit followed by treatment with the polyamide resin. The additional step significantly improved the purity of the DNA templates, especially at high humic acid concentrations, based on qPCR analysis of the bacterial 16S rRNA genes. The new method has the advantages of being inexpensive, simple, and rapid and should provide a valuable addition to protocols in the field of petroleum and soil microbiology. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Microbiological and molecular biological methods for monitoring microbial inoculants and their effects in the soil environment

    NARCIS (Netherlands)

    Elsas, van J.D.; Duarte, G.F.; Rosado, A.S.; Smalla, K.

    1998-01-01

    As the use of biotechnology products, such as genetically modified microorganisms (GMMs), in the environment might bring about undesirable ecological effects, it is important that the environmental fate of inoculant organisms, as well as any effects of their release, are assessed. Ideally, pilot stu

  13. Early childhood environment related to microbial exposure and the occurrence of atopic disease at school age

    NARCIS (Netherlands)

    de Meer, G; Janssen, NAH; Brunekreef, B

    2005-01-01

    Background: There is a growing body of evidence that the early childhood environment with respect to day care attendance, older siblings, pet ownership, and early life airway infections may protect from developing atopic disease. Few studies have distinguished between atopic sensitization and sympto

  14. USE OF STABLE CARBON ISOTOPE RATIOS OF FATTY ACIDS TO EVALUATE MICROBIAL CARBON SOURCES IN TERRESTRIAL ENVIRONMENTS

    Science.gov (United States)

    We use measurements of the concentration and stable carbon isotopic ratio (D 13C) of individual microbial phospholipid fatty acids (PLFAs) in soils as indicators of live microbial biomass levels and microbial carbon source. We found that intensive sugar cane cultivation leads to ...

  15. Community Structure and Function of High-temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-06-01

    Full Text Available Six phototrophic microbial mat communities from different geothermal springs (YNP were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average~ 53 Mbp/site were subjected to multiple taxonomic, phylogenetic and functional analyses. All methods, including G+C content distribution, MEGAN analyses and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7 and Fischerella-like populations at White Creek (WC_6. Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp. were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae, and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria population from Bath Lake Vista Annex (BLVA_20. Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes; however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional

  16. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments.

    Science.gov (United States)

    Klatt, Christian G; Inskeep, William P; Herrgard, Markus J; Jay, Zackary J; Rusch, Douglas B; Tringe, Susannah G; Niki Parenteau, M; Ward, David M; Boomer, Sarah M; Bryant, Donald A; Miller, Scott R

    2013-01-01

    Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average ∼53 Mbp/site) were subjected to multiple taxonomic, phylogenetic, and functional analyses. All methods, including G + C content distribution, MEGAN analyses, and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7) and Fischerella-like populations at White Creek (WC_6). Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp.) were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae), and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria) population from Bath Lake Vista Annex (BLVA_20). Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes); however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional

  17. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    Directory of Open Access Journals (Sweden)

    Lucie Musilova

    2016-07-01

    Full Text Available Secondary plant metabolites (SPMEs play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs and polyaromatic hydrocarbons (PAHs. Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

  18. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    Science.gov (United States)

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  19. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    Science.gov (United States)

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-03-10

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.

  20. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.

    Science.gov (United States)

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-07-29

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

  1. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    KAUST Repository

    Thompson, Luke R

    2013-05-11

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. 2013 The

  2. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

    Science.gov (United States)

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  3. Microbial diversity in a permanently cold and alkaline environment in Greenland

    DEFF Research Database (Denmark)

    Glaring, Mikkel Andreas; Vester, Jan Kjølhede; Lylloff, Jeanette Eva

    2015-01-01

    representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups...... with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California....

  4. Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes.

    Science.gov (United States)

    Dusny, Christian; Schmid, Andreas

    2015-06-01

    Life is based on the cell as the elementary replicative and self-sustaining biological unit. Each single cell constitutes an independent and highly dynamic system with a remarkable individuality in a multitude of physiological traits and responses to environmental fluctuations. However, with traditional population-based cultivation set-ups, it is not possible to decouple inherent stochastic processes and extracellular contributions to phenotypic individuality for two central reasons: the lack of environmental control and the occlusion of single-cell dynamics by the population average. With microfluidic single-cell analysis as a new cell assay format, these issues can now be addressed, enabling cultivation and time-resolved analysis of single cells in precisely manipulable extracellular environments beyond the bulk. In this article, we explore the interplay of cellular physiology and environment at a single-cell level. We review biological basics that govern the functional state of the cell and put them in context with physical fundamentals that shape the extracellular environment. Furthermore, the significance of single-cell growth rates as pivotal descriptors for global cellular physiology is discussed and highlighted by selected studies. These examples illustrate the unique opportunities of microfluidic single-cell cultivation in combination with growth rate analysis, addressing questions of fundamental bio(techno)logical interest.

  5. ComBase: a common database on microbial responses to food environments.

    Science.gov (United States)

    Baranyi, József; Tamplin, Mark L

    2004-09-01

    The advancement of predictive microbiology relies on available data that describe the behavior of microorganisms in different environmental matrices. For such information to be useful to the predictive microbiology research community, data must be organized in a manner that permits efficient access and data retrieval. Here, we describe a database protocol that encompasses observations of bacterial responses to food environments, resulting in a database (ComBase) for predictive microbiology purposes. The data included in ComBase were obtained from cooperating research institutes and from the literature and are publicly available via the Internet.

  6. Incorporating rosemary diterpenes in lamb diet to improve microbial quality of meat packed in different environments.

    Science.gov (United States)

    Ortuño, Jordi; Serrano, Rafael; Bañón, Sancho

    2017-01-31

    The dietary use of phytochemicals may contribute to improving lamb meat preservation under different packing atmospheres. The objective was to test the preservative potential of a dietary rosemary extract (RE) containing carnosic acid and carnosol (at 1:1 w:w) in chilled lamb patties packed in air, vacuum and 70/30 O2 /CO2 modified atmosphere. Three experimental diets, (C) control, (RE) C plus 600 mg RE/kg feed and (E) C plus 600 mg vitamin E/kg, were given to fattening lambs. Unlike the C- and E-diets, the RE-diet had a double antimicrobial and antioxidant effect on the lamb patties packed in all the environments studied. The RE-diet inhibited total viable and lactic acid bacteria and Enterobacteriaceae, but not Brochothrix thermosphacta and Pseudomonas spp. and also improved oxidative stability (measured as CIE Lab color and thiobarbituric reagent substances), appearance and odor. The E-diet had a better antioxidant effect than the RE-diet but had no antimicrobial effects. Escherichia coli and Salmonella spp. were not detected. The dietary use of RE was most suitable for preserving vacuum-packed meat, which is more exposed to spoilage by anaerobic bacteria, while the use of dietary vitamin E allowed better control of oxidation in the meat packed in a bacteriostatic and oxidizing environment.

  7. Microbial cellulases – Diversity & biotechnology with reference to mangrove environment: A review

    Directory of Open Access Journals (Sweden)

    B.C. Behera

    2017-06-01

    Full Text Available Cellulose is an abundant natural biopolymer on earth, found as a major constituent of plant cell wall in lignocellulosic form. Unlike other compounds cellulose is not easily soluble in water hence enzymatic conversion of cellulose has become a key technology for biodegradation of lignocellulosic materials. Microorganisms such as aerobic bacteria, fungi, yeast and actinomycetes produce cellulase that degrade cellulose by hydrolysing the β-1, 4-glycosidic linkages of cellulose. In contrast to aerobic bacteria, anaerobic bacteria lack the ability to effectively penetrate into the cellulosic material which leads to the development of complexed cellulase systems called cellulosome. Among the different environments, the sediments of mangrove forests are suitable for exploring cellulose degrading microorganisms because of continuous input of cellulosic carbon in the form of litter which then acts as a substrate for decomposition by microbe. Understanding the importance of cellulase, the present article overviews the diversity of cellulolytic microbes from different mangrove environments around the world. The molecular mechanism related to cellulase gene regulation, expression and various biotechnological application of cellulase is also discussed.

  8. Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility

    Directory of Open Access Journals (Sweden)

    Nieto Pamela A

    2008-11-01

    Full Text Available Abstract Background Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer A. thiooxidans and A. caldus (sulfur oxidizers that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below. Results Acidithiobacilli have predicted FeoB-like Fe(II and Nramp-like Fe(II-Mn(II transporters. They also have 14 different TonB dependent ferri-siderophore transporters of diverse siderophore affinity, although they do not produce classical siderophores. Instead they have predicted novel mechanisms for dicitrate synthesis and possibly also for phosphate-chelation mediated iron uptake. It is hypothesized that the unexpectedly large number and diversity of Fe(III-uptake systems confers versatility to this group of acidophiles, especially in higher pH environments (pH 4–5 where soluble iron may not be abundant. In contrast, Leptospirilla have only a FtrI-Fet3P-like permease and three TonB dependent ferri-dicitrate siderophore systems. This paucity of iron

  9. Pulmonary infection by Yersinia pestis rapidly establishes a permissive environment for microbial proliferation.

    Science.gov (United States)

    Price, Paul A; Jin, Jianping; Goldman, William E

    2012-02-21

    Disease progression of primary pneumonic plague is biphasic, consisting of a preinflammatory and a proinflammatory phase. During the long preinflammatory phase, bacteria replicate to high levels, seemingly uninhibited by normal pulmonary defenses. In a coinfection model of pneumonic plague, it appears that Yersinia pestis quickly creates a localized, dominant anti-inflammatory state that allows for the survival and rapid growth of both itself and normally avirulent organisms. Yersinia pseudotuberculosis, the relatively recent progenitor of Y. pestis, shows no similar trans-complementation effect, which is unprecedented among other respiratory pathogens. We demonstrate that the effectors secreted by the Ysc type III secretion system are necessary but not sufficient to mediate this apparent immunosuppression. Even an unbiased negative selection screen using a vast pool of Y. pestis mutants revealed no selection against any known virulence genes, demonstrating the transformation of the lung from a highly restrictive to a generally permissive environment during the preinflammatory phase of pneumonic plague.

  10. Microbial indicators, pathogens and methods for their monitoring in water environment.

    Science.gov (United States)

    Saxena, Gaurav; Bharagava, Ram Naresh; Kaithwas, Gaurav; Raj, Abhay

    2015-06-01

    Water is critical for life, but many people do not have access to clean and safe drinking water and die because of waterborne diseases. The analysis of drinking water for the presence of indicator microorganisms is key to determining microbiological quality and public health safety. However, drinking water-related illness outbreaks are still occurring worldwide. Moreover, different indicator microorganisms are being used in different countries as a tool for the microbiological examination of drinking water. Therefore, it becomes very important to understand the potentials and limitations of indicator microorganisms before implementing the guidelines and regulations designed by various regulatory agencies. This review provides updated information on traditional and alternative indicator microorganisms with merits and demerits in view of their role in managing the waterborne health risks as well as conventional and molecular methods proposed for monitoring of indicator and pathogenic microorganisms in the water environment. Further, the World Health Organization (WHO) water safety plan is emphasized in order to develop the better approaches designed to meet the requirements of safe drinking water supply for all mankind, which is one of the major challenges of the 21st century.

  11. Effects of electron donors on the microbial reductive dechlorination of hexachlorocyclohexane and on the environment.

    Science.gov (United States)

    Cui, Zhaojie; Meng, Fanli; Hong, Jinglan; Li, Xiangzhi; Ren, Xiaohua

    2012-06-01

    The reductive biotransformation of α-, β-, γ-, and δ-hexachlorocyclohexane isomers was investigated using five alternative electron donors (i.e., glucose plus methanol, glucose only, methanol only, acetate, and ethanol) in a batch assay of an HCH-dechlorinating anaerobic culture. In addition, a life cycle assessment was conducted using the IMPACT2002+ method to evaluate the environmental effects of HCH bioremediation with the aforementioned electron donors. Results showed that the electron donors methanol plus glucose, ethanol, glucose, and methanol can significantly enhance the biotransformation of each HCH isomer. However, the amended electron donors and the byproduct of the anoxic/anaerobic systems may negatively affect the environment (e.g., respiratory inorganic, land occupation, global warming, and non-renewable energy categories). These effects are attributed to the electron donor production processes. To avoid secondary pollutants, a linear relationship between the upper bound electron donor applications and HCH concentration was observed from an environmental perspective. Results indicated that the methanol scenario was the most suitable option for the current research.

  12. The potential of autochthonous microbial culture encapsulation in a confined environment for phenol biodegradation.

    Science.gov (United States)

    Azaizeh, Hassan; Kurzbaum, Eyal; Said, Ons; Jaradat, Husain; Menashe, Ofir

    2015-10-01

    Olive mill wastewater (OMWW) is claimed to be one of the most polluting effluents produced by agro-food industries, providing high contaminants load that encase cytotoxic agents such as phenolic and polyphenolic compounds. Therefore, a significant and continuous stress episode is induced once the mixed liquor of the wastewater treatment plants (WWTP's) is being exposed to OMWW. The use of bio-augmentation treatment procedures can be useful to eliminate or reduce such stress episodes. In this study, we have estimated the use of autochthonous biomass implementation within small bioreactor platform (SBP) particles as a bio-augmentation method to challenge against WWTPs stress episodes. Our results showed that SBP particles significantly reduced the presence of various phenolics: tannic, gallic and caffeic acid in a synthetic medium and in crude OMWW matrix. Moreover, the SBP particles succeeded to biodegrade a very high concentration of phenol blend (3000 mg L(-1)). Our findings indicated that the presence of the SBP microfiltration membrane has reduced the phenol biodegradation rate by 50 % compared to the same suspended culture. Despite the observed reduction in biodegradation rate, encapsulation in a confined environment can offer significant values such as overcoming the grazing forcers and dilution, thus achieving a long-term sufficient biomass. The potential for reducing stress episodes caused by cytotoxic agents through bio-augmentation treatment procedure using the SBP technology is discussed.

  13. Conjunctival microbial flora of clinically normal persons who work in a hospital environment

    Directory of Open Access Journals (Sweden)

    Trindade Rita de Cássia

    2000-01-01

    Full Text Available The objective of the work was to study the microbiota of the conjunctival secretion of health professionals. Samples were collected from the clinically normal eyes of 40 health professionals in four different sectors, Proctology, General Intensive Care Unit (ICU, Male Ward, and Oncology of Hospital das Clínicas Dr. Augusto Leite, Aracaju, SE, Brazil. Ten professionals from each sector were selected. The samples were inoculated into various culture media: blood agar, Chapman agar, EMB medium (Teague, and Sabouraud dextrose agar with chloramphenicol. The bacteria most frequently isolated from all the sectors were Staphylococcus epidermidis (45.0% and Bacillus sp (29.0%. The least frequent bacteria were Proteus sp (6.1%, Staphylococcus aureus (4.1%, Enterobacter sp (4.1%, Alcaligenes sp (4.1%, Citrobacter sp (2.1%, Moraxella sp (2.1%, and Proteus mirabilis (2.1%. Fungi were not isolated. These results confirm the continuous contamination of the conjunctival sac of these professionals by the external environment, while at the same time confirming that the mechanisms of local defence continue to be intact, preventing the fixation of invading microorganisms.

  14. Microbial communities in large-scale wood piles and their effects on wood quality and the environment.

    Science.gov (United States)

    Noll, Matthias; Jirjis, Raida

    2012-08-01

    The demand of renewable energy sources, i.e. biomass, is steadily increasing worldwide to reduce the need of fossil energy sources. Biomass such as energy crops, woody species, forestry and agricultural residues are the most common renewable energy sources. Due to uneven demand for wood fuel, the material is mostly stored outdoors in chip piles or as logs until utilisation. Storage of biomass is accompanied by chemical, physical and biological processes which can significantly reduce the fuel quality. However, heating plants require high-quality biomass to ensure efficient operation, thereby minimising maintenance costs. Therefore, optimised storage conditions and duration times for chipped wood and tree logs have to be found. This paper aims at reviewing available knowledge on the pathways of microbial effects on stored woody biomass and on investigations of the fungal and bacterial community structure and identity. Moreover, potential functions of microorganisms present in wood chip piles and logs are discussed in terms of (1) reduction of fuel quality, (2) catalysing self-ignition processes, and (3) constituting health risk and unfriendly work environment.

  15. Environmental Shortcourse Final report [Joint US-EC Short Course on Environmental Biotechnology: Microbial Catalysts for the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Zylstra, Gerben; van der Meer, Jan Roelof

    2013-03-05

    The Joint US-EC Short Course on Environmental Biotechnology is designed for several purposes. One of the central tenets is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that will set the groundwork for future overseas collaborative interactions. The course is also designed to give the scientists hands-on experience in modern, up-to-date biotechnological methods for the analysis of microbes and their activities pertinent to the remediation of pollutants in the environment. The 2011 course covered multiple theoretical and practical topics in environmental biotechnology. The practical part was centered around a full concise experiment to demonstrate the possibility for targeted remediation of contaminated soil. Experiments included chemical, microbiological, and molecular analyses of sediments and/or waters, contaminant bioavailability assessment, seeded bioremediation, gene probing, PCR amplification, microbial community analysis based on 16S rRNA gene diversity, and microarray analyses. Each of these topics is explained in detail. The practical part of the course was complemented with two lectures per day, given by distinguished scientists from the US and from Europe, covering a research area related to what the students are doing in the course.

  16. Microbial and Metabolic Diversity of the Alkaline Hot Springs of Paoha Island: A Late Archean and Proterozoic Ocean Analogue Environment.

    Science.gov (United States)

    Foster, I. S.; Demirel, C.; Hyde, A.; Motamedi, S.; Frantz, C. M.; Stamps, B. W.; Nunn, H. S.; Oremland, R. S.; Rosen, M.; Miller, L. G.; Corsetti, F. A.; Spear, J. R.

    2016-12-01

    Paoha Island formed 450 years ago within Mono Lake, California, as a result of magmatic activity in the underlying Long Valley Caldera. Previous studies of Paoha Island hot springs focused on the presence of novel organisms adapted to high levels of arsenic (114-138 µM). However, the microbial community structure, relationship with Mono Lake, and preservation potential of these communities remains largely unexplored. Here, we present water chemistry, 16S and 18S rRNA gene sequences, and metagenomic data for spring water and biofilms sampled on a recently exposed mudflat along the shoreline of Paoha Island. Spring waters were hypoxic, alkaline, and saline, had variable temperature (39-70 °C near spring sources) and high concentrations of arsenic, sulfide and reduced organic compounds. Thermodynamic modeling based on spring water chemistry indicated that sulfide and methane oxidation were the most energetically favorable respiratory metabolisms. 16S rRNA gene sequencing revealed distinct communities in different biofilms: red biofilms were dominated by arsenite-oxidizing phototrophs within the Ectothiorhodospiraceae, while OTUs most closely related to the cyanobacterial genus Arthrospira were present in green biofilms, as well as a large proportion of sequences assigned to sulfur-oxidizing bacteria. Metagenomic analysis identified genes related to arsenic resistance, arsenic oxidation/reduction, sulfur oxidation and photosynthesis. Eukaryotic rRNA gene sequencing analyses revealed few detectable taxa in spring biofilms and waters compared to Mono Lake; springs receiving splash from the lake were dominated by the alga Picocystis. The co-occurrence of hypoxia, high pH, and close proximity of anoxygenic and oxygenic phototrophic mats makes this site a potential Archean/Proterozoic analogue environment, but suggests that similar environments if preserved in the rock record, may not preserve evidence for community dynamics or the existence of photosynthetic metabolisms.

  17. Insight into the microbial community structure of a Norwegian deep-water coral reef environment

    Science.gov (United States)

    Jensen, Sigmund; Neufeld, Josh D.; Birkeland, Nils-Kåre; Hovland, Martin; Murrell, J. Colin

    2008-11-01

    Deep-water coral reefs support rich biological communities below the photic zone of fjords and continental shelves around the world. In this environment, life is enclosed within cold permanent darkness, in stark contrast to life in tropical coral reefs. We collected samples of water, sediment and a Desmacidon sp. sponge from a deep-water coral reef off the coast of Norway, and characterised bacterial communities with focus on primary producers in the dark. Following DNA extraction, PCR amplification and 16S rRNA gene library sequencing, bioinformatic analyses demonstrated significant differences between bacterial communities associated with the three samples. The finding that 50% of the clones showed cultured bacteria reflects the novel and uncharacterised diversity associated with these deep-water coral reefs. A total of 13 bacterial phyla were identified. Acidobacteria dominated the sponge library and Proteobacteria dominated the bacterioplankton and sediment libraries. Phylogenetic analysis revealed a possible new clade of sponge-associated Acidobacteria, which includes representatives from the Desmacidon sp. (Norway), Rhopaloeides odorabile (Australia) and Discodermia dissoluta (Curacao). Furthermore, the targeted recovery of a particulate methane monooxygenase ( pmoA) gene from the Desmacidon sp. DNA extract suggests that as yet uncultivated type I methanotrophs may mediate methane oxidation in this deep-water coral reef. Methanotrophs were not identified in the 16S rRNA gene libraries, but the presence of a high number (8%) of clones related to sulfide-, nitrite- and iodide-oxidising bacteria suggests chemosynthesis to be involved with maintenance of the deep-water coral reef ecosystem.

  18. Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane

    KAUST Repository

    Jeong, Sanghyun

    2017-07-25

    Four dual media filters (DMFs) were operated in a biofiltration mode with different engineered environments (DMF I and II: coagulation with/without acidification and DMF III and IV: without/with chlorination). Designed biofilm enrichment reactors (BERs) containing the removable reverse osmosis (RO) coupons, were connected at the end of the DMFs in parallel to analyze the biofilm on the RO membrane by DMF effluents. Filtration performances were evaluated in terms of dissolved organic carbon (DOC) and assimilable organic carbon (AOC). Organic foulants on the RO membrane were also quantified and fractionized. The bacterial community structures in liquid (seawater and effluent) and biofilm (DMF and RO) samples were analyzed using 454-pyrosequencing. The DMF IV fed with the chlorinated seawater demonstrated the highest reductions of DOC including LMW-N as well as AOC among the other DMFs. The DMF IV was also effective in reducing organic foulants on the RO membrane surface. The bacterial community structure was grouped according to the sample phase (i.e., liquid and biofilm samples), sampling location (i.e., DMF and RO samples), and chlorination (chlorinated and non-chlorinated samples). In particular, the biofilm community in the DMF IV differed from the other DMF treatments, suggesting that chlorination exerted as stronger selective pressure than pH adjustment or coagulation on the biofilm community. In the DMF IV, several chemoorganotrophic chlorine-resistant biofilm-forming bacteria such as Hyphomonas, Erythrobacter, and Sphingomonas were predominant, and they may enhance organic carbon degradation efficiency. Diverse halophilic or halotolerant organic degraders were also found in other DMFs (i.e., DMF I, II, and III). Various kinds of dominant biofilm-forming bacteria were also investigated in RO membrane samples; the results provided possible candidates that cause biofouling when DMF process is applied as the pretreatment option for the RO process.

  19. BIOMEX (Biology and Mars Experiment): Preliminary results on Antarctic black cryptoendolithic fungi in ground based experiments

    OpenAIRE

    C. Pacelli; Selbmann, L.; S. Onofri; de Vera, J.P.P.

    2014-01-01

    The main goal for astrobiologists is to find traces of present or past life in extraterrestrial environment or in meteorites. Biomolecules, such as lipids, pigments or polysaccharides, may be useful to establish the presence of extant or extinct life (Simoneit, B et al., 1998). BIOMEX (Biology and Mars Experiment) aims to measure to what extent biomolecules, such as pigments and cellular components, preserve their stability under space and Mars-like conditions. The experiment has just been la...

  20. Comparative microbial diversity and redox environments of black shale and stromatolite facies in the Mesoproterozoic Xiamaling Formation

    Science.gov (United States)

    Luo, Genming; Hallmann, Christian; Xie, Shucheng; Ruan, Xiaoyan; Summons, Roger E.

    2015-02-01

    The composition of microbial communities and their relationship to ocean redox structure in the Precambrian are topics of continuing interest in geobiology. Our knowledge of organismic diversity and environmental conditions during this time are mostly based on fragmentary paleontological and geochemical records and might be skewed accordingly. In North China the Xiamaling Formation (∼1.37 Ga) is characterized by black shales of relatively low thermal maturity (Tmax is ∼445 °C) and has been identified as a potential petroleum source rock. To date, however, the biological sources of the organic matter and the environmental conditions prevalent during the deposition of these sediments remain unclear. In this study we analyzed the hydrocarbon biomarker compositions of the Xiamaling Formation shales and a superjacent stromatolitic carbonate in order to shed light on the microbial diversity in the sedimentary environments they represent. The hydrocarbons extracted from both sediments are dominated by low-molecular-weight n-alkanes with a maximum at C15-18, suggesting that bacteria and/or algae were primary biotic precursors. Our inability to detect steranes in bitumen I, and only traces of rearranged steranes in bitumen II of black shales, indicates that modern eukaryotic algae were either ecologically insignificant or not preserved due to a taphonomic bias. The high relative concentration of hopanes and diahopanes ranging from C27 to C35, as well as monomethylalkanes, suggests that cyanobacteria may have been the dominant primary producers and could have contributed to the biologically available nitrogen pool through N2-fixation. This observation is supported by the low nitrogen isotopic composition of the kerogens. Even though all facies zones appear to have been anoxic but not sulfidic on the basis of biomarker ratios and trace metals, subtle but distinct molecular differences are observed between the stromatolite and the black shales, which can be attributed to

  1. Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

    Science.gov (United States)

    Alvaro, J J; Clausen, S

    2010-03-01

    The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.

  2. Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

    DEFF Research Database (Denmark)

    Steen, Andrew; Ziervogel, K.; Arnosti, C.

    2010-01-01

    Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult...

  3. The architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in freshwater and marine environments

    Directory of Open Access Journals (Sweden)

    Clara S Chan

    2016-06-01

    Full Text Available Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to

  4. Seasonal patterns in immune indices reflect microbial loads on birds but not microbes in the wider environment

    NARCIS (Netherlands)

    Horrocks, N.P.C.; Matson, K.D.; Shobrak, M.; Tinbergen, J.M.; Tieleman, B.I.

    2012-01-01

    Documenting patterns in immune function is a first step to understanding immune variation, but to comprehend causes and consequences, antigen and parasite exposure that may drive such variation must be determined. We measured host-independent microbial exposure in five species of larks (Alaudidae) i

  5. Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment.

    Science.gov (United States)

    González-Toril, Elena; Santofimia, Esther; Blanco, Yolanda; López-Pamo, Enrique; Gómez, Manuel J; Bobadilla, Miguel; Cruz, Rolando; Palomino, Edwin Julio; Aguilera, Ángeles

    2015-11-01

    The exposure of fresh sulfide-rich lithologies by the retracement of the Nevado Pastoruri glacier (Central Andes, Perú) is increasing the presence of heavy metals in the water as well as decreasing the pH, producing an acid rock drainage (ARD) process in the area. We describe the microbial communities of an extreme ARD site in Huascarán National Park as well as their correlation with the water physicochemistry. Microbial biodiversity was analyzed by FLX 454 sequencing of the 16S rRNA gene. The suggested geomicrobiological model of the area distinguishes three different zones. The proglacial zone is located in the upper part of the valley, where the ARD process is not evident yet. Most of the OTUs detected in this area were related to sequences associated with cold environments (i.e., psychrotolerant species of Cyanobacteria or Bacteroidetes). After the proglacial area, an ARD-influenced zone appeared, characterized by the presence of phylotypes related to acidophiles (Acidiphilium) as well as other species related to acidic and cold environments (i.e., acidophilic species of Chloroflexi, Clostridium and Verrumicrobia). Sulfur- and iron-oxidizing acidophilic bacteria (Acidithiobacillus) were also identified. The post-ARD area was characterized by the presence of OTUs related to microorganisms detected in soils, permafrost, high mountain environments, and deglaciation areas (Sphingomonadales, Caulobacter or Comamonadaceae).

  6. Environment

    DEFF Research Database (Denmark)

    Valentini, Chiara

    2017-01-01

    The term environment refers to the internal and external context in which organizations operate. For some scholars, environment is defined as an arrangement of political, economic, social and cultural factors existing in a given context that have an impact on organizational processes and structures....... For others, environment is a generic term describing a large variety of stakeholders and how these interact and act upon organizations. Organizations and their environment are mutually interdependent and organizational communications are highly affected by the environment. This entry examines the origin...... and development of organization-environment interdependence, the nature of the concept of environment and its relevance for communication scholarships and activities....

  7. Pseudoracemization (Biological Accumulation of D-amino Acids) in the Antarctic Cryptoendolithic Microbial Ecosystem, a Model for Oceans, Sediments, and Soils

    Science.gov (United States)

    Sun, H. J.; McDonald, G. D.; McKay, C. P.; Friedmann, I. E.

    2006-12-01

    Amino acids exist in right-handed and left-handed forms, different in that they are mirror images of each other. In organisms, with few exceptions, only left-handed forms are present. In non-living systems, left-handed forms slowly convert, through the physico-chemical process of racemization, into right-handed ones until the two forms reach equilibrium. We found that in microorganisms in Antarctic rocks right-handed amino acids accumulate from bacterial cell walls, through the biological process pseudoracemization. We suggest that the same process is responsible for the fact that large amounts of right-handed amino acids exist in oceans, sediments and soils.

  8. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

    Directory of Open Access Journals (Sweden)

    Yang Zamin K

    2010-05-01

    Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

  9. C3H7NO2S effect on concrete steel-rebar corrosion in 0.5 M H2SO4 simulating industrial/microbial environment

    Science.gov (United States)

    Okeniyi, Joshua Olusegun; Nwadialo, Christopher Chukwuweike; Olu-Steven, Folusho Emmanuel; Ebinne, Samaru Smart; Coker, Taiwo Ebenezer; Okeniyi, Elizabeth Toyin; Ogbiye, Adebanji Samuel; Durotoye, Taiwo Omowunmi; Badmus, Emmanuel Omotunde Oluwasogo

    2017-02-01

    This paper investigates C3H7NO2S (Cysteine) effect on the inhibition of reinforcing steel corrosion in concrete immersed in 0.5 M H2SO4, for simulating industrial/microbial environment. Different C3H7NO2S concentrations were admixed, in duplicates, in steel-reinforced concrete samples that were partially immersed in the acidic sulphate environment. Electrochemical monitoring techniques of open circuit potential, as per ASTM C876-91 R99, and corrosion rate, by linear polarization resistance, were then employed for studying anticorrosion effect in steel-reinforced concrete samples by the organic hydrocarbon admixture. Analyses of electrochemical test-data followed ASTM G16-95 R04 prescriptions including probability distribution modeling with significant testing by Kolmogorov-Smirnov and student's t-tests statistics. Results established that all datasets of corrosion potential distributed like the Normal, the Gumbel and the Weibull distributions but that only the Weibull model described all the corrosion rate datasets in the study, as per the Kolmogorov-Smirnov test-statistics. Results of the student's t-test showed that differences of corrosion test-data between duplicated samples with the same C3H7NO2S concentrations were not statistically significant. These results indicated that 0.06878 M C3H7NO2S exhibited optimal inhibition efficiency η = 90.52±1.29% on reinforcing steel corrosion in the concrete samples immersed in 0.5 M H2SO4, simulating industrial/microbial service-environment.

  10. Microbial corrosion and cracking in steel. Fundamental studies on the electrochemical behaviour of carbon steel exposed in sulphide and sulphate-reducing environments

    Energy Technology Data Exchange (ETDEWEB)

    Rischel Hilbert, Lisbeth

    1998-08-01

    The aim of the report is to give a fundamental understanding of the response of different electrochemical techniques on carbon steel in a sulphide environment as well as in a biologically active sulphate-reducing environment (SRB). This will form the basis for further studies and for recommendations in regards to electrochemical monitoring of MIC. The work presented here and further studies are also planned to lead to a Ph.D. thesis on `MIC monitoring based on mechanisms on corrosion`. The results of laboratory experiments conducted in the period 1995 to 1997 are summarised. Conclusions will be based on results from the entire 3 year period, but only selected experimental data primarily from the latest experiments will be presented in detail here. Microbial corrosion of carbon steel under influence of sulphate-reducing bacteria (SRB) is characterised by the formation of both biofilm and corrosion products (ferrous sulphides) on the metal surface. Experiments have been conducted on carbon steel exposed in near neutral (pH 6 to 8.5) saline hydrogen sulphide environment (0 to 100 mg/l total dissolved sulphide) for a period of 14 days. Furthermore coupons have been exposed in a bioreactor for a period of up to 120 days in sulphide-producing environment controlled by biological activity of (SRB). (au)

  11. Extensive microbial mats and their influences on the erosional and depositional dynamics of a siliciclastic cold water environment (Lower Arenigian, Montagne Noire, France)

    Science.gov (United States)

    Noffke, N.

    2000-11-01

    Lower Arenigian (Ordovician) rocks of the Montagne Noire, France, represent a shallow-marine environment of a high latitude position along the northern margin of Gondwana. Within the weakly metamorphosed siliciclastics six depositional units were recognized: (1) outer shelf; (2) foreshore zone, below wave base; (3) foreshore zone, above wave base; (4) sand bars of shoreface zone; (5) intertidal deposits; and (6) lagoonal zone. Wrinkle structures and various other phenomena were mediated by coherent (cyano-)bacterial mats. The structures can be related to the different facies zones of the paleoenvironment. Whereas the muddy outer shelf, and the high-energetic sand bars were not overgrown by any mat-constructing microbial populations, fine sands of the foreshore zone, the tidal flats and lagoonal areas were widely colonized. Restriction of mats due to competition of space by endobenthic macroorganisms, or by grazers was low. The microbially induced structures are composed of organic material, pyrite, clay minerals (illite, chamsonite, chlorite), and chert. The minerals precipitated in situ during degradation of the organic layers by the activity of heterotrophic bacteria at low temperatures. Because the microorganisms formed a dense organic carpet covering extensive areas of the ancient sea-bottom, they influenced significantly the erosional and depositional dynamics of the sedimentary system of the local Arenigian. Biostabilization counteracted erosion, and baffling, trapping and binding enriched mineral particles. Additionally, the in situ formed minerals contributed to the total amount of sediment. The biotic influence lead to increased accumulation of sediment within the depositional area. The study shows that microbial mats of great extension occur within Phanerozoic siliciclastics of cold paleoclimate zones, and that preservation of the mat fabrics was possible. The significant mats influenced the local sedimentary system, an aspect scarcely taken into account

  12. Subtask 1.22 - Microbial Cycling of CH4, CO2, and N2O in a Wetlands Environment

    Energy Technology Data Exchange (ETDEWEB)

    Dingyi Ye; Bethany Kurz; Marc Kurz

    2008-12-31

    Soil microbial metabolic activities play an important role in determining CO{sub 2}, CH{sub 4}, and N{sub 2}O fluxes from terrestrial ecosystems. To verify and evaluate CO{sub 2} sequestration potential by wetland restoration in the Prairie Pothole Region (PPR), as well as to address concern over restoration effects on CH{sub 4} and N{sub 2}O emissions, laboratory and in situ microcosm studies on microbial cycling of CO{sub 2}, CH{sub 4}, and N{sub 2}O were initiated. In addition, to evaluate the feasibility of the use of remote sensing to detect soil gas flux from wetlands, a remote-sensing investigation was also conducted. Results of the laboratory microcosm study unequivocally proved that restoration of PPR wetlands does sequester atmospheric CO{sub 2}. Under the experimental conditions, the simulated restored wetlands did not promote neither N{sub 2}O nor CH{sub 4} fluxes. Application of ammonia enhanced both N{sub 2}O and CH{sub 4} emission, indicating that restoration of PPR wetlands may reduce both N{sub 2}O and CH{sub 4} emission by cutting N-fertilizer input. Enhancement of CO{sub 2} emission by the N-fertilizer was observed, and this observation revealed an overlooked fact that application of N-fertilizer may potentially increase CO{sub 2} emission. In addition, the CO{sub 2} results also demonstrate that wetland restoration sequesters atmospheric carbon not only by turning soil conditions from aerobic to anoxic, but also by cutting N-fertilizer input that may enhance CO{sub 2} flux. The investigation on microbial community structure and population dynamics showed that under the experimental conditions restoration of the PPR wetlands would not dramatically increase population sizes of those microorganisms that produce N{sub 2}O and CH{sub 4}. Results of the in situ study proved that restoration of the PPR wetland significantly reduced CO{sub 2} flux. Ammonia enhanced the greenhouse gas emission and linearly correlated to the CO{sub 2} flux within the

  13. Linking geology, fluid chemistry, and microbial activity of basalt- and ultramafic-hosted deep-sea hydrothermal vent environments.

    Science.gov (United States)

    Perner, M; Hansen, M; Seifert, R; Strauss, H; Koschinsky, A; Petersen, S

    2013-07-01

    Hydrothermal fluids passing through basaltic rocks along mid-ocean ridges are known to be enriched in sulfide, while those circulating through ultramafic mantle rocks are typically elevated in hydrogen. Therefore, it has been estimated that the maximum energy in basalt-hosted systems is available through sulfide oxidation and in ultramafic-hosted systems through hydrogen oxidation. Furthermore, thermodynamic models suggest that the greatest biomass potential arises from sulfide oxidation in basalt-hosted and from hydrogen oxidation in ultramafic-hosted systems. We tested these predictions by measuring biological sulfide and hydrogen removal and subsequent autotrophic CO2 fixation in chemically distinct hydrothermal fluids from basalt-hosted and ultramafic-hosted vents. We found a large potential of microbial hydrogen oxidation in naturally hydrogen-rich (ultramafic-hosted) but also in naturally hydrogen-poor (basalt-hosted) hydrothermal fluids. Moreover, hydrogen oxidation-based primary production proved to be highly attractive under our incubation conditions regardless whether hydrothermal fluids from ultramafic-hosted or basalt-hosted sites were used. Site-specific hydrogen and sulfide availability alone did not appear to determine whether hydrogen or sulfide oxidation provides the energy for primary production by the free-living microbes in the tested hydrothermal fluids. This suggests that more complex features (e.g., a combination of oxygen, temperature, biological interactions) may play a role for determining which energy source is preferably used in chemically distinct hydrothermal vent biotopes.

  14. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

    Science.gov (United States)

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-11-25

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

  15. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

    Science.gov (United States)

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-01-01

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies. PMID:27886221

  16. Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs

    NARCIS (Netherlands)

    Liebensteiner, M.; Tsesmetzis, N.; Stams, A.J.M.; Lomans, B.P.

    2014-01-01

    The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of m

  17. Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF and Their Association with Lower Airways Infections.

    Directory of Open Access Journals (Sweden)

    Alya Heirali

    Full Text Available Cystic fibrosis (CF airways are colonized by a polymicrobial community of organisms, termed the CF microbiota. We sought to define the microbial constituents of the home environment of individuals with CF and determine if it may serve as a latent reservoir for infection.Six patients with newly identified CF pathogens were included. An investigator collected repeat sputum and multiple environmental samples from their homes. Bacteria were cultured under both aerobic and anaerobic conditions. Morphologically distinct colonies were selected, purified and identified to the genus and species level through 16S rRNA gene sequencing. When concordant organisms were identified in sputum and environment, pulsed-field gel electrophoresis (PFGE was performed to determine relatedness. Culture-independent bacterial profiling of each sample was carried out by Illumina sequencing of the V3 region of the 16s RNA gene.New respiratory pathogens prompting investigation included: Mycobacterium abscessus(2, Stenotrophomonas maltophilia(3, Pseudomonas aeruginosa(3, Pseudomonas fluorescens(1, Nocardia spp.(1, and Achromobacter xylosoxidans(1. A median 25 organisms/patient were cultured from sputum. A median 125 organisms/home were cultured from environmental sites. Several organisms commonly found in the CF lung microbiome were identified within the home environments of these patients. Concordant species included members of the following genera: Brevibacterium(1, Microbacterium(1, Staphylococcus(3, Stenotrophomonas(2, Streptococcus(2, Sphingomonas(1, and Pseudomonas(4. PFGE confirmed related strains (one episode each of Sphinogomonas and P. aeruginosa from the environment and airways were identified in two patients. Culture-independent assessment confirmed that many organisms were not identified using culture-dependent techniques.Members of the CF microbiota can be found as constituents of the home environment in individuals with CF. While the majority of isolates from

  18. Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture.

    Science.gov (United States)

    Zhao, Zelong; Wang, Jing; Han, Ying; Chen, Jingwen; Liu, Guangfei; Lu, Hong; Yan, Bin; Chen, Shiaoshing

    2017-01-01

    With the rapid development of aquaculture, the large amounts of pollutants were discharged into the aquatic environment, where the detected antibiotic resistance genes (ARGs) have drawn increasing attention due to their potential threats to ecological environment and human health. Thus, the impact of mariculture on ARGs was assessed and the underlying mechanism of their propagation was explained. Sediments from eight sampling sites were collected along a mariculture drainage ditch, and the sediment in Yellow River Delta National Park was used as a non-mariculture control. Microbial ARGs qPCR array and illumina sequencing of 16S rRNA gene were applied to examine the changing patterns of ARGs and bacterial communities. Results showed that 18 ARGs (3 fluoroquinolone, 1 aminoglycoside, 3 macrolide-lincosamide-streptogramin B, 2 tetracycline, and 9 beta-lactam resistance genes) were influenced by mariculture, and ARGs abundance and diversity were significantly increased in mariculture sediments (p < 0.05). A remarkable shift in bacterial community structure and composition was also observed. The abundance of most of ARGs were significantly decreased in the estuary samples, implying that seawater had a significant dilution effect on the ARGs emission from the mariculture sites. Partial redundancy analysis showed that nutrients, heavy metals, and bacteria communities might directly and indirectly contribute to ARGs propagation, suggesting that the profile and dissemination of ARGs were driven by the combined effects of multiple factors in mariculture-impacted sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Christian A Lindensmith

    Full Text Available 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.

  20. Exploring the functional diversity of the supraglacial environment: Microbial degradation of the pesticide 2,4-D on the Greenland Ice Sheet

    Science.gov (United States)

    Stibal, M.; Bælum, J.; Holben, W. E.; Jacobsen, C. S.

    2012-12-01

    The surface of the Greenland ice sheet (GrIS) harbours a diverse community of heterotrophic microorganisms. Organic compounds of anthropogenic origin, including pesticides, are deposited on the GrIS; however, the fate of these compounds in the ice is currently unknown. In this study we determine the potential of the microbial community from the surface of the GrIS to mineralise the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D). It is one of the most easily degraded compounds among the phenoxyacetic acid pesticides, and the ability to mineralise 2,4-D has been found to be widespread in microbial communities around the globe. Functional genes involved in the degradation pathway have also been characterised. Thus, 2,4-D represents a very suitable model compound to use in order to gain an insight into pollutant degradation dynamics in the rapidly changing Arctic region. We collected surface ice cores on the GrIS and incubated them for up to 529 days in microcosms simulating in situ conditions. We measured mineralisation of side-chain- and ring-labelled 14C-2,4-D in the samples and performed quantitative PCR targeting the tfdA gene, encoding an enzyme catalysing the first step in the degradation pathway of 2,4-D, in the DNA extracted from the ice after the experiments. We show that the microbial community on the surface of the GrIS is of low diversity, but contains microbes capable of degrading 2,4-D. The low diversity of the community and the similarity of the detected clones to those from other icy environment clones suggest that the bacterial community on the GrIS is selected from a pool of propagules deposited on the surface of the ice sheet, based on the level of adaptation to the conditions in the surface ice. The 2,4-D degraders are likely present in very low numbers, and they can mineralise 2,4-D at a rate of up to 1 nmol per m2 per day, equivalent to ~26 ng C m-2 d-1. We contend that the surface of the GrIS should not be considered to be a mere reservoir of

  1. Microbial degradation and fate in the environment of methyl tert-butyl ether and related fuel oxygenates.

    Science.gov (United States)

    Fayolle, F; Vandecasteele, J P; Monot, F

    2001-08-01

    Oxygenates, mainly methyl tert-butyl ether (MTBE), are commonly added to gasoline to enhance octane index and improve combustion efficiency. Other oxygenates used as gasoline additives are ethers such as ethyl tert-butyl ether (ETBE), tert-amyl methyl ether (TAME), and alcohols such as tert-butyl alcohol (TBA). As a result of its wide use, MTBE has been detected, mainly in the USA, in groundwater and surface waters, and is a cause of concern because of its possible health effects and other undesirable consequences. MTBE is a water-soluble and mobile compound that generates long pollution plumes in aquifers impacted by gasoline releases from leaking tanks. Field observations concur in estimating that, because of recalcitrance to biodegradation, natural attenuation is slow (half-life of at least 2 years). However, quite significant advances have been made in recent years concerning the microbiology of the degradation of MTBE and other oxygenated gasoline additives. The recalcitrance of these compounds results from the presence in their structure of an ether bond and of a tertiary carbon structure. For the most part, only aerobic microbial degradation systems have been reported so far. Consortia capable of mineralizing MTBE have been selected. Multiple instances of the cometabolism of MTBE with pure strains or with microflorae, growing on n-alkanes, isoalkanes, cyclohexane or ethers (diethyl ether, ETBE), have been described. MTBE was converted into TBA in all cases and was sometimes further degraded, but it was not used as a carbon source by the pure strains. However, mineralization of MTBE and TBA by several pure bacterial strains using these compounds as sole carbon and energy source has recently been reported. The pathways of metabolism of MTBE involve the initial attack by a monooxygenase. In several cases, the enzyme was characterized as a cytochrome P-450. After oxygenation, the release of a C -unit as formaldehyde or formate leads to the production of TBA

  2. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part I.

    Science.gov (United States)

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-01-31

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking experimental research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He also wrote extensively on potential health consequences of a progressive loss of contact with natural environments (now referred to as green or blue space), arguing that Paleolithic experiences have created needs, particularly in the mental realm, that might not be met in the context of rapid global urbanization. He posited that humans would certainly adapt to modern urban landscapes and high technology, but there might be a toll to be paid in the form of higher psychological distress (symptoms of anxiety and depression) and diminished quality of life. In particular, there might be an erosion of humanness, exemplified by declines in altruism/empathy. Here in the first of a two-part review, we examine contemporary research related to natural environments and question to what extent Dubos might have been correct in some of his 50-year-old assertions.

  3. Microbially influenced corrosion: studies on enterobacteria isolated from seawater environment and influence of toxic metals on bacterial biofilm and bio-corrosion

    Energy Technology Data Exchange (ETDEWEB)

    Bermond-Tilly, D.; Pineau, S.; Dupont-Morral, I. [Corrodys, 50 - Equeurdreville (France); Janvier, M.; Grimont, P.A.D. [Institut Pasteur, Unite BBPE, 75 - Paris (France)

    2004-07-01

    Full text of publication follows: The most widely involved bacteria in Microbially Induced Corrosion (MIC usually called bio-corrosion) are sulfate/thiosulfate-reducing bacteria. The sulfate-reducing bacteria (SRB) are major contributors to the anaerobic bio-corrosion of steel. However, corrosion process of pipelines (or off shores platforms) was found to be associated with many other bacteria. These bacteria are able to produce sulfides from the reduction of thiosulfate in anaerobic conditions. By this way, a thiosulfate-reducing non sulfate-reducing bacteria, Dethiosulfovibrio peptidovorans, showed a significant corrosive activity similar to or higher than that recorded for SRB involved in bio-corrosion, (Magot et al., 1997). Furthermore, a bacteria, Citrobacter amalonaticus, which belongs to the family of the Enterobacteriaceae, is involved in severe pitting corrosion process (Angeles Chavez et al., 2002). Recently, some bacteria (Citrobacter freundii, Proteus mirabilis and Klebsiella planticola characterized as belonging to the family of Enterobacteriaceae) were isolated from biofilm developed on carbon steel coupons immersed in natural seawater. The latter bacteria were also associated in severe pitting corrosion process on carbon steel coupons (Bermond-Tilly et al., 2003). Biofilm forms a protective layer, reducing the exposure of the metal surface to the external environment. However, bacteria included in the biofilm could also cause localized corrosion by consuming cathodic hydrogen from the steel or by producing corrosive metabolic end products and by the Extracellular Polymeric Substances (EPS) production. Thus, EPS can also play an important role in the corrosion of the metals (e.g. can complex metal ions). However, sulfate/thiosulfate-reducing bacteria and some Enterobacteria are highly efficient to bioremediation by precipitation of toxic metals from wastewater as metal sulfides. Recently it was shown that toxic metal may be involved in the formation

  4. On using rational enzyme redesign to improve enzyme-mediated microbial dehalogenation of recalcitrant substances in deep-subsurface environments

    Energy Technology Data Exchange (ETDEWEB)

    Ornstein, R.L.

    1993-06-01

    Heavily halogenated hydrocarbons are one of the most prevalent classes of man-made recalcitrant environmental contaminants and often make their way into subsurface environments. Biodegradation of heavily chlorinated compounds in the deep subsurface often occurs at extremely slow rates because native enzymes of indigenous microbes are unable to efficiently metabolize such synthetic substances. Cost-effective engineering solutions do not exist for dealing with disperse and recalcitrant pollutants in the deep subsurface (i.e., ground water, soils, and sediments). Timely biodegradation of heavily chlorinated compounds in the deep subsurface may be best accomplished by rational redesign of appropriate enzymes that enhance the ability of indigenous microbes to metabolize these substances. The isozyme family cytochromes P450 are catalytically very robust and are found in all aerobic life forms and may be active in may anaerobes as well. The author is attempting to demonstrate proof-of-principle rational enzyme redesign of cytochromes P450 to enhance biodehalogenation.

  5. Ocean microbial metagenomics

    Science.gov (United States)

    Kerkhof, Lee J.; Goodman, Robert M.

    2009-09-01

    Technology for accessing the genomic DNA of microorganisms, directly from environmental samples without prior cultivation, has opened new vistas to understanding microbial diversity and functions. Especially as applied to soils and the oceans, environments on Earth where microbial diversity is vast, metagenomics and its emergent approaches have the power to transform rapidly our understanding of environmental microbiology. Here we explore select recent applications of the metagenomic suite to ocean microbiology.

  6. Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird

    Directory of Open Access Journals (Sweden)

    Danielle June Whittaker

    2016-08-01

    Full Text Available Chemical signaling is an underappreciated means of communication among birds, as may be the potential contributions of symbiotic microbes to animal chemical communication in general. The dark-eyed junco (Junco hyemalis produces and detects volatile compounds that may be important in reproductive behavior. These compounds are found in preen oil secreted by the uropygial gland, and this gland supports diverse bacterial communities including genera known to produce some of these volatile compounds. We investigated the relative contributions of shared environments and genetic relatedness in shaping juncos’ symbiotic bacterial communities, and investigated whether these bacterial communities underlie juncos’ chemical signaling behavior. We sampled parents and nestlings at 9 junco nests during one breeding season at Mountain Lake Biological Station in Virginia, USA. From each individual, we collected swabs of the uropygial gland and the cloaca, preen oil, and a small blood sample for paternity testing. We characterized junco bacterial communities through 16S rRNA gene surveys and preen oil volatile compounds via gas chromatography-mass spectrometry. Nest membership and age class had the strongest influence on the structure of bacterial and volatile profiles. We compared father-offspring similarity based on paternity, and nestling similarity in nests containing full siblings and half siblings, and found that relatedness did not noticeably affect bacterial or volatile profiles. While we cannot rule out an influence of genetic relatedness on these profiles, it is clear that shared environments are more influential in shaping bacterial and volatile profiles among juncos.We did not find significant covariation between individual bacterial and volatile profiles. Possible explanations for this result include: 1 bacteria do not underlie volatile production; 2 ample redundancy in volatile production among bacterial types obscures covariation; or 3 the

  7. Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria

    Directory of Open Access Journals (Sweden)

    JD Medeiros

    Full Text Available This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

  8. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Moberly, James G [ORNL; Shakya, Migun [ORNL; Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Elias, Dwayne A [ORNL

    2014-01-01

    Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na2SO4 and NH4H2PO4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22 2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46 0.25 g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU s having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.

  9. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.

    Science.gov (United States)

    Jay, Z J; Rusch, D B; Tringe, S G; Bailey, C; Jennings, R M; Inskeep, W P

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.

  10. In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria.

    Science.gov (United States)

    McBeth, Joyce M; Emerson, David

    2016-01-01

    Microbiologically influenced corrosion (MIC) is a complex biogeochemical process involving interactions between microbes, metals, minerals, and their environment. We hypothesized that sediment-derived iron-oxidizing bacteria (FeOB) would colonize and become numerically abundant on steel surfaces incubated in coastal marine environments. To test this, steel coupons were incubated on sediments over 40 days, and samples were taken at regular intervals to examine microbial community succession. The experiments were conducted at two locations: (1) a brackish salt marsh stream and (2) a coastal marine bay. We analyzed DNA extracted from the MIC biofilms for bacterial diversity using high-throughput amplicon sequencing of the SSU rRNA gene, and two coupons from the coastal site were single cell sorted and screened for the SSU rRNA gene. We quantified communities of Zetaproteobacteria, sulfate-reducing bacteria (SRB), and total bacteria and archaea using qPCR analyses. Zetaproteobacteria and SRB were identified in the sequencing data and qPCR analyses for samples collected throughout the incubations and were also present in adjacent sediments. At the brackish site, the diversity of Zetaproteobacteria was lower on the steel compared to sediments, consistent with the expected enrichment of FeOB on steel. Their numbers increased rapidly over the first 10 days. At the marine site, Zetaproteobacteria and other known FeOB were not detected in sediments; however, the numbers of Zetaproteobacteria increased dramatically within 10 days on the steel surface, although their diversity was nearly clonal. Iron oxyhydroxide stalk biosignatures were observed on the steel and in earlier enrichment culture studies; this is evidence that the Zetaproteobacteria identified in the qPCR, pyrosequencing, and single cell data were likely FeOB. In the brackish environment, members of freshwater FeOB were also present, but were absent in the fully marine site. This work indicates there is a

  11. Lactic Acid Bacteria Improves Peyer's Patch Cell-Mediated Immunoglobulin A and Tight-Junction Expression in a Destructed Gut Microbial Environment.

    Science.gov (United States)

    Kim, Sung Hwan; Jeung, Woonhee; Choi, Il-Dong; Jeong, Ji-Woong; Lee, Dong Eun; Huh, Chul-Sung; Kim, Geun-Bae; Hong, Seong Soo; Shim, Jae-Jung; Lee, Jung Lyoul; Sim, Jae-Hun; Ahn, Young-Tae

    2016-06-28

    To evaluate the effects of lactic acid bacteria (LAB) on Peyer's patch cells, mice were treated with a high dose of kanamycin to disturb the gut microbial environment. The overarching goal was to explore the potential of LAB for use as a dietary probiotic that buffers the negative consequences of antibiotic treatment. In vitro, LAB stimulated the production of immunoglobulin A (IgA) from isolated Peyer's patch cells. Inflammation-related genes (TNF-α, IL-1β, and IL-8) were up-regulated in Caco-2 cells stimulated with lipopolysaccharide (LPS), while tight-junction-related genes (ZO-1 and occludin) were down-regulated; the effects of LPS on inflammatory gene and tight-junction gene expression were reversed by treatment with LAB. Mice treated with a high dose of kanamycin showed increased serum IgE levels and decreases in serum IgA and fecal IgA levels; the number of Peyer's patch cells decreased with kanamycin treatment. However, subsequent LAB treatment was effective in reducing the serum IgE level and recovering the serum IgA and fecal IgA levels, as well as the number of Peyer's patch cells. In addition, ZO-1 and occludin mRNA levels were up-regulated in the ileum tissues of mice receiving LAB treatment. Lactic acid bacteria can enhance the intestinal immune system by improving the integrity of the intestinal barrier and increasing the production of IgA in Peyer's patches. Lactic acid bacteria should be considered a potential probiotic candidate for improving intestinal immunity, particularly in mitigating the negative consequences of antibiotic use.

  12. Counting viruses and bacteria in photosynthetic microbial mats

    NARCIS (Netherlands)

    Carreira, C; Staal, M.; Middelboe, M.; Brussaard, C.P.D.

    2015-01-01

    Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures

  13. Laser Induced Fluorescence Emission (L.I.F.E.): In Situ Non-Destructive Detection of Microbial Life on Supraglacial Environments

    Science.gov (United States)

    Sattler, B.; Tilg, M.; Storrie-Lombardi, M.; Remias, D.; Psenner, R.

    2012-04-01

    Laser-induced fluorescence emission (L.I.F.E.) is an in situ laser scanning technique to detect photoautotrophic pigments such as phycoerythrin of an ice ecosystem such as supraglacial environments without contamination. The sensitivity of many psychrophiles to even moderate changes in temperature, and the logistical difficulties associated with either in situ analysis or sampling makes it difficult to study microbial metabolism in ice ecosystems in a high resolution. Surface communities of cold ecosystems are highly autotrophic and therefor ideal systems for L.I.F.E examinations. 532nm green lasers excite photopigments in cyanobacteria and produce multiple fluorescence signatures between 550nm and 750nm including carotenoids, phycobiliproteins which would enable a non-invasive in-situ measurement. The sensitivity of many psychrophiles to even moderate changes in temperature, and the logistical difficulties associated with either in situ analysis or sampling makes it difficult to study these cryosphere ecosystems. In general, the ice habitat has to be disrupted using techniques that usually include coring, sawing, and melting. Samples are also often chosen blindly, with little indication of probable biomass. The need for an in situ non-invasive, non-destructive technique to detect, localize, and sample cryosphere biomass in the field is therefore of considerable importance. L.I.F.E has already been tested in remote ecosystems like Antarctica (Lake Untersee, Lake Fryxell), supraglacial environments in the Kongsfjord region in the High Arctic and High Alpine glaciers but until now no calibration was set to convert the L.I.F.E. signal into pigment concentration. Here we describe the standardization for detection of Phycobiliproteins (Phycoerythrine) which are found in red algae, cyanobacteria, and cryptomonads. Similar methods are already used for detection of phytoplankton in liquid systems like oceans and lakes by NASÁs Airborne Oceanographic LIDAR since 1979. The

  14. 40 CFR 158.2110 - Microbial pesticides data requirements.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2110 Microbial pesticides data requirements. (a) For all microbial pesticides. (1) The following § 158.2120 through §...

  15. 40 CFR 158.2100 - Microbial pesticides definition and applicability.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2100 Microbial pesticides definition and applicability. (a) This subpart applies to all living or dead microbial pesticides as...

  16. Anti-Microbial Resistance Profiles Of E. Coli Isolated From Free Range Chickens In Urban And Rural Environments Of Imo State, Nigeria

    OpenAIRE

    Okoli IC

    2006-01-01

    Information on the resistance profiles of normal intestinal flora of extensively reared chickens that hardly receive antibiotics in the developing countries can serve as important means of understanding the human/animal pathogens drug resistance interactions in the zone. Three hundred and fifty E. coli isolates, comprising 133 from urban and 217 from rural sites in Imo state, Nigeria, were screened for anti-microbial resistance profile against 10 antibiotics using the disc diffusion method. O...

  17. Organic geochemistry of endoevaporitic environments: Microbial diversity and lipid biomarkers from gypsum deposits at the E.S.S.A Salt Works, Guerrero Negro, Baja, Mexico

    Science.gov (United States)

    Vogel, M. B.; Des Marais, D. J.; Jahnke, L. L.; Turk, K. A.; Kubo, M. D.

    2006-12-01

    We report lipid biomarker distributions and microbial diversity of endoevaporitic microbial communities from the gypsum crystallizer pond (Pond #9; ~170 % salinity) at the Exportadora de Sal, (ESSA) salt works in Guerrero Negro, Baja California Sur, Mexico. According to phylogenetic analysis using 16S rRNA sequences, gypsum crusts from this system host stratified communities of unicellular cyanobacteria (orange Euhalothece), filamentous cyanobacteria (green Oscillatoria), purple sulfur bacteria (Chromatium), and other halophilic microorganisms. Lipids collected from spatially discrete horizons of the crust indicate a shift in C16, C18 and C19 fatty acids from lower concentrations in the upper aerobic layers to higher concentrations in the deeper anaerobic zones of the crust. Compound specific isotopic analyses (CSIA) of fatty acids differentiate the more abundant C16, C18 and C19 homologues as isotopically lighter (~ -20% to -25% δ13C VPDB) from C15, C17 and C20 homologues which are isotopically heavier (~ -14% to -19% δ13C VPDB) and occur in lower abundance. CSIA of multiple compound classes reveals that gypsum domain lipids have significantly lighter δ13C values than those of lipids from the laminated benthic microbial mats living at lower salinities (i.e. ~100% to 115% salinity) in the ESSA system. This isotopic effect is consistent with intensive internal nutrient cycling within the crust. Squalane/squalene were detected in extracts from the gypsum crust indicating the presence of archaea. Diploptene is the most abundant triterpenoid of the C28 C32 hopanoids. Branched alkanes with quaternary substituted carbons (BAQCs) were also detected. These compounds have been linked with sulfur oxidizing microbial activity, which is known to be a major respiratory process in the crust's internal O2 budget (Sørensen et al., 2004). Abundant organosulfur compounds (OSC) and thiacycloalkanes in extracts indicate a vigorous internal sulfur cycle that influences both

  18. Usage of microbial mats in depostional environment interpretation and sea level changes: A study of carbonate deposits of members 1 to 2 of the Mila Group (Deh-Sufiyan Formation in Central Alborz

    Directory of Open Access Journals (Sweden)

    Aram Bayetgol

    2015-05-01

    Full Text Available Carbonate deposits of members 1 to 2 of the Mila Group (Middle Cambrian in Central Alborz that call Deh-Sufiyan Formation in this research, were studied in Shahmirzad, Tueh-Darvar, Mila-Kuh and Deh-Molla sections. These sediments were deposited in four facies belts on a carbonate ramp including basinal environments, outer ramp (deep subtidal sequences, mid ramp (shallow subtidal to lower intertidal sequences, and inner ramp (shoal and upper intertidal to supratidal sequences. Various microbialites were recognized in the shallow-water sediments (includes subtidal and intertidal of this unit. Based on this study, microbial mats have various morphology of form and type of growth structure and inluding laminar to wavy-laminar, domal or hemispheroidal, bulbous, columnar, regular flabellate columns, unlaminated, loaf- to mound-shaped thrombolities. Facies associations of Deh-Sufiyan Formation are arranged in small-scale of peritidal, shallow subtidal, and deep subtidal cycles and microbial mats are the major features of them. The trends of vertical changes of facies in shallowing-upward and deepening-upward cycles and distribution of various types of microbialites in these cycles had been related to depostional environments and their postions on carbonate ramp. Basal classification method used in this study can provide valuable informations for application of microbiali mats in paleo-environmental and sequence stratigraphy analysis.

  19. Comparative microbial ecology study of the sediments and the water column of the Río Tinto, an extreme acidic environment.

    Science.gov (United States)

    García-Moyano, Antonio; González-Toril, Elena; Aguilera, Ángeles; Amils, Ricardo

    2012-08-01

    Due to its highly metalliferous waters and low pH, the Rio Tinto has shown its potential for modelling both acid mine drainage systems and biohydrometallurgical operations. Most geomicrobiological studies of these systems have focused on the oxic water column. A sequence-based approach in combination with in situ detection techniques enabled us to examine the composition and structure of the microbial communities associated with the suboxic and anoxic sediments along the river course and to compare them with the planktonic communities inhabiting the water column. The results obtained with the different approaches were consistent and revealed some major patterns: higher cell density and higher richness (75 vs. 48 operational taxonomic units) in the sediments than in the water column. The microbial communities were related but the river sediments appear to be enriched in certain populations, some of which have not previously been reported in the Rio Tinto basin. The differences detected between sampling stations along the river correlate with certain environmental parameters (e.g. iron concentration gradient). The biological and geochemical data show the importance of the sediments as representing a phase of particular high diversity, probably related to key metabolic processes within both the iron and the sulfur cycles.

  20. Anti-Microbial Resistance Profiles Of E. Coli Isolated From Free Range Chickens In Urban And Rural Environments Of Imo State, Nigeria

    Directory of Open Access Journals (Sweden)

    Okoli IC

    2006-07-01

    Full Text Available Information on the resistance profiles of normal intestinal flora of extensively reared chickens that hardly receive antibiotics in the developing countries can serve as important means of understanding the human/animal pathogens drug resistance interactions in the zone. Three hundred and fifty E. coli isolates, comprising 133 from urban and 217 from rural sites in Imo state, Nigeria, were screened for anti-microbial resistance profile against 10 antibiotics using the disc diffusion method. Overall percentage anti-microbial resistance of the isolates against cotrimoxazole, ampicillin, nalidixic acid, chloramphenicol and nitrofurantoin (72–92% were very high. The organisms were highly sensitive to other antibiotics, especially gentamicin and ciprofloxacin. The 59.5% overall mean percentage resistance recorded at the urban area was significantly higher than the 46.8% recorded at the rural area (p<0.05. With the exception of the figures for cotrimoxazole and ampicillin, resistance values obtained against the other antibiotics at the urban sites were statistically higher than those obtained at the rural sites (p<0.05. Zero resistance was recorded against the fluoroquinolones, norfloxacin and ciprofloxacin at all the rural sites except at Enyiogwugwu where a 28.6% resistance was obtained against norfloxacin. Since free-range chickens rarely receive antibiotic medication, it is concluded that the highly resistant E. coli organisms isolated from them may be reflecting consequences of human drug use in the study areas.

  1. Application of Multi-Species Microbial Bioassay to Assess the Effects of Engineered Nanoparticles in the Aquatic Environment: Potential of a Luminous Microbial Array for Toxicity Risk Assessment (LumiMARA on Testing for Surface-Coated Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    YounJung Jung

    2015-07-01

    Full Text Available Four different manufactured surface-coated silver nanoparticles (AgNPs with coating of citrate, tannic acid, polyethylene glycol, and branched polyethylenimine were used in this study. The toxicity of surface-coated AgNPs was evaluated by a luminous microbial array for toxicity risk assessment (LumiMARA using multi-species of luminescent bacteria. The salt stability of four different AgNPs was measured by UV absorbance at 400 nm wavelength, and different surface-charged AgNPs in combination with bacteria were observed using scanning electron microscopy (SEM. Both branched polyethylenimine (BPEI-AgNPs and polyethylene glycol (PEG-AgNPs were shown to be stable with 2% NaCl (non-aggregation, whereas both citrate (Cit-AgNPs and tannic acid (Tan-AgNPs rapidly aggregated in 2% NaCl solution. The values of the 50% effective concentration (EC50 for BPEI-AgNPs in marine bacteria strains (1.57 to 5.19 mg/L were lower than those for the other surface-coated AgNPs (i.e., Cit-AgNPs, Tan-AgNPs, and PEG-AgNPs. It appears that the toxicity of AgNPs could be activated by the interaction of positively charged AgNPs with the negatively charged bacterial cell wall from the results of LumiMARA. LumiMARA for toxicity screening has advantageous compared to a single-species bioassay and is applicable for environmental samples as displaying ranges of assessment results.

  2. Bioerosion by microbial euendoliths in benthic foraminifera from heavy metal-polluted coastal environments of Portovesme (South-Western Sardinia, Italy

    Directory of Open Access Journals (Sweden)

    A. Cherchi

    2012-08-01

    Full Text Available A monitoring survey of the coastal area facing the industrial area of Portoscuso-Portovesme (South-Western Sardinia, Italy revealed intense bioerosional processes. Benthic foraminifera collected at the same depth (about 2 m but at different distances from the pollution source show extensive microbial infestation, anomalous Mg/Ca molar ratios and high levels of heavy metals in the shell associated with a decrease in foraminifera richness, population density and biodiversity with the presence of morphologically abnormal specimens. We found that carbonate dissolution induced by euendoliths is selective, depending on the Mg content and morpho-structural types of foraminiferal taxa. This study provides evidences for a connection between heavy metal dispersion, decrease in pH of the sea-water and bioerosional processes on foraminifera.

  3. Microbial reduction of iodate

    Science.gov (United States)

    Councell, T.B.; Landa, E.R.; Lovley, D.R.

    1997-01-01

    The different oxidation species of iodine have markedly different sorption properties. Hence, changes in iodine redox states can greatly affect the mobility of iodine in the environment. Although a major microbial role has been suggested in the past to account for these redox changes, little has been done to elucidate the responsible microorganisms or the mechanisms involved. In the work presented here, direct microbial reduction of iodate was demonstrated with anaerobic cell suspensions of the sulfate reducing bacterium Desulfovibrio desulfuricans which reduced 96% of an initial 100 ??M iodate to iodide at pH 7 in 30 mM NaHCO3 buffer, whereas anaerobic cell suspensions of the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens were unable to reduce iodate in 30 mM NaHCO3 buffer (pH 7). Both D. desulfuricans and S. putrefaciens were able to reduce iodate at pH 7 in 10 mM HEPES buffer. Both soluble ferrous iron and sulfide, as well as iron monosulfide (FeS) were shown to abiologically reduce iodate to iodide. These results indicate that ferric iron and/or sulfate reducing bacteria are capable of mediating both direct, enzymatic, as well as abiotic reduction of iodate in natural anaerobic environments. These microbially mediated reactions may be important factors in the fate and transport of 129I in natural systems.

  4. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  5. Microbial biosensors for environmental monitoring

    Directory of Open Access Journals (Sweden)

    David VOGRINC

    2015-12-01

    Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

  6. Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

    Directory of Open Access Journals (Sweden)

    Katherine S Dawson

    2016-05-01

    Full Text Available Stable isotope probing (SIP is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS, allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S and elemental ratio (C/CN and S/CN profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs into 5 distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

  7. Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

    Science.gov (United States)

    Dawson, K.; Scheller, S.; Dillon, J. G.; Orphan, V. J.

    2016-12-01

    Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned 2200 cellular regions of interest (ROIs) into 5 distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

  8. MBR和CAS工艺污泥在贫营养培养条件下的微生物群落结构研究%Microbial community structure of sludge in MBR and CAS under oligotrophic environment

    Institute of Scientific and Technical Information of China (English)

    胡怡杉; 孙宝盛; 王盛勇

    2011-01-01

    采用聚合酶链式-变性梯度凝胶电泳(PCR-DGGE)技术,研究了膜生物反应器(MBR)和传统活性污泥工艺(CAS)反应器中微生物在贫营养条件下的总细菌群落结构.结果表明,在培养过程中,污泥的微生物种群经历了一个比较明显的变化过程,且以CAS污泥微生物种群的变化更为明显,演替过程中既有原始优势种群的消亡,又有新的优势种群的增强,故优势种群的功能地位处于动态变化中.两种污泥的来源、工艺进水水质和运行条件的不同造成了活性污泥中菌群结构的差异.两种污泥中主要存在的优势菌种大部分为未经培养菌种(uncultured%Total microbial community structure in membrane bio-reactor(MBR) and conventional activated sludge(CAS) processes operated under oligotrophic environment was investigated using PCR-denaturing gradient gel electrophoresis(PCR-DGGE).Investigation results show that microbial population of the two types of sludge had significant changes during cultivation process,especially for the sludge in CAS process.In the evolvement of microbial population,the original dominant species was replaced by new species gradually and the original dominant species was even died out from the system.The state of the dominant populations was dynamically changing.Different sludge sources,influent water quality and operating conditions of the two systems lead to the differences of microbial community structure in activated sludge.The main dominant bacteria in the two types of sludge are uncultured bacterium,e.g.Arcobacter,Pseudomonas,Bacillus and gamma proteobacterium bacteria.Moreover,there also exist some pathogenic microorganisms,such as Arcobacter,Serratia and Klebsiella species.

  9. Microbial degradation of petroleum hydrocarbons.

    Science.gov (United States)

    Varjani, Sunita J

    2017-01-01

    Petroleum hydrocarbon pollutants are recalcitrant compounds and are classified as priority pollutants. Cleaning up of these pollutants from environment is a real world problem. Bioremediation has become a major method employed in restoration of petroleum hydrocarbon polluted environments that makes use of natural microbial biodegradation activity. Petroleum hydrocarbons utilizing microorganisms are ubiquitously distributed in environment. They naturally biodegrade pollutants and thereby remove them from the environment. Removal of petroleum hydrocarbon pollutants from environment by applying oleophilic microorganisms (individual isolate/consortium of microorganisms) is ecofriendly and economic. Microbial biodegradation of petroleum hydrocarbon pollutants employs the enzyme catalytic activities of microorganisms to enhance the rate of pollutants degradation. This article provides an overview about bioremediation for petroleum hydrocarbon pollutants. It also includes explanation about hydrocarbon metabolism in microorganisms with a special focus on new insights obtained during past couple of years. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Degradation of microbial polyesters.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P

    2004-08-01

    Microbial polyhydroxyalkanoates (PHAs), one of the largest groups of thermoplastic polyesters are receiving much attention as biodegradable substitutes for non-degradable plastics. Poly(D-3-hydroxybutyrate) (PHB) is the most ubiquitous and most intensively studied PHA. Microorganisms degrading these polyesters are widely distributed in various environments. Although various PHB-degrading microorganisms and PHB depolymerases have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. Distributions of PHB-degrading microorganisms, factors affecting the biodegradability of PHB, and microbial and enzymatic degradation of PHB are discussed in this review. We also propose an application of a new isolated, thermophilic PHB-degrading microorganism, Streptomyces strain MG, for producing pure monomers of PHA and useful chemicals, including D-3-hydroxycarboxylic acids such as D-3-hydroxybutyric acid, by enzymatic degradation of PHB.

  11. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  12. Aggregation and removal of copper oxide (CuO) nanoparticles in wastewater environment and their effects on the microbial activities of wastewater biofilms.

    Science.gov (United States)

    Miao, Lingzhan; Wang, Chao; Hou, Jun; Wang, Peifang; Ao, Yanhui; Li, Yi; Geng, Nan; Yao, Yu; Lv, Bowen; Yang, Yangyang; You, Guoxiang; Xu, Yi

    2016-09-01

    The transport behaviors of copper oxide (CuO) NPs in wastewater matrix and their possible impacts on microbial activities of stable wastewater biofilms cultivated in a lab scale rotating biological contactor (RBC) were investigated. Significant aggregation of CuO NPs was observed in the wastewater samples, depending on their mass concentrations. Extracellular polymeric substance (EPS)-adsorbed copper accounted for a large proportion of the total copper accumulated in biofilms. The microelectrode profiles showed that a single pulse exposure to 50mg/L CuO resulted in a deeper penetration depth of oxygen in biofilms compared to the CuO NP free biofilms. The maximum oxygen consumption rate shifted to the deeper parts of biofilms, indicating that the respiration activities of bacteria in the top region of the biofilms was significantly inhibited by CuO NPs. Biofilms secreted more EPS in response to the nano-CuO stress, with higher production of proteins compared to polysaccharides. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

    Stams, A.J.M.; Bok, de F.A.M.; Plugge, C.M.; Eekert, van M.H.A.; Dolfing, J.; Schraa, G.

    2006-01-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory

  14. Microbial cell surfaces and secretion systems

    NARCIS (Netherlands)

    Tommassen, J.P.M.; Wosten, H.A.B.

    2015-01-01

    Microbial cell surfaces, surface-exposed organelles, and secreted proteins are important for the interaction with the environment, including adhesion to hosts, protection against host defense mechanisms, nutrient acquisition, and intermicrobial competition. Here, we describe the structures of the ce

  15. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

    Stams, A.J.M.; Bok, de F.A.M.; Plugge, C.M.; Eekert, van M.H.A.; Dolfing, J.; Schraa, G.

    2006-01-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory

  16. Microbial diversity--insights from population genetics.

    Science.gov (United States)

    Mes, Ted H M

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

  17. Microbial Risk Assessment

    Science.gov (United States)

    Ott, C. M.; Mena, K. D.; Nickerson, C.A.; Pierson, D. L.

    2009-01-01

    Historically, microbiological spaceflight requirements have been established in a subjective manner based upon expert opinion of both environmental and clinical monitoring results and the incidence of disease. The limited amount of data, especially from long-duration missions, has created very conservative requirements based primarily on the concentration of microorganisms. Periodic reevaluations of new data from later missions have allowed some relaxation of these stringent requirements. However, the requirements remain very conservative and subjective in nature, and the risk of crew illness due to infectious microorganisms is not well defined. The use of modeling techniques for microbial risk has been applied in the food and potable water industries and has exceptional potential for spaceflight applications. From a productivity standpoint, this type of modeling can (1) decrease unnecessary costs and resource usage and (2) prevent inadequate or inappropriate data for health assessment. In addition, a quantitative model has several advantages for risk management and communication. By identifying the variable components of the model and the knowledge associated with each component, this type of modeling can: (1) Systematically identify and close knowledge gaps, (2) Systematically identify acceptable and unacceptable risks, (3) Improve communication with stakeholders as to the reasons for resource use, and (4) Facilitate external scientific approval of the NASA requirements. The modeling of microbial risk involves the evaluation of several key factors including hazard identification, crew exposure assessment, dose-response assessment, and risk characterization. Many of these factors are similar to conditions found on Earth; however, the spaceflight environment is very specialized as the inhabitants live in a small, semi-closed environment that is often dependent on regenerative life support systems. To further complicate modeling efforts, microbial dose

  18. Microbial Metalloproteomics

    Directory of Open Access Journals (Sweden)

    Peter-Leon Hagedoorn

    2015-12-01

    Full Text Available Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.

  19. Microbial Ecosystems, Protection of

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning.

  20. Microbial Ecosystems, Protection of

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning. Introdu

  1. Medium-chain triglyceride as an alternative of in-feed colistin sulfate to improve growth performance and intestinal microbial environment in newly weaned pigs.

    Science.gov (United States)

    Yen, Hung-Che; Lai, Wei-Kang; Lin, Chuan-Shun; Chiang, Shu-Hsing

    2015-01-01

    Five hundred and twenty-eight newly weaned pigs were given four treatments, with eight replicates per treatment. Sixteen to 18 pigs were assigned per replicate and were fed diets supplemented with 0 or 3% medium-chain triglyceride (MCT) and 0 or 40 ppm colistin sulfate (CS) in a 2 × 2 factorial arrangement for 2 weeks. The results showed that dietary supplementation with MCT improved the gain-to-feed ratio during days 3-7 and in the overall period (P environment and the feed utilization efficiency of newly weaned pigs.

  2. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  3. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping

    2004-01-01

    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  4. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAOGuo-ping

    2004-01-01

    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  5. 40 CFR 158.2170 - Experimental use permit data requirements-microbial pesticides.

    Science.gov (United States)

    2010-07-01

    ... requirements-microbial pesticides. 158.2170 Section 158.2170 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2170 Experimental use permit data requirements—microbial pesticides. (a) For all microbial pesticides. (1)...

  6. The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters.

    Science.gov (United States)

    Malham, Shelagh K; Rajko-Nenow, Paulina; Howlett, Eleanor; Tuson, Karen E; Perkins, Tracy L; Pallett, Denise W; Wang, Hui; Jago, Colin F; Jones, Davey L; McDonald, James E

    2014-09-20

    Anthropogenic activities have increased the load of faecal bacteria, pathogenic viruses and nutrients in rivers, estuaries and coastal areas through point and diffuse sources such as sewage discharges and agricultural runoff. These areas are used by humans for both commercial and recreational activities and are therefore protected by a range of European Directives. If water quality declines in these zones, significant economic losses can occur. Identifying the sources of pollution, however, is notoriously difficult due to the ephemeral nature of discharges, their diffuse source, and uncertainties associated with transport and transformation of the pollutants through the freshwater-marine interface. Further, significant interaction between nutrients, microorganisms and particulates can occur in the water column making prediction of the fate and potential infectivity of human pathogenic organisms difficult to ascertain. This interaction is most prevalent in estuarine environments due to the formation of flocs (suspended sediment) at the marine-freshwater interface. A range of physical, chemical and biological processes can induce the co-flocculation of microorganisms, organic matter and mineral particles resulting in pathogenic organisms becoming potentially protected from a range of biotic (e.g. predation) and abiotic stresses (e.g. UV, salinity). These flocs contain and retain macro- and micro- nutrients allowing the potential survival, growth and transfer of pathogenic organisms to commercially sensitive areas (e.g. beaches, shellfish harvesting waters). The flocs can either be transported directly to the coastal environment or can become deposited in the estuary forming cohesive sediments where pathogens can survive for long periods. Especially in response to storms, these sediments can be subsequently remobilised releasing pulses of potential pathogenic organisms back into the water column leading to contamination of marine waters long after the initial

  7. Counting Viruses and Bacteria in Photosynthetic Microbial Mats

    OpenAIRE

    Carreira, C.; Staal, M.; Middelboe, M.; Brussaard, C.P.D.

    2015-01-01

    Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures typically used in benthic viral ecology were applied to the complex matrix of microbial mats but were found to inefficiently extract viruses. Here, we present a method for extraction and quantifica...

  8. Rapid Detection of Staphylococcus aureus and Related Species Isolated from Food, Environment, Cosmetics, a Medical Device, and Clinical Samples Using the VITEK MS Microbial Identification System.

    Science.gov (United States)

    Sulaiman, Irshad M; Banerjee, Pratik; Hsieh, Ying-Hsin; Miranda, Nancy; Simpson, Steven; Kerdahi, Khalil

    2017-09-15

    Staphylococcus spp. is considered as one of the most common human-pathogenic bacteria, causing illnesses ranging from nonthreatening skin infections to lethal diseases, including sepsis, pneumonia, bloodstream infections, and food poisoning. The emergence of methicillin-resistant Staphylococcus aureus strains has increased morbidity and mortality and resulted in a major healthcare burden worldwide. Single and multilocus sequence typing have been extensively used in the identification of Staphylococcus species. Nevertheless, these assays are relatively time-consuming and require high-quality DNA. Matrix-assisted laser desorption ionization-time-of-flight has been used recently for the rapid identification of several bacterial species. In this study, we have examined 47 Staphylococcus isolates recovered from food, environment, clinical samples, cosmetic products, and a medical device and 3 American Type Culture Collection Staphylococcus reference isolates using bioMérieux VITEK MS and VITEK 2 systems to determine isolate identity. Sequencing of the 16S ribosomal RNA gene was performed to confirm and compare the species identification data generated by VITEK 2 and VITEK MS systems. Although the VITEK 2 system could not identify one of the isolates, VITEK MS identified all 50 Staphylococcus spp. isolates tested. Results of this study clearly suggest that VITEK MS can be used in the rapid identification of Staphylococcus isolates of public health importance.

  9. The fluctuating environment associated with the episodic biotic crisis during the Permo/Triassic transition:Evidence from microbial biomarkers in Changxing,Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The environmental conditions and the biotic crisis during the Permo-Triassic (Tr/P) transition received increasing attention in the past decades. Presented herein are the molecular fossil records of cyano-bacteria and green sulfur bacteria,the base of the marine ecosystem,to highlight the episodic nature of both the environment and the biotic crisis during this critical period. At least two episodes of cyano-bacterial expansion are documented by 2-methylhopanes ranging from C28 to C32 in carbon number,indicative of the instable marine ecosystem and the fluctuant aquatic nutrients. Meanwhile,the index of 2-alkyl-1,3,4-trimethylbenzenes (biomarkers of green sulfur bacteria) and the ratio of pristane to phy-tane (Pr/Ph) witness the fluctuation of sedimentary environmental redox conditions. The above mo-lecular evidence suggests the occurrence of highly fluctuating environmental conditions during the Tr/P transition,which is consistent with,and probably the cause of,the multi-phased biotic crisis and the prolonged faunal recovery.

  10. Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

    KAUST Repository

    Röthig, Till

    2017-03-17

    Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

  11. System and method for preparing near-surface heavy oil for extraction using microbial degradation

    Science.gov (United States)

    Busche, Frederick D.; Rollins, John B.; Noyes, Harold J.; Bush, James G.

    2011-04-12

    A system and method for enhancing the recovery of heavy oil in an oil extraction environment by feeding nutrients to a preferred microbial species (bacteria and/or fungi). A method is described that includes the steps of: sampling and identifying microbial species that reside in the oil extraction environment; collecting fluid property data from the oil extraction environment; collecting nutrient data from the oil extraction environment; identifying a preferred microbial species from the oil extraction environment that can transform the heavy oil into a lighter oil; identifying a nutrient from the oil extraction environment that promotes a proliferation of the preferred microbial species; and introducing the nutrient into the oil extraction environment.

  12. Microbial communities in microcosm soils treated with battery waste

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Battery waste is one of the most destructive hazards to our environment, especially to the soil. In order to understand the effects of the battery waste on the microbial communities in soil, microcosm soils were treated with the powder made from the battery waste. Microbial biomass and respiration were measured after 15, 30, 45, and 60 days of the treatment, and catabolic capability and Biolog profile were determined after 60 days. Microbial biomass was declined by all treatments, while microbial respiration and catabolic capability were enhanced. Although microbial biomass recovered after a period of incubation, microbial respiratory quotient, catabolic capability and community structure remained significantly affected. Our results also suggest that microbial respiratory quotient and Biolog parameters are more sensitive than microbial biomass to the battery stress on bioavailability.

  13. Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

    Energy Technology Data Exchange (ETDEWEB)

    Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

    2009-07-01

    Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)

  14. Modeling Approaches for Describing Microbial Population Heterogeneity

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita

    , ethanol and biomass throughout the reactor. This work has proven that the integration of CFD and population balance models, for describing the growth of a microbial population in a spatially heterogeneous reactor, is feasible, and that valuable insight on the interplay between flow and the dynamics......Although microbial populations are typically described by averaged properties, individual cells present a certain degree of variability. Indeed, initially clonal microbial populations develop into heterogeneous populations, even when growing in a homogeneous environment. A heterogeneous microbial......) to predict distributions of certain population properties including particle size, mass or volume, and molecular weight. Similarly, PBM allow for a mathematical description of distributed cell properties within microbial populations. Cell total protein content distributions (a measure of cell mass) have been...

  15. Patterns and Scales in Gastrointestinal Microbial Ecology

    Science.gov (United States)

    Rawls, John F.

    2016-01-01

    The body surfaces of humans and other animals are colonized at birth by microorganisms. The majority of microbial residents on the human body exist within gastrointestinal (GI) tract communities, where they contribute to many aspects of host biology and pathobiology. Recent technological advances have expanded our ability to perceive the membership and physiologic traits of microbial communities along the GI tract. To translate this information into a mechanistic and practical understanding of host-microbe and microbe-microbe relationships, it is necessary to recast our conceptualization of the GI tract and its resident microbial communities in ecological terms. This review depicts GI microbial ecology in the context of 2 fundamental ecological concepts: (1) the patterns of biodiversity within the GI tract and (2) the scales of time, space, and environment within which we perceive those patterns. We show how this conceptual framework can be used to integrate our existing knowledge and identify important open questions in GI microbial ecology. PMID:19457423

  16. Microbial activity at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  17. Biotechnological Processes in Microbial Amylase Production

    Directory of Open Access Journals (Sweden)

    Subash C. B. Gopinath

    2017-01-01

    Full Text Available Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi amylase is discussed along with its production methods from the laboratory to industrial scales.

  18. Biofilm and dental implant: The microbial link

    OpenAIRE

    Sangeeta Dhir

    2013-01-01

    Mouth provides a congenial environment for the growth of the microorganisms as compared to any other part of the human body by exhibiting an ideal nonshedding surface. Dental plaque happens to be a diverse community of the microorganisms found on the tooth surface. Periodontal disease and the peri-implant disease are specific infections that are originating from these resident microbial species when the balance between the host and the microbial pathogenicity gets disrupted. This review discu...

  19. APPLICATION OF MICROBIAL TECHNOLOGY TO MINERAL PROCESSING

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The application of microbial technology to mineral processing has been reviewed with respect to the bioleaching of metals from minerals, the influence of biotreatment on flotation, the biobene ficiation of nonmetallic minerals, and the biotreatment for mine waste reclamation.The application of microbial technology to mineral processing has shown the advantages of high efficiency, low energy and reagent consumption, low capital and operating costs, and low pollution of the environment.

  20. Antarctic microfungi as models for exobiology

    Science.gov (United States)

    Onofri, S.; Selbmann, L.; Zucconi, L.; Pagano, S.

    2004-01-01

    Microfungi living in different Antarctic environments are generally well adapted to high stress conditions such as low temperatures, wide thermal fluctuations, high UV irradiance, and low water and nutrients availability; for this reason they could be investigated in order to explore limits of microbial life. Microfungi living in simple cryptoendolithic microbial communities inside the porosity of rocks in the Antarctic Dry Valleys, the closest terrestrial analogue of Mars, are particularly suitable for exobiological studies. Until now studies on exobiology focused mainly on prokaryotes; since cryptoendolithic black meristematic fungi are able to tolerate hard desiccation, high UV exposure, extremely low temperatures and wide thermal fluctuations, they are proposed as the best eukaryotic models for the biological exploration of Mars. Indeed, their adaptive strategies could be crucial as predictive tools in investigating the limits of life.

  1. Universality of human microbial dynamics

    Science.gov (United States)

    Bashan, Amir; Gibson, Travis E.; Friedman, Jonathan; Carey, Vincent J.; Weiss, Scott T.; Hohmann, Elizabeth L.; Liu, Yang-Yu

    2016-06-01

    Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.

  2. Microbial transport : Adaptations to natural environments

    NARCIS (Netherlands)

    Konings, Wil N.

    2006-01-01

    The cytoplasmic membrane of bacteria is the matrix for metabolic energy transducing processes such as proton motive force generation and solute transport. Passive permeation of protons across the cytoplasmic membrane is a crucial determinant in the proton motive generating capacity of the organisms.

  3. Microbial conversions of terpenoids

    OpenAIRE

    Parshikov, Igor A

    2015-01-01

    The monograph describes examples of the application of microbial technology for obtaining of derivatives of terpenoids. Obtaining new derivatives of terpenoids, including artemisinin derivatives with increased antimalarial activity, is an important goal of research in microbial biotechnology and medicinal chemistry.

  4. Microbial Community and Urban Water Quality

    Institute of Scientific and Technical Information of China (English)

    YANG Jun; ZHANG Yongyu; LIU Lemian; WANG Changfu; YU Xiaoqing

    2012-01-01

    Urbanization of China is substantial and growing, and water resources are crucial for both economic and social sustainable development. Unfortunately, the frequency and intensity of water contamination events are increasing at an unprecedented rate and often accompanied by increased pollutant loading due to human activities such as irreversible industrialization and urbanization. The impacts of human pollution are most evident and of greatest concern at the microbial level. The research of the Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, has been focusing mainly on aquatic microorganisms in the urban environment, from drinking water and landscape water to waste water. Its projects fall into three categories: biomonitoring and bioassessment, microbial ecology and diversity, ecotoxicology and environmental microbiology. Its scientific topics include the aquatic ecological safety and microbial food web.

  5. Microbial interactions: ecology in a molecular perspective.

    Science.gov (United States)

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

  6. Microbial interactions: ecology in a molecular perspective

    Directory of Open Access Journals (Sweden)

    Raíssa Mesquita Braga

    Full Text Available ABSTRACT The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

  7. Determination of the feasibility of using open path FTIR to monitor levels of 3-methylfuran and 1-octen-3-ol for the purpose of detecting microbial contamination in indoor environments

    Energy Technology Data Exchange (ETDEWEB)

    Olive, Brent [Univ. of Alabama, Birmingham, AL (United States)

    1996-03-01

    Studies have shown that the presence of microbial growth correlates with health complaints associated with sick building syndrome. Microbial growth may be found in damp places within a building, and may be dispersed to other areas if present in the HVAC system. Certain individuals may be especially sensitive to the presence of these microorganisms, and may experience adverse reactions at extremely low concentrations. Unfortunately, the source of the problem may not be discovered because many times the microbial growth is not visible. However, there are some volatile organic compounds that are given off by certain microorganisms which may be used to determine the presence of microbial contamination. 3-Methylfuran is an excellent indicator of growing fungi. It is produced by a majority of fungi, and can be used as an indicator of ongoing growth. 1-Octen-3-ol is also produced by a number of fungi, and has been used in the past as an indicator of such. These two compounds and many other volatiles given off by microorganisms have been termed microbial volatile organic compounds (MVOCs). Many of these compounds are commonly found in indoor air, and thus, may be present even when there is not microbial contamination.

  8. Exploring Subglacial Microbial Ecology (Invited)

    Science.gov (United States)

    Mikucki, J.; Mitchell, A. C.; Johnson, S. S.; Grzymski, J.

    2009-12-01

    Subglacial environments were long thought to be abiotic. We now know that microbial life exists below glaciers, but know relatively little about the in situ metabolic processes they mediate and how their activity transforms the geochemistry of subglacial efflux. It has been hypothesized that subglacial systems, driven to anoxia in the presence of sufficient organic matter, will follow a continuum of redox chemistries utilizing electron acceptors with decreasing reduction potential (i.e. Fe (III), sulfate, CO2). Indeed, sulfate reduction and methanogenesis have been detected in studies of polythermal glaciers. However, it is unclear whether there is sufficient organic matter to sustain highly reducing conditions below Antarctic ice. Here we present a broad overview of the microbial ecology of subglacial ecosystems and describe the links between microbial diversity and community function in these chemically complex environments. The subglacial environment below the Taylor Glacier, Antarctica provides an example where biogeochemical measurements made on subglacial efflux can inform specific mechanisms of microbial metabolism. We have tested the validity of these mechanisms using environmental genomic surveys and biogeochemical measurements of subglacial fluids to describe an active community that cycles iron and sulfur below Taylor Glacier. Examples include the incorporation of radiolabeled bicarbonate by cells in the outflow and detection of functional genes responsible for CO2-fixation (i.e. RuBisCO), and isotopic composition of sulfate sulfur and oxygen in the outflow indicative of sulfate reduction with the presence of functional genes of the sulfur cycle (i.e. APS reductase). Moving forward in our exploration of subglacial ecosystems, key questions regarding microbial energetics include: 1) How microorganisms cycle mineral substrates below glaciers to gain energy for growth 2) Whether subglacial microorganisms grow syntrophically in order to metabolize iron and

  9. Microfluidics and microbial engineering.

    Science.gov (United States)

    Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

    2016-02-01

    The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

  10. Childhood microbial keratitis

    Directory of Open Access Journals (Sweden)

    Abdullah G Al Otaibi

    2012-01-01

    Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

  11. Hydrological controls on glacially exported microbial assemblages

    Science.gov (United States)

    Dubnick, Ashley; Kazemi, Sina; Sharp, Martin; Wadham, Jemma; Hawkings, Jon; Beaton, Alexander; Lanoil, Brian

    2017-05-01

    The Greenland Ice Sheet (GrIS) exports approximately 400 km3 of freshwater annually to downstream freshwater and marine ecosystems. These meltwaters originate in a wide range of well-defined habitats that can be associated with very different physical environments within the ice sheet, ranging from oxygenated surface environments that are exposed to light and supplied with nutrients from atmospheric/aeolian sources to subglacial environments that are permanently dark, isolated from the atmosphere, and potentially anoxic. Hydrological conditions in the latter likely favor prolonged rock-water contact. The seasonally evolving hydrological system that drains meltwaters from the GrIS connects these distinct microbial habitats and exports the microbes contained within them to downstream ecosystems. The microbial assemblages exported in glacier meltwater may have an impact on downstream ecosystem function and development. We explored how the seasonal development of a glacial drainage system influences the character of microbial assemblages exported from the GrIS by monitoring the seasonal changes in hydrology, water chemistry, and microbial assemblage composition of meltwaters draining from a glacier in southwest Greenland. We found that the microbial assemblages exported in meltwaters varied in response to glacier hydrological flow path characteristics. Whether or not meltwaters passed through the subglacial environment was the first-order control on the composition of the microbial assemblages exported from the glacier, while water source (i.e., supraglacial or extraglacial) and subglacial residence times were second-order controls. Glacier hydrology therefore plays a fundamental role in determining the microbial exports from glaciated watersheds.

  12. Microbial stress priming: a meta-analysis.

    Science.gov (United States)

    Andrade-Linares, Diana R; Lehmann, Anika; Rillig, Matthias C

    2016-04-01

    Microbes have to cope with complex and dynamic environments, making it likely that anticipatory responses provide fitness benefits. Mild, previous stressors can prepare microbes (stress priming) to further and potentially damaging stressors (triggering). We here quantitatively summarize the findings from over 250 trials of 34 studies including bacteria and fungi, demonstrating that priming to stress has a beneficial impact on microbial survival. In fact, survival of primed microbes was about 10-fold higher compared with that in non-primed microbes. Categorical moderators related to microbial taxonomy and the kind of stress applied as priming or as triggering revealed significant differences of priming effect size among 14 different microbial species, 6 stress categories and stressor combination. We found that priming by osmotic, physiological and temperature stress had the highest positive effect sizes on microbial response. Cross-protection was evident for physiological, temperature and pH stresses. Microbes are better prepared against triggering by oxidative, temperature and osmotic stress. Our finding of an overall positive mean effect of priming regardless of the microbial system and particular stressor provides unprecedentedly strong evidence of the broad ecological significance of microbial stress priming. These results further suggest that stress priming may be an important factor in shaping microbial communities.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  15. Guiding bioprocess design by microbial ecology.

    Science.gov (United States)

    Volmer, Jan; Schmid, Andreas; Bühler, Bruno

    2015-06-01

    Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies.

  16. Which Microbial Communities Are Present? Sequence-Based Metagenomics

    Science.gov (United States)

    Caffrey, Sean M.

    The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment's microbial community and activities, metagenomic analysis is an essential tool.

  17. Microbial shaping of sedimentary wrinkle structures

    Science.gov (United States)

    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.

  18. Effects of Elevated Carbon Dioxide and Salinity on the Microbial Diversity in Lithifying Microbial Mats

    Directory of Open Access Journals (Sweden)

    Steven R. Ahrendt

    2014-03-01

    Full Text Available Atmospheric levels of carbon dioxide (CO2 are rising at an accelerated rate resulting in changes in the pH and carbonate chemistry of the world’s oceans. However, there is uncertainty regarding the impact these changing environmental conditions have on carbonate-depositing microbial communities. Here, we examine the effects of elevated CO2, three times that of current atmospheric levels, on the microbial diversity associated with lithifying microbial mats. Lithifying microbial mats are complex ecosystems that facilitate the trapping and binding of sediments, and/or the precipitation of calcium carbonate into organosedimentary structures known as microbialites. To examine the impact of rising CO2 and resulting shifts in pH on lithifying microbial mats, we constructed growth chambers that could continually manipulate and monitor the mat environment. The microbial diversity of the various treatments was compared using 16S rRNA gene pyrosequencing. The results indicated that elevated CO2 levels during the six month exposure did not profoundly alter the microbial diversity, community structure, or carbonate precipitation in the microbial mats; however some key taxa, such as the sulfate-reducing bacteria Deltasulfobacterales, were enriched. These results suggest that some carbonate depositing ecosystems, such as the microbialites, may be more resilient to anthropogenic-induced environmental change than previously thought.

  19. Microbial Profiling Of Cyanobacteria From VIT Lake

    Directory of Open Access Journals (Sweden)

    Swati Singh

    2015-08-01

    Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

  20. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  1. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  2. 40 CFR 158.2130 - Microbial pesticides residue data requirements table.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides residue data... (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2130 Microbial pesticides residue data requirements table. (a) General. Sections 158.100 through 158.130 describe how to...

  3. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides product analysis... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2120 Microbial pesticides product analysis data requirements table. (a) General. Sections 158.100 through...

  4. Microbial activity in bentonite buffers. Literature study

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, M.; Itavaara, M.

    2012-07-01

    The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokaryotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7-8 MPa, the amount of free water is low and the average pore and pore throat diameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. Literature on the environmental limits of microbial life in extreme conditions and the occurrence of sulphatereducing prokaryotes in extreme environments is reviewed briefly and the results of published studies characterizing microbes and microbial processes in repository conditions or in relevant subsurface environments are presented. The presence of bacteria, including SRBs, has been confirmed in deep groundwater and bentonite-based materials. Sulphate reducers have been detected in various high-pressure environments, and sulphate-reduction based on hydrogen as an energy source is considered a major microbial process in deep subsurface environments. In bentonite, microbial activity is strongly suppressed, mainly due to the low amount of free water and small pores, which limit the transport of microbes and nutrients. Spore-forming bacteria have been shown to survive in compacted bentonite as dormant spores, and they are able to resume a metabolically active state after decompaction. Thus, microbial sulphide production may increase in repository conditions if the dry density of the bentonite buffer is locally reduced. (orig.)

  5. Multifactorial diversity sustains microbial community stability

    NARCIS (Netherlands)

    Erkus, O.; Jager, de V.C.L.; Spus, M.; Alen-Boerrigter, van I.J.; Rijswijck, van I.M.H.; Hazelwood, L.; Janssen, P.W.; Hijum, van S.A.F.T.; Kleerebezem, M.; Smid, E.J.

    2013-01-01

    Maintenance of a high degree of biodiversity in homogeneous environments is poorly understood. A complex cheese starter culture with a long history of use was characterized as a model system to study simple microbial communities. Eight distinct genetic lineages were identified, encompassing two spec

  6. Microbial Biogeography of the Arctic Cryosphere

    DEFF Research Database (Denmark)

    Hauptmann, Aviaja Zenia Edna Lyberth

    communities. This has considerably improved our understanding that even harsh and seemingly barren environments such as the cryosphere, the frozen parts of our planet, is inhabited by diverse life. This thesis presents three studies in microbial biogeography of the Arctic cryosphere utilizing a range of NGS...

  7. Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

    DEFF Research Database (Denmark)

    Modrzynski, Jakub Jan

    -induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient......Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution...

  8. Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

    DEFF Research Database (Denmark)

    Modrzynski, Jakub Jan

    Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution......-induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient...

  9. An Economic Framework of Microbial Trade.

    Science.gov (United States)

    Tasoff, Joshua; Mee, Michael T; Wang, Harris H

    2015-01-01

    A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century.

  10. An Economic Framework of Microbial Trade.

    Directory of Open Access Journals (Sweden)

    Joshua Tasoff

    Full Text Available A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century.

  11. Microbial life in a liquid asphalt desert.

    Science.gov (United States)

    Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M; Guinan, Edward; Lehto, Harry J; Hallam, Steven J

    2011-04-01

    Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

  12. Microbial Life in a Liquid Asphalt Desert

    Science.gov (United States)

    Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C.; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M.; Guinan, Edward; Lehto, Harry J.; Hallam, Steven J.

    2011-04-01

    Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 107 cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

  13. Manipulating soil microbial communities in extensive green\\ud roof substrates

    OpenAIRE

    Molineux, Chloe; Connop, Stuart; Gange, Alan

    2014-01-01

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated,we added mycorrhizal fungi and a microbial mixture (‘compost tea’) to green...

  14. Enhancing Metagenomics Investigations of Microbial Interactions with Biofilm Technology

    Directory of Open Access Journals (Sweden)

    Kavita S. Kakirde

    2013-11-01

    Full Text Available Investigations of microbial ecology and diversity have been greatly enhanced by the application of culture-independent techniques. One such approach, metagenomics, involves sample collections from soil, water, and other environments. Extracted nucleic acids from bulk environmental samples are sequenced and analyzed, which allows microbial interactions to be inferred on the basis of bioinformatics calculations. In most environments, microbial interactions occur predominately in surface-adherent, biofilm communities. In this review, we address metagenomics sampling and biofilm biology, and propose an experimental strategy whereby the resolving power of metagenomics can be enhanced by incorporating a biofilm-enrichment step during sample acquisition.

  15. Enhancing metagenomics investigations of microbial interactions with biofilm technology.

    Science.gov (United States)

    McLean, Robert J C; Kakirde, Kavita S

    2013-11-11

    Investigations of microbial ecology and diversity have been greatly enhanced by the application of culture-independent techniques. One such approach, metagenomics, involves sample collections from soil, water, and other environments. Extracted nucleic acids from bulk environmental samples are sequenced and analyzed, which allows microbial interactions to be inferred on the basis of bioinformatics calculations. In most environments, microbial interactions occur predominately in surface-adherent, biofilm communities. In this review, we address metagenomics sampling and biofilm biology, and propose an experimental strategy whereby the resolving power of metagenomics can be enhanced by incorporating a biofilm-enrichment step during sample acquisition.

  16. MICROBIAL FUEL CELL

    DEFF Research Database (Denmark)

    2008-01-01

    A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

  17. Biofilms: A microbial home

    Science.gov (United States)

    Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

    2011-01-01

    Microbial biofilms are mainly implicated in etiopathogenesis of caries and periodontal disease. Owing to its properties, these pose great challenges. Continuous and regular disruption of these biofilms is imperative for prevention and management of oral diseases. This essay provides a detailed insight into properties, mechanisms of etiopathogenesis, detection and removal of these microbial biofilms. PMID:21976832

  18. Biofilms: A microbial home

    OpenAIRE

    Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

    2011-01-01

    Microbial biofilms are mainly implicated in etiopathogenesis of caries and periodontal disease. Owing to its properties, these pose great challenges. Continuous and regular disruption of these biofilms is imperative for prevention and management of oral diseases. This essay provides a detailed insight into properties, mechanisms of etiopathogenesis, detection and removal of these microbial biofilms.

  19. Microbial Life in a Liquid Asphalt Desert

    CERN Document Server

    Schulze-Makuch, Dirk; Antonio, Marina Resendes de Sousa; Ali, Denzil; Hosein, Riad; Song, Young C; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M; Guinan, Edward; Lehto, Harry J; Hallam, Steven J

    2010-01-01

    An active microbiota, reaching up to 10 E+7 cells/g, was found to inhabit a naturally occurring asphalt lake characterized by low water activity and elevated temperature. Geochemical and molecular taxonomic approaches revealed novel and deeply branching microbial assemblages mediating anaerobic hydrocarbon degradation, metal respiration and C1 utilization pathways. These results open a window into the origin and adaptive evolution of microbial life within recalcitrant hydrocarbon matrices, and establish the site as a useful analog for the liquid hydrocarbon environments on Saturn's moon Titan.

  20. Flat laminated microbial mat communities

    Science.gov (United States)

    Franks, Jonathan; Stolz, John F.

    2009-10-01

    Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

  1. Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

    KAUST Repository

    Kiely, Patrick D.

    2011-01-01

    Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H2 gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current. © 2010 Elsevier Ltd.

  2. Microbial extracellular electron transfer and its relevance to iron corrosion.

    Science.gov (United States)

    Kato, Souichiro

    2016-03-01

    Extracellular electron transfer (EET) is a microbial metabolism that enables efficient electron transfer between microbial cells and extracellular solid materials. Microorganisms harbouring EET abilities have received considerable attention for their various biotechnological applications, including bioleaching and bioelectrochemical systems. On the other hand, recent research revealed that microbial EET potentially induces corrosion of iron structures. It has been well known that corrosion of iron occurring under anoxic conditions is mostly caused by microbial activities, which is termed as microbiologically influenced corrosion (MIC). Among diverse MIC mechanisms, microbial EET activity that enhances corrosion via direct uptake of electrons from metallic iron, specifically termed as electrical MIC (EMIC), has been regarded as one of the major causative factors. The EMIC-inducing microorganisms initially identified were certain sulfate-reducing bacteria and methanogenic archaea isolated from marine environments. Subsequently, abilities to induce EMIC were also demonstrated in diverse anaerobic microorganisms in freshwater environments and oil fields, including acetogenic bacteria and nitrate-reducing bacteria. Abilities of EET and EMIC are now regarded as microbial traits more widespread among diverse microbial clades than was thought previously. In this review, basic understandings of microbial EET and recent progresses in the EMIC research are introduced.

  3. Microbial ecological associations in the surface sediments of Bohai strait

    Science.gov (United States)

    Wang, Bin; Liu, Hongmei; Tang, Haitian; Hu, Xiaoke

    2017-09-01

    Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China (average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational difference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.

  4. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

    NARCIS (Netherlands)

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-01-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with.

  5. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

    NARCIS (Netherlands)

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-01-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. It

  6. Humans differ in their personal microbial cloud

    Directory of Open Access Journals (Sweden)

    James F. Meadow

    2015-09-01

    Full Text Available Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

  7. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    Directory of Open Access Journals (Sweden)

    Darine Trabelsi

    2013-01-01

    Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

  8. Inferring Microbial Fitness Landscapes

    Science.gov (United States)

    2016-02-25

    experiments on evolving microbial populations. Although these experiments have produced examples of remarkable phenomena – e.g. the emergence of mutator...what specific mutations, avian influenza viruses will adapt to novel human hosts; or how readily infectious bacteria will escape antibiotics or the...infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND

  9. Evaluation of Microalgae as Microbial Fertilizer

    Directory of Open Access Journals (Sweden)

    Onder Uysal

    2015-06-01

    Full Text Available Microalgal biomass is utilized in many fields such as food, agriculture, energy, and cosmetic sectors. It is very well known that chemical fertilizer adversely affect soil, plant, and environment. To reduce this effect in recent years, interest to organic farming has been increasing. In this study, microbial fertilizers obtained from microalgae was applied to maize and wheat plants. Microbial fertilizers at four different doses were applied, namely, S1 (control: 0,00 dose-non fertilizer, S2 (0.50 dose, S3 (1.00 dose, and S4 (1.50 dose. All measurements were made at the end of 30th days.  The best results were determined for S3 dose applications. During the experiment, the soil temperature between 15 and 30⁰C and soil pH values between 6.5 and 8.5 were maintained. The results showed that the amount of soil organic matter and the water holding capacity were improved. Finally, microbial fertilizers obtained from microalgae can be reported to have positive effects on soil, plants and therefore environment. Keywords: Microalgae, biomass, agriculture, fertilizer, microbial

  10. Review of Micro/Nanotechnologies for Microbial Biosensors

    Directory of Open Access Journals (Sweden)

    Ji Won eLim

    2015-05-01

    Full Text Available A microbial biosensor is an analytical device with a biologically integrated transducer that generates a measurable signal indicating the analyte concentration. This method is ideally suited for the analysis of extracellular chemicals and the environment, and for metabolic sensory-regulation. Although microbial biosensors show promise for application in various detection fields, some limitations still remain such as poor selectivity, low sensitivity, and impractical portability. To overcome such limitations, microbial biosensors have been integrated with many recently developed micro/nanotechnologies and applied to a wide range of detection purposes. This review article discusses micro/nanotechnologies that have been integrated with microbial biosensors and summarizes recent advances and the applications achieved through such novel integration. Future perspectives on the combination of micro/nanotechnologies and microbial biosensors will be discussed, and the necessary developments and improvements will be strategically deliberated.

  11. A Review of Methods for Studying Microbial Diversity in Soils

    Institute of Scientific and Technical Information of China (English)

    LIU Bing-Ru; JIA Guo-Mei; CHEN Jian; WANG Gang

    2006-01-01

    Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients,and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. However, understanding the diversity of this complex microbial community in the soil environment is a challenging task. Thus, it is important to master and comprehend appropriate methods for studying soil microbial diversity. Concepts of soil microbial diversity and major methods of study are briefly introduced in this paper. Then, the application of biochemical-based and molecularbased techniques in this area, and their advantages and disadvantages are evaluated. Based on recent related research,perspectives for studying microbial diversity in soils are presented.

  12. Designing the Microbial Research Commons

    Energy Technology Data Exchange (ETDEWEB)

    Uhlir, Paul F. [Board on Research Data and Information Policy and Global Affairs, Washington, DC (United States)

    2011-10-01

    Recent decades have witnessed an ever-increasing range and volume of digital data. All elements of the pillars of science--whether observation, experiment, or theory and modeling--are being transformed by the continuous cycle of generation, dissemination, and use of factual information. This is even more so in terms of the re-using and re-purposing of digital scientific data beyond the original intent of the data collectors, often with dramatic results. We all know about the potential benefits and impacts of digital data, but we are also aware of the barriers, the challenges in maximizing the access, and use of such data. There is thus a need to think about how a data infrastructure can enhance capabilities for finding, using, and integrating information to accelerate discovery and innovation. How can we best implement an accessible, interoperable digital environment so that the data can be repeatedly used by a wide variety of users in different settings and with different applications? With this objective: to use the microbial communities and microbial data, literature, and the research materials themselves as a test case, the Board on Research Data and Information held an International Symposium on Designing the Microbial Research Commons at the National Academy of Sciences in Washington, DC on 8-9 October 2009. The symposium addressed topics such as models to lower the transaction costs and support access to and use of microbiological materials and digital resources from the perspective of publicly funded research, public-private interactions, and developing country concerns. The overall goal of the symposium was to stimulate more research and implementation of improved legal and institutional models for publicly funded research in microbiology.

  13. Microbial ecology and adaptation in cystic fibrosis airways

    DEFF Research Database (Denmark)

    Yang, Lei; Jelsbak, Lars; Molin, Søren

    2011-01-01

    Chronic infections in the respiratory tracts of cystic fibrosis (CF) patients are important to investigate, both from medical and from fundamental ecological points of view. Cystic fibrosis respiratory tracts can be described as natural environments harbouring persisting microbial communities...... constitute the selective forces that drive the evolution of the microbes after they migrate from the outer environment to human airways. Pseudomonas aeruginosa adapts to the new environment through genetic changes and exhibits a special lifestyle in chronic CF airways. Understanding the persistent...... colonization of microbial pathogens in CF patients in the context of ecology and evolution will expand our knowledge of the pathogenesis of chronic infections and improve therapeutic strategies....

  14. Microbial Extremophiles in Evolutionary Aspect

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2007-01-01

    The microflora of the cryosphere of planet Earth provides the best analogs for life forms that might be found in the permafrost or polar ice caps of Mars, near the surface of the cometary nuclei, or in the liquid water beneath the ice crusts of icy moons of Jupiter and Saturn. For astrobiology the focus on the study alkaliphilic microorganisms was enhanced by the findings of abundant carbonates and carbonate globules rimmed with possibly biogenic magnetites in association with the putative microfossils in the ALH84001 meteorite. Although the ALH84001 "nanofossils" were to small and simple to be unambiguously recognized as biogenic, they stimulated Astrobiology research and studies of microbial extremophiles and biomarkers in ancient rocks and meteorites. Recent studies of CI and CM carbonaceous meteorites have resulted in the detection of the well-preserved mineralized remains of coccoidal and" filamentous microorganisms in cyanobacterial mats. Energy Dispersive X-ray Analysis has shown anomalous biogenic element ratios clearly indicating they are not recent biological contaminants. This paper reviews microbial extremophiles in context of their significance to Astrobiology and the evolution of life. Extremophilic microorganisms on Earth are models for life that might endure high radiation environments in the ice near the surface of comets or on the icy moons of Jupiter and Saturn and in the seafloor deep beneath the icy crusts of Europa and Enceladus.

  15. Microbial responses to environmental arsenic.

    Science.gov (United States)

    Páez-Espino, David; Tamames, Javier; de Lorenzo, Víctor; Cánovas, David

    2009-02-01

    Microorganisms have evolved dynamic mechanisms for facing the toxicity of arsenic in the environment. In this sense, arsenic speciation and mobility is also affected by the microbial metabolism that participates in the biogeochemical cycle of the element. The ars operon constitutes the most ubiquitous and important scheme of arsenic tolerance in bacteria. This system mediates the extrusion of arsenite out of the cells. There are also other microbial activities that alter the chemical characteristics of arsenic: some strains are able to oxidize arsenite or reduce arsenate as part of their respiratory processes. These type of microorganisms require membrane associated proteins that transfer electrons from or to arsenic (AoxAB and ArrAB, respectively). Other enzymatic transformations, such as methylation-demethylation reactions, exchange inorganic arsenic into organic forms contributing to its complex environmental turnover. This short review highlights recent studies in ecology, biochemistry and molecular biology of these processes in bacteria, and also provides some examples of genetic engineering for enhanced arsenic accumulation based on phytochelatins or metallothionein-like proteins.

  16. Nitrogen cycle in microbial mats: completely unknown?

    Science.gov (United States)

    Coban, O.; Bebout, B.

    2015-12-01

    Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results

  17. 广西隆安下石炭统都结微生物岩微相特征与沉积环境研究%Sedimentary Environment and Microfacies Analysis of the Lower Carboniferous Microbial Carbonates in the Dujie Village, Long’an County,Guangxi

    Institute of Scientific and Technical Information of China (English)

    苗卓伟; 张永利; 巩恩普; 关长庆; 阮氏梅香; 黄文韬; 王邓

    2016-01-01

    Objectives:The thick-bedded Dujie microbial carbonates are widespread and well exposed in Long ’an county,Guangxi.The microbial carbonates occur in the middle—upper part of Du’an Formation.Until recently, Early Carboniferous carbonate buildups were reported as relatively rare in south China,and very few work on Dujie microbial carbonates has been done.In this study,we focus on the microfacies analysis to establish depositional facies models and identify sedimentary environment. Methods:Microfacies is considered as the total of all sedimentological and paleontological data which can be described and classified from thin sections,polished slabs,rock samples and so on.Microfacies analysis consists of two parts of work:① Field geology,including mapping and profiling,is a prerequisite for successful microfacies analysis;② Thin-section studies,observing microscopic features of limestones by polarizing microscope and using microfacies criteria in describing and classifying limestones. Results:Dujie microbial carbonates contain various organisms including microbe,foraminifera,echinoderm, calcisphere,brachiopod etc..Fossiliferous grainstones and boundstones are two common lithofacies in the microbial carbonates.Eight microfacies types grouped into three facies zones are recognized by petrographic analysis.They are (MF1)Coated bioclastic grainstone;(MF2)Peloidal grainstone with shell;(MF3)Non-laminated peloidal grainstone;(MF4)Aggregate-grain grainstone;(MF5)Densely laminated bindstone;(MF6)Ooid grainstone with intraclast;(MF7 ) Ooid grainstone;(MF8 ) Dolomitic ooid grainstone.The sedimentary processes of Dujie microbial carbonates include (FZ1 )the shoal of platform margin facies,(FZ2 )the open platform facies and (FZ3 )the restricted platform facies. Conclusions:Thus,the established depositional facies models and geologic foundation data indicate that:①Dujie microbial carbonates are distributed in shallow water carbonate platform within low latitudes;② Dujie

  18. Application of AFM from microbial cell to biofilm.

    Science.gov (United States)

    Wright, Chris J; Shah, Maia Kierann; Powell, Lydia C; Armstrong, Ian

    2010-01-01

    Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes.

  19. [Biomass energy utilization in microbial fuel cells: potentials and challenges].

    Science.gov (United States)

    Huang, Liping; Cheng, Shaoan

    2010-07-01

    Microbial fuel cells (MFCs) that can harvest biomass energy from organic wastes through microbial catalysis have garnered more and more attention within the past decade due to its potential benefits to ecological environment. In this article, the updated progress in MFCs is reviewed, with a focus on frontier technologies such as chamber configurations, feedstock varieties and the integration of MFCs with microbial electrolysis cells for hydrogen production. And on the other hand, the challenges like development of cost-effective electrode materials, improvement of biomass energy recovery and power output, design and optimization of commercial MFC devices are presented.

  20. Microbial growth and physiology in space - A review

    Science.gov (United States)

    Cioletti, Louis A.; Mishra, S. K.; Pierson, Duane L.

    1991-01-01

    An overview of microbial behavior in closed environments is given with attention to data related to simulated microgravity and actual space flight. Microbes are described in terms of antibiotic sensitivity, subcellular structure, and physiology, and the combined effects are considered of weightlessness and cosmic radiation on human immunity to such microorganisms. Space flight results report such effects as increased phage induction, accelerated microbial growth rates, and the increased risk of disease communication and microbial exchange aboard confining spacecraft. Ultrastructural changes are also noted in the nuclei, cell membranes, and cytoplasmic streaming, and it appears that antibiotic sensitivity is reduced under both actual and simulated conditions of spaceflight.

  1. A new perspective on microbial landscapes within food production.

    Science.gov (United States)

    Bokulich, Nicholas A; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

    2016-02-01

    High-throughput, 'next-generation' sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems.

  2. Deicing/Propylene Glycol (PG) Microbial Remediation Technology

    Science.gov (United States)

    2011-05-01

    Deicing /Propylene Glycol (PG) Microbial Remediation Technology Environment, Energy Security, & Sustainability (E2S2) Symposium & Exhibition Ernest N...DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Deicing /Propylene Glycol (PG) Microbial Remediation Technology 5a. CONTRACT...Issues C. PG Remediation Project D. Summary E. Questions 2 3 Background • Aircraft deicing fluids (ADF) work planes fly in the winter o Military

  3. A new perspective on microbial landscapes within food production

    OpenAIRE

    Bokulich, Nicholas A.; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

    2016-01-01

    High-throughput, ‘next-generation’ sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights...

  4. Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

    Science.gov (United States)

    Birmele, Michele; Caro, Janicce; Newsham, Gerard; Roberts, Michael; Morford, Megan; Wheeler, Ray

    2012-01-01

    Microbial detection, identification, and control are essential for the maintenance and preservation of spacecraft water systems. Requirements set by NASA put limitations on the energy, mass, materials, noise, cost, and crew time that can be devoted to microbial control. Efforts are being made to attain real-time detection and identification of microbial contamination in microgravity environments. Research for evaluating technologies for capability enhancement on-orbit is currently focused on the use of adenosine triphosphate (ATP) analysis for detection purposes and polymerase chain reaction (peR) for microbial identification. Additional research is being conducted on how to control for microbial contamination on a continual basis. Existing microbial control methods in spacecraft utilize iodine or ionic silver biocides, physical disinfection, and point-of-use sterilization filters. Although these methods are effective, they require re-dosing due to loss of efficacy, have low human toxicity thresholds, produce poor taste, and consume valuable mass and crew time. Thus, alternative methods for microbial control are needed. This project also explores ultraviolet light-emitting diodes (UV-LEDs), surface passivation methods for maintaining residual biocide levels, and several antimicrobial materials aimed at improving current microbial control techniques, as well as addressing other materials presently under analysis and future directions to be pursued.

  5. Microbial life in the deep terrestrial subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B. [E.I. DuPont de Nemours and Co., Aiken, SC (United States). Savannah River Lab.; Balkwill, D.L. [Florida State Univ., Tallahassee, FL (United States); Beeman, R.E. [Univ. of Oklahoma, Norman, OK (United States)] [and others

    1988-12-31

    The distribution and function of microorganisms is a vital issue in microbial ecology. The US Department of Energy`s Program, ``Microbiology of the Deep Subsurface,`` concentrates on establishing fundamental scientific information about organisms at depth, and the use of these organisms for remediation of contaminants in deep vadose zone and groundwater environments. This investigation effectively extends the Biosphere hundreds of meters into the Geosphere and has implications to a variety of subsurface activities.

  6. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System

    Science.gov (United States)

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems. PMID:28261160

  7. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System.

    Science.gov (United States)

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.

  8. Microbial deprivation, inflammation and cancer.

    Science.gov (United States)

    von Hertzen, Leena C; Joensuu, H; Haahtela, T

    2011-06-01

    Dysregulated immune function is involved in the pathogenesis of many common human diseases. Living in urban, microbe-poor environment may have a profound influence on the immune function and eventually also on carcinogenesis. Unfortunately, few studies have thus far addressed the role of exposure to the environmental microbiota on the risk of cancer. Which mechanisms are broken in individuals prone to develop chronic inflammation in response to exposure that does not cause harm in others? Recent work in immunology has revealed that Th17 cells, a third subset of Th cells, and inflammatory cytokines, particularly IL-23, are closely linked with tumour-associated inflammation. Albeit the precise role of Th17 cells in cancer is still unclear and a matter of debate, accumulating evidence shows that Th17 cells are enriched in a wide range of human tumours, and that these tumour-derived Th17 cells may promote angiogenesis, tumour growth and inflammation. Regulatory T cells, in turn, appear to have counter-regulatory effects on Th17 cells and can inhibit their function. Thus, the regulatory network, induced and strengthened by continuous exposure to environmental microbiota, may play an important role in tumour immunobiology in preventing the establishment of chronic inflammation in its early phases. In addition, the discovery of the Toll-like receptor (TLR) system has brought micro-organisms to new light; continuous signalling via these TLRs and other receptors that sense microbial components is necessary for epithelial cell integrity, tissue repair, and recovery from injury. In this communication, we summarise the epidemiological data of living in environments with diverse microbial exposures and the risk of cancer, and discuss the related immunological mechanisms, focusing on the links between environmental microbiota, the Th17/IL-23 axis and cancer-associated inflammation.

  9. Expansion of Microbial Forensics.

    Science.gov (United States)

    Schmedes, Sarah E; Sajantila, Antti; Budowle, Bruce

    2016-08-01

    Microbial forensics has been defined as the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes. Over the past 15 years, technology, particularly massively parallel sequencing, and bioinformatics advances now allow the characterization of microorganisms for a variety of human forensic applications, such as human identification, body fluid characterization, postmortem interval estimation, and biocrimes involving tracking of infectious agents. Thus, microbial forensics should be more broadly described as the discipline of applying scientific methods to the analysis of microbial evidence in criminal and civil cases for investigative purposes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  10. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    microbial identifier (GMI) initiative, aims to build a database of whole microbial genome sequencing data linked to relevant metadata, which can be used to identify microorganisms, their communities and the diseases they cause. It would be a platform for storing whole genome sequencing (WGS) data......) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open......-source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global...

  11. The Microbial Olympics

    Science.gov (United States)

    Youle, Merry; Rohwer, Forest; Stacy, Apollo; Whiteley, Marvin; Steel, Bradley C.; Delalez, Nicolas J.; Nord, Ashley L.; Berry, Richard M.; Armitage, Judith P.; Kamoun, Sophien; Hogenhout, Saskia; Diggle, Stephen P.; Gurney, James; Pollitt, Eric J. G.; Boetius, Antje; Cary, S. Craig

    2014-01-01

    Every four years, the Olympic Games plays host to competitors who have built on their natural talent by training for many years to become the best in their chosen discipline. Similar spirit and endeavour can be found throughout the microbial world, in which every day is a competition to survive and thrive. Microorganisms are trained through evolution to become the fittest and the best adapted to a particular environmental niche or lifestyle, and to innovate when the ‘rules of the game’ are changed by alterations to their natural habitats. In this Essay, we honour the best competitors in the microbial world by inviting them to take part in the inaugural Microbial Olympics. PMID:22796885

  12. Microbial Diversity of Impact-Generated Habitats

    Science.gov (United States)

    Pontefract, Alexandra; Osinski, Gordon R.; Cockell, Charles S.; Southam, Gordon; McCausland, Phil J. A.; Umoh, Joseph; Holdsworth, David W.

    2016-10-01

    Impact-generated lithologies have recently been identified as viable and important microbial habitats, especially within cold and arid regions such as the polar deserts on Earth. These unique habitats provide protection from environmental stressors, such as freeze-thaw events, desiccation, and UV radiation, and act to trap aerially deposited detritus within the fissures and pore spaces, providing necessary nutrients for endoliths. This study provides the first culture-independent analysis of the microbial community structure within impact-generated lithologies in a Mars analog environment, involving the analysis of 44,534 16S rRNA sequences from an assemblage of 21 rock samples that comprises three shock metamorphism categories. We find that species diversity increases (H = 2.4-4.6) with exposure to higher shock pressures, which leads to the development of three distinct populations. In each population, Actinobacteria were the most abundant (41%, 65%, and 59%), and the dominant phototrophic taxa came from the Chloroflexi. Calculated porosity (a function of shock metamorphism) for these samples correlates (R2 = 0.62) with inverse Simpson indices, accounting for overlap in populations in the higher shock levels. The results of our study show that microbial diversity is tied to the amount of porosity in the target substrate (as a function of shock metamorphism), resulting in the formation of distinct microbial populations.

  13. EVAPORITE MICROBIAL FILMS, MATS, MICROBIALITES AND STROMATOLITES

    Energy Technology Data Exchange (ETDEWEB)

    Brigmon, R; Penny Morris, P; Garriet Smith, G

    2008-01-28

    Evaporitic environments are found in a variety of depositional environments as early as the Archean. The depositional settings, microbial community and mineralogical composition vary significantly as no two settings are identical. The common thread linking all of the settings is that evaporation exceeds precipitation resulting in elevated concentrations of cations and anions that are higher than in oceanic systems. The Dead Sea and Storrs Lake are examples of two diverse modern evaporitic settings as the former is below sea level and the latter is a coastal lake on an island in the Caribbean. Each system varies in water chemistry as the Dead Sea dissolved ions originate from surface weathered materials, springs, and aquifers while Storrs Lake dissolved ion concentration is primarily derived from sea water. Consequently some of the ions, i.e., Sr, Ba are found at significantly lower concentrations in Storrs Lake than in the Dead Sea. The origin of the dissolved ions are ultimately responsible for the pH of each system, alkaline versus mildly acidic. Each system exhibits unique biogeochemical properties as the extreme environments select certain microorganisms. Storrs Lake possesses significant biofilms and stromatolitic deposits and the alkalinity varies depending on rainfall and storm activity. The microbial community Storrs Lake is much more diverse and active than those observed in the Dead Sea. The Dead Sea waters are mildly acidic, lack stromatolites, and possess a lower density of microbial populations. The general absence of microbial and biofilm fossilization is due to the depletion of HCO{sub 3} and slightly acidic pH.

  14. Altering petrology through microbial dissimilatory phosphite oxidation

    Science.gov (United States)

    Zhu, H.; Figueroa, I.; Coates, J. D.

    2013-12-01

    Microbial enhanced oil recovery (MEOR) takes advantage of various microbial metabolisms to increase hydrocarbon and energy yield by improving oil flow and flood water sweep in a reservoir during tertiary recovery. Wormholing at the injection well is believed to be the result of the large drop in pressure when water exits the injection well and enters the unconsolidated reservoir matrix. One possible means of prevent this event is to consolidate the rock matrix immediately around the injection well to create a permeable zone of stable petrology. Many microbial processes are known to result in the precipitation of ionic components into their environment creating solid-phase minerals. Such processes could be judiciously applied to bind unconsolidated matrices in order to form a permeable concreted rock matrix, which would minimize wormholing events and thus improve floodwater sweep. However, to date, apart from the application of urea oxidation creating calcium carbonate precipitation, there has been little investigation of the applicability of these precipitated bioconcretions to MEOR strategies and none to control wormholing events. Here we present a novel approach to altering rock petrology to concrete unconsolidated matrices in the near well environment by the biogenesis of authigenic minerals through microbial dissimilatory phosphite oxidation. Desulfotignum phosphitoxidans, strain FiPS-3 is currently the only isolated organism capable of using phosphite (HPO32-) as an electron donor for growth. This process, known as dissimilatory phosphite oxidation (DPO), can be coupled to either sulfate reduction or homoacetogenesis and leads to the accumulation of inorganic phosphate in the medium. The resulting insoluble mineral phases can coat the rock environment resulting in a concretion binding the unconsolidated matrix particles into a single phase. In this study we demonstrate that DPO can effectively produce calcium or magnesium phosphate minerals in packed glass

  15. Microbial community degradation of widely used quaternary ammonium disinfectants.

    Science.gov (United States)

    Oh, Seungdae; Kurt, Zohre; Tsementzi, Despina; Weigand, Michael R; Kim, Minjae; Hatt, Janet K; Tandukar, Madan; Pavlostathis, Spyros G; Spain, Jim C; Konstantinidis, Konstantinos T

    2014-10-01

    Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments.

  16. Environmental sensing of heavy metals through whole cell microbial biosensors: a synthetic biology approach.

    Science.gov (United States)

    Bereza-Malcolm, Lara Tess; Mann, Gülay; Franks, Ashley Edwin

    2015-05-15

    Whole cell microbial biosensors are offering an alternative means for rapid, on-site heavy metal detection. Based in microorganisms, biosensing constructs are designed and constructed to produce both qualitative and quantitative outputs in response to heavy metal ions. Previous microbial biosensors designs are focused on single-input constructs; however, development of multiplexed systems is resulting in more flexible designs. The movement of microbial biosensors from laboratory based designs toward on-site, functioning heavy metal detectors has been hindered by the toxic nature of heavy metals, along with the lack of specificity of heavy metals promoter elements. Applying a synthetic biology approach with alternative microbial chassis may increase the robustness of microbial biosensors and mitigate these issues. Before full applications are achieved, further consideration has to be made regarding the risk and regulations of whole cell microbial biosensor use in the environment. To this end, a standard framework for future whole cell microbial biosensor design and use is proposed.

  17. Molecular ecology of microbial mats

    NARCIS (Netherlands)

    H. Bolhuis; M.S. Cretoiu; L.J. Stal

    2014-01-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

  18. Microbial ecology of biotechnological processes

    OpenAIRE

    Fraraccio, Serena

    2015-01-01

    The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete...

  19. Microbial Weathering of Olivine

    Science.gov (United States)

    McKay, D. S.; Longazo, T. G.; Wentworth, S. J.; Southam, G.

    2002-01-01

    Controlled microbial weathering of olivine experiments displays a unique style of nanoetching caused by biofilm attachment to mineral surfaces. We are investigating whether the morphology of biotic nanoetching can be used as a biosignature. Additional information is contained in the original extended abstract.

  20. Diazotrophic microbial mats

    NARCIS (Netherlands)

    Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

    2010-01-01

    Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically stra

  1. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  2. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    Science.gov (United States)

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213). Seagrasses ...

  3. Microbial keratitis in children.

    Science.gov (United States)

    Kunimoto, D Y; Sharma, S; Reddy, M K; Gopinathan, U; Jyothi, J; Miller, D; Rao, G N

    1998-02-01

    Microbial keratitis is a major cause of corneal blindness worldwide. This problem is particularly relevant to children, because most of their visual life is ahead of them, and they are uniquely at risk for irreversible ocular deficits, such as those resulting from amblyopia. The objective of this study was to determine the etiologic agents and predisposing factors in childhood infectious keratitis and to examine the outcome of treatment in terms of structure and visual acuity. The study design was a retrospective cases series. The authors studied 113 eyes in 107 children 16 years of age and younger who were treated for (nonviral) microbial keratitis at the LV Prasad Eye Institute in Hyderabad, India, during the 4.5-year period between February 1, 1991, and June 30, 1995. The patients who met the following criteria were included in the study: (1) corneal stromal infiltrate was present on slit-lamp examination; and (2) a corneal scraping was taken at the time of examination for suspected microbial keratitis. Etiologic micro-organisms, predisposing factors, treatment method, structural treatment outcome, and visual acuity treatment outcome of the infectious keratitis episode were measured. The principal predisposing factors identified in this study were trauma (21.2%), ocular disease (17.7%), systemic disease (15.9%), and prior penetrating keratoplasty in the same eye (8.8%). Vitamin A deficiency was an important factor within the category of severe systemic disease, and contact lens wear was not involved in any of the cases. A total of 85 organisms were isolated in cultures of corneal scrapings from 64 (56.6%) of the 113 cases. Staphylococcus species (43.7%), Streptococcus pneumoniae (18.8%), and fungi (17.2%) were the most common isolates. Eighteen eyes (15.9%) required surgery, and 28 (36.4%) of the 77 patients on whom visual acuity was assessed at last follow-up achieved an unaided visual acuity of 20/60 or better at last follow-up. This work represents the

  4. Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Cristiane C. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Amaral, Gilda R. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Campeão, Mariana [Univ. of Rio de Janeiro (UFRJ) (Brazil); Edwards, Robert A. [Univ. of Rio de Janeiro (UFRJ) (Brazil); San Diego State Univ., CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Dutilh, Bas E. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Radbould Univ., Nijmegen (Netherlands); Ussery, David W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sawabe, Tomoo [Hokkaido Univ., Hakodate (Japan); Swings, Jean [Univ. of Rio de Janeiro (UFRJ) (Brazil); Ghent Univ. (Belgium); Thompson, Fabiano L. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Advanced Systems Laboratory Production Management COPPE / UFRJ, Rio de Janeiro (Brazil)

    2014-12-23

    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

  5. Research and application of marine microbial enzymes: status and prospects.

    Science.gov (United States)

    Zhang, Chen; Kim, Se-Kwon

    2010-06-23

    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.

  6. Research and Application of Marine Microbial Enzymes: Status and Prospects

    Directory of Open Access Journals (Sweden)

    Chen Zhang

    2010-06-01

    Full Text Available 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.

  7. Research and Application of Marine Microbial Enzymes: Status and Prospects

    Science.gov (United States)

    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

  8. Balance Trees Reveal Microbial Niche Differentiation.

    Science.gov (United States)

    Morton, James T; Sanders, Jon; Quinn, Robert A; McDonald, Daniel; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Navas-Molina, Jose A; Song, Se Jin; Metcalf, Jessica L; Hyde, Embriette R; Lladser, Manuel; Dorrestein, Pieter C; Knight, Rob

    2017-01-01

    Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available.

  9. Microbially Induced Precipitation of Strontianite Nanoparticles.

    Science.gov (United States)

    Kang, Serku; Yumi Kim; Lee, Young Jae; Roh, Yul

    2015-07-01

    The objectives of this study were to investigate the microbially mediated precipitation of strontium by microorganisms, and to examine the mineralogical characteristics of the precipitates. Wu Do-1 (Proteus mirabilis) enriched from rhodoliths was used to precipitate strontium at room temperature under aerobic environment. The growth of Wu Do-1 gradually increased over 16 days (OD600 = 2.6) and then decreased until 22 days (OD600 = 2.0) during microbial incubation for strontium precipitation. Also, the pH decreased from 6.5 to 5.3 over 4 days of incubation due to microbial oxidation of organic acids, and then the pH increased up to 8.6 at 25 days of incubation due to NH3+ generation. The Sr2+ concentration in the biotic group sharply decreased from 2,953 mg/L to 5.7 mg/L over 29 days of incubation. XRD, SEM-/TEM-EDS analyses revealed that the precipitates formed by Wu Do-1 (Proteus mirabilis) were identified as 20-70 nm sized strontianite (SrCO3). Therefore, these results suggested that formation of sparingly soluble Sr precipitates mediated by Wu Do-1 (Proteus mirabilis) sequesters strontium and carbon dioxide into a more stable and less toxic form such as strontianite (SrCO3). These results also suggest that bioremediation of metal-contaminated water and biominealization of carbonate minerals may be feasible in the marine environment.

  10. Balance Trees Reveal Microbial Niche Differentiation

    Science.gov (United States)

    Morton, James T.; Sanders, Jon; Quinn, Robert A.; McDonald, Daniel; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Navas-Molina, Jose A.; Metcalf, Jessica L.; Hyde, Embriette R.; Lladser, Manuel; Dorrestein, Pieter C.

    2017-01-01

    ABSTRACT Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available. PMID:28144630

  11. Counting viruses and bacteria in photosynthetic microbial mats.

    Science.gov (United States)

    Carreira, Cátia; Staal, Marc; Middelboe, Mathias; Brussaard, Corina P D

    2015-03-01

    Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures typically used in benthic viral ecology were applied to the complex matrix of microbial mats but were found to inefficiently extract viruses. Here, we present a method for extraction and quantification of viruses from photosynthetic microbial mats using epifluorescence microscopy (EFM) and flow cytometry (FCM). A combination of EDTA addition, probe sonication, and enzyme treatment applied to a glutaraldehyde-fixed sample resulted in a substantially higher viral (5- to 33-fold) extraction efficiency and reduced background noise compared to previously published methods. Using this method, it was found that in general, intertidal photosynthetic microbial mats harbor very high viral abundances (2.8 × 10(10) ± 0.3 × 10(10) g(-1)) compared with benthic habitats (10(7) to 10(9) g(-1)). This procedure also showed 4.5- and 4-fold-increased efficacies of extraction of viruses and bacteria, respectively, from intertidal sediments, allowing a single method to be used for the microbial mat and underlying sediment.

  12. Microbial diversity and metabolic networks in acid mine drainage habitats

    Directory of Open Access Journals (Sweden)

    Celia eMendez-Garcia

    2015-05-01

    Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  13. Hydrodynamics of microbial filter feeding

    DEFF Research Database (Denmark)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia

    2017-01-01

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequat...... predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling....

  14. Microbial corrosion of metallic materials in a deep nuclear-waste repository

    Directory of Open Access Journals (Sweden)

    Stoulil J.

    2016-06-01

    Full Text Available The study summarises current knowledge on microbial corrosion in a deep nuclear-waste repository. The first part evaluates the general impact of microbial activity on corrosion mechanisms. Especially, the impact of microbial metabolism on the environment and the impact of biofilms on the surface of structure materials were evaluated. The next part focuses on microbial corrosion in a deep nuclear-waste repository. The study aims to suggest the development of the repository environment and in that respect the viability of bacteria, depending on the probable conditions of the environment, such as humidity of bentonite, pressure in compact bentonite, the impact of ionizing radiation, etc. The last part is aimed at possible techniques for microbial corrosion mechanism monitoring in the conditions of a deep repository. Namely, electrochemical and microscopic techniques were discussed.

  15. Design, construction, and characterization methodologies for synthetic microbial consortia.

    Science.gov (United States)

    Bernstein, Hans C; Carlson, Ross P

    2014-01-01

    Engineered microbial consortia are of growing interest to a range of scientists including bioprocess engineers, systems biologists, and microbiologists because of their ability to simultaneously optimize multiple tasks, to test fundamental systems science, and to understand the microbial ecology of environments like chronic wounds. Metabolic engineering, synthetic biology, and microbial ecology provide a sound scientific basis for designing, building, and analyzing consortium-based microbial platforms.This chapter outlines strategies and protocols useful for (1) in silico network design, (2) experimental strain construction, (3) consortia culturing including biofilm growth methods, and (4) physiological characterization of consortia. The laboratory and computational methods given here may be adapted for synthesis and characterization of other engineered consortia designs.

  16. Factors Affecting Microbial Contamination of Market Eggs: A Review

    Directory of Open Access Journals (Sweden)

    Svobodová J.

    2015-01-01

    Full Text Available The aim of the review was to analyze the ways of microbial contamination, the protective mechanism of egg, and factors that affect the quantity of contamination and microbial penetration. Eggs can be contaminated during their formation in the infected reproductive organs of hens or after laying, when eggs are exposed to contaminated environment. The eggs are equipped against microbial contamination by several protective mechanisms comprising the presence of cuticle, eggshell, eggshell membranes, occurrence of some antibacterial proteins, and high pH value of albumen. There are several factors that affect the quantity of microbial contamination and penetration such as species of bacteria, the amount of microorganisms, storage conditions, quality of eggshell or number of pores.

  17. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India.

    Science.gov (United States)

    Rao, Subramanya; Chan, Yuki; Bugler-Lacap, Donnabella C; Bhatnagar, Ashish; Bhatnagar, Monica; Pointing, Stephen B

    2016-03-01

    A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system.

  18. Microbial nitrogen metabolism: response to warming and resource supply

    Science.gov (United States)

    Buckeridge, K. M.; Min, K.; Lehmeier, C.; Ballantyne, F.; Billings, S. A.

    2013-12-01

    Ecosystem nitrogen (N) dynamics are dependent on microbial metabolic responses to a changing climate. Most studies that investigate soil microbial N dynamics in response to temperature employ measurements reflective of many interacting and confounding phenomena, as altering soil temperature can simultaneously alter moisture regime, substrate availability, and competitive dynamics between microbial populations. As a result, it is difficult to discern how temperature alone can alter patterns of microbial N metabolism using whole soils. Without that knowledge, it is impossible to parse temperature effects on soil N fluxes from other drivers. We address this issue by exploring the sensitivity of microbial partitioning of N between assimilation (growing biomass) and dissimilation (releasing N to the environment) in response to changes in temperature and quality (C:N ratio) of substrate, using a chemostat approach in which a microbial population is maintained at steady state. We perform our experiments using a Gram-negative bacterium (Pseudomonas fluorescens), ubiquitous in soils and dependent on organic compounds to satisfy its resource demand. Individual chemostat runs, all conducted at similar microbial growth rates, generate data describing microbial biomass N, solution N pools and microbial biomass and solution d15N. With these data we can calculate d15N enrichment (d15N microbial biomass - d15N nutrient solution) a proxy for microbial N partitioning. From a recently published model of microbial biomass d15N drivers, fractionation of N occurs with both uptake and excretion of NH3+ so that microbes with a net dissimilation become 15N enriched relative to their source. Because a related study has demonstrated increased microbial C demand with temperature, we predict that in a warming environment microorganisms will become relatively C limited. Accordingly, we hypothesize that warming will enhance microbial dissimilation, and that this N release will be exacerbated as

  19. Microbial Transformations of Actinides and Other Radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Francis,A.J.; Dodge, C. J.

    2009-01-07

    Microorganisms can affect the stability and mobility of the actinides and other radionuclides released from nuclear fuel cycle and from nuclear fuel reprocessing plants. Under appropriate conditions, microorganisms can alter the chemical speciation, solubility and sorption properties and thus could increase or decrease the concentrations of radionuclides in solution in the environment and the bioavailability. Dissolution or immobilization of radionuclides is brought about by direct enzymatic action or indirect non-enzymatic action of microorganisms. Although the physical, chemical, and geochemical processes affecting dissolution, precipitation, and mobilization of radionuclides have been extensively investigated, we have only limited information on the effects of microbial processes and biochemical mechanisms which affect the stability and mobility of radionuclides. The mechanisms of microbial transformations of the major and minor actinides U, Pu, Cm, Am, Np, the fission products and other radionuclides such as Ra, Tc, I, Cs, Sr, under aerobic and anaerobic conditions in the presence of electron donors and acceptors are reviewed.

  20. Algal and microbial exopolysaccharides: new insights as biosurfactants and bioemulsifiers.

    Science.gov (United States)

    Paniagua-Michel, José de Jesús; Olmos-Soto, Jorge; Morales-Guerrero, Eduardo Roberto

    2014-01-01

    Currently, efforts are being made to utilize more natural biological systems as alternatives as a way to replace fossil forms of carbon. There is a growing concern at global level to have nontoxic, nonhazardous surface-active agents; contrary to synthetic surfactants, their biological counterparts or biosurfactants play a primary function, facilitating microbial presence in environments dominated by hydrophilic-hydrophobic interfaces. Algal and microbial biosurfactants/bioemulsifiers from marine and deep-sea environments are attracting major interest due to their structural and functional diversity as molecules actives of surface and an alternative biomass to replace fossil forms of carbon. Algal and microbial surfactants are lipid in nature and classified as glycolipids, phospholipids, lipopeptides, natural lipids, fatty acids, and lipopolysaccharides. These metabolic bioactive products are applicable in a number of industries and processes, viz., food processing, pharmacology, and bioremediation of oil-polluted environments. This chapter presents an update of the progress and potentialities of the principal producers of exopolysaccharide (EPS)-type biosurfactants and bioemulsifiers, viz., macro- and microalgae (cyanobacteria and diatoms) and bacteria from marine and extreme environments. Particular interest is centered into new sources and applications, viz., marine and deep-sea environments and promissory uses of these EPSs as biosurfactants/emulsifiers and other polymeric roles. The enormous benefits of these molecules encourage their discovery, exploitation, and development of new microbial EPSs that could possess novel industrial importance and corresponding innovations.

  1. Forensic microbiology: Evolving from discriminating distinct microbes to characterizing entire microbial communities on decomposing remains

    Science.gov (United States)

    The body of an animal encompasses a multitude of compositionally and functionally unique microbial environments, from the skin to the gastrointestinal system. Each of these systems harbor microbial communities that have adapted in order to cohabitate with their specific host resulting in a distinct...

  2. Rhizosphere microbial community and its response to plant species and soil history

    NARCIS (Netherlands)

    Garbeva, P.V.; van Elsas, J.D.; Van Veen, J.A.

    2008-01-01

    The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. Two important factors determining the structure of microbial community present in the vicinity of plant roots are plant species and soil

  3. Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms

    Science.gov (United States)

    Organic farming is a growing field of agriculture that is benign on the environment but there are contradictory reports about the impact of these practices on the soil microbial community, i.e. some studies showed higher microbial diversity in organic farms but others showed no differences in divers...

  4. 40 CFR 158.2171 - Experimental use permit microbial pesticides product analysis data requirements table.

    Science.gov (United States)

    2010-07-01

    ... pesticides product analysis data requirements table. 158.2171 Section 158.2171 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2171 Experimental use permit microbial pesticides product analysis data requirements...

  5. 40 CFR 158.2172 - Experimental use permit microbial pesticides residue data requirements table.

    Science.gov (United States)

    2010-07-01

    ... pesticides residue data requirements table. 158.2172 Section 158.2172 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2172 Experimental use permit microbial pesticides residue data requirements table. (a)...

  6. Metalliferous Biosignatures for Deep Subsurface Microbial Activity

    Science.gov (United States)

    Parnell, John; Brolly, Connor; Spinks, Sam; Bowden, Stephen

    2016-03-01

    The interaction of microbes and metals is widely assumed to have occurred in surface or very shallow subsurface environments. However new evidence suggests that much microbial activity occurs in the deep subsurface. Fluvial, lacustrine and aeolian `red beds' contain widespread centimetre-scale reduction spheroids in which a pale reduced spheroid in otherwise red rocks contains a metalliferous core. Most of the reduction of Fe (III) in sediments is caused by Fe (III) reducing bacteria. They have the potential to reduce a range of metals and metalloids, including V, Cu, Mo, U and Se, by substituting them for Fe (III) as electron acceptors, which are all elements common in reduction spheroids. The spheroidal morphology indicates that they were formed at depth, after compaction, which is consistent with a microbial formation. Given that the consequences of Fe (III) reduction have a visual expression, they are potential biosignatures during exploration of the terrestrial and extraterrestrial geological record. There is debate about the energy available from Fe (III) reduction on Mars, but the abundance of iron in Martian soils makes it one of the most valuable prospects for life there. Entrapment of the microbes themselves as fossils is possible, but a more realistic target during the exploration of Mars would be the colour contrasts reflecting selective reduction or oxidation. This can be achieved by analysing quartz grains across a reduction spheroid using Raman spectroscopy, which demonstrates its suitability for life detection in subsurface environments. Microbial action is the most suitable explanation for the formation of reduction spheroids and may act as metalliferous biosignatures for deep subsurface microbial activity.

  7. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1992-03-01

    The objective of this project is to perform a microbial enhanced oil recovery field pilot in the Southeast Vassar Vertz Sand Unit (SEVVSU) in Payne County, Oklahoma. Indigenous, anaerobic, nitrate reducing bacteria will be stimulated to selectively plug flow paths which have been referentially swept by a prior waterflood. This will force future flood water to invade bypassed regions of the reservoir and increase sweep efficiency. This report covers progress made during the second year, January 1, 1990 to December 31, 1990, of the Microbial Field Pilot Study project. Information on reservoir ecology, surface facilities design, operation of the unit, core experiments, modeling of microbial processes, and reservoir characterization and simulation are presented in the report. To better understand the ecology of the target reservoir, additional analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. The results of the produced and injected water analysis show increasing sulfide concentrations with respect to time. In March of 1990 Mesa Limited Partnership sold their interest in the SEVVSU to Sullivan and Company. In April, Sullivan and Company assumed operation of the field. The facilities for the field operation of the pilot were refined and implementation was begun. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. The experiments were performed at SEVVSU temperature using fluids and inoculum from the unit. The model described in last year's report was further validated using results from a core flood experiment. The model was able to simulate the results of one of the core flood experiments with good quality.

  8. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1992-03-01

    The objective of this project is to perform a microbial enhanced oil recovery field pilot in the Southeast Vassar Vertz Sand Unit (SEVVSU) in Payne County, Oklahoma. Indigenous, anaerobic, nitrate reducing bacteria will be stimulated to selectively plug flow paths which have been referentially swept by a prior waterflood. This will force future flood water to invade bypassed regions of the reservoir and increase sweep efficiency. This report covers progress made during the second year, January 1, 1990 to December 31, 1990, of the Microbial Field Pilot Study project. Information on reservoir ecology, surface facilities design, operation of the unit, core experiments, modeling of microbial processes, and reservoir characterization and simulation are presented in the report. To better understand the ecology of the target reservoir, additional analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. The results of the produced and injected water analysis show increasing sulfide concentrations with respect to time. In March of 1990 Mesa Limited Partnership sold their interest in the SEVVSU to Sullivan and Company. In April, Sullivan and Company assumed operation of the field. The facilities for the field operation of the pilot were refined and implementation was begun. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. The experiments were performed at SEVVSU temperature using fluids and inoculum from the unit. The model described in last year`s report was further validated using results from a core flood experiment. The model was able to simulate the results of one of the core flood experiments with good quality.

  9. Forum of Microbial Threats

    Science.gov (United States)

    2011-06-01

    and ―disease‖. Studies on leafcutter ants have revealed a complex web of symbiotic interactions, among ants, bacteria , and fungi that are associated...strains of bacteria and viruses are treatable with only a single drug, and some no longer have effective treatments. The disease burden from multi...microbes have played in driving adaptation and evolution of organisms. To date, most microbiome or microbial ecology studies have focused on bacteria

  10. Microbial desulfurization of coal

    Energy Technology Data Exchange (ETDEWEB)

    Danzet, C.; Buonfiglio, V.; Polidoro, M.; Valenti, P. (Rome Univ. La Sapienza (Italy). Ist. di Microbiologia)

    This paper reviews the biochemical and economics aspects of coal desulfurization processes involving the use of thermophile microorganisms such as sulfolobus, currently believed to be the the only type of microorganism capable of degrading both inorganic (pyrite-containing) and organic sulfur compounds. Comments are also made on the feasibility of the development of an in-lab, microbial based method for the transformation of the lignin component, obtained in the processing, by anaerobic fermentation, of lignocellulosic biomass, into humic acid.

  11. Preparing near-surface heavy oil for extraction using microbial degradation

    Energy Technology Data Exchange (ETDEWEB)

    Busche, Frederick D.; Rollins, John B.; Noyes, Harold J.; Bush, James G.

    2017-05-30

    In one embodiment, the invention provides a system including at least one computing device for enhancing the recovery of heavy oil in an underground, near-surface crude oil extraction environment by performing a method comprising sampling and identifying microbial species (bacteria and/or fungi) that reside in the underground, near-surface crude oil extraction environment; collecting rock and fluid property data from the underground, near-surface crude oil extraction environment; collecting nutrient data from the underground, near-surface crude oil extraction environment; identifying a preferred microbial species from the underground, near-surface crude oil extraction environment that can transform the heavy oil into a lighter oil; identifying a nutrient from the underground, near-surface crude oil extraction environment that promotes a proliferation of the preferred microbial species; and introducing the nutrient into the underground, near-surface crude oil extraction environment.

  12. Advances in microbial amylases.

    Science.gov (United States)

    Pandey, A; Nigam, P; Soccol, C R; Soccol, V T; Singh, D; Mohan, R

    2000-04-01

    This review makes a comprehensive survey of microbial amylases, i.e. alpha-amylase, beta-amylase and glucoamylase. Amylases are among the most important enzymes and are of great significance in present-day biotechnology. Although they can be derived from several sources, such as plants, animals and micro-organisms, the enzymes from microbial sources generally meet industrial demands. Microbial amylases could be potentially useful in the pharmaceutical and fine-chemical industries if enzymes with suitable properties could be prepared. With the advent of new frontiers in biotechnology, the spectrum of amylase application has widened in many other fields, such as clinical, medicinal and analytical chemistries, as well as their widespread application in starch saccharification and in the textile, food, brewing and distilling industries. In this review, after a brief description of the sources of amylases, we discuss the molecular biology of amylases, describing structures, cloning, sequences, and protoplast fusion and mutagenesis. This is followed by sections on their production and finally the properties of various amylases.

  13. Microbial biosurfactants and biodegradation.

    Science.gov (United States)

    Ward, Owen P

    2010-01-01

    Microbial biosurfactants are amphipathic molecules having typical molecular weights of 500-1500 Da, made up of peptides, saccharides or lipids or their combinations. In biodegradation processes they mediate solubilisation, mobilization and/or accession of hydrophobic substrates to microbes. They may be located on the cell surface or be secreted into the extracellular medium and they facilitate uptake of hydrophobic molecules through direct cellular contact with hydrophobic solids or droplets or through micellarisation. They are also involved in cell physiological processes such as biofilm formation and detachment, and in diverse biofilm associated processes such as wastewater treatment and microbial pathogenesis. The protection of contaminants in biosurfactants micelles may also inhibit uptake of contaminants by microbes. In bioremediation processes biosurfactants may facilitate release of contaminants from soil, but soils also tend to bind surfactants strongly which makes their role in contaminant desorption more complex. A greater understanding of the underlying roles played by biosurfactants in microbial physiology and in biodegradative processes is developing through advances in cell and molecular biology.

  14. Microbial Monitoring of the International Space Station

    Science.gov (United States)

    Pierson, Duane L.; Botkin, Douglas J.; Bruce, Rebekah J.; Castro, Victoria A.; Smith, Melanie J.; Oubre, Cherie M.; Ott, C. Mark

    2013-01-01

    Humans living and working in the harsh environment of space present many challenges for habitability engineers and microbiologists. Spacecraft must provide an internal environment in which physical (gas composition, pressure, temperature, and humidity), chemical, and biological environmental parameters are maintained at safe levels. Microorganisms are ubiquitous and will accompany all human-occupied spacecraft, but if biological contamination were to reach unacceptable levels, long-term human space flight would be impossible. Prevention of microbiological problems, therefore, must have a high priority. Historically, prevention of infectious disease in the crew has been the highest priority, but experience gained from the NASA-Mir program showed that microbial contamination of vehicle and life-support systems, such as biofouling of water and food, are of equal importance. The major sources of microbiological risk factors for astronauts include food, drinking water, air, surfaces, payloads, research animals, crew members, and personnel in close contact with the astronauts. In our efforts to eliminate or mitigate the negative effects of microorganisms in spacecraft, the National Aeronautics and Space Administration (NASA) implemented comprehensive microbial analyses of the major risk factors. This included the establishment of acceptability requirements for food, water, air, surfaces, and crew members. A robust monitoring program was then implemented to verify that the risks were within acceptable limits. Prevention of microbiological problems is preferred over mitigation of problems during flight, and preventive steps must begin very early in the design phase. Spacecraft development must include requirements to control free water from humidity, condensate, hygiene activities, and other releases. If water is available, microbes are likely to grow because sufficient nutrients are potentially available. Materials selected for the spacecraft must not promote or support

  15. Microbial populations in contaminant plumes

    Science.gov (United States)

    Haack, Sheridan K.; Bekins, Barbara A.

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

  16. Suitable microscopic entropy for the origin of microbial life: microbiological methods are challenges.

    Science.gov (United States)

    Trevors, J T

    2010-12-01

    A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.

  17. Monitoring Microbes in the Spacecraft Environment by Mass Spectrometry of Ribosomal RNA Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The unique stresses in the spacecraft environment including isolation, containment, weightlessness, increased radiation exposure, and enhanced microbial...

  18. Unravelling microbial communities with DNA-microarrays: challenges and future directions

    NARCIS (Netherlands)

    Wagner, M.; Smidt, H.; Loy, A.; Zhou, J.

    2007-01-01

    High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbi

  19. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification

    NARCIS (Netherlands)

    Direito, S.O.L.; Zaura, E.; Little, M.; Ehrenfreund, P.; Röling, W.F.M.

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement amplific

  20. Dual active ionic liquids and organic salts for inhibition of microbially influenced corrosion.

    Science.gov (United States)

    Seter, Marianne; Thomson, Melanie J; Stoimenovski, Jelena; MacFarlane, Douglas R; Forsyth, Maria

    2012-06-18

    We describe a series of novel compounds designed to combat the bacterial growth that leads to microbially induced corrosion on steel in the marine environment. A synergistic effect of the ionic components in these dual active organic salts is demonstrated.

  1. Microbial community structure in three deep-sea carbonate crusts

    NARCIS (Netherlands)

    Heijs, S. K.; Aloisi, G.; Bouloubassi, I.; Pancost, R. D.; Pierre, C.; Damste, J. S. Sinninghe; Gottschal, J. C.; van Elsas, J. D.; Forney, L. J.

    2006-01-01

    Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eas

  2. Probiotic legacy effects on gut microbial assembly in tilapia larvae

    NARCIS (Netherlands)

    Giatsis, Christos; Sipkema, Detmer; Ramiro-Garcia, Javier; Bacanu, Gianina M.; Abernathy, Jason; Verreth, Johan; Smidt, Hauke; Verdegem, Marc

    2016-01-01

    The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbi

  3. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    Science.gov (United States)

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-07-05

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

  4. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  5. Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

    Science.gov (United States)

    Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

    2016-05-01

    The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

  6. Applying "-omics" Data in Marine Microbial Oceanography

    Science.gov (United States)

    Fuhrman, Jed; Follows, Mick; Forde, Samantha

    2013-07-01

    Due to biotechnological advances and the ever-decreasing cost of sequencing in recent years, there has been a major shift in microbial oceanography to include data on the sequences of genes, gene transcripts, and proteins from environmentally relevant organisms and naturally occurring mixed communities in studies of marine ecosystems. This research area is collectively called "-omics," referring to genomics, transcriptomics, and proteomics of individual organisms and metagenomics, metatranscriptomics, and metaproteomics of mixed communities. These data provide information about how organisms interact with their environment.

  7. The effect of initial pH on hydrogen production of microbial community from marine environment%起始pH值对海洋混合菌群产氢量的影响

    Institute of Scientific and Technical Information of China (English)

    刘洪艳; 王广策

    2011-01-01

    对采自天津潮间带的污泥进行热休克处理,厌氧条件下富集混合菌群进行产氢试验;设置起始pH从4.0到8.0(间隔0.5个单位),比较混合菌群在不同pH培养条件下产氢量;利用变性梯度凝胶电泳(DGGE)分析不同起始pH培养条件下的混合菌群组成。结果表明,在起始pH为7.0时,混合菌群产氢量最高。不同起始pH对产氢量的影响,依次为pH6.5〉pH7.5〉pH8.0〉pH6.0〉pH5.5〉pH5.0〉pH4.5〉pH4.0。混合菌16S rRNA基因的PCR扩增产物经DGGE分离,电泳图谱表明,不同起始pH条件下混合菌群的优势菌相同,PCR产物的测序结果与Clostridium sp.存在比较高相似度(98%)。Fe-氢酶基因扩增产物在DGGE电泳图谱中存在一条特异条带,其测定序列与Clostridium perfringens氢酶基因相似度为98%。不同起始pH条件下混合菌群的产氢菌基本相同,混合菌群产氢量之间的差异可能在于起始pH对混合菌群Fe-氢酶基因活性的影响,有待进一步研究确定。%Sludge, collected from the intertidal zone of a bathing beach in Tianjin, was pretreated by the heat-shock method and enriched under anaerobic condition for hydrogen-production. Hydrogen production was investigated under various initial pHs, ranging from 4.0 to 8.0. The composition of microbial community under various initial pHs was analyzed by denaturing gradient gel electrophoresis (DGGE). The result showed that hydrogen production potential of the mixed culture was the highest at the optimal pH of 7.0. The effects of initial pHs on hydrogen production followed the order ofpH 6.5〉 pH 7.5 〉 pH 8.0 〉 pH 6.0 〉 pH 5.5 〉 pH 5.0 〉 pH 4.5 〉 pH 4.0. The 16S rRNA gene was PCR amplified and analyzed by DGGE. The dominant bands obtained on DGGE of 16S rRNA gene were identical at various pH values. These bands were cloned and sequenced. NCBI blast indicated that the segment of 16S rRNA gene

  8. Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina).

    Science.gov (United States)

    Urbieta, María Sofía; González-Toril, Elena; Bazán, Ángeles Aguilera; Giaveno, María Alejandra; Donati, Edgardo

    2015-03-01

    Copahue is a natural geothermal field (Neuquén province, Argentina) dominated by the Copahue volcano. As a consequence of the sustained volcanic activity, Copahue presents many acidic pools, hot springs and solfataras with different temperature and pH conditions that influence their microbial diversity. The occurrence of microbial biofilms was observed on the surrounding rocks and the borders of the ponds, where water movements and thermal activity are less intense. Microbial biofilms are particular ecological niches within geothermal environments; they present different geochemical conditions from that found in the water of the ponds and hot springs which is reflected in different microbial community structure. The aim of this study is to compare microbial community diversity in the water of ponds and hot springs and in microbial biofilms in the Copahue geothermal field, with particular emphasis on Cyanobacteria and other photosynthetic species that have not been detected before in Copahue. In this study, we report the presence of Cyanobacteria, Chloroflexi and chloroplasts of eukaryotes in the microbial biofilms not detected in the water of the ponds. On the other hand, acidophilic bacteria, the predominant species in the water of moderate temperature ponds, are almost absent in the microbial biofilms in spite of having in some cases similar temperature conditions. Species affiliated with Sulfolobales in the Archaea domain are the predominant microorganism in high temperature ponds and were also detected in the microbial biofilms.

  9. Counteraction of antibiotic production and degradation stabilizes microbial communities

    OpenAIRE

    Kelsic, Eric D.; Zhao, Jeffrey; Vetsigian, Kalin; Kishony, Roy

    2015-01-01

    Summary A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity 1-8 , and in particular how antibiotic producing, sensitive and resistant species coexist 9-15 . While cyclic “rock-paper-scissors” interactions can stabilize communities in spatial environments 9-11 , coexistence in unstructured environments remains an enigma 12,16 . Here, using simulations and analytical models, we show that the opposing actions of antibiotic product...

  10. Iron oxyhydroxide mineralization on microbial extracellular polysaccharides

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Clara S.; Fakra, Sirine C.; Edwards, David C.; Emerson, David; Banfield, Jillian F.

    2010-06-22

    Iron biominerals can form in neutral pH microaerophilic environments where microbes both catalyze iron oxidation and create polymers that localize mineral precipitation. In order to classify the microbial polymers that influence FeOOH mineralogy, we studied the organic and mineral components of biominerals using scanning transmission X-ray microscopy (STXM), micro X-ray fluorescence ({mu}XRF) microscopy, and high-resolution transmission electron microscopy (HRTEM). We focused on iron microbial mat samples from a creek and abandoned mine; these samples are dominated by iron oxyhydroxide-coated structures with sheath, stalk, and filament morphologies. In addition, we characterized the mineralized products of an iron-oxidizing, stalk-forming bacterial culture isolated from the mine. In both natural and cultured samples, microbial polymers were found to be acidic polysaccharides with carboxyl functional groups, strongly spatially correlated with iron oxyhydroxide distribution patterns. Organic fibrils collect FeOOH and control its recrystallization, in some cases resulting in oriented crystals with high aspect ratios. The impact of polymers is particularly pronounced as the materials age. Synthesis experiments designed to mimic the biomineralization processes show that the polysaccharide carboxyl groups bind dissolved iron strongly but release it as mineralization proceeds. Our results suggest that carboxyl groups of acidic polysaccharides are produced by different microorganisms to create a wide range of iron oxyhydroxide biomineral structures. The intimate and potentially long-term association controls the crystal growth, phase, and reactivity of iron oxyhydroxide nanoparticles in natural systems.

  11. Biofilm and dental implant: The microbial link

    Directory of Open Access Journals (Sweden)

    Sangeeta Dhir

    2013-01-01

    Full Text Available Mouth provides a congenial environment for the growth of the microorganisms as compared to any other part of the human body by exhibiting an ideal nonshedding surface. Dental plaque happens to be a diverse community of the microorganisms found on the tooth surface. Periodontal disease and the peri-implant disease are specific infections that are originating from these resident microbial species when the balance between the host and the microbial pathogenicity gets disrupted. This review discusses the biofilms in relation to the peri-implant region, factors affecting its presence, and the associated treatment to manage this complex microbial colony. Search Methodology: Electronic search of the medline was done with the search words: Implants and biofilms/dental biofilm formation/microbiology at implant abutment interface/surface free energy/roughness and implant, periimplantitis/local drug delivery and dental implant. Hand search across the journals - clinical oral implant research, implant dentistry, journal of dental research, international journal of oral implantology, journal of prosthetic dentistry, perioodntology 2000, journal of periodontology were performed. The articles included in the review comprised of in vivo studies, in vivo (animal and human studies, abstracts, review articles.

  12. Biofilm and dental implant: The microbial link

    Science.gov (United States)

    Dhir, Sangeeta

    2013-01-01

    Mouth provides a congenial environment for the growth of the microorganisms as compared to any other part of the human body by exhibiting an ideal nonshedding surface. Dental plaque happens to be a diverse community of the microorganisms found on the tooth surface. Periodontal disease and the peri-implant disease are specific infections that are originating from these resident microbial species when the balance between the host and the microbial pathogenicity gets disrupted. This review discusses the biofilms in relation to the peri-implant region, factors affecting its presence, and the associated treatment to manage this complex microbial colony. Search Methodology: Electronic search of the medline was done with the search words: Implants and biofilms/dental biofilm formation/microbiology at implant abutment interface/surface free energy/roughness and implant, periimplantitis/local drug delivery and dental implant. Hand search across the journals – clinical oral implant research, implant dentistry, journal of dental research, international journal of oral implantology, journal of prosthetic dentistry, perioodntology 2000, journal of periodontology were performed. The articles included in the review comprised of in vivo studies, in vivo (animal and human) studies, abstracts, review articles. PMID:23633764

  13. Microbial desulfurization of coal by thermophilic archaea

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Gunnel

    1994-04-01

    The investigation was focused on the removal of pyrite as well as organic sulfur. One major objective was to identify and outline difficulties associated with microbial desulfurization of coal. The work has particularly been concentrated on the desulfurization environment of the microorganisms, the reprecipitation of dissolved sulfate as jarosite, the effect of microbial treatment on the properties of the coal and the comparison of different thermophilic archaea suggested for coal desulfurization. The investigated microorganisms were the thermophilic archaea Acidianus brierleyi, Sulfolobus acidocaldarius and Sulfolobus solfataricus and for comparison the mesophilic bacterium Thiobacillus ferrooxidans. The major part of the work has been done with Acidianus brierleyi. Compounds leached from coal may seriously affect the growth of microorganisms suggested for coal desulfurization. Degradation of pyritic sulfur with the used strains of S. solfataricus and S. acidocaldarius, was observed to be impossible. However, both the thermophilic archaeon Acidianus brierleyi and the mesophilic bacterium Thiobacillus ferrooxidans, were capable of degrading pure pyrite as well as pyrite from low-sulfur coals. Up to 85% removal of pyritic sulfur was obtained for coals when staring with a pyrite sulfur content of 0.5-0.7%. From kinetic studies, it was shown that A. brierleyi and T. ferrooxidans remove sulfur from coal at roughly the same rate, at least for the coals investigated in this study. However, the rate for microbial oxidation of pure pyrite was seen to be much higher for A. brierleyi than for T. ferroxidans. 62 refs, 16 figs, 5 tabs

  14. Simulation modeling for microbial risk assessment.

    Science.gov (United States)

    Cassin, M H; Paoli, G M; Lammerding, A M

    1998-11-01

    Quantitative microbial risk assessment implies an estimation of the probability and impact of adverse health outcomes due to microbial hazards. In the case of food safety, the probability of human illness is a complex function of the variability of many parameters that influence the microbial environment, from the production to the consumption of a food. The analytical integration required to estimate the probability of foodborne illness is intractable in all but the simplest of models. Monte Carlo simulation is an alternative to computing analytical solutions. In some cases, a risk assessment may be commissioned to serve a larger purpose than simply the estimation of risk. A Monte Carlo simulation can provide insights into complex processes that are invaluable, and otherwise unavailable, to those charged with the task of risk management. Using examples from a farm-to-fork model of the fate of Escherichia coli O157:H7 in ground beef hamburgers, this paper describes specifically how such goals as research prioritization, risk-based characterization of control points, and risk-based comparison of intervention strategies can be objectively achieved using Monte Carlo simulation.

  15. Explicitly representing soil microbial processes in Earth system models

    Science.gov (United States)

    Wieder, William R.; Allison, Steven D.; Davidson, Eric A.; Georgiou, Katerina; Hararuk, Oleksandra; He, Yujie; Hopkins, Francesca; Luo, Yiqi; Smith, Matthew J.; Sulman, Benjamin; Todd-Brown, Katherine; Wang, Ying-Ping; Xia, Jianyang; Xu, Xiaofeng

    2015-10-01

    Microbes influence soil organic matter decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) will make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here we review the diversity, advantages, and pitfalls of simulating soil biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models, we suggest the following: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.

  16. Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

    Directory of Open Access Journals (Sweden)

    Farai eMaphosa

    2012-10-01

    Full Text Available Organohalide compounds such as chloroethenes, chloroethanes and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.

  17. Human and environmental impacts on river sediment microbial communities.

    Directory of Open Access Journals (Sweden)

    Sean M Gibbons

    Full Text Available Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA, comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼ 65,000 microbial 'species' identified and most novel (93% of OTUs do not match known microbial diversity ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.

  18. Microbial communities associated with wet flue gas desulfurization systems

    Directory of Open Access Journals (Sweden)

    Bryan P. Brown

    2012-11-01

    Full Text Available Flue gas desulfurization (FGD systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal fired electricity generation facilities were evaluated using culture-dependent and –independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.

  19. Implementation of microbial fuel cell in harvesting energy using wastewater

    Science.gov (United States)

    Ramli, N. L.; Wahab, M. S. Abdul; Sharif, S. A. Md; Ramly, N. H.

    2016-02-01

    In this century, most of the companies use the electricity from the fossils fuels such as oil, gas and coal. This method will give negative impact to the environment and the fossils fuel will be run out. This project is to develop a microbial fuels cell that can produce electricity. There are several types of the microbial fuel cell, which are a single chamber, double chamber and continuous. In this paper, the double chamber microbial fuel cell was selected to investigate the effect of suspended sludge into the double chamber microbial fuels cell. The salt bridge will construct between both chambers of the double chamber microbial fuels cell. Carbon graphite rod is selected as an electrode at the cathode and anode to transfer the electron from the anode to the cathode. Electricity is generated from the anaerobic oxidation of organic matter by bacteria. At the end of this project, the microbial fuels cell was successful in generating electricity that can be used for a specific application.

  20. Potential microbial contamination during sampling of permafrost soil assessed by tracers.

    Science.gov (United States)

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

    2017-02-23

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

  1. Temporal dynamics of microbial communities in microcosms in response to pollutants.

    Science.gov (United States)

    Jiao, Shuo; Zhang, Zhengqing; Yang, Fan; Lin, Yanbing; Chen, Weimin; Wei, Gehong

    2017-02-01

    Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.

  2. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    Science.gov (United States)

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    2017-01-01

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

  3. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    Science.gov (United States)

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    2017-02-01

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

  4. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.

    Science.gov (United States)

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-10-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

  5. Connecting Water Quality With Air Quality Through Microbial Aerosols

    Science.gov (United States)

    Dueker, M. Elias

    Aerosol production from surface waters results in the transfer of aquatic materials (including nutrients and bacteria) to air. These materials can then be transported by onshore winds to land, representing a biogeochemical connection between aquatic and terrestrial systems not normally considered. In urban waterfront environments, this transfer could result in emissions of pathogenic bacteria from contaminated waters. Despite the potential importance of this link, sources, near-shore deposition, identity and viability of microbial aerosols are largely uncharacterized. This dissertation focuses on the environmental and biological mechanisms that define this water-air connection, as a means to build our understanding of the biogeochemical, biogeographical, and public health implications of the transfer of surface water materials to the near-shore environment in both urban and non-urban environments. The effects of tidal height, wind speed and fog on coastal aerosols and microbial content were first quantified on a non-urban coast of Maine, USA. Culture-based, culture-independent, and molecular methods were used to simultaneously sample microbial aerosols while monitoring meteorological parameters. Aerosols at this site displayed clear marine influence and high concentrations of ecologically-relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height, onshore wind speed, and fog presence. Tidal height and fog presence did not significantly influence total microbial aerosol concentrations, but did have a significant effect on culturable microbial aerosol fallout. Molecular analyses of the microbes settling out of near-shore aerosols provided further evidence of local ocean to terrestrial transport of microbes. Aerosol and surface ocean bacterial communities shared species and in general were dominated by organisms previously sampled in marine environments. Fog presence strengthened the microbial connection between water and land through

  6. The microbial genomics of arsenic.

    Science.gov (United States)

    Andres, Jérémy; Bertin, Philippe N

    2016-03-01

    Arsenic, which is a major contaminant of many aquatic ecosystems worldwide, is responsible for serious public health issues. However, life has evolved various strategies for coping with this toxic element. In particular, prokaryotic organisms have developed processes enabling them to resist and metabolize this chemical. Studies based on genome sequencing and transcriptome, proteome and metabolome profiling have greatly improved our knowledge of prokaryotes' metabolic potential and functioning in contaminated environments. The increasing number of genomes available and the development of descriptive and comparative approaches have made it possible not only to identify several genetic determinants of the arsenic metabolism, but also to elucidate their phylogenetic distribution and their modes of regulation. In addition, studies using functional genomic tools have established the pleiotropic character of prokaryotes' responses to arsenic, which can be either common to several species or species-specific. These approaches also provide promising means of deciphering the functioning of microbial communities including uncultured organisms, the genetic transfers involved and the possible occurrence of metabolic interactions as well as the evolution of arsenic resistance and metabolism.

  7. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Coates, J.D.; Chisholm, J.L.

    1993-05-01

    A multi-well microbially enhanced oil recovery field pilot has been performed in the Southeast Vassar Vertz Sand Unit in Payne County, Oklahoma. The primary emphasis of the experiment was preferential plugging of high permeability zones for the purpose of improving waterflood sweep efficiency. Studies were performed to determine reservoir chemistry, ecology, and indigenous bacteria populations. Growth experiments were used to select a nutrient system compatible with the reservoir that encouraged growth of a group of indigenous nitrate-using bacteria and inhibit growth of sulfate-reducing bacteria. A specific field pilot area behind an active line drive waterflood was selected. Surface facilities were designed and installed. Injection protocols of bulk nutrient materials were prepared to facilitate uniform distribution of nutrients within the pilot area. By the end of December, 1991, 82.5 tons (75.0 tonnes) of nutrients had been injected in the field. A tracer test identified significant heterogeneity in the SEVVSU and made it necessary to monitor additional production wells in the field. The tracer tests and changes in production behavior indicate the additional production wells monitored during the field trial were also affected. Eighty two and one half barrels (13.1 m[sup 3]) of tertiary oil have been recovered. Microbial activity has increased CO[sub 2] content as indicated by increased alkalinity. A temporary rise in sulfide concentration was experienced. These indicate an active microbial community was generated in the field by the nutrient injection. Pilot area interwell pressure interference test results showed that significant permeability reduction occurred. The interwell permeabilities in the pilot area between the injector and the three pilot production wells were made more uniform which indicates a successful preferential plugging enhanced oil recovery project.

  8. Redox regime shifts in microbially mediated biogeochemical cycles

    Science.gov (United States)

    Bush, T.; Butler, I. B.; Free, A.; Allen, R. J.

    2015-06-01

    Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  9. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Directory of Open Access Journals (Sweden)

    Peter Larsen

    Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  10. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Science.gov (United States)

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  11. Manipulating soil microbial communities in extensive green roof substrates.

    Science.gov (United States)

    Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

    2014-09-15

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition.

  12. Urea transformation of wetland microbial communities.

    Science.gov (United States)

    Thorén, Ann-Karin

    2007-02-01

    Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12 degrees C) with the use of the 14C-urea tracer method, which measures the release of 14CO2 as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12-22 mmol urea-N m(-2) day(-1)) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1-0.2 mmol urea-N m(-2) day(-1)). The epiphytic activity of leaves of Typha latifolia was lower (0.001-0.03 mmol urea-N m(-2) day(-1)), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity-in the range of 23-33 m2 of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2-7 mmol urea-N m(-2) day(-1) and was in the same magnitude as the urea transformation in the sediment.

  13. Toward a microbial Neolithic revolution in buildings.

    Science.gov (United States)

    Thaler, David S

    2016-03-29

    The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes but starting with the gut we continue our hundred-year project of approaching the ability to assess and cultivate benign microbiomes in our bodies. Buildings are analogous to the body and it is time to ask what it means to cultivate benign microbiomes in our built environment. A critical distinction is that we have not found, or invented, niches in buildings where healthful microbial metabolism occurs and/or could be cultivated. Key events affecting the health and healthfulness of buildings such as a hurricane leading to a flood or a burst pipe occur only rarely and unpredictably. The cause may be transient but the effects can be long lasting and, e.g., for moisture damage, cumulative. Non-invasive "building tomography" could find moisture and "sentinel microbes" could record the integral of transient growth. "Seed" microbes are metabolically inert cells able to grow when conditions allow. All microbes and their residue present actinic molecules including immunological epitopes (molecular shapes). The fascinating hygiene and microbial biodiversity hypotheses propose that a healthy immune system requires exposure to a set of microbial epitopes that is rich in diversity. A particular conjecture is that measures of the richness of diversity derived from microbiome next-generation sequencing (NGS) can be mechanistically coupled to--rather than merely correlated with some measures of--human health. These hypotheses and conjectures inspire workers and funders but an alternative is also consequent to the first Neolithic revolution: That the genetic uniformity of contemporary foods may also decrease human exposure to molecular biodiversity in a heath-relevant manner. Understanding the consequences--including the unintended

  14. Microbial response to triepthylphosphate

    Energy Technology Data Exchange (ETDEWEB)

    Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

    1997-05-01

    The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior to the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.

  15. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-12-23

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

  16. Les hydrocarbures aromatiques polycycliques dans l'environnement. Deuxième partie : La dégradation par voie microbienne Polycyclic Aromatic Hydrocarbons in the Environment. Part Two: Microbial Degradation

    Directory of Open Access Journals (Sweden)

    Bouchez M.

    2006-11-01

    (PAH is a rapidly progressing area. Research aims both at developing the knowledge of the fate of these ubiquitous and genotoxic pollutants in the environment and at promoting the utilization of microbiological processes for the remediation of industrial soils contaminated with these compounds. A review of present knowledge in this field is presented here. Degradative organisms are essentially bacteria and fungi. The biodegradation processes involved are aerobic and are initiated by oxygenases. Bacteria utilize two to four cycle-PAH as growth substrates, leading to their mineralization. In addition, lignolytic fungi, as well as bacteria, carry out a cometabolic attack of PAH. A survey of the various microorganisms degrading PAH and of the metabolic pathways involved is presented. The mechanisms by which these scarcely soluble compounds are made accessible to the degradative microorganisms is discussed. Studies completed with bacteria had shown that two distinct mechanisms are involved, namely transfer by dissolution in the aqueous phase and direct interfacial uptake. Another important aspect is the fate of PAH in terms of carbon balances during the bacterial degradation of individual PAH and of PAH mixtures. High levels of mineralization can be obtained. In the case of PAH mixtures such high mineralization levels are obtained using complex microflora involving a large participation of cometabolism. Progress achieved in recent years leads to give up considering PAH as intrinsically biodegradation-recalcitrant compounds. In the environment, an important parameter limiting PAH degradation is their accessibility to microorganisms.

  17. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  18. Microbial interactions during carrion decomposition

    Science.gov (United States)

    This addresses the microbial ecology of carrion decomposition in the age of metagenomics. It describes what is known about the microbial communities on carrion, including a brief synopsis about the communities on other organic matter sources. It provides a description of studies using state-of-the...

  19. Web Resources for Microbial Data

    Institute of Scientific and Technical Information of China (English)

    Qinglan Sun; Li Liu; Linhuan Wu; Wei Li; Quanhe Liu; Jianyuan Zhang; Di Liug; Juncai Ma

    2015-01-01

    There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.

  20. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  1. Microbial conversions of nitrogenous heterocycles

    OpenAIRE

    Parshikov, Igor A

    2015-01-01

    The monography describes examples of the application of microbial technologies for obtaining of derivatives from a series of nitrogen heterocycles (saturated nitrogen heterocycles, azaarenes and quinolones). It is proposed alternative ways for synthesize substances that are difficult to obtain by the methods of organic chemistry. Microbial technologies of synthesis of organic compounds may find out a practical application in the production of various drugs.

  2. A microbial world within us

    NARCIS (Netherlands)

    Zoetendal, E.G.; Vaughan, E.E.; Vos, de W.M.

    2006-01-01

    The microbial world within us includes a vast array of gastrointestinal (GI) tract communities that play an important role in health and disease. Significant progress has been made in recent years in describing the intestinal microbial composition based on the application of 16S ribosomal RNA (rRNA)

  3. Models of microbiome evolution incorporating host and microbial selection.

    Science.gov (United States)

    Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

    2017-09-25

    Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

  4. The role of coastal fog in increased viability of marine microbial aerosols

    Science.gov (United States)

    Dueker, M.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

    2011-12-01

    Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. Despite the ubiquity of these bacteria (concentration estimates range from 1 x 10^4 to 6 x 10^5 cells m-3), much is still being learned about their source, viability, and interactions with climatic controls. They can be attached to ambient aerosol particles or exist singly in the air. They affect climate by serving as ice, cloud, and fog nucleators, and have the metabolic potential to alter atmospheric chemistry. Fog presence in particular has been shown to greatly increase the deposition of viable microbial aerosols in both urban and coastal environments, but the mechanisms behind this are not fully understood. To address this gap, we examined the diversity of culturable microbial aerosols from a relatively pristine coastal environment in Maine (USA) and determined the effect of fog presence on viability and community composition of microbial aerosols. 16S rRNA sequencing of culturable ocean surface bacteria and depositing microbial aerosols (under clear and foggy conditions) resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66% of all sequences. Seventy-five percent of the viable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. The fog and ocean surface sequence libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries. These findings support a dual role for fog in enhancing the fallout of viable marine microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms. The dominant presence of marine bacteria in coastal microbial aerosols provides a strong case for

  5. Final Report: Role of microbial synergies in immobilization of metals

    Energy Technology Data Exchange (ETDEWEB)

    Slava Epstein, Ph.D. and Kim Lewis, Ph.D.

    2012-11-14

    This Subsurface Microbial Ecology and Community Dynamics project tested the following hypothesis: synergistic groups of microorganisms immobilize heavy elements more efficiently than do individual species. We focused on groundwater at several DOE FRC and their microbial communities affecting the fate of U, Tc, and Cr. While we did not obtain evidence to support the original hypothesis, we developed a platform to accessing novel species from the target environments. We implemented this technology and discovered and isolated novel species capable of immobilization of uranium and species with exceptionally high resistances to the extant toxic factors. We have sequenced their genomes are are in the process of investigating the genomic contents behind these surprising resistances.

  6. Microbial community structure in the rhizosphere of rice plants

    Directory of Open Access Journals (Sweden)

    Björn eBreidenbach

    2016-01-01

    Full Text Available The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e. rhizosphere versus bulk soil had a greater effect on the community structure than did time (e.g. plant growth stage. Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g. Geobacter, Anaeromyxobacter and fermenters (e.g. Clostridiaceae, Opitutaceae were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.

  7. Microbial Biofilm Growth on Irradiated, Spent Nuclear Fuel Cladding

    Energy Technology Data Exchange (ETDEWEB)

    S.M. Frank

    2009-02-01

    A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 × 103 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments.

  8. Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Taillefert, Martial [Georgia Tech Research Corporation, Atlanta, GA (United States)

    2015-04-01

    This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined that both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".

  9. Soil microbial community diversity and driving mechanisms

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To study the structure of soil microbial communities, DNA was extracted from different environmental soil samples, and 16S rDNA clone libraries were constructed. The diversity of these 16S libraries were analyzed with restriction fragment length polymorphism based on amplification ribosomal DNA restriction analysis (RFLP-ARDRA)method. The results reveal a high diversity of the soil microbial communities, and striking differences in community structure at different depths. In the surface soil environment, there is no dominant gene pattern, but in the subsurface samples some dominant gene patterns are much more common. With the increasing depth the preference dominance becomes more significant. A spatial isolation hypothesis is proposed to explain the different community structures at different soil depths. Microcosms are set to simulate competition between populations at different degrees of spatial isolation. These studies reveal that spatial isolation caused by low moisture affects the competitive interactions of the two populations. In the two-strain microcosm there is one dominant population at high moisture, and no dominance in very dry environments

  10. Anaerobic microbial degradation of organochlorine insecticides Aldrin

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, T.C.; Yen, J.H.; Wang, Y.S. [National Taiwan Univ. (Taiwan)

    2004-09-15

    Aldrin (1,2,3,4,10,10-hexachloro-1,4,4a,5,8,8a-hexahydro-1,4-endo-exo-5,8-dimethanonnaphthalene), a cyclodiene organochlorine insecticide, was banned by nations and classified as B2 carcinogen by United States Environmental Protection Agency (EPA). Because of its chemical stability and lipophilicity, aldrin is regarded as a persistent and recalcitrant compound. Aldrin is easily adsorbed to soil and sediment after spreading to the environments, furthermore, it may be accumulated in animal's tissue or milk and then cause adverse effects by food-chain. The dissipation process of aldrin in environments has continuously been paid much attention by researchers. In general, the dissipation of aldrin has been thought as relating to three mechanisms: photo-degradation, chemical hydrolysis, and microbial degradation. And it has been well known that microbial degradation is the most important agent for breakdown of organochlorine pesticides. There has been shown that aldrin could be transformed to its metabolites, such as dieldrin or photo-dieldrin, by microorganisms under aerobic conditions, however, limited information has been shown under anaerobic conditions. For this reason, the degradation potential of aldrin by anaerobic microorganisms obtained from indigenous river sediment was evaluated, and the effect of environmental factors such as temperatures and nutrients on the aldrin degradation was also investigated in this study.

  11. Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

    Science.gov (United States)

    Nadeau, Jay; Lindensmith, Chris; Deming, Jody W.; Fernandez, Vicente I.; Stocker, Roman

    2016-10-01

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

  12. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    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 to 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.

  13. Monitoring Microbially Influenced Corrosion

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    Abstract Microbially influenced corrosion (MIC) of carbon steel may occur in media with microbiological activity of especially sulphate-reducing bacteria (SRB). The applicability and reliability of a number of corrosion monitoring techniques for monitoring MIC has been evaluated in experiments...... and diffusional effects and unreliable corrosion rates, when biofilm and ferrous sulphide corrosion products cover the steel surface. Corrosion rates can be overestimated by a factor of 10 to 100 by electrochemical techniques. Weight loss coupons and ER are recommended as necessary basic monitoring techniques....... EIS might be used for detection of MIC as the appearance of very large capacitances can be attributed to the combined ferrous sulphide and biofilm formation. Capacitance correlates directly with sulphide concentration in sterile sulphide media. Keywords: Corrosion monitoring, carbon steel, MIC, SRB...

  14. New microbial growth factor

    Science.gov (United States)

    Bok, S. H.; Casida, L. E., Jr.

    1977-01-01

    A screening procedure was used to isolate from soil a Penicillium sp., two bacterial isolates, and a Streptomyces sp. that produced a previously unknown microbial growth factor. This factor was an absolute growth requirement for three soil bacteria. The Penicillium sp. and one of the bacteria requiring the factor, an Arthrobacter sp., were selected for more extensive study concerning the production and characteristics of the growth factor. It did not seem to be related to the siderochromes. It was not present in soil extract, rumen fluid, or any other medium component tested. It appears to be a glycoprotein of high molecular weight and has high specific activity. When added to the diets for a meadow-vole mammalian test system, it caused an increased consumption of diet without a concurrent increase in rate of weight gain.

  15. Preserved filamentous microbial biosignatures in the Brick Flat gossan, Iron Mountain, California

    Science.gov (United States)

    Williams, Amy J.; Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A

    2015-01-01

    A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous

  16. Preserved Filamentous Microbial Biosignatures in the Brick Flat Gossan, Iron Mountain, California.

    Science.gov (United States)

    Williams, Amy J; Sumner, Dawn Y; Alpers, Charles N; Karunatillake, Suniti; Hofmann, Beda A

    2015-08-01

    A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous

  17. Microbial Field Pilot Study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1990-11-01

    This report covers progress made during the first year of the Microbial Field Pilot Study project. Information on reservoir ecology and characterization, facility and treatment design, core experiments, bacterial mobility, and mathematical modeling are addressed. To facilitate an understanding of the ecology of the target reservoir analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. A preliminary design of facilities for the operation of the field pilot test was prepared. In addition, procedures for facilities installation and for injection treatments are described. The Southeast Vassar Vertz Sand Unit (SEVVSU), the site of the proposed field pilot study, is described physically, historically, and geologically. The fields current status is presented and the ongoing reservoir simulation is discussed. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. Two possible mechanisms, relative permeability effects and changes in the capillary number, are discussed and related to four Berea core experiments' results. The experiments were conducted at reservoir temperature using SEVVSU oil, brine, and bacteria. The movement and activity of bacteria in porous media were investigated by monitoring the growth of bacteria in sandpack cores under no flow conditions. The rate of bacteria advancement through the cores was determined. A mathematical model of the MEOR process has been developed. The model is a three phase, seven species, one dimensional model. Finite difference methods are used for solution. Advection terms in balance equations are represented with a third- order upwind differencing scheme to reduce numerical dispersion and oscillations. The model is applied to a batch fermentation example. 52 refs., 26 figs., 21 tabs.

  18. Origin of microbial biomineralization and magnetotaxis during the Archean.

    Science.gov (United States)

    Lin, Wei; Paterson, Greig A; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A; Zhu, Rixiang; Kirschvink, Joseph L; Pan, Yongxin

    2017-02-28

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

  19. Origin of microbial biomineralization and magnetotaxis during the Archean

    Science.gov (United States)

    Paterson, Greig A.; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A.; Zhu, Rixiang; Kirschvink, Joseph L.; Pan, Yongxin

    2017-01-01

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time. PMID:28193877

  20. Origin of microbial biomineralization and magnetotaxis during the Archean

    Science.gov (United States)

    Lin, Wei; Paterson, Greig A.; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A.; Zhu, Rixiang; Kirschvink, Joseph L.; Pan, Yongxin

    2017-02-01

    Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

  1. Geomicrobiological processes in extreme environments: A review

    Institute of Scientific and Technical Information of China (English)

    Hailiang Dong; Bingsong Yu

    2007-01-01

    @@ The last decade has seen an extraordinary growth of Geomicrobiology. Microorganisms have been studied in numerous extreme environments on Earth, ranging from crystalline rocks from the deep subsurface, ancient sedimentary rocks and hypersaline lakes, to dry deserts and deep-ocean hydrothermal vent systems. In light of this recent progress, we review several currently active research frontiers: deep continental subsurface microbiology, microbial ecology in saline lakes, microbial formation of dolomite, geomicrobiology in dry deserts,fossil DNA and its use in recovery of paleoenvironmental conditions, and geomicrobiology of oceans.Throughout this article we emphasize geomicrobiological processes in these extreme environments.

  2. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.

    Science.gov (United States)

    Ho, Adrian; Angel, Roey; Veraart, Annelies J; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L E

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.

  3. Responses of soil microbial community to experimental warming and precipitation manipulation

    Science.gov (United States)

    Li, G.; Kim, S.; Park, M. J.; Han, S. H.; Lee, J.; Son, Y.

    2015-12-01

    An experimental nursery was established with two-year-old Pinus densiflora seedlings at Korea University to study soil microbial community responses to air warming (+3°C) and precipitation manipulation (-30% and +30%). Soil samplings were collected monthly from July to November, 2014. Substrate utilization profile of microbial community was examined using BIOLOG EcoPlate. Microbial community composition was assessed by high-throughput sequencing technology. The results showed that warming significantly affected the substrate utilization profile of microbial community (P0.05). In contrast, compared with unwarmed and precipitation control treatment, the bacterial community richness in the others were increased, but community abundance and diversity in those treatments were decreased (all P>0.05). These changes in microbial community structure resulted in the changes in community functional composition, which microbial metabolic functions were higher in warming plots than unwarmed plots. Since microorganisms differ in their susceptibility to stressors, changes in the soil environment affect the microbial community. Therefore, the results indicated that effects of warming and precipitation manipulation on soil microbial community might be related to warming and precipitation manipulation-induced changes in soil moisture. We suggested that shifts in the microbial community may be important implications for soil carbon and nitrogen dynamics in a warmer world. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

  4. Astrobiological Significance of Microbial Extremophiles

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2007-01-01

    The microflora of the cryosphere of planet Earth provides the best analogs for life forms that might be found in the permafrost or polar ice caps of Mars, near the surface of the cometary nuclei, or in the liquid water beneath and the ice crusts of icy moons of Jupiter and Saturn. The importance of study alkaliphilic microorganisms for astrobiology was enhanced by the findings of abundant carbonates and carbonate globules rimmed with possibly biogenic magnetites in association with the putative microfossils in the ALH84001 meteorite. Although the ALH84001 "nanofossils" were to small and simple to be unambiguously recognized as biogenic, they stimulated Astrobiology research and studies of microbial extremophiles and biomarkers in ancient rocks and meteorites. Recent studies of CI and CM carbonaceous meteorites have resulted in the detection of the well-preserved mineralized remains of coccoidal and filamentous microorganisms in cyanobacterial mats. Energy Dispersive X-ray Analysis has shown anomalous biogenic element ratios clearly indicating they are not recent biological contaminants. This paper reviews microbial extremophiles in context of their significance to Astrobiology. The study of halophilic microorganisms was started from work with saline soils and lakes, and one of the record of good growth for Haloferax mediterranei was shown at 30 percent NaC1. Although alkali-tolerant nitrifying bacteria had previously been reported, the first described alkaliphilic microorganism was the bacterium Streptococcus faecalis. Halophilic and alkaliphilic forms are relevant to conditions that might be found in closed impact basins and craters on Mars filled with evaporite deposits. The first obligately acidophilic bacterium described was Acidithiobacillus ferrooxydans (formally Thiobacillus ferrooxidans). Later thermophilic lithotrophic acidophiles were found, and the hyperacidophilic moderately thermophilic species of the genus Picrophilus were found to grow at negative p

  5. The microbial ecology of permafrost

    DEFF Research Database (Denmark)

    Jansson, Janet; Tas, Neslihan

    2014-01-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

  6. Principal methods for isolation and identification of soil microbial communities.

    Science.gov (United States)

    Stefanis, Christos; Alexopoulos, Athanasios; Voidarou, Chrissa; Vavias, Stavros; Bezirtzoglou, Eugenia

    2013-01-01

    Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes.

  7. Prevention of microbial communities: novel approaches based natural products.

    Science.gov (United States)

    Mogosanu, George D; Grumezescu, Alexandru M; Huang, Keng-Shiang; Bejenaru, Ludovic E; Bejenaru, Cornelia

    2015-01-01

    Firmly attached to different living or non-living, solid or fluid surfaces rich in nutrients and moisture, microbial biofilm is a matter of great interest due to its major importance for the healthcare community. Depending on common strategies such as mutual protection and hibernation (quiescent bacteria), the resistance, survival and virulence of microbial communities have large implications for human pathology, clinical environment and biomedical devices. The microbial biofilm is continuously changing, stimulating inflammation, increasing vascular permeability and preventing the action of macrophages. About 80% of human infections affecting the gastrointestinal, genitourinary and respiratory systems, oral mucosa and teeth, eyes, middle ear and skin are caused by biofilm-associated microorganisms. Therefore, the search for modern strategies is even more important as microbial biofilms resistant to conventional antibiotics, antiseptics and disinfectants are involved in the frequent treatment failures of some chronic inflammatory diseases and wounds. Natural products containing secondary metabolites, such as aromatic compounds, sulphurated derivatives, terpenoids (essential oils) and alkaloids as quorum-sensing inhibitors and biofilm disruptors, are promising alternatives for the prophylaxis and treatment of chronic infections. Surface modification of medical devices with non-polar functionalized nanoparticles stabilizes the natural compounds antibiofilm activity and inhibits microbial adhesion and biofilm formation and growth for a longer period of time. In this regard, an interdisciplinary approach is needed due to the large number of natural derivatives alone or in combination with biocompatible and biodegradable micro-/ nano-engineered materials.

  8. Redox regime shifts in microbially-mediated biogeochemical cycles

    Science.gov (United States)

    Bush, T.; Butler, I. B.; Free, A.; Allen, R. J.

    2015-02-01

    Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the sulfur and nitrogen cycles in the present-day natural environment, and may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  9. Microbial ecology and biogeochemistry of continental Antarctic soils

    Directory of Open Access Journals (Sweden)

    Don A Cowan

    2014-04-01

    Full Text Available 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 harbour 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.

  10. Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

    Science.gov (United States)

    Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

    2013-01-01

    The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the

  11. Teaching Microbial Growth by Simulation.

    Science.gov (United States)

    Ruiz, A. Fernandez; And Others

    1989-01-01

    Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

  12. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    1993-01-01

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and sulfid

  13. Microbial production of gaseous hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Hideo

    1987-10-20

    Microbial production of ethylene, isobutane and a saturated gaseous hydrocarbon mixture was described. Microbial ethylene production was studied with Penicillium digitatum IFO 9372 and a novel pathway of the ethylene biosynthesis through alpha-ketoglutarate was proposed. Rhodotorula minuta IFO 1102 was selected for the microbial production of isobutane and the interesting actions of L-leucine and L-phenylalanine for the isobutane production were found. It was finally presented about the microbial production of a saturated gaseous hydrocarbon mixture with Rhizopus japonicus IFO 4758 was described. A gas mixture was produced through a chemical reaction of SH compounds and some cellular component such as squalene under aerobic conditions. (4 figs, 7 tabs, 41 refs)

  14. The microbial ecology of permafrost.

    Science.gov (United States)

    Jansson, Janet K; Taş, Neslihan

    2014-06-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.

  15. Microbial hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, P.F.; Maness, P.C.; Martin, S. [National Renewable Energy Lab., Golden, CO (United States)] [and others

    1995-09-01

    Photosynthetic bacteria inhabit an anaerobic or microaerophilic world where H{sub 2} is produced and consumed as a shared intermediary metabolite. Within a given bacterial isolate there are as many as 4 to 6 distinct enzymes that function to evolve or consume H{sub 2}. Three of the H{sub 2}-evolving physiologies involving three different enzymes from photosynthetic bacteria have been examined in detail for commercial viability. Nitrogenase-mediated H{sub 2} production completely dissimilates many soluble organic compounds to H{sub 2} and CO{sub 2} at rates up to 131 {mu}mol H{sub 2}{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} and can remain active for up to 20 days. This metabolism is very energy intensive, however, which limits solar conversion efficiencies. Fermentative hydrogenase can produce H{sub 2} at rates of 440 {mu}mol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} at low levels of irradiation over indefinite periods. The equilibrium for this activity is low (<0.15 atmospheres), thereby requiring gas sparging, vacuuming, or microbial scavenging to retain prolonged activity. Microbial H{sub 2} production from the CO component of synthesis or producer gases maximally reaches activities of 1.5 mmol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1}. Mass transport of gaseous CO into an aqueous bacterial suspension is the rate-limiting step. Increased gas pressure strongly accelerates these rates. Immobilized bacteria on solid supports at ambient pressures also show enhanced shift activity when the bulk water is drained away. Scaled-up bioreactors with 100-200 cc bed volume have been constructed and tested. The near-term goal of this portion of the project is to engineer and economically evaluate a prototype system for the biological production of H{sub 2} from biomass. The CO shift enables a positive selection technique for O{sub 2}-resistant, H{sub 2}-evolving bacterial enzymes from nature.

  16. New insights into microbial adaptation to extreme saline environments

    Directory of Open Access Journals (Sweden)

    Vauclare P.

    2014-02-01

    Full Text Available Extreme halophiles are microorganisms adapted to low water activity living at the upper salt concentration that life can tolerate. We review here recent data that specify the main factors, which determine their peculiar salt-dependent biochemistry. The data suggested that evolution proceeds by stage to modify the molecular dynamics properties of the entire proteome. Extreme halophiles therefore represent tractable models to understand how fast and to what extent microorganisms adapt to environmental changes. Halophiles are also robust organisms, capable to resist multiple stressors. Preliminary studies indicated that they have developed a cellular response specifically aimed to survive when the salt condition fluctuates. Because of these properties halophilic organisms deserve special attention in the search for traces of life on other planets.

  17. Microbial Oxidation of Iron Sulfides in Anaerobic Environments

    DEFF Research Database (Denmark)

    Vaclavkova, Sarka

    processes in natural anoxic soils is supported by the fact that about 17 % of drinking water wells in Denmark were lately found to be contaminated by NO3- in concentrations exceeding the allowed limit of 50 mgL-1. This study experimentally documented potential for MISON in a range of anoxic aquatic......Abstract (shortened): Iron sulfides (FeSx), representing 0.04-10 % of Danish dry soil weight, oxidize in a presence of oxygen, releasing sulfuric acid and free iron. Environmental impact of FeSx oxidation is commonly seen on agricultural sites cultivated by drainage as acid sulfate soil formation...

  18. Microbial genomes: Blueprints for life

    Energy Technology Data Exchange (ETDEWEB)

    Relman, David A.; Strauss, Evelyn

    2000-12-31

    Complete microbial genome sequences hold the promise of profound new insights into microbial pathogenesis, evolution, diagnostics, and therapeutics. From these insights will come a new foundation for understanding the evolution of single-celled life, as well as the evolution of more complex life forms. This report is an in-depth analysis of scientific issues that provides recommendations and will be widely disseminated to the scientific community, federal agencies, industry and the public.

  19. Microbial dynamics in natural aquifers

    OpenAIRE

    Bajracharya, Bijendra Man

    2016-01-01

    Microorganisms in groundwater form ecosystems that can transform chemical compounds. Quantitatively understanding microbial dynamics in soils and groundwater is thus essential for pollutant dynamics and biogeochemistry in the subsurface. This dissertation addresses three factors influencing microbial dynamics in aquifers and soils, namely: (1) the influence of grazing on bacteria in eutrophic aquifers, posing the question whether the carrying capacity of bacteria, which has been observed i...

  20. Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge.

    Science.gov (United States)

    Mikucki, J A; Lee, P A; Ghosh, D; Purcell, A M; Mitchell, A C; Mankoff, K D; Fisher, A T; Tulaczyk, S; Carter, S; Siegfried, M R; Fricker, H A; Hodson, T; Coenen, J; Powell, R; Scherer, R; Vick-Majors, T; Achberger, A A; Christner, B C; Tranter, M

    2016-01-28

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

  1. Effects of microbial inhibitors on anaerobic degradation of DDT

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

    2004-09-15

    Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

  2. Limited recovery of soil microbial activity after transient exposure to gasoline vapors

    DEFF Research Database (Denmark)

    Modrzyński, Jakub J.; Christensen, Jan H.; Mayer, Philipp

    2016-01-01

    During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial...... functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial...... microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient...

  3. Mining Seasonal Marine Microbial Pattern with Greedy Heuristic Clustering and Symmetrical Nonnegative Matrix Factorization

    Directory of Open Access Journals (Sweden)

    Fei Liu

    2014-01-01

    Full Text Available With the development of high-throughput and low-cost sequencing technology, a large number of marine microbial sequences were generated. The association patterns between marine microbial species and environment factors are hidden in these large amount sequences. Mining these association patterns is beneficial to exploit the marine resources. However, very few marine microbial association patterns are well investigated in this field. The present study reports the development of a novel method called HC-sNMF to detect the marine microbial association patterns. The results show that the four seasonal marine microbial association networks have characters of complex networks, the same environmental factor influences different species in the four seasons, and the correlative relationships are stronger between OTUs (taxa than with environmental factors in the four seasons detecting community.

  4. Prediction of Competitive Microbial Growth.

    Science.gov (United States)

    Fujikawa, Hiroshi

    2016-01-01

     Prediction of competitive microbial growth is becoming important for microbial food safety. There would be two approaches to predict competitive microbial growth with mathematical models. The first approach is the development of a growth model for competitive microbes. Among several candidates for the competition model considered, the combination of the primary growth model of the new logistic (NL) model and the competition model of the Lotka-Vorttera (LV) model showed the best performance in predicting microbial competitive growth in the mixed culture of two species. This system further successfully predicted the growth of three competitive species in mixed culture. The second approach is the application of the secondary model especially for the parameter of the maximum cell population in the primary growth model. The combination of the NL model and a polynomial model for the maximum population successfully predicted Salmonella growth in raw ground beef. This system further successfully predicted Salmonella growth in beef at various initial concentrations and temperatures. The first approach requires microbial growth data in monoculture for analysis. The second approach to the prediction of competitive growth from the viewpoint of microbial food safety would be more suitable for practical application.

  5. Molecular ecology of microbial mats.

    Science.gov (United States)

    Bolhuis, Henk; Cretoiu, Mariana Silvia; Stal, Lucas J

    2014-11-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep and fluctuating physicochemical microgradients, that are the result of the ever changing environmental conditions and of the microorganisms' own activities, give rise to a plethora of potential niches resulting in the formation of one of the most diverse microbial ecosystems known to date. For several decades, microbial mats have been studied extensively and more recently molecular biological techniques have been introduced that allowed assessing and investigating the diversity and functioning of these systems. These investigations also involved metagenomics analyses using high-throughput DNA and RNA sequencing. Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring, and hypersaline). We also present a comparison of the available metagenomic data sets from mats emphasizing the major differences between them as well as elucidating the overlap in overall community composition.

  6. Microbial Transformation of Arsenic

    Science.gov (United States)

    Stolz, J. F.

    2004-12-01

    Whether the source is natural or anthropogenic, it has become evident that arsenic is readily transformed by a great diversity of microbial species and has a robust biogeochemical cycle. Arsenic cycling primarily involves the oxidation of As(III) and the reduction of As(V). Over thirty arsenite oxidizing prokaryotes have been reported and include alpha, beta, and gamma Proteobacteria , Deinocci and Crenarchaeota. At least twenty species of arsenate-respiring prokaryotes are now known and include Crenarchaeota, thermophilic bacteria, low and high G+C gram positive bacteria, and gamma, delta, and epsilon Proteobacteria. These organisms are metabolically diverse, and depending on the species, capable of using other terminal electron acceptors (e.g., nitrate, selenate, fumarate, sulfate). In addition to inorganic forms (e.g., sodium arsenate) organoarsenicals can be utilized as a substrate. The feed additive roxarsone (3-nitro-4-hydroxyphenyl arsonic acid) has been shown to readily degrade leading to the release of inorganic arsenic (e.g., As(V)). Degradation proceeds via the cleavage of the arsenate functional group or the reduction of the nitro functional group and deamination. The rapid degradation (within 3 days) of roxarsone by Clostridium sp. strain OhILAs appears to follow the latter pathway and may involve Stickland reactions. The activities of these organisms affect the speciation and mobilization of arsenic, ultimately impacting water quality.

  7. Chaos and microbial systems

    Energy Technology Data Exchange (ETDEWEB)

    Kot, M.

    1990-07-01

    A recurrent theme of much recent research is that seemingly random fluctuations often occur as the result of simple deterministic mechanisms. Hence, much of the recent work in nonlinear dynamics has centered on new techniques for identifying order in seemingly chaotic systems. To determine the robustness of these techniques, chaos must, to some extent, be brought into the laboratory. Preliminary investigations of the forced double-Monod equations, a model for a predator and a prey in a chemostat with periodic variation in inflowing substrate concentration, suggest that simple microbial systems may provide the perfect framework for determining the efficacy and relevance of the new nonlinear dynamics in dealing with complex population dynamics. This research has two main goals, that is the mathematical analysis and computer simulation of the periodically forced double-Monod equations and of related models; and experimental (chemostat) population studies that evaluate the accuracy and generality of the models, and that judge the usefulness of various new techniques of nonlinear dynamics to the study of populations.

  8. Microbial production of biovanillin

    Directory of Open Access Journals (Sweden)

    A. Converti

    2010-10-01

    Full Text Available This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  9. Microbial Sulfur Geochemistry in Mine Systems (Invited)

    Science.gov (United States)

    Warren, L. A.; Norlund, K. L.; Hitchcock, A.

    2010-12-01

    Acid mine drainage (AMD), metal laden, acidic water, is the most pressing mining environmental issue on a global scale. While it is well recognized that the activity of autotrophic Fe and S bacteria amplify the oxidation of the sulfidic wastes, thereby generating acidity and leaching metals; the underlying microbial geochemistry is not well described. This talk will highlight results revealing the importance of microbial cooperation associated with a novel sulfur-metabolizing consortium enriched from mine waters. Results generated by an integrated approach, combining field characterization, geochemical experimentation, scanning transmission X-ray microscopy (STXM), and fluorescence in situ hybridization (FISH) [1]describing the underlying ecological drivers, the functionally relevant biogeochemical architecture of the consortial macrostructure as well as the identities of this environmental sulphur redox cycling consortium will be presented. The two common mine bacterial strains involved in this consortium, Acidithiobacillus ferroxidans and Acidiphilium sp., are specifically spatially segregated within a macrostructure (pod) of extracellular polymeric substance (EPS) that enables coupled sulphur oxidation and reduction reactions despite bulk, oxygenated conditions. Identical pod formation by type culture strains was induced and linked to ecological conditions. The proposed sulphur geochemistry associated with this bacterial consortium produces 40-90% less acid than expected based on abiotic AMD models, with implications for both AMD mitigation and AMD carbon flux modeling. We are currently investigating the implications of these sulphur-processing pods for metal dynamics in mine systems. These results demonstrate how microbes can orchestrate their geochemical environment to facilitate metabolism, and underscore the need to consider microbial interactions and ecology in constraining their geochemical impacts. [1] Norlund, Southam, Tyliszcczak, Hu, Karunakaran, Obst

  10. Threatened corals provide underexplored microbial habitats.

    Directory of Open Access Journals (Sweden)

    Shinichi Sunagawa

    Full Text Available Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these "rare" organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1% were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under

  11. Rock glacier ice as a microbial habitat

    Science.gov (United States)

    Florentine, C. E.; Skidmore, M. L.; Montross, S. N.

    2010-12-01

    Rock glaciers are ubiquitous geomorphic features in alpine environments, recognizable by a talus mantle, steep-toe, lobate shape and that flow due to the inferred presence of internal ice. Rock glaciers consist of both ice and debris, and are abundant in mountain ranges such as the Rocky Mountains, the Andes and the European Alps. Rock glacier ice has not previously been considered as a microbial habitat. However, given recent research showing debris-rich basal layers in glaciers harbor viable microbes, the debris-rich ice in a rock glacier has potential as a microbial habitat. The glacier research has demonstrated increased cell numbers in the debris rich basal ice relative to the clean glacier ice, and the finely-ground debris is considered to be a source of nutrients for the microbes. In August 2009 3 m of surface talus was excavated from the Lone Peak rock glacier, one of ~ 380 in Southwest Montana, to expose the underlying rock glacier ice. The ice contained numerous large rocks making sampling difficult, but 25 cm thick blocks with layers of clean and amber (~ 0.01% debris) ice were sampled. The isotopic, microbiological, and geochemical composition of the clean and amber ice was analyzed. The isotopic data provides some relative age dating for the ice and the geochemical data information on nutrient availability. Differences were observed between the microbial communities in the clean and amber ice by both cell counts and culturing techniques suggesting that as in glacier ice the debris-rich (amber) ice is a more amenable habitat for microbes.

  12. Microbial oceanography of anoxic oxygen minimum zones.

    Science.gov (United States)

    Ulloa, Osvaldo; Canfield, Donald E; DeLong, Edward F; Letelier, Ricardo M; Stewart, Frank J

    2012-10-02

    Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

  13. Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

    Directory of Open Access Journals (Sweden)

    Alan D. W. Dobson

    2010-03-01

    Full Text Available The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.

  14. Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

    Science.gov (United States)

    Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

  15. Targeted Proteomics Approaches To Monitor Microbial Activity In Basalt Aquifer

    Science.gov (United States)

    Paszczynski, A. J.; Paidisetti, R.

    2007-12-01

    Microorganisms play a major role in biogeochemical cycles of the Earth. Information regarding microbial community composition can be very useful for environmental monitoring since the short generation times of microorganisms allows them to respond rapidly to changing environmental conditions. Microbial mediated attenuation of toxic chemicals offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. Current knowledge regarding the structure and functional activities of microbial communities is limited, but more information is being acquired every day through many genomic- and proteomic- based methods. As of today, only a small fraction of the Earth's microorganisms has been cultured, and so most of the information regarding the biodegradation and therapeutic potentials of these uncultured microorganisms remains unknown. Sequence analysis of DNA and/or RNA has been used for identifying specific microorganisms, to study the community composition, and to monitor gene expression providing limited information about metabolic state of given microbial system. Proteomic studies can reveal information regarding the real-time metabolic state of the microbial communities thereby aiding in understanding their interaction with the environment. In research described here the involvement of microbial communities in the degradation of anthropogenic contaminants such as trichloroethylene (TCE) was studied using mass spectrometry-based proteomics. The co- metabolic degradation of TCE in the groundwater of the Snake River Plain Aquifer at the Test Area North (TAN) site of Idaho National Laboratory (INL) was monitored by the characterization of peptide sequences of enzymes such as methane monooxygenases (MMOs). MMOs, expressed by methanotrophic bacteria are involved in the oxidation of methane and non-specific co-metabolic oxidation of TCE. We developed a time- course cell lysis method to release proteins from complex microbial

  16. Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

    Science.gov (United States)

    Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

    2013-01-01

    Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

  17. Microbial degradation of chlorinated compounds. Application of specialized bacteria in the treatment of contaminated soil and waste water.

    NARCIS (Netherlands)

    Oldenhuis, Roelof

    1992-01-01

    The development of (aerobic) treatment technologies for polluted environments and waste streams will require an understanding of the microbial potential and the ecophysiology of the most suitable organisms. Therefore, we have studied physiological pathways and some kinetic aspects of the

  18. Microbial biogeochemistry of uranium mill tailings

    Science.gov (United States)

    Landa, Edward R.

    2005-01-01

    Uranium mill tailings (UMT) are the crushed ore residues from the extraction of uranium (U) from ores. Among the radioactive wastes associated with the nuclear fuel cycle, UMT are unique in terms of their volume and their limited isolation from the surficial environment. For this latter reason, their management and long-term fate has many interfaces with environmental microbial communities and processes. The interactions of microorganisms with UMT have been shown to be diverse and with significant consequences for radionuclide mobility and bioremediation. These radionuclides are associated with the U-decay series. The addition of organic carbon and phosphate is required to initiate the reduction of the U present in the groundwater down gradient of the mills. Investigations on sediment and water from the U-contaminated aquifer, indicates that the addition of a carbon source stimulates the rate of U removal by microbial reduction. Moreover, most attention with respect to passive or engineered removal of U from groundwaters focuses on iron-reducing and sulfate-reducing bacteria.

  19. Physiological characterization of sugarcane's endophytic microbial community

    Directory of Open Access Journals (Sweden)

    Anar Janet Rodríguez Cheang

    2007-02-01

    Full Text Available Excessive application of chemical nitrogen fertilisers and pesticides has badly affected the environment. This has led to great interest being shown in studying a crop's native microbial community and its benefit for plants. This paper was thus aimed at characterising sugarcane's endophytic microbial community. 5 sugar cane strains and 50 isolates were used. Gas chromatography was used for measuring nitrogenase activity and the influence of carbon and nitrogen sources and pH on cultures. Indol acetic (IAA production was detected by Dot-Immunobinding and Salkowski's method. These results show that 19 strains and isolates had nitrogenase activity, values ranging from 100 to SOOO/zg/mL; 6 of them produced IAA (values ranging from 1,7 to 2,5 //g/mL: Gluconacetobacter diazotrophicus PAl-5, Gluconacetobacter diazotrophicus 1-05, Gluconacetobacter diazotrophicus 4-02,17,30 and 305. It was demonstrated that culture medium nutrient sources and pH affected the nitrogenase activity of the strains representing the endophytic community. Key words: endophytic community, sugarcane, nitrogenase activity, indolacetic acid.

  20. Chronic kidney disease alters intestinal microbial flora.

    Science.gov (United States)

    Vaziri, Nosratola D; Wong, Jakk; Pahl, Madeleine; Piceno, Yvette M; Yuan, Jun; DeSantis, Todd Z; Ni, Zhenmin; Nguyen, Tien-Hung; Andersen, Gary L

    2013-02-01

    The population of microbes (microbiome) in the intestine is a symbiotic ecosystem conferring trophic and protective functions. Since the biochemical environment shapes the structure and function of the microbiome, we tested whether uremia and/or dietary and pharmacologic interventions in chronic kidney disease alters the microbiome. To identify different microbial populations, microbial DNA was isolated from the stools of 24 patients with end-stage renal disease (ESRD) and 12 healthy persons, and analyzed by phylogenetic microarray. There were marked differences in the abundance of 190 bacterial operational taxonomic units (OTUs) between the ESRD and control groups. OTUs from Brachybacterium, Catenibacterium, Enterobacteriaceae, Halomonadaceae, Moraxellaceae, Nesterenkonia, Polyangiaceae, Pseudomonadaceae, and Thiothrix families were markedly increased in patients with ESRD. To isolate the effect of uremia from inter-individual variations, comorbid conditions, and dietary and medicinal interventions, rats were studied 8 weeks post 5/6 nephrectomy or sham operation. This showed a significant difference in the abundance of 175 bacterial OTUs between the uremic and control animals, most notably as decreases in the Lactobacillaceae and Prevotellaceae families. Thus, uremia profoundly alters the composition of the gut microbiome. The biological impact of this phenomenon is unknown and awaits further investigation.

  1. Microbial Induction of Immunity, Inflammation And Cancer

    Directory of Open Access Journals (Sweden)

    Stephen John O'Keefe

    2011-01-01

    Full Text Available The human microbiota presents a highly active metabolic that influences the state of health of our gastrointestinal tracts as well as our susceptibility to disease. Although much of our initial microbiota is adopted from our mothers, its final composition and diversity is determined by environmental factors. Westernization has significantly altered our microbial function. Extensive experimental and clinical evidence indicates that the westernized diet, rich in animal products and low in complex carbohydrates, plus the overuse of antibiotics and underuse of breastfeeding, leads to a heightened inflammatory potential of the microbiota. Chronic inflammation leads to the expression of certain diseases in genetically predisposed individuals. Antibiotics and a ‘clean’ environment, termed the ‘hygiene hypothesis’, has been linked to the rise in allergy and inflammatory bowel disease, due to impaired beneficial bacterial exposure and education of the gut immune system, which comprises the largest immune organ within the body. The elevated risk of colon cancer is associated with the suppression of microbial fermentation and butyrate production, as butyrate provides fuel for the mucosa and is anti-inflammatory and anti-proliferative. This article will summarize the work to date highlighting the complicated and dynamic relationship between the gut microbiota and immunity, inflammation and carcinogenesis.

  2. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  3. Applying landscape genetics to the microbial world.

    Science.gov (United States)

    Dudaniec, Rachael Y; Tesson, Sylvie V M

    2016-07-01

    Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.

  4. 30年不同设施条件和栽培方式下土壤养分和微生物群落功能多样性的变化%Changes of soil nutrients and microbial community diversity in responses to different growth environments and cultivation practices in 30 years

    Institute of Scientific and Technical Information of China (English)

    张雪艳; 田蕾; 吴萍; 高艳明; 李建设

    2015-01-01

    相对CK处理则显著降低其含量,其中全氮、有机质、速效钾、铵态氮和硝态氮含量分别显著降低41.46%、50.26%、51.47%、26.72%和54.11%,CS3 和CS4 处理全氮、速效磷、速效钾、硝态氮均显著低于其他处理. 全氮、速效养分均与B/F、微生物总量、微生物多样性指数呈负相关,铵态氮与其均呈极显著负相关,速效磷与B/F、微生物总量呈极显著负相关. [结论]30年温室连作黄瓜土壤养分累积严重,夏季填闲毛豆/花生可显著降低硝态氮累积和增加微生物多样性;30年温室大棚单一连作黄瓜显著降低微生物群落多样性;30年露地种植绿叶菜以及大棚后两年露地种植叶菜的微生物数量均较高,且养分累积最低.%[Objectives] With the elongation of vegetable cultivation ,the soil bio-ecosystems will change greatly . Systematically research on the changes in soil nutrient availabilities and the microbial community will provide theoretical support for the sustainable vegetable production .[Methods] The soils consecutively used for vegetable production over 30-years under different growth environments and cultivation practices were chosen for the investigation .Double cucumber cropping followed by fallow in summer in greenhouse was used as control ( CK ) , double cucumber followed by green soybean/peanut in summer ( CS1 ) , double cucumber cropping in plastics greenhouse (CS2), double cucumber in plastics greenhouse for the first 28 years and followed by two-years green leafy vegetables in open filed (CS3), and consecutive green leafy vegetables in the open filed (CS4) were used. The soil samples of 0-20 cm depth were collected in 2009 , and the soil nutrient contents and microbial quantity were measured with conventional methods .The microbial community diversity was evaluated with the values of Average Well Color Development ( AWCD) , the utilization of six C sources with the principal component analysis ( PCA) .[Results] The

  5. [Microbial geochemical calcium cycle].

    Science.gov (United States)

    Zavarzin, G A

    2002-01-01

    The participation of microorganisms in the geochemical calcium cycle is the most important factor maintaining neutral conditions on the Earth. This cycle has profound influence on the fate of inorganic carbon, and, thereby, on the removal of CO2 from the atmosphere. The major part of calcium deposits was formed in the Precambrian, when prokaryotic biosphere predominated. After that, calcium recycling based on biogenic deposition by skeletal organisms became the main process. Among prokaryotes, only a few representatives, e.g., cyanobacteria, exhibit a special calcium function. The geochemical calcium cycle is made possible by the universal features of bacteria involved in biologically mediated reactions and is determined by the activities of microbial communities. In the prokaryotic system, the calcium cycle begins with the leaching of igneous rock predominantly through the action of the community of organotrophic organisms. The release of carbon dioxide to the soil air by organotrophic aerobes leads to leaching with carbonic acid and soda salinization. Under anoxic conditions, of major importance is the organic acid production by primary anaerobes (fermentative microorganisms). Calcium carbonate is precipitated by secondary anaerobes (sulfate reducers) and to a smaller degree by methanogens. The role of the cyanobacterial community in carbonate deposition is exposed by stromatolites, which are the most common organo-sedimentary Precambrian structures. Deposition of carbonates in cyanobacterial mats as a consequence of photoassimilation of CO2 does not appear to be a significant process. It is argued that carbonates were deposited at the boundary between the "soda continent", which emerged as a result of subaerial leaching with carbonic acid, and the ocean containing Ca2+. Such ecotones provided favorable conditions for the development of the benthic cyanobacterial community, which was a precursor of stromatolites.

  6. Microbial taxonomy in the post-genomic era: rebuilding from scratch?

    Science.gov (United States)

    Thompson, Cristiane C; Amaral, Gilda R; Campeão, Mariana; Edwards, Robert A; Polz, Martin F; Dutilh, Bas E; Ussery, David W; Sawabe, Tomoo; Swings, Jean; Thompson, Fabiano L

    2015-04-01

    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

  7. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  8. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

    OpenAIRE

    Igor Shuryak; Ekaterina Dadachova

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil co...

  9. Physico-Chemical and Microbial Analysis of Selected Borehole Water in Mahikeng, South Africa

    OpenAIRE

    Lobina Palamuleni; Mercy Akoth

    2015-01-01

    Groundwater is generally considered a “safe source” of drinking water because it is abstracted with low microbial load with little need for treatment before drinking. However, groundwater resources are commonly vulnerable to pollution, which may degrade their quality. An assessment of microbial and physicochemical qualities of borehole wate