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Sample records for archaea ecology metabolism

  1. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Julie Maupin- Furlow

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  2. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  3. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Imke Schroeder

    2008-09-18

    The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  4. 2003 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Richard F. Shand

    2004-09-21

    The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, ''free time'' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier-breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. If you wish any further details, please feel free to contact me. Thank you, Dr. Richard F. Shand, 2003 Conference Chair.

  5. 2001 Gordon Research Conference on Archaea: Ecology [sic], Metabolism. Final progress report [agenda and attendee list

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, Charles

    2001-08-10

    The Gordon Research Conference on Archaea: Ecology, Metabolism [and Molecular Biology] was held at Proctor Academy, Andover, New Hampshire, August 5-10, 2001. The conference was attended by 135 participants. The attendees represented the spectrum of endeavor in this field, coming from academia, industry, and government laboratories, and included US and foreign scientists, senior researchers, young investigators, and students. Emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate discussion about the key issues in the field today. Session topics included the following: Ecology and genetic elements; Genomics and evolution; Ecology, genomes and gene regulation; Replication and recombination; Chromatin and transcription; Gene regulation; Post-transcription processing; Biochemistry and metabolism; Proteomics and protein structure; Metabolism and physiology. The featured speaker addressed the topic: ''Archaeal viruses, witnesses of prebiotic evolution?''

  6. Metabolic ecology.

    Science.gov (United States)

    Humphries, Murray M; McCann, Kevin S

    2014-01-01

    Ecological theory that is grounded in metabolic currencies and constraints offers the potential to link ecological outcomes to biophysical processes across multiple scales of organization. The metabolic theory of ecology (MTE) has emphasized the potential for metabolism to serve as a unified theory of ecology, while focusing primarily on the size and temperature dependence of whole-organism metabolic rates. Generalizing metabolic ecology requires extending beyond prediction and application of standardized metabolic rates to theory focused on how energy moves through ecological systems. A bibliometric and network analysis of recent metabolic ecology literature reveals a research network characterized by major clusters focused on MTE, foraging theory, bioenergetics, trophic status, and generalized patterns and predictions. This generalized research network, which we refer to as metabolic ecology, can be considered to include the scaling, temperature and stoichiometric models forming the core of MTE, as well as bioenergetic equations, foraging theory, life-history allocation models, consumer-resource equations, food web theory and energy-based macroecology models that are frequently employed in ecological literature. We conclude with six points we believe to be important to the advancement and integration of metabolic ecology, including nomination of a second fundamental equation, complementary to the first fundamental equation offered by the MTE. PMID:24028511

  7. Ammonia-oxidising archaea--physiology, ecology and evolution.

    Science.gov (United States)

    Schleper, Christa; Nicol, Graeme W

    2010-01-01

    Nitrification is a microbially mediated process that plays a central role in the global cycling of nitrogen and is also of economic importance in agriculture and wastewater treatment. The first step in nitrification is performed by ammonia-oxidising microorganisms, which convert ammonia into nitrite ions. Ammonia-oxidising bacteria (AOB) have been known for more than 100 years. However, metagenomic studies and subsequent cultivation efforts have recently demonstrated that microorganisms of the domain archaea are also capable of performing this process. Astonishingly, members of this group of ammonia-oxidising archaea (AOA), which was overlooked for so long, are present in almost every environment on Earth and typically outnumber the known bacterial ammonia oxidisers by orders of magnitudes in common environments such as the marine plankton, soils, sediments and estuaries. Molecular studies indicate that AOA are amongst the most abundant organisms on this planet, adapted to the most common environments, but are also present in those considered extreme, such as hot springs. The ecological distribution and community dynamics of these archaea are currently the subject of intensive study by many research groups who are attempting to understand the physiological diversity and the ecosystem function of these organisms. The cultivation of a single marine isolate and two enrichments from hot terrestrial environments has demonstrated a chemolithoautotrophic mode of growth. Both pure culture-based and environmental studies indicate that at least some AOA have a high substrate affinity for ammonia and are able to grow under extremely oligotrophic conditions. Information from the first available genomes of AOA indicate that their metabolism is fundamentally different from that of their bacterial counterparts, involving a highly copper-dependent system for ammonia oxidation and electron transport, as well as a novel carbon fixation pathway that has recently been discovered in

  8. Global Ecological Pattern of Ammonia-Oxidizing Archaea

    OpenAIRE

    Huiluo Cao; Jean-Christophe Auguet; Ji-Dong Gu

    2013-01-01

    BACKGROUND: The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. METHODOLOGY AND RESULTS: We condu...

  9. Global ecological pattern of ammonia-oxidizing archaea.

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    Huiluo Cao

    Full Text Available BACKGROUND: The global distribution of ammonia-oxidizing archaea (AOA, which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. METHODOLOGY AND RESULTS: We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. CONCLUSION AND SIGNIFICANCE: Based on an up-to-date amoA phylogeny, this

  10. Distribution of Bathyarchaeota (MCG) archaea in the South China Sea sediments and implication of its ecological roles

    Science.gov (United States)

    Tiantian, Y.; Wang, F.; MingYang, N.

    2015-12-01

    Tiantian Yu1,2, Mingyang Niu1,2 and Fengping Wang1,2 1State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai, 200240, China; 2State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China ABSTRACT: Archaea of Bathyarchaeota Phylum (Miscellaneous Crenarchaeotal Group, MCG) are widespread and abundant in various marine and continental environments. However, very little is understood on the metabolisms and ecological roles of this cosmopolitan sedimentary archaea , partly due to obstacles of cultivation. Bathyarchaeota could be divided into large members of subgroups with potentially high genetic heterogeneity, implying different metabolic capabilities and functions in different subgroups. Here, we report our work on investigating Bathyarchaeota abundance and types of subgroups in the South China Sea(SCS) sediments, aim to understand their ecological roles in the carbon cycling. Bathyarchaeota were found the most dominant archaeal group in the sediments of SCS , most of which belong to subgroups MCG-8, MCG-15, MCG-17 and MCG-3. A new pair of 16S rRNA gene primers was designed as the published primers could not cover MCG-15 and MCG-17, which are the most dominant subgroups in the SCS sediments. Comparing with previous primers which used for quantifying the abundance of Bathyarchaeota via Q-PCR, the new primer revealed about an order of magnitude higher abundance in all South China Sea sediments. The relationship of geochemical parameters and MCG subgroups will further be explored to provide the basis for further understanding the metabolic function and biogeochemical roles of these poor-understood sedimentary archaea.

  11. Novel Cardiolipins from Uncultured Methane-Metabolizing Archaea

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    Marcos Y. Yoshinaga

    2012-01-01

    Full Text Available Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noting that cardiolipin analogues from the seep archaeal communities are composed of four isoprenoidal chains, which may contain differences in chain length (20 and 25 carbon atoms and degrees of unsaturation and the presence of a hydroxyl group. Two novel diether lipids, structurally related to the BPGs, are described and interpreted as degradation products of archaeal cardiolipin analogues. Since archaeal communities in seep sediments are dominated by anaerobic methanotrophs, our observations have implications for characterizing structural components of archaeal membranes, in which BPGs are presumed to contribute to modulation of cell permeability properties. Whether BPGs facilitate interspecies interaction in syntrophic methanotrophic consortia remains to be tested.

  12. Distribution of Metabolically Active Prokaryotes (Archaea and Bacteria) throughout the Profiles of Chernozem and Brown Semidesert Soil

    Science.gov (United States)

    Semenov, M. V.; Manucharova, N. A.; Stepanov, A. L.

    2016-02-01

    The distribution of metabolically active cells of archaea and bacteria in the profiles of typical chernozems (Voronezh oblast) and brown semidesert soils (Astrakhan oblast) of natural and agricultural ecosystems was studied using the method of fluorescent in situ hybridization (FISH). The studied soils differed sharply in the microbial biomass and in the numbers of metabolically active cells of archaea and bacteria. The number of active bacterial cells was 3.5-7.0 times greater than that of archaea. In the arable chernozem, the numbers of active cells of archaea and bacteria were 2.6 and 1.5 times, respectively, lower than those in the chernozem under the shelterbelt. The agricultural use of the brown semidesert soil had little effect on the abundances of bacteria and archaea. The soil organic carbon content was the major factor controlling the numbers of metabolically active cells of both domains. However, the dependence of the abundance of bacteria on the organic matter content was more pronounced. The decrease in the organic carbon and total nitrogen contents down the soil profiles was accompanied by the decrease in the bacteria: archaea ratio attesting to a better adaptation of archaea to the permanent deficiency of carbon and nitrogen. The bacteria: archaea ratio can serve as an ecotrophic indicator of the state of soil microbial communities.

  13. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea

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    Inês A. C. ePereira

    2011-04-01

    Full Text Available The number of sequenced genomes of sulfate-reducing organisms (SRO has increased significantly in the recent years, providing an opportunity for a broader perspective into the energy metabolism of such organisms. In this work we carried out a comparative survey of energy metabolism genes found in twenty-five available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H+-pyrophosphatases, complex I homologues, Rnf and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H2, formate, pyruvate, NAD(PH, β-oxidation and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.

  14. Marxism, social metabolism, and ecologically unequal exchange

    OpenAIRE

    MARTÍNEZ ALIER, Joan

    2004-01-01

    Authors working on "industrial metabolism" or "social metabolism" look at the economy in terms of flows of energy and materials. Together with the ecological economists, they see the economy as a subsystem of a larger physical system. Marx and Engels followed with a few years' delay many of the remarkable scientific and technical novelties of their time.

  15. Archaea in biogeochemical cycles.

    Science.gov (United States)

    Offre, Pierre; Spang, Anja; Schleper, Christa

    2013-01-01

    Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored.

  16. Methanogenic archaea

    International Nuclear Information System (INIS)

    This chapter outlines procedures for enumerating, isolating, culturing and storing methanogens from ruminal digesta. The methanogens, a large and diverse group of Archaea, have unique features that separate them from the bacteria and the eukaryotes. They are the only recognized ruminal microbes belonging to the Archaea and are an integral part of the rumen microbial ecosystem. By scavenging hydrogen gas, methanogens play a key ecological role in keeping the partial pressure of hydrogen low so that fermentation can proceed efficiently. Although about 70 methanogenic species belonging to 2 1 genera have been identified from anaerobic environments, and a range of different methanogens co-exist in the rumen, to date only seven ruminal species have been isolated and purified. The population densities of methanogens in the rumen appear to be influenced by diet, and in particular by the fibre content of the diet. Sheep and cattle fed diets rich in concentrates contained 107-108 and 108- 109 ruminal methanogens/g, respectively, whereas sheep and dairy cows grazing pasture contained 109-1010 ruminal methanogens/g (G.N. Jarvis and K.N. Joblin, unpublished data). With careful application, methanogen population densities can readily be determined using culture methods. These appear to be similar to the population densities determined by culture-independent methods (P. Evans and K.N. Joblin, unpublished data)

  17. Bioenergetics of the Archaea

    OpenAIRE

    Schäfer, Günter; Engelhard, Martin; Müller, Volker

    1999-01-01

    In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the mol...

  18. Archaea on human skin.

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    Alexander J Probst

    Full Text Available The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.

  19. Research on metabolic network of extremely halophilic archaea%极端嗜盐古菌代谢网络研究

    Institute of Scientific and Technical Information of China (English)

    丁德武

    2012-01-01

    Extremely halophilic archaea belonging to the euryarchaeota halobium branch, it is a typical population in archaea, and very important to microbial resources. In this article, we mainly study the structure and function of metabolic network about one extremely halophilic archaea: Halobacterium salinarum Rl. We obtain a list of all metabolic reactions in Halobacterium salinarum Rl from published high-quality metabolic models, and represent it with metabolite graph. We analyze functional modules and hubs of the network, and discussed their biological signification.%极端嗜盐古菌(extremely thermophilic archaea)属于广域古菌界盐杆菌科,是古菌域中的典型生理类群,也是重要的极端微生物资源.文章主要对一种极端嗜盐古菌——盐沼盐杆菌(Halobacterium salinarum R1)——代谢网络的结构与功能进行了分析.对高质量盐沼盐杆菌代谢网络数据进行整理,构建了其中所有的代谢反应列表,并用代谢物图来表示.分析了该网络的功能模块和关键节点,并讨论了它们的生物学功能意义.

  20. Archaea in Symbioses

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    Christoph Wrede

    2012-01-01

    Full Text Available During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.

  1. Saccharomyces cerevisiae metabolism in ecological context

    Science.gov (United States)

    Jouhten, Paula; Ponomarova, Olga; Gonzalez, Ramon; Patil, Kiran R.

    2016-01-01

    The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype–metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype–phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype–environment–phenotype relationships. PMID:27634775

  2. Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

    Science.gov (United States)

    Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

    2015-12-01

    Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

  3. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups.

    Directory of Open Access Journals (Sweden)

    Dongying Wu

    Full Text Available With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as "marker" genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ∼30 commonly used, and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible

  4. An urban metabolism and ecological footprint assessment of Metro Vancouver.

    Science.gov (United States)

    Moore, Jennie; Kissinger, Meidad; Rees, William E

    2013-07-30

    As the world urbanizes, the role of cities in determining sustainability outcomes grows in importance. Cities are the dominant form of human habitat, and most of the world's resources are either directly or indirectly consumed in cities. Sustainable city analysis and management requires understanding the demands a city places on a wider geographical area and its ecological resource base. We present a detailed, integrated urban metabolism of residential consumption and ecological footprint analysis of the Vancouver metropolitan region for the year 2006. Our overall goal is to demonstrate the application of a bottom-up ecological footprint analysis using an urban metabolism framework at a metropolitan, regional scale. Our specific objectives are: a) to quantify energy and material consumption using locally generated data and b) to relate these data to global ecological carrying capacity. Although water is the largest material flow through Metro Vancouver (424,860,000 m(3)), it has the smallest ecological footprint (23,100 gha). Food (2,636,850 tonnes) contributes the largest component to the ecological footprint (4,514,400 gha) which includes crop and grazing land as well as carbon sinks required to sequester emissions from food production and distribution. Transportation fuels (3,339,000 m(3)) associated with motor vehicle operation and passenger air travel comprises the second largest material flow through the region and the largest source of carbon dioxide emissions (7,577,000 tonnes). Transportation also accounts for the second largest component of the EF (2,323,200 gha). Buildings account for the largest electricity flow (17,515,150 MWh) and constitute the third largest component of the EF (1,779,240 gha). Consumables (2,400,000 tonnes) comprise the fourth largest component of the EF (1,414,440 gha). Metro Vancouver's total Ecological Footprint in 2006 was 10,071,670 gha, an area approximately 36 times larger than the region itself. The EFA reveals that

  5. [Microbial metabolic characteristics and ecological controlling in petroleum reservoir--a review].

    Science.gov (United States)

    Gao, Peike; Ma, Ting; Liu, Rulin

    2011-06-01

    Petroleum reservoir has a variety of microbes with diverse metabolic characteristics and great diversity. These microbes play an important role in geochemical cycle. Research on their metabolism and ecological relationships enables the understanding of Microbial Enhanced Oil Recovery (MEOR). Based on the present researches, we review the microbial metabolic characteristics and ecological relationships in oil reservoir. PMID:21866693

  6. Archaea on human skin

    OpenAIRE

    Alexander J Probst; Auerbach, Anna K.; Christine Moissl-Eichinger

    2013-01-01

    The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin mi...

  7. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

    OpenAIRE

    Magalhães, Catarina M.; Machado, Ana; Frank-Fahle, Béatrice; Lee, Charles K; Cary, S. Craig

    2014-01-01

    The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Va...

  8. Archaea in Yellowstone Lake

    OpenAIRE

    Kan, Jinjun; Clingenpeel, Scott; Macur, Richard E.; Inskeep, William P.; Lovalvo, Dave; Varley, John; Gorby, Yuri; McDermott, Timothy R.; Nealson, Kenneth

    2011-01-01

    The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (∼51 ...

  9. Functional Encyclopedia of Bacteria and Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Blow, M. J.; Deutschbauer, A. M.; Hoover, C. A.; Lamson, J.; Lamson, J.; Price, M. N.; Waters, J.; Wetmore, K. M.; Bristow, J.; Arkin, A. P.

    2013-03-20

    Bacteria and Archaea exhibit a huge diversity of metabolic capabilities with fundamental importance in the environment, and potential applications in biotechnology. However, the genetic bases of these capabilities remain unclear due largely to an absence of technologies that link DNA sequence to molecular function. To address this challenge, we are developing a pipeline for high throughput annotation of gene function using mutagenesis, growth assays and DNA sequencing. By applying this pipeline to annotate gene function in 50 diverse microbes we hope to discover thousands of new gene functions and produce a proof of principle `Functional Encyclopedia of Bacteria and Archaea?.

  10. Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.

    Directory of Open Access Journals (Sweden)

    Kirill Borziak

    Full Text Available Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs, is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA, which in archaea is typically encoded by two genes (LplA-N and LplA-C, or by a lipoyl(octanoyl transferase (LipB or LipM plus a lipoic acid synthetase (LipA. Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across

  11. Evolution of specialization and ecological character displacement: metabolic plasticity matters.

    NARCIS (Netherlands)

    C.J.M. Egas

    2005-01-01

    An important question in evolutionary biology, especially with respect to herbivorous arthropods, is the evolution of specialization. In a previous paper, the combined evolutionary dynamics of specialization and ecological character displacement was studied, focusing on the role of herbivore foragin

  12. Gene decay in archaea

    Directory of Open Access Journals (Sweden)

    M. W. J. van Passel

    2007-01-01

    Full Text Available The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

  13. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

    Directory of Open Access Journals (Sweden)

    Catarina Maria Magalhães

    2014-09-01

    Full Text Available The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four Dry Valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity. Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA, revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.

  14. Genetic techniques for the archaea.

    Science.gov (United States)

    Farkas, Joel A; Picking, Jonathan W; Santangelo, Thomas J

    2013-01-01

    Genetic techniques for the Archaea have undergone a rapid expansion in complexity, resulting in increased exploration of the role of Archaea in the environment and detailed analyses of the molecular physiology and information-processing systems in the third domain of life. Complementary gains in describing the ever-increasing diversity of archaeal organisms have allowed these techniques to be leveraged in new and imaginative ways to elucidate shared and unique aspects of archaeal diversity and metabolism. In this review, we introduce the four archaeal clades for which advanced genetic techniques are available--the methanogens, halophiles, Sulfolobales, and Thermococcales--with the aim of providing an overall profile of the advantages and disadvantages of working within each clade, as essentially all of the genetically accessible archaeal organisms require unique culturing techniques that present real challenges. We discuss the full repertoire of techniques possible within these clades while highlighting the recent advances that have been made by taking advantage of the most prominent techniques and approaches.

  15. Biology and population ecology of uncultured Archaea in natural environments analyzed by taxon-specific molecular markers = Biología y ecología poblacional de Archaeas no cultivadas en ambientes naturales analizadas mediante marcadores moleculares específicos

    OpenAIRE

    Restrepo Ortiz, Claudia Ximena

    2016-01-01

    Tesi realitzada al Centre d'Estudis Avançats de Blanes (CEAB-CSIC) The annual dynamics of three different ammonia-oxidizing archaea (AOA) ecotypes (amoA gene) and of the SAGMCG-1 (Nitrosotalea-like aquatic Thaumarchaeota) group (16S rRNA gene) were studied by newly designed specific primers and quantitative PCR analysis in a deep oligotrophic high mountain lake (Lake Redon, Limnological Observatory of the Pyrenees, Spain). We observed segregated distributions of the main AOA populations, p...

  16. Biodiversity, ecological determinants, and metabolic exploitation of sourdough microbiota.

    Science.gov (United States)

    De Vuyst, L; Vrancken, G; Ravyts, F; Rimaux, T; Weckx, S

    2009-10-01

    Sourdough is a microbial ecosystem of lactic acid bacteria (LAB) and yeasts in a matrix of mainly cereal flour and water. Culture-dependent and culture-independent microbiological analysis together with metabolite target analyses of different sourdoughs enabled to understand this complex fermentation process. It is difficult to link the species diversity of the sourdough microbiota with the (geographical) type of sourdough and the flour used, although the type and quality of the latter is the main source of autochthonous LAB in spontaneous sourdough fermentations and plays a key role in establishing stable microbial consortia within a short time. Carbohydrate fermentation targeted towards maltose catabolism, the use of external alternative electron acceptors, amino acid transamination reactions, and/or the arginine deiminase pathway are metabolic activities that favour energy production, cofactor (re)cycling, and/or tolerance towards acid stress, and hence contribute to the competitiveness and dominance of certain species of LAB found in sourdoughs. Also, microbial interactions play an important role. The availability of genome sequences for several LAB species that are of importance in sourdough as well as technological advances in the fields of functional genomics, transcriptomics, and proteomics enable new approaches to study sourdough fermentations beyond the single species level and will allow an integral analysis of the metabolic activities and interactions taking place in sourdough. Finally, the implementation of selected starter cultures in sourdough technology is of pivotal importance for the industrial production of sourdoughs to be used as flavour carrier, texture-improving, or health-promoting dough ingredient.

  17. Spatial variation in the ecological relationships among the components of Beijing's carbon metabolic system.

    Science.gov (United States)

    Xia, Linlin; Fath, Brian D; Scharler, Ursula M; Zhang, Yan

    2016-02-15

    In this paper, we construct a spatially explicit model of carbon metabolism for the flows of carbon among the components of an urban area. We used the model to identify spatial heterogeneity in the ecological relationships within a carbon metabolic network. We combined land-use and cover type maps for Beijing from 1990 to 2010 with empirical coefficients and socioeconomic data to quantify the flows. We used utility analysis to determine the ecological relationships between the components of the system and analyzed their changes during urban development. We used ArcGIS to analyze their spatial variation. We found that the positive utilities in Beijing decreased over time and that negative relationships mostly outweighed positive relationships after 2000. The main ecological relationships were distributed throughout the entire urban area before 2000; subsequently, exploitation, control, and mutualism relationships became concentrated in the southeast, leaving competition relationships to dominate the northwest. Mutualism relationships were most common for natural components, but were not stable because they were easily disturbed by urban expansion. Transportation and industrial land and urban land were the most important contributors to exploitation and control relationships and may be important indicators of spatial adjustment. Increasing competition relationships unbalanced the carbon metabolism, and limitations on the area of land available for development and on the water resources led to increasingly serious competition. The results provide an objective basis for planning adjustments to Beijing's land-use patterns to improve its carbon metabolism and reduce carbon emission.

  18. Tropical Archaea: Diversity associated with the surface microlayer of corals

    Science.gov (United States)

    Kellogg, C.A.

    2004-01-01

    Recent 16S rDNA studies have focused on detecting uncultivated bacteria associated with Caribbean reef corals in an effort to address the ecological roles of coral-associated microbes. Reports of Archaea associated with fishes and marine invertebrates raised the question of whether Archaea might also be part of the coral-associated microbial community. DNA analysis of mucus from 3 reef-building species of Caribbean corals, Montastraea annularis complex, Diploria strigosa and D. labyrinthiformis in the US Virgin Islands yielded 34 groups of archaeal 16S ribotypes (defined at the level of 97% similarity). The majority (75%) was most closely matched by BLAST searches to sequences derived from marine water column samples, whereas the remaining ribotypes were most similar to sequences isolated from anoxic environments (15%) and hydrothermal vents (9%). Unlike previous 16S studies of coral-associated Bacteria, the results do not suggest specific associations between particular archaeal sequences and individual coral species. Marine Archaea (Groups I, II and III) in addition to Thermoplasma-like, methanogen, and marine benthic crenarchaeote phylotypes, were detected in the mucus of tropical corals. The finding of sequences from coral-associated Archaea that are closely related to strict and facultative anaerobes, as well as to uncultivated Archaea from other types of anoxic environments, suggests that anaerobic micro-niches may exist in coral mucus layers. Archaea, with their unique biogeochemical capabilities, broaden the scope of possible interactions between corals and their associated microbial communities.

  19. Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation

    Energy Technology Data Exchange (ETDEWEB)

    Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot , Casey M.; Young, VIncent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan A.

    2016-01-19

    Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date analyses of such multi-meta-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites' abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributors. Focusing on two independent vaginal microbiome datasets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that significantly contribute to these predictions. Interestingly, our analysis also detects metabolites for which predicted variation negatively correlates with measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome datasets reveals similar trends,including prediction of bile acid metabolite shifts. This framework is an important first step towards a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease.

  20. Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals.

    Science.gov (United States)

    Balcom, Ian N; Driscoll, Heather; Vincent, James; Leduc, Meagan

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

  1. Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism

    Directory of Open Access Journals (Sweden)

    Ron S. Ronimus

    2003-01-01

    Full Text Available Enzymes of the gluconeogenic/glycolytic pathway (the Embden-Meyerhof-Parnas (EMP pathway, the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle and the Entner-Doudoroff pathway are widely distributed and are often considered to be central to the origins of metabolism. In particular, several enzymes of the lower portion of the EMP pathway (the so-called trunk pathway, including triosephosphate isomerase (TPI; EC 5.3.1.1, glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12/13, phosphoglycerate kinase (PGK; EC 2.7.2.3 and enolase (EC 4.2.1.11, are extremely well conserved and universally distributed among the three domains of life. In this paper, the distribution of enzymes of gluconeogenesis/glycolysis in hyperthermophiles—microorganisms that many believe represent the least evolved organisms on the planet—is reviewed. In addition, the phylogenies of the trunk pathway enzymes (TPIs, GAPDHs, PGKs and enolases are examined. The enzymes catalyzing each of the six-carbon transformations in the upper portion of the EMP pathway, with the possible exception of aldolase, are all derived from multiple gene sequence families. In contrast, single sequence families can account for the archaeal and hyperthermophilic bacterial enzyme activities of the lower portion of the EMP pathway. The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.

  2. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Martinez, Asuncion; Mincer, Tracy J;

    2006-01-01

    Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light......-driven proton translocation across the cell membrane. So far, proteorhodopsin genes have been well documented only in proteobacteria and a few other bacterial groups. Here we report the presence and distribution of proteorhodopsin genes in Archaea affiliated with the order Thermoplasmatales, in the ocean......'s upper water column. The genomic context and phylogenetic relationships of the archaeal and proteobacterial proteorhodopsins indicate its probable lateral transfer between planktonic Bacteria and Archaea. About 10% of the euryarchaeotes in the photic zone contained the proteorhodopsin gene adjacent...

  3. Are There Rab GTPases in Archaea?

    Science.gov (United States)

    Surkont, Jaroslaw; Pereira-Leal, Jose B

    2016-07-01

    A complex endomembrane system is one of the hallmarks of Eukaryotes. Vesicle trafficking between compartments is controlled by a diverse protein repertoire, including Rab GTPases. These small GTP-binding proteins contribute identity and specificity to the system, and by working as molecular switches, trigger multiple events in vesicle budding, transport, and fusion. A diverse collection of Rab GTPases already existed in the ancestral Eukaryote, yet, it is unclear how such elaborate repertoire emerged. A novel archaeal phylum, the Lokiarchaeota, revealed that several eukaryotic-like protein systems, including small GTPases, are present in Archaea. Here, we test the hypothesis that the Rab family of small GTPases predates the origin of Eukaryotes. Our bioinformatic pipeline detected multiple putative Rab-like proteins in several archaeal species. Our analyses revealed the presence and strict conservation of sequence features that distinguish eukaryotic Rabs from other small GTPases (Rab family motifs), mapping to the same regions in the structure as in eukaryotic Rabs. These mediate Rab-specific interactions with regulators of the REP/GDI (Rab Escort Protein/GDP dissociation Inhibitor) family. Sensitive structure-based methods further revealed the existence of REP/GDI-like genes in Archaea, involved in isoprenyl metabolism. Our analysis supports a scenario where Rabs differentiated into an independent family in Archaea, interacting with proteins involved in membrane biogenesis. These results further support the archaeal nature of the eukaryotic ancestor and provide a new insight into the intermediate stages and the evolutionary path toward the complex membrane-associated signaling circuits that characterize the Ras superfamily of small GTPases, and specifically Rab proteins. PMID:27034425

  4. Testing the Role of Microbial Ecology, Redox-Mediated Deep Water Production and Hypersalinity on TEX86: Lipids and 16s Sequences from Archaea and Bacteria in the Water Column and Sediments of Orca Basin

    Science.gov (United States)

    Warren, C.; Romero, I.; Ellis, G.; Goddard, E.; Krishnan, S.; Nigro, L. M.; Super, J. R.; Zhang, Y.; Zhuang, G.; Hollander, D. J.; Pagani, M.

    2014-12-01

    Mesophilic marine archaea and bacteria are known to substantially contribute to the oceanic microbial biomass and play critical roles in global carbon, nitrogen and nutrient cycles. The Orca Basin, a 2400 meter deep bathymetric depression on the continental slope of the north-central Gulf of Mexico, is an ideal environment to examine how redox-dependent biochemical processes control the input and cycling of bacterial and archaea-derived lipid compounds from formation in near-surface water, through secondary recycling processes operating at the redox-transition in the water column, to sedimentary diagenetic processes operating in oxic to anoxic zones within the basin. The lowermost 180 meters of the Orca Basin is characterized by an anoxic, hypersaline brine that is separated from the overlying oxic seawater by a well-defined redox sequence associated with a systematic increasing in salinity from 35 - 250‰. While surface water conditions are viewed as normal marine with a seasonally productive water column, the sub-oxic to anoxic transition zones within the deep-water column and the sediment spans over 200 m allowing the unique opportunity for discrete sampling of resident organisms and lipids. Here we present 16s rRNA sequence data of Bacteria and Archaea collected parallel to GDGT lipid profiles and in situ environmental measurements from the sediment and overlying water column in the intermediate zone of the basin, where movements of chemical transition zones are preserved. We evaluated GDGTs and corresponding taxa across the surface water, chlorophyll maximum, thermocline, and the deep redox boundary, including oxygenation, denitrification, manganese, iron and sulfate reduction zones, to determine if GDGTs are being produced under these conditions and how surface-derived GDGT lipids and the TEX86 signal may be altered. The results have implications for the application of the TEX86 paleotemperature proxy.

  5. Impact of a synbiotic food on the gut microbial ecology and metabolic profiles

    Directory of Open Access Journals (Sweden)

    Candela Marco

    2010-01-01

    Full Text Available Abstract Background The human gut harbors a diverse community of microorganisms which serve numerous important functions for the host wellbeing. Functional foods are commonly used to modulate the composition of the gut microbiota contributing to the maintenance of the host health or prevention of disease. In the present study, we characterized the impact of one month intake of a synbiotic food, containing fructooligosaccharides and the probiotic strains Lactobacillus helveticus Bar13 and Bifidobacterium longum Bar33, on the gut microbiota composition and metabolic profiles of 20 healthy subjects. Results The synbiotic food did not modify the overall structure of the gut microbiome, as indicated by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE. The ability of the probiotic L. helveticus and B. longum strains to pass through the gastrointestinal tract was hypothesized on the basis of real-time PCR data. In spite of a stable microbiota, the intake of the synbiotic food resulted in a shift of the fecal metabolic profiles, highlighted by the Gas Chromatography Mass Spectrometry Solid Phase Micro-Extraction (GC-MS/SPME analysis. The extent of short chain fatty acids (SCFA, ketones, carbon disulfide and methyl acetate was significantly affected by the synbiotic food consumption. Furthermore, the Canonical discriminant Analysis of Principal coordinates (CAP of GC-MS/SPME profiles allowed a separation of the stool samples recovered before and after the consumption of the functional food. Conclusion In this study we investigated the global impact of a dietary intervention on the gut ecology and metabolism in healthy humans. We demonstrated that the intake of a synbiotic food leads to a modulation of the gut metabolic activities with a maintenance of the gut biostructure. In particular, the significant increase of SCFA, ketones, carbon disulfide and methyl acetate following the feeding period suggests potential health

  6. The metabolic theory of ecology: prospects and challenges for plant biology.

    Science.gov (United States)

    Price, Charles A; Gilooly, James F; Allen, Andrew P; Weitz, Joshua S; Niklas, Karl J

    2010-11-01

    The metabolic theory of ecology (MTE) as applied to the plant sciences aims to provide a general synthesis for the structure and functioning of plants from organelles to ecosystems. MTE builds from simple assumptions of individual metabolism to make predictions about phenomena across a wide range of scales, from individual plant structure and function to community dynamics and global nutrient cycles. The scope of its predictions include morphological allometry, biomass partitioning, vascular network design, and life history phenomena at the individual level; size-frequency distributions, population growth rates, and energetic equivalence at the community level; and the flux, turnover and storage of nutrients at the ecosystem level. Here, we provide an overview of MTE, by considering its assumptions and predictions at these different levels of organization and explaining how the model integrates phenomena among all of these scales. We highlight the model's many successes in predicting novel patterns and draw attention to areas in which gaps remain between observations and MTE's assumptions and predictions. Considering the theory as a whole, we argue that MTE has made a significant contribution in furthering our understanding of those unifying aspects of the structure and function of plants, populations, communities, and ecosystems.

  7. On the Response of Halophilic Archaea to Space Conditions

    Directory of Open Access Journals (Sweden)

    Stefan Leuko

    2014-02-01

    Full Text Available Microorganisms are ubiquitous and can be found in almost every habitat and ecological niche on Earth. They thrive and survive in a broad spectrum of environments and adapt to rapidly changing external conditions. It is of great interest to investigate how microbes adapt to different extreme environments and with modern human space travel, we added a new extreme environment: outer space. Within the last 50 years, technology has provided tools for transporting microbial life beyond Earth’s protective shield in order to study in situ responses to selected conditions of space. This review will focus on halophilic archaea, as, due to their ability to survive in extremes, they are often considered a model group of organisms to study responses to the harsh conditions associated with space. We discuss ground-based simulations, as well as space experiments, utilizing archaea, examining responses and/or resistance to the effects of microgravity and UV in particular. Several halophilic archaea (e.g., Halorubrum chaoviator have been exposed to simulated and actual space conditions and their survival has been determined as well as the protective effects of halite shown. Finally, the intriguing potential of archaea to survive on other planets or embedded in a meteorite is postulated.

  8. River basins as social-ecological systems: linking levels of societal and ecosystem water metabolism in a semiarid watershed

    Directory of Open Access Journals (Sweden)

    Violeta Cabello

    2015-09-01

    Full Text Available River basin modeling under complexity requires analytical frameworks capable of dealing with the multiple scales and dimensions of environmental problems as well as uncertainty in the evolution of social systems. Conceptual and methodological developments can now be framed using the wide socio-eco-hydrological approach. We add hierarchy theory into the mix to discuss the conceptualization of river basins as complex, holarchic social-ecological systems. We operationalize the social-ecological systems water metabolism framework in a semiarid watershed in Spain, and add the governance dimension that shapes human-environment reciprocity. To this purpose, we integrate an eco-hydrological model with the societal metabolism accounting scheme for land use, human activity, and water use. We explore four types of interactions: between societal organization and water uses/demands, between ecosystem organization and their water requirements/supplies, between societal metabolism and aquatic ecosystem health, and between water demand and availability. Our results reveal a metabolic pattern of a high mountain rural system striving to face exodus and agricultural land abandonment with a multifunctional economy. Centuries of social-ecological evolution shaping waterscapes through traditional water management practices have influenced the eco-hydrological functioning of the basin, enabling adaptation to aridity. We found a marked spatial gradient on water supply, use pattern, and impact on water bodies from the head to the mouth of the basin. Management challenges posed by the European water regulatory framework as a new driver of social-ecological change are highlighted.

  9. Biosignatures of methanogenic archaea by Confocal Raman Microspectroscopy (CRM)

    OpenAIRE

    Serrano, P.; Hermelink, A.; Lasch, P.; de Vera, J.P.; Böttger, U.; Wagner, D

    2014-01-01

    Methanogenic archaea are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. In particular, methanogens from Siberian permafrost are extremely resistant against different types of environmental stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. Raman spectroscopy is a vibrational spectroscopic technique that ha...

  10. Potential environmental functions of widespread, abundant, uncultured marine archaea

    Science.gov (United States)

    Lloyd, K. G.; Schreiber, L.; Petersen, D. G.; Schramm, A.; Jorgensen, B.

    2012-12-01

    The vast majority of marine subsurface microorganisms are uncultivated, and therefore have unknown metabolisms. Much of the prokaryotes present in the marine subsurface are archaea, and, in turn, much of the archaea fall into the Miscellaneous Crenarchaeotal Group. These organisms are widely distributed globally and are phylogenetically diverse, comprising 17 distinct subgroups, defined by 16S rRNA genes (Kubo et al. 2012). The subgroups do not seem to have any well-defined environmental distribution (i.e., they are all present in different types of marine and terrestrial environments). However, the abundance of sequences from a certain environment type differs among subgroups, and may provide clues to their role in these environments. We sequenced the genome of a single cell of MCG extracted directly from marine sediments. Although coverage was low (~30%), the data quality was high. Conserved genes show that MCG is deeply branching within the newly named "Thaumarchaeota", and contains a complete pathway for the degradation or extracellular proteins. A further search through metagenomic data shows that this process may be widespread in marine sediments. We hypothesize that MCG archaea may be important in anaerobic protein decomposition in marine sediments. Reference Kubo et al., 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments. ISME Journal, in press, doi:10.1038/ismej.2012.37.

  11. Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals

    Science.gov (United States)

    Balcom, Ian N.; Driscoll, Heather; Vincent, James; Leduc, Meagan

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

  12. Ecology

    OpenAIRE

    Pough, F. H.; Andrews, R.M.

    1985-01-01

    We measured the oxygen consumption (aerobic energy cost) and lactic acid production (anaerobic energy cost) of scincid lizards, Chalcides ocellatus, eating domestic crickets. Aerobic metabolism accounted for 90% or more of the total energy cost of subduing and swallowing prey. The time required to subdue and swallow a cricket was linearly correlated with oxygen consumption. Oxygen consumption increased as a power function of cricket mass, but the maximum size of crickets swallowed by the liza...

  13. Ecological network analysis of an urban metabolic system based on input-output tables: model development and case study for Beijing.

    Science.gov (United States)

    Zhang, Yan; Zheng, Hongmei; Fath, Brian D; Liu, Hong; Yang, Zhifeng; Liu, Gengyuan; Su, Meirong

    2014-01-15

    If cities are considered as "superorganisms", then disorders of their metabolic processes cause something analogous to an "urban disease". It is therefore helpful to identify the causes of such disorders by analyzing the inner mechanisms that control urban metabolic processes. Combining input-output analysis with ecological network analysis lets researchers study the functional relationships and hierarchy of the urban metabolic processes, thereby providing direct support for the analysis of urban disease. In this paper, using Beijing as an example, we develop a model of an urban metabolic system that accounts for the intensity of the embodied ecological elements using monetary input-output tables from 1997, 2000, 2002, 2005, and 2007, and use this data to compile the corresponding physical input-output tables. This approach described the various flows of ecological elements through urban metabolic processes and let us build an ecological network model with 32 components. Then, using two methods from ecological network analysis (flow analysis and utility analysis), we quantitatively analyzed the physical input-output relationships among urban components, determined the ecological hierarchy of the components of the metabolic system, and determined the distribution of advantage-dominated and disadvantage-dominated relationships, thereby providing scientific support to guide restructuring of the urban metabolic system in an effort to prevent or cure urban "diseases".

  14. Expansion of the Genomic Encyclopedia of Bacteria and Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Rinke, Christian; Sczyrba, Alex; Malfatti, Stephanie; Lee, Janey; Cheng, Jan-Fang; Stepanauskas, Ramunas; Eisen, Jonathan A.; Hallam, Steven; Inskeep, William P.; Hedlund, Brian P.; Sievert, Stefan M.; Liu, Wen-Tso; Tsiamis, George; Hugenholtz, Philip; Woyke, Tanja

    2011-06-02

    To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed at systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99 percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

  15. Expansion of the Genomic Encyclopedia of Bacteria and Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Rinke, Christian; Sczyrba, Alex; Malfatti, Stephanie; Lee, Janye; Cheng, Jan-Fang; Stepanauskas, Ramunas; Eisen, Jonathan A.; Hallam, Steven; Inskeep, William P.; Hedlund, Brian P.; Sievert, Stefan M.; Liu, Wen-Tso; Tsiamis, George; Hugenholtz, Philip; Woyke, Tanja

    2011-03-20

    To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed to systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

  16. amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China

    OpenAIRE

    Jian eYang; Hongchen eJiang; Hailiang eDong; Huanye eWang; Geng eWu; Weiguo eHou; Weiguo eLiu; Chuanlun eZhang; Yongjuan eSun; Zhongping eLai

    2013-01-01

    All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol we...

  17. Regulated polyploidy in halophilic archaea.

    Directory of Open Access Journals (Sweden)

    Sebastian Breuert

    Full Text Available Polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. We have used two independent methods to determine the genome copy number in halophilic archaea, 1 cell lysis in agarose blocks and Southern blot analysis, and 2 Real-Time quantitative PCR. Fast growing H. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their ploidy is downregulated to 15 copies in early stationary phase. The chromosome copy number is identical in cultures with a twofold lower growth rate, in contrast to the results reported for several other prokaryotic species. Of three additional replicons of H. salinarum, two have a low copy number that is not growth-phase regulated, while one replicon even shows a higher degree of growth phase-dependent regulation than the main replicon. The genome copy number of H. volcanii is similarly high during exponential phase (on average 18 copies/cell, and it is also downregulated (to 10 copies as the cells enter stationary phase. The variation of genome copy numbers in the population was addressed by fluorescence microscopy and by FACS analysis. These methods allowed us to verify the growth phase-dependent regulation of ploidy in H. salinarum, and they revealed that there is a wide variation in genome copy numbers in individual cells that is much larger in exponential than in stationary phase. Our results indicate that polyploidy might be more widespread in archaea (or even prokaryotes in general than previously assumed. Moreover, the presence of so many genome copies in a prokaryote raises questions about the evolutionary significance of this strategy.

  18. Environmental and ecological controls of coral community metabolism on Palmyra Atoll

    Science.gov (United States)

    Koweek, David; Dunbar, Robert B.; Rogers, Justin S.; Williams, Gareth J.; Price, Nichole; Mucciarone, David; Teneva, Lida

    2015-03-01

    Accurate predictions of how coral reefs may respond to global climate change hinge on understanding the natural variability to which these ecosystems are exposed and to which they contribute. We present high-resolution estimates of net community calcification (NCC) and net community production (NCP) from Palmyra Atoll, an uninhabited, near-pristine coral reef ecosystem in the central Pacific. In August-October 2012, we employed a combination of Lagrangian and Eulerian frameworks to establish high spatial (~2.5 km2) and temporal (hourly) resolution coral community metabolic estimates. Lagrangian drifts, all conducted during daylight hours, resulted in NCC estimates of -51 to 116 mmol C m-2 h-1, although most NCC estimates were in the range of 0-40 mmol C m-2 h-1. Lagrangian drift NCP estimates ranged from -7 to 67 mmol C m-2 h-1. In the Eulerian setup, we present carbonate system parameters (dissolved inorganic carbon, total alkalinity, pH, and pCO2) at sub-hourly resolution through several day-night cycles and provide hourly NCC and NCP rate estimates. We compared diel cycles of all four carbonate system parameters to the offshore surface water (0-50 m depth) and show large departures from offshore surface water chemistry. Hourly Eulerian estimates of NCC aggregated over the entire study ranged from 14 to 53 mmol C m-2 h-1, showed substantial variability during daylight hours, and exhibited a diel cycle with elevated NCC in the afternoons and depressed, but positive, NCC at night. The Eulerian NCP range was very high (-55 to 177 mmol C m-2 h-1) and exhibited strong variability during daylight hours. Principal components analysis revealed that NCC and NCP were most closely aligned with diel cycle forcing, whereas the NCC/NCP ratio was most closely aligned with reef community composition. Our analysis demonstrates that ecological community composition is the primary determinant of coral reef biogeochemistry on a near-pristine reef and that reef biogeochemistry is

  19. Comparison of communities of both methane-producing and metabolizing archaea and bacteria in sediments between the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

    Directory of Open Access Journals (Sweden)

    Zhichao eZhou

    2015-02-01

    Full Text Available Communities of methanogens, anaerobic methanotrophic (ANME archaea and aerobic methantrophic bacteria were compared by profiling mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clade 1,2 and Methanomassiliicoccus like groups of methanogens were the most abundant constitutional parts in nSCS sediment samples . Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was completely updated. Mai Po mangrove wetland surface layer exhibited lower diversity than subsurface, but similar community structures were shared in both layers. Quantitative PCR was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4~3.9×106 copies per gram dry weight and of intertidal mudflat (5.5~5.8×106 copies per gram dry weight was observed, but higher abundance (6.9×106 to 1.02×108 copies per gram dry weight was found in subsurface samples of both sediment types. Aerobic methanotrophic bacteria were more abundant in surface layers (6.7~11.1×105 copies per gram dry weight than the subsurface layers (1.2~5.9×105copies per gram dry weight based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal, but fewer abundant pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51×108 copies per g dry weight and pmoA gene (1.56×107 copies per g dry weight.

  20. A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea

    OpenAIRE

    Chistoserdova, Ludmila; Vorholt, Julia A.; Lidstrom, Mary E.

    2005-01-01

    Recent sequencing of the genome and proteomic analysis of a model aerobic methanotrophic bacterium, Methylococcus capsulatus (Bath) has revealed a highly versatile metabolic potential. In parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis.

  1. Serpins in unicellular Eukarya, Archaea, and Bacteria:

    DEFF Research Database (Denmark)

    Roberts, T.H.; Hejgaard, Jørn; Saunders, N.F.W;

    2004-01-01

    in unicellular eukaryotes: the green alga Chlamydomonas reinhardtii, the dinoflagellate Alexandrium tamarense, and the human pathogens Entamoeba spp., Eimera tenella, Toxoplasma gondii, and Giardia lamblia. We compare these sequences to others, particularly those in the complete genome sequences of Archaea...

  2. Where does DNA replication start in archaea?

    OpenAIRE

    Vas, Amit; Leatherwood, Janet

    2000-01-01

    Genome-wide measures of DNA strand composition have been used to find archaeal DNA replication origins. Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication factors are more like those of eukaryotes.

  3. Viruses of the Archaea: a unifying view

    DEFF Research Database (Denmark)

    Prangishvili, David; Forterre, Patrick; Garrett, Roger Antony

    2006-01-01

    DNA viruses of the Archaea have highly diverse and often exceptionally complex morphotypes. Many have been isolated from geothermally heated hot environments, raising intriguing questions about their origins, and contradicting the widespread notion of limited biodiversity in extreme environments...

  4. From metabolism to ecology: cross-feeding interactions shape the balance between polymicrobial conflict and mutualism

    OpenAIRE

    Estrela, Sylvie; Trisos, Christopher H; Brown, Sam P.

    2012-01-01

    Polymicrobial interactions are widespread in nature, and play a major role in maintaining human health and ecosystems. Whenever one organism uses metabolites produced by another organism as energy or nutrient sources, this is called cross-feeding. The ecological outcomes of cross-feeding interactions are poorly understood and potentially diverse: mutualism, competition, exploitation or commensalism. A major reason for this uncertainty is the lack of theoretical approaches linking microbial me...

  5. Diversity and seasonal dynamics of airborne archaea

    Science.gov (United States)

    Fröhlich-Nowoisky, J.; Ruzene Nespoli, C.; Pickersgill, D. A.; Galand, P. E.; Müller-Germann, I.; Nunes, T.; Gomes Cardoso, J.; Almeida, S. M.; Pio, C.; Andreae, M. O.; Conrad, R.; Pöschl, U.; Després, V. R.

    2014-11-01

    Archaea are widespread and abundant in many terrestrial and aquatic environments, and are thus outside extreme environments, accounting for up to ~10% of the prokaryotes. Compared to bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of archaea in the atmosphere. By means of DNA analysis and Sanger sequencing targeting the 16S rRNA (435 sequences) and amoA genes in samples of air particulate matter collected over 1 year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne archaea. The detected archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b) being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase in bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly predicted methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands (72 sequences) and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role in the dispersal of archaea, including assumed ammonia-oxidizing Thaumarchaeota and methanogens.

  6. Lipid metabolism in employees of the Poles'e state radiation-ecological reserve

    International Nuclear Information System (INIS)

    The results of the investigation show significant deviation in indexes of lipid metabolism typical for Chernobyl liquidators and employees of the reserve, living on territories with density of 137Cs contamination exceeding 15 Ci/km2 thus they are at a higher risk of atherosclerosis

  7. Biochemical trade-offs: evidence for ecologically linked secondary metabolism of the sponge Oscarella balibaloi.

    Directory of Open Access Journals (Sweden)

    Julijana Ivanisevic

    Full Text Available Secondary metabolite production is assumed to be costly and therefore the resource allocation to their production should be optimized with respect to primary biological functions such as growth or reproduction. Sponges are known to produce a great diversity of secondary metabolites with powerful biological activities that may explain their domination in some hard substrate communities both in terms of diversity and biomass. Oscarella balibaloi (Homoscleromorpha is a recently described, highly dynamic species, which often overgrows other sessile marine invertebrates. Bioactivity measurements (standardized Microtox assay and metabolic fingerprints were used as indicators of the baseline variations of the O. balibaloi secondary metabolism, and related to the sponge reproductive effort over two years. The bioactivity showed a significant seasonal variation with the lowest values at the end of spring and in early summer followed by the highest bioactivity in the late summer and autumn. An effect of the seawater temperature was detected, with a significantly higher bioactivity in warm conditions. There was also a tendency of a higher bioactivity when O. balibaloi was found overgrowing other sponge species. Metabolic fingerprints revealed the existence of three principal metabolic phenotypes: phenotype 1 exhibited by a majority of low bioactive, female individuals, whereas phenotypes 2 and 3 correspond to a majority of highly bioactive, non-reproductive individuals. The bioactivity was negatively correlated to the reproductive effort, minimal bioactivities coinciding with the period of embryogenesis and larval development. Our results fit the Optimal Defense Theory with an investment in the reproduction mainly shaping the secondary metabolism variability, and a less pronounced influence of other biotic (species interaction and abiotic (temperature factors.

  8. Archaea: From Genomics to Physiology and the Origin of Life

    Science.gov (United States)

    Vothknecht, Ute C.; Tumbula, Debra L.

    1999-01-01

    This document represents a report on a meeting about Archaea. The meeting had an unusually diversified mix of topics all related to Archaea highlighting their differences and similarities with other kingdoms of life. Thus, a large number of scientists from others areas of biology participated in this conference. One-third of the speakers (11 of 33) represented laboratories whose main interests have not been archaea and who have not previously participated in similar symposia or workshops. Thus, this symposium provided a unique opportunity for archaeal researchers to interact in a wider forum. Because of the broad range of topics covered, the conference also introduced many of the participants to new areas of archaeal research. The discussions of genomics, molecular mechanisms of transcription, metabolic pathways and evolution were at a very high level. Talks and posters provided detailed discussions of the state of the current knowledge in RNA processing, transcriptional initiation, chromatin structure, aminoacyl-tRNA synthetases, autotrophic CO2 fixation, Upid biosynthesis and a wide range of other topics. In addition to providing overviews, major areas of scientific argument were clearly delineated, particularly in the discussions of genomics and evolution. Some of the questions raised included: how representative are individual gene trees of organismal evolution, how prevalent is horizontal evolution, how reliable are functional assignments in genomics? On these topics, the different points of view were well represented. The future of any field depends on the enthusiasm and intellectual engagement of young scientists working in the area. Therefore, the participation of 29 graduate and postdoctoral students (out of about 135 participants) was a highlight of the meeting. This was the consequence of funding contributions by NSF and NASA.

  9. Challenges and Opportunities of Long-Term Continuous Stream Metabolism Measurements at the National Ecological Observatory Network

    Science.gov (United States)

    Goodman, K. J.; Lunch, C. K.; Baxter, C.; Hall, R.; Holtgrieve, G. W.; Roberts, B. J.; Marcarelli, A. M.; Tank, J. L.

    2013-12-01

    Recent advances in dissolved oxygen sensing and modeling have made continuous measurements of whole-stream metabolism relatively easy to make, allowing ecologists to quantify and evaluate stream ecosystem health at expanded temporal and spatial scales. Long-term monitoring of continuous stream metabolism will enable a better understanding of the integrated and complex effects of anthropogenic change (e.g., land-use, climate, atmospheric deposition, invasive species, etc.) on stream ecosystem function. In addition to their value in the particular streams measured, information derived from long-term data will improve the ability to extrapolate from shorter-term data. With the need to better understand drivers and responses of whole-stream metabolism come difficulties in interpreting the results. Long-term trends will encompass physical changes in stream morphology and flow regime (e.g., variable flow conditions and changes in channel structure) combined with changes in biota. Additionally long-term data sets will require an organized database structure, careful quantification of errors and uncertainties, as well as propagation of error as a result of the calculation of metabolism metrics. Parsing of continuous data and the choice of modeling approaches can also have a large influence on results and on error estimation. The two main modeling challenges include 1) obtaining unbiased, low-error daily estimates of gross primary production (GPP) and ecosystem respiration (ER), and 2) interpreting GPP and ER measurements over extended time periods. The National Ecological Observatory Network (NEON), in partnership with academic and government scientists, has begun to tackle several of these challenges as it prepares for the collection and calculation of 30 years of continuous whole-stream metabolism data. NEON is a national-scale research platform that will use consistent procedures and protocols to standardize measurements across the United States, providing long

  10. Protein Acetylation in Archaea, Bacteria, and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Jörg Soppa

    2010-01-01

    Full Text Available Proteins can be acetylated at the alpha-amino group of the N-terminal amino acid (methionine or the penultimate amino acid after methionine removal or at the epsilon-amino group of internal lysines. In eukaryotes the majority of proteins are N-terminally acetylated, while this is extremely rare in bacteria. A variety of studies about N-terminal acetylation in archaea have been reported recently, and it was revealed that a considerable fraction of proteins is N-terminally acetylated in haloarchaea and Sulfolobus, while this does not seem to apply for methanogenic archaea. Many eukaryotic proteins are modified by differential internal acetylation, which is important for a variety of processes. Until very recently, only two bacterial proteins were known to be acetylation targets, but now 125 acetylation sites are known for E. coli. Knowledge about internal acetylation in archaea is extremely limited; only two target proteins are known, only one of which—Alba—was used to study differential acetylation. However, indications accumulate that the degree of internal acetylation of archaeal proteins might be underestimated, and differential acetylation has been shown to be essential for the viability of haloarchaea. Focused proteomic approaches are needed to get an overview of the extent of internal protein acetylation in archaea.

  11. Metabolism

    Science.gov (United States)

    ... also influenced by body composition — people with more muscle and less fat generally have higher BMRs. previous continue Things That Can Go Wrong With Metabolism Most of the time your metabolism works effectively ...

  12. Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008255 Serum adiponectin level declines in the elderly with metabolic syndrome.WU Xiaoyan(吴晓琰),et al.Dept Geriatr,Huashan Hosp,Fudan UnivShanghai200040.Chin J Geriatr2008;27(3):164-167.Objective To investigate the correlation between ser-um adiponectin level and metabolic syndrome in the elderly·Methods Sixty-one subjects with metabolic syndrome and140age matched subjects without metabolic

  13. Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.

    Science.gov (United States)

    DeLorenzo, M.E.; Lewitus, A.J.; Scott, G.I.; Ross, P.E.

    2001-10-01

    Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer

  14. ECOLOGY OF PLANT SECONDARY METABOLISM%植物次生代谢生态学

    Institute of Scientific and Technical Information of China (English)

    阎秀峰

    2001-01-01

    @@ 植物次生代谢(Plant secondary metabolism)的概念最早是由Kossel于1891年明确提出的.次生代谢是相对于初生代谢或称基本代谢(Primarymetabolism)而言的.与维持细胞生命活动所必需的初生代谢产物(Primary metabolites)不同,次生代谢产物(Secondary metabolites,也称次生产物、次生物质)是指植物中一大类对于细胞生命活动或植物生长发育正常进行并非必需的小分子有机化合物,这些在植物体内含量不等的化合物均有自己独特的代谢途径,通常由初生代谢派生而来(陈晓亚等,1998).

  15. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

    Directory of Open Access Journals (Sweden)

    Muammar eMansor

    2015-08-01

    Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

  16. The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Ambrust, E.V.; Berges, J.; Bowler, C.; Green, B.; Martinez, D.; Putnam, N.; Zhou, S.; Allen, A.; Apt, K.; Bechner, M.; Brzezinski, M.; Chaal, B.; Chiovitti, A.; Davis, A.; Goodstein, D.; Hadi, M.; Hellsten,U.; Hildebrand, M.; Jenkins, B.; Jurka, J.; Kapitonov, V.; Kroger, N.; Lau, W.; Lane, T.; Larimer, F.; Lippmeier, J.; Lucas, S.; Medina, M.; Montsant, A.; Obornik, M.; Parker, M. Schnitzler; Palenik, B.; Pazour,G.; Richardson, P.; Rynearson, T.; Saito, M.; Schwartz, D.; Thamatrakoln,K.; Valentin, K.; Vardi, A.; Wilkerson, F.; Rokhsar, D.; Vardi, A.; Wilkerson, F.P.; Rokhsar, D.S.

    2004-09-01

    different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.

  17. The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution and Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Armbrust, E V; Berges, J A; Bowler, C; Green, B R; Martinez, D; Putnam, N H; Zhou, S; Allen, A E; Apt, K E; Bechner, M; Brzezinski, M A; Chaal, B K; Chiovitti, A; Davis, A K; Demarest, M S; Detter, J C; del Rio, T G; Goodstein, D; Hadi, M Z; Hellsten, U; Hildebrand, M; Jenkins, B D; Jurka, J; Kapitonov, V V; Kroger, N; Lau, W Y; Lane, T W; Larimer, F W; Lippmeier, J C; Lucas, S; Medina, M; Montsant, A; Obornik, M; Parker, M S; Palenik, B; Pazour, G J; Richardson, P M; Rynearson, T A; Saito, M A; Schwartz, D C; Thamatrakoln, K; Valentin, K; Vardi, A; Wilkerson, F P; Rokhsar, D S

    2005-11-14

    different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.

  18. Archaea: Evolution, Physiology, and Molecular Biology

    DEFF Research Database (Denmark)

    to honor the archaea pioneers Wolfram Zillig and Karl O. Stetter, the book provides a thorough survey of the field from its controversial beginnings to its ongoing expansion to include aspects of eukaryotic biology. The editors have assembled articles from the premier researchers in this rapidly burgeoning...... and technological context, and include accounts of cutting-edge research developments. The book spans archaeal evolution, physiology, and molecular and cellular biology and will be an essential reference for both graduate students and researchers....

  19. Role of microbes in the ecology of marine environment

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; DeSouza, M.J.B.D.; LokaBharathi, P.A.

    Microbes are mostly unicellular microscopic living entities falling under the domains Bacteria, Archaea and Eukarya. They have multiple roles to play in the environment both for their own survival and towards maintaining ecological balance. A few...

  20. Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters.

    Science.gov (United States)

    Reitschuler, Christoph; Hofmann, Katrin; Illmer, Paul

    2016-06-01

    The objectives of this study were to assess abundances and community compositions of Archaea within a heterogeneous set of freshwater systems in the Austrian Alps. Seasonal changes and geographical differences within Archaea, considering abiotic and biotic factors (e.g. temperature, pH, total organic carbon (TOC), NH4 (+), bacteria, fungi), were analysed in this context. Water samples were collected from 8 lakes, 10 creeks and the river Inn in 2014. Qualitative-quantitative data were derived via a comprehensive set of (quantitative) PCR assays and PCR-DGGE (denaturing gradient gel electrophoresis) based methodology, which was evaluated concerning specificity and reliability either previously or in this study. QPCR-derived archaeal abundances reached values of 10(3) copies mL(-1) on average, with a peak in winter-spring ('Cold Peak'), and covered 0-15 % (average: 1 %) of the microbial populations. This peak correlated with significantly raised TOC and low NH4 (+) levels during the cold seasons. Stagnant waters showed significantly higher archaeal abundances and diversities than flowing ones. Among methanogens, Methanosarcinales were the most common order. PCR-DGGE data showed that the archaeal communities were site-specific and could function as an ecological marker, in contrast to the more heterogeneous and unsteady bacterial and fungal community. This is attributable to the highly heterogeneous community of methanogenic Archaea (MA, Euryarchaeota), while only two species, Nitrosopumilus maritimus and Ca. Nitrososphaera gargensis, were found to be the ubiquitous representatives of ammonia-oxidizing Archaea (AOA, Thaumarchaeota) in Alpine freshwaters. This work emphasises the diversity, distribution and seasonality of non-extremophilic Archaea in Alpine freshwaters, with a first insight into their ecophysiological potential. PMID:27002962

  1. Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

    Science.gov (United States)

    Zarsky, Jakub D.; Stibal, Marek; Hodson, Andy; Sattler, Birgit; Schostag, Morten; Hansen, Lars H.; Jacobsen, Carsten S.; Psenner, Roland

    2013-09-01

    The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier.

  2. An intertwined evolutionary history of methanogenic archaea and sulfate reduction.

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    Dwi Susanti

    Full Text Available Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420-dependent sulfite reductase (Fsr where N- and C-terminal halves (Fsr-N and Fsr-C are homologs of F(420H(2 dehydrogenase and dissimilatory sulfite reductase (Dsr, respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP, both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest, carrying a coupled siroheme-[Fe(4-S(4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex, with group I features, a Dsr-type peripheral [Fe(4-S(4] cluster and an additional [Fe(4-S(4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4-S(4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420H(2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago biologically produced sulfide deposit.

  3. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.

    Science.gov (United States)

    Wegener, Gunter; Krukenberg, Viola; Riedel, Dietmar; Tegetmeyer, Halina E; Boetius, Antje

    2015-10-22

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. In marine sediments, AOM is performed by dual-species consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) inhabiting the methane-sulfate transition zone. The biochemical pathways and biological adaptations enabling this globally relevant process are not fully understood. Here we study the syntrophic interaction in thermophilic AOM (TAOM) between ANME-1 archaea and their consortium partner SRB HotSeep-1 (ref. 6) at 60 °C to test the hypothesis of a direct interspecies exchange of electrons. The activity of TAOM consortia was compared to the first ANME-free culture of an AOM partner bacterium that grows using hydrogen as the sole electron donor. The thermophilic ANME-1 do not produce sufficient hydrogen to sustain the observed growth of the HotSeep-1 partner. Enhancing the growth of the HotSeep-1 partner by hydrogen addition represses methane oxidation and the metabolic activity of ANME-1. Further supporting the hypothesis of direct electron transfer between the partners, we observe that under TAOM conditions, both ANME and the HotSeep-1 bacteria overexpress genes for extracellular cytochrome production and form cell-to-cell connections that resemble the nanowire structures responsible for interspecies electron transfer between syntrophic consortia of Geobacter. HotSeep-1 highly expresses genes for pili production only during consortial growth using methane, and the nanowire-like structures are absent in HotSeep-1 cells isolated with hydrogen. These observations suggest that direct electron transfer is a principal mechanism in TAOM, which may also explain the enigmatic functioning and specificity of other methanotrophic ANME-SRB consortia. PMID:26490622

  4. Metabolism

    Science.gov (United States)

    ... a particular food provides to the body. A chocolate bar has more calories than an apple, so ... More Common in People With Type 1 Diabetes Metabolic Syndrome Your Child's Weight Healthy Eating Endocrine System Blood ...

  5. Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology.

    Science.gov (United States)

    Khelaifia, S; Drancourt, M

    2012-09-01

    We herein review the state of knowledge regarding the in vitro and in vivo susceptibility of archaea to antimicrobial agents, including some new molecules. Indeed, some archaea colonizing the human microbiota have been implicated in diseases such as periodontopathy. Archaea are characterized by their broad-spectrum resistance to antimicrobial agents. In particular, their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents interfering with peptidoglycan biosynthesis. Archaea are, however, susceptible to the protein synthesis inhibitor fusidic acid and imidazole derivatives. Also, squalamine, an antimicrobial agent acting on the cell wall, proved effective against human methanogenic archaea. In vitro susceptibility data could be used to design protocols for the decontamination of complex microbiota and the selective isolation of archaea in anaerobic culture. PMID:22748132

  6. Geochemistry and Mixing Drive the Spatial Distribution of Free-living Archaea and Bacteria in Yellowstone Lake

    Directory of Open Access Journals (Sweden)

    Jinjun eKan

    2016-02-01

    Full Text Available Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8 µm, 0.8-3.0 µm, and 3.0-20 µm were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV. Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water to 25:1 (vent water. Microbial population structures (both Bacteria and Archaea were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 & V2 regions of 16S rRNA genes. Nonmetric multidimensional scaling (NMDS analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the Lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon, DOC (dissolved organic carbon, SO42-, O2 and metals were likely the major drivers for microbial population structures, however mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (>3 µm and contained higher predicted OTU richness and microbial diversities (genus level than free-living ones (< 0.8 µm. Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

  7. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.

    Science.gov (United States)

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L; McDermott, Timothy R; Macur, Richard E; Inskeep, William P; Nealson, Kenneth H

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur. PMID:26973602

  8. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

    Science.gov (United States)

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L.; McDermott, Timothy R.; Macur, Richard E.; Inskeep, William P.; Nealson, Kenneth H.

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur. PMID:26973602

  9. Bioenergetic and physiological studies of hyperthermophilic archaea. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, R.M.

    1999-03-01

    This project focuses on physiological and bioenergetic characteristics of two representative hyperthermophilic archaea: Thermococcus litoralis (T{sub opt} 88 C) and Pyrococcus furiosus (T{sub opt} 98 C). Both are obligately anaerobic heterotrophs which grow in the presence or absence of reducible sulfur compounds. T. litoralis was studied in relation to information previously developed for P. furiosus: effect of sulfur reduction on bioenergetics, preferred fermentation patterns, tungsten requirement, etc. A defined medium was developed for T. litoralis consisting of amino acids, vitamins and nucleotides. This serves as the basis for continuous culture studies probing metabolic response to media changes. P. furiosus and T. litoralis have also been found to produce a polysaccharide in the presence of maltose and yeast extract. The composition and chemical structure of this polysaccharide was investigated as well as the metabolic motivation for its production. A novel and, perhaps, primitive intracellular proteolytic complex (previously designated as protease S66) in P. furiosus was isolated and the gene encoding the subunit of the complex was cloned, sequenced and the protease expressed in active form in Eschericia coli. Among other issues, the role of this complex in protein turnover and stress response was examined in the context of this organism in addition to comparing it to other complexes in eubacterial and eukaryotic cells. Biochemical characteristics of the protease have been measured in addition to examining other proteolytic species in P. furiosus.

  10. Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

    Science.gov (United States)

    Ding, Jing; Fu, Liang; Ding, Zhao-Wei; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

    2016-01-01

    The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage. PMID:26394860

  11. A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea

    Directory of Open Access Journals (Sweden)

    Pau Richard N

    2003-12-01

    Full Text Available Abstract Background The transition metal molybdenum is essential for life. Escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an ABC transport system. In E. coli and other Proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor ModE. Results Orthologues of ModE are widespread amongst diverse prokaryotes, but not ubiquitous. We identified probable ModE-binding sites upstream of genes implicated in molybdenum metabolism in green sulphur bacteria and methanogenic Archaea as well as in Proteobacteria. We also present evidence of horizontal transfer of nitrogen fixation genes between green sulphur bacteria and methanogenic Archaea. Conclusions Whereas most of the archaeal helix-turn-helix-containing transcription factors belong to families that are Archaea-specific, ModE is unusual in that it is found in both Archaea and Bacteria. Moreover, its cognate upstream DNA recognition sequence is also conserved between Archaea and Bacteria, despite the fundamental differences in their core transcription machinery. ModE is the third example of a transcriptional regulator with a binding signal that is conserved in Bacteria and Archaea.

  12. Methanogenic Archaea and oral infections – ways to unravel the black box

    Directory of Open Access Journals (Sweden)

    Hans-Peter Horz

    2011-02-01

    Full Text Available Archaea, organisms that make up the third domain of cellular life are members of the human oral microflora. They are strikingly less diverse than oral bacteria and appear to be relatively rare with respect to their numerical abundance. Since they have been exclusively found in association with oral infections such as periodontitis and apical periodontitis and given their unique physiology and energy metabolism, it is highly plausible that they are more than just secondary colonizers of infected areas, but instead are actively involved in the overall poly-microbial infection process. Conversely, it is a highly challenging task to clearly demonstrate their possible active participation – mostly due to the difficulty to grow them in routine microbiology laboratories. This current review points out the importance for understanding the medical impact of methanogens and aims at devising strategies for elucidating the true function of archaea in the oral ecosystem.

  13. Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling

    Energy Technology Data Exchange (ETDEWEB)

    Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.; Hug, Laura A.; Brown, Christopher T.; Wilkins, Michael J.; Frischkorn, Kyle R.; Tringe, Susannah G.; Singh, Andrea; Markillie, Lye Meng; Taylor, Ronald C.; Williams, Kenneth H.; Banfield, Jillian F.

    2015-03-01

    Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within the DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an archaeon from this phylum that is only 0.8 Mb in length and lacks almost all core biosynthetic pathways, but has genes encoding enzymes predicted to interact with bacterial cell walls, consistent with a symbiotic lifestyle. The second new phylum, for which we propose the name Pacearchaeota, was defined based on 46 newly sampled archaeal genomes. This phylum includes the first non-methanogen with an intermediate Type II/III RuBisCO. We also reconstructed a complete (1.24 Mb) genome for another DPANN archaeon, a member of the Diapherotrites phylum. Metabolic prediction and transcriptomic data indicate that this organism has a fermentation-based lifestyle. In fact, genomic analyses consistently indicate lack of recognizable pathways for sulfur, nitrogen, methane, oxygen, and metal cycling, and suggest that symbiotic and fermentation-based lifestyles are widespread across the DPANN superphylum. Thus, as for a recently identified superphylum of bacteria with small genomes and no

  14. Archaea: The First Domain of Diversified Life

    Directory of Open Access Journals (Sweden)

    Gustavo Caetano-Anollés

    2014-01-01

    Full Text Available The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston’s generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.

  15. Diurnally entrained anticipatory behavior in archaea.

    Directory of Open Access Journals (Sweden)

    Kenia Whitehead

    Full Text Available By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal. This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms. The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature on O(2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

  16. Swimming behavior of selected species of Archaea.

    Science.gov (United States)

    Herzog, Bastian; Wirth, Reinhard

    2012-03-01

    The swimming behavior of Bacteria has been studied extensively, at least for some species like Escherichia coli. In contrast, almost no data have been published for Archaea on this topic. In a systematic study we asked how the archaeal model organisms Halobacterium salinarum, Methanococcus voltae, Methanococcus maripaludis, Methanocaldococcus jannaschii, Methanocaldococcus villosus, Pyrococcus furiosus, and Sulfolobus acidocaldarius swim and which swimming behavior they exhibit. The two Euryarchaeota M. jannaschii and M. villosus were found to be, by far, the fastest organisms reported up to now, if speed is measured in bodies per second (bps). Their swimming speeds, at close to 400 and 500 bps, are much higher than the speed of the bacterium E. coli or of a very fast animal, like the cheetah, each with a speed of ca. 20 bps. In addition, we observed that two different swimming modes are used by some Archaea. They either swim very rapidly, in a more or less straight line, or they exhibit a slower kind of zigzag swimming behavior if cells are in close proximity to the surface of the glass capillary used for observation. We argue that such a "relocate-and-seek" behavior enables the organisms to stay in their natural habitat.

  17. A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria

    International Nuclear Information System (INIS)

    The sensitivity of nitrifiers to crude oil released by the BP Deepwater Horizon oil spill in Gulf of Mexico was examined using characterized ammonia-oxidizing bacteria and archaea to develop a bioassay and to gain further insight into the ecological response of these two groups of microorganisms to marine oil spills. Inhibition of nitrite production was observed among all the tested ammonia-oxidizing organisms at 100 ppb crude oil. Nitrosopumilus maritimus, a cultured representative of the abundant Marine Group I Archaea, showed 20% inhibition at 1 ppb, a much greater degree of sensitivity to petroleum than the tested ammonia-oxidizing and heterotrophic bacteria. The differing susceptibility may have ecological significance since a shift to bacterial dominance in response to an oil spill could potentially persist and alter trophic interactions influenced by availability of different nitrogen species. - Oil spills potentially induce a change of major nitrifying prokaryotes from the archaea to the bacteria.

  18. Astrobiological studies with extremely halophilic Archaea

    Science.gov (United States)

    Fendrihan, S.; Lotter, H. Stan

    2007-08-01

    Extremely halophilic Archaea were isolated and characterized by both classical and modern molecular biological methods from hypersaline and haloalkaline lakes, salted soils, solar salterns and rock salt deposits (1). The survival of these micro-organisms after embedding in laboratory-made halite was investigated. Their presence in fluid inclusions was demonstrated by staining with the BacLight LIVE/DEAD kit and observation of their fluorescence by microscopy. Following resuspension of cells from halite crystals, a survival of about 0.5 - 4% according to colony forming units was obtained. In previous studies which focussed on the resistance of halophilic archaea to UV radiation or the space environment, survival of a dose of 110 J/m2 (using liquid cultures) and up to 10 000 J/m2 at a range of 200 - 400 nm was reported, when dried Haloarcula sp. in a single layer were exposed on the Biopan facility (2). We exposed a few haloarchaeal strains to a Martian UV simulator lamp with a range of 200 - 400 nm and an intensity of 41.2 W/m2, obtaining a viability of about 51- 67% of cells following different exposure times. Other studies focus on the detection of haloarchaea in halite by Raman microspectroscopy and by NIR-FT-Raman spectroscopy, which are considered to be important future tools for Mars exploration (3). Using the Dilor XY Raman spectrometer with laser excitation at 514.5 nm, equipped with a confocal microscope BX40 (Olympus Corp., Japan) and a Bruker IFS 66 + FRA106 with laser excitation at 1064 nm (Bruker, Germany), instruments, we obtained characteristic carotenoid peaks contained by these microorganisms. 1. Fendrihan S., Legat A., Pfaffenhuemer M., Gruber C., Weidler G., Gerbl F. Stan Lotter H. (2006) Extremely halophilic archaea and the issue of long-term microbial survival. Review. Environ. Sci. Biotechnol. 5: 203-218. 2. Mancinelli R. L., White M. R., Rothschild L. J. (1998) Biopan survival I : exposure of the osmophiles Synechococcus sp. (Nägeli) and

  19. Ecological network analysis for carbon metabolism of eco-industrial parks: a case study of a typical eco-industrial park in Beijing.

    Science.gov (United States)

    Lu, Yi; Chen, Bin; Feng, Kuishuang; Hubacek, Klaus

    2015-06-16

    Energy production and industrial processes are crucial economic sectors accounting for about 62% of greenhouse gas (GHG) emissions globally in 2012. Eco-industrial parks are practical attempts to mitigate GHG emissions through cooperation among businesses and the local community in order to reduce waste and pollution, efficiently share resources, and help with the pursuit of sustainable development. This work developed a framework based on ecological network analysis to trace carbon metabolic processes in eco-industrial parks and applied it to a typical eco-industrial park in Beijing. Our findings show that the entire metabolic system is dominated by supply of primary goods from the external environment and final demand. The more carbon flows through a sector, the more influence it would exert upon the whole system. External environment and energy providers are the most active and dominating part of the carbon metabolic system, which should be the first target to mitigate emissions by increasing efficiencies. The carbon metabolism of the eco-industrial park can be seen as an evolutionary system with high levels of efficiency, but this may come at the expense of larger levels of resilience. This work may provide a useful modeling framework for low-carbon design and management of industrial parks.

  20. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

    Science.gov (United States)

    Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; Berthrong, Sean; Buckley, Daniel H.

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  1. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

    Directory of Open Access Journals (Sweden)

    Charles ePepe-Ranney

    2016-05-01

    Full Text Available We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP. Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs, respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

  2. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil.

    Science.gov (United States)

    Pepe-Ranney, Charles; Campbell, Ashley N; Koechli, Chantal N; Berthrong, Sean; Buckley, Daniel H

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  3. HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea

    DEFF Research Database (Denmark)

    Jørgensen, Mikkel G; Pandey, Deo P; Jaskolska, Milena;

    2009-01-01

    Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins...

  4. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

    Directory of Open Access Journals (Sweden)

    Xuefeng ePeng

    2013-07-01

    Full Text Available Ammonia-oxidizing archaea (AOA have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs, where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA. The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP AOA assemblages was investigated using principal component analysis (PCA and redundancy analysis (RDA. In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.

  5. Experimental fossilisation of viruses from extremophilic Archaea

    Directory of Open Access Journals (Sweden)

    F. Orange

    2011-06-01

    Full Text Available The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 – Sulfolobus islandicus rod-shaped virus 2, TPV1 – Thermococcus prieurii virus 1, and PAV1 – Pyrococcus abyssi virus 1. Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles.

  6. amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China

    Directory of Open Access Journals (Sweden)

    Jian eYang

    2013-11-01

    Full Text Available All known ammonia-oxidizing archaea (AOA belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of AEA in freshwater lakes have been well-studied, little is known about amoA gene-encoding archaea (AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai-Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g/L. The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g/L. The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.

  7. AN ANALYSIS OF HATCHLING RESTING METABOLISM - IN SEARCH OF ECOLOGICAL CORRELATES THAT EXPLAIN DEVIATIONS FROM ALLOMETRIC RELATIONS

    NARCIS (Netherlands)

    KLAASSEN, M; DRENT, R

    1991-01-01

    From data in the literature, an allometric equation is compiled for hatchling resting metabolic rate and an attempt is made to explain residual variation in terms of hatchling type, yolk and water content, embryonic and postnatal growth rate, and environmental circumstances (latitudinal distribution

  8. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat

    Directory of Open Access Journals (Sweden)

    Steven J Biller

    2012-07-01

    Full Text Available Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA, with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.

  9. Archaea and Bacteria in deep lake hypolimnion: in situ dark inorganic carbon uptake

    Directory of Open Access Journals (Sweden)

    Cristiana Callieri

    2014-02-01

    Full Text Available The interest for microorganisms inhabiting the hypolimnion and for their role in biogeochemical cycles of lakes is considerable, but knowledge is far from complete. The presence of chemolithoautotrophic Bacteria and mesophilic Archaea (e.g., Thaumarchaeota assimilating inorganic carbon in the deep hypolimnion of lakes has been ascertained. We measured, for the first time at 350 m in Lake Maggiore (Northern Italy, the prokaryotic in situ dark [14C]HCO3 incorporation with a new custom-made apparatus, which takes samples and adds tracers in situ. Thereby stress factors affecting prokaryotes during sample recovery from the depth were avoided. We tested the new instrument at different depths and conditions, performing parallel conventional on board incubations. We found that dark [14C]HCO3 incorporations had lower standard deviation in in situ incubations with respect to the on board ones, but their means were not statistically different. At 350 m we estimated an uptake of 187.7±15 μg C m–3 d–1, which is in line with the published uptake rates in aquatic systems. By inhibiting the bacterial metabolism, we found that Archaea were responsible for 28% of the total CO2 uptake. At the same depth, Thaumarchaeota, on average, constituted 11% of total DAPI counts. Dark [14C]HCO3 incorporation integrated along the aphotic water column was 65.8±5.2 mg C m–2 d–1 which corresponds to 87% of picophytoplanktonic autotrophic fixation in the euphotic layer. This study provides the first evidence of Bacteria and Archaea dark CO2 fixation in the deep hypolimnion of a subalpine lake and indicates a potentially significant prokaryotic CO2 sink.

  10. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens

    Directory of Open Access Journals (Sweden)

    Éric Bapteste

    2005-01-01

    Full Text Available We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO2 are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO2, formate, acetate, methylated C-1 compounds, these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.

  11. Phylogenetic and functional analysis of metagenome sequence from high-temperature archaeal habitats demonstrate linkages between metabolic potential and geochemistry

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-05-01

    Full Text Available Geothermal habitats in Yellowstone National Park (YNP provide an unparalled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40-45 Mbase Sanger sequencing per site was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G+C content and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH. These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high temperature systems of YNP.

  12. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

    Science.gov (United States)

    Inskeep, William P; Jay, Zackary J; Herrgard, Markus J; Kozubal, Mark A; Rusch, Douglas B; Tringe, Susannah G; Macur, Richard E; Jennings, Ryan deM; Boyd, Eric S; Spear, John R; Roberto, Francisco F

    2013-01-01

    Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.

  13. Halophilic archaea on Earth and in space: growth and survival under extreme conditions.

    Science.gov (United States)

    Oren, Aharon

    2014-12-13

    Salts are abundant on Mars, and any liquid water that is present or may have been present on the planet is expected to be hypersaline. Halophilic archaea (family Halobacteriaceae) are the microorganisms best adapted to life at extremes of salinity on Earth. This paper reviews the properties of the Halobacteriaceae that may make the group good candidates for life also on Mars. Many species resist high UV and gamma radiation levels; one species has survived exposure to vacuum and radiation during a space flight; and there is at least one psychrotolerant species. Halophilic archaea may survive for millions of years within brine inclusions in salt crystals. Many species have different modes of anaerobic metabolism, and some can use light as an energy source using the light-driven proton pump bacteriorhodopsin. They are also highly tolerant to perchlorate, recently shown to be present in Martian soils, and some species can even use perchlorate as an electron acceptor to support anaerobic growth. The presence of characteristic carotenoid pigments (α-bacterioruberin and derivatives) makes the Halobacteriaceae easy to identify by Raman spectroscopy. Thus, if present on Mars, such organisms may be detected by Raman instrumentation planned to explore Mars during the upcoming ExoMars mission. PMID:25368347

  14. Genomic Analysis of Deeply-Branching Bacteria and Archaea from IODP Leg 347: Baltic Sea Paleoenvironment

    Science.gov (United States)

    Bird, J. T.; Lloyd, K. G.

    2014-12-01

    Among the diverse inhabitants of the marine subsurface are "deeply-branching" bacteria and archaea, whose recent evolutionary ancestors have eluded isolation and characterization by traditional culture-based methods. By using single-cell genomics, we were able to target members of common deeply-branching mircorganisms found in a sediment core acquired during IODP Leg 347. Cells were separated from sediment layers (37 and 84 meters below the seafloor) deposited at site 60, hole B, near Anholt Island tens to hundreds of thousands of years ago. Ten single amplified genomes from 4 bacterial and 1 archaeal lineages were chosen from the 60 successfully sorted cells. The lineages include: Desulfobacterium sp., OPB41, OP8, NT-B2, Marine Group II archaea. Two lineages have not been genomically sampled before, while all 5 are frequently found in a variety of marine sediment habitats. The genome assemblies range in completeness from 45 - 85% and contain a number of phylogenetically relevant genes that has helped to anchor their position in the tree of life. The metabolic strategies, including putative sulfate reduction and carbon degradation pathways, employed by these cells have allowed them to survive in an environment with diminishing sources of labile carbon substrates.

  15. Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal

    NARCIS (Netherlands)

    Verhaart, M.R.A.; Bielen, A.A.M.; Oost, van der J.; Stams, A.J.M.; Kengen, S.W.M.

    2010-01-01

    Hydrogen produced from biomass by bacteria and archaea is an attractive renewable energy source. However, to make its application more feasible, microorganisms are needed with high hydrogen productivities. For several reasons, hyperthermophilic and extremely thermophilic bacteria and archaea are pro

  16. In-Vitro Archaeacidal Activity of Biocides against Human-Associated Archaea

    OpenAIRE

    Saber Khelaifia; Jean Michel Brunel; Michel Drancourt

    2013-01-01

    BACKGROUND: Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea. METHODOLOGY: The minimal archaeacidal concentration (MAC) of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea inclu...

  17. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China

    Science.gov (United States)

    Zu, Qianhui; Zhong, Linghao; Deng, Ye; Shi, Yu; Wang, Baozhan; Jia, Zhongjun; Lin, Xiangui; Feng, Youzhi

    2016-01-01

    Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology. PMID:27679621

  18. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China.

    Science.gov (United States)

    Zu, Qianhui; Zhong, Linghao; Deng, Ye; Shi, Yu; Wang, Baozhan; Jia, Zhongjun; Lin, Xiangui; Feng, Youzhi

    2016-01-01

    Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology. PMID:27679621

  19. Hyperthermophilic archaea produce membrane vesicles that can transfer DNA

    NARCIS (Netherlands)

    Gaudin, M.; Gauliard, E.; Schouten, S.; Houel-Renault, L.; Lenormand, P.; Marguet, E.; Forterre, P.

    2013-01-01

    Thermococcales are hyperthermophilic archaea found in deep-sea hydrothermal vents. They have been recently reported to produce membrane vesicles (MVs) into their culture medium. Here, we have characterized the mode of production and determined the biochemical composition of MVs from two species of T

  20. Molecular characterization of hydrolytic enzymes from hyperthermophilic archaea.

    NARCIS (Netherlands)

    Voorhorst, W.G.B.

    1998-01-01

    Hyperthermophiles are recently discovered microorganisms which are able to grow optimally above 85 °C. Most hyperthermophiles belong to the Archaea, the third domain of life. One of the main interests in hyperthermophiles to deepen the insight in the way their proteins are stabilized and how to appl

  1. Engineering of ß-glycosidases from hyperthermophilic Archaea

    NARCIS (Netherlands)

    Kaper, T.

    2001-01-01

    Hyperthermophilic Archaea are microorganisms that grow optimally above 80°C. To be able to live at these temperature extremes their cell components display extreme resistance towards thermal degradation. This characteristic is an attractive feature for use of their

  2. Archaea were widespread in sediments of the Messinian Salinity Crisis

    Science.gov (United States)

    Birgel, Daniel; Peckmann, Jörn

    2015-04-01

    The Messinian salinity crisis (MSC) was among the most extreme and short-lived paleooceanographic events in Earth history and dramatically impacted the depositional environments of the Mediterranean. Many of the Messinian sedimentary sequences reflect environmental variability on extremely short time scales, typified by phenomena like evaporation and high salinities, anoxia, and desiccation. Only few organisms tolerate such severe conditions. Among those are archaea, many of which are especially well adapted to extreme conditions. We studied various MSC locations and deposits to shed light onto the role of archaea in the MSC, focusing on lipid biomarkers. These are (1) primary gypsum with abundant, yet problematic filamentous microfossils from various locations in the Mediterranean, (2) Calcare di Base, limestones from Sicily and Calabria, and (3) Calcare Solfifero, authigenic carbonates associated with native sulfur from Sicily. (1) Primary gypsum beds with abundant filamentous fossils are widespread in the Mediterranean. Archaea were found as important contributor of organic matter in these evaporites. The filaments, however, have previously been interpreted to represent cyanobacteria based on the extraction and amplification of cyanobacterial DNA. Cyanobacteria produce specific and long-lasting biomarkers, but no such compounds were found in the studied deposits, thus, the assignment of the filaments to cyanobacteria necessitates further verification. (2) The Calcare di Base are widespread, genetically heterogeneous Messinian limestones, which are particularly common in Sicily and Calabria. The environmental conditions during their deposition, as well as mechanisms and timing of formation are a matter of debate. The studied Calcare di Base samples were found to contain specific halophilic archaeal signatures and numerous pseudomorphs after halite. (3) The Calcare Solfifero, authigenic carbonates accompanied by elemental sulfur formed in the course of microbial

  3. Copepod community growth rates in relation to body size, temperature, and food availability in the East China Sea: a test of metabolic theory of ecology

    Directory of Open Access Journals (Sweden)

    K. Y. Lin

    2012-11-01

    Full Text Available Zooplankton play an essential role in marine food webs and understanding how community-level growth rates of zooplankton vary in the field is critical for predicting how marine ecosystem function may vary in the face of environmental changes. Here, we used the artificial cohort method to examine the effects of temperature, body size, and chlorophyll concentration (a proxy for food on weight-specific growth rates for copepod communities in the East China Sea. Specifically, we tested the hypothesis that copepod community growth rates can be described by the metabolic theory of ecology (MTE, linking spatio-temporal variation of copepod growth rate with temperature and their body size. Our results generally agree with predictions made by the MTE and demonstrate that weight-specific growth rates of copepod communities in our study area are positively related with temperature and negatively related to body size. However, the regression coefficients of body size do not approach the theoretical predictions. Furthermore, we find that the deviation from the MTE predictions may be partly attributed to the effect of food availability (which is not explicitly accounted for by the MTE. In addition, significant difference in the coefficients of temperature and body size exists among taxonomic groups. Our results suggest that considering the effects of food limitation and taxonomy is necessary to better understand copepod growth rates under in situ conditions, and such effects on the MTE-based prediction needs further investigation.

  4. Copepod community growth rates in relation to body size, temperature, and food availability in the East China Sea: a test of metabolic theory of ecology

    Science.gov (United States)

    Lin, K. Y.; Sastri, A. R.; Gong, G. C.; Hsieh, C. H.

    2013-03-01

    Zooplankton play an essential role in marine food webs, and understanding how community-level growth rates of zooplankton vary in the field is critical for predicting how marine ecosystem function may vary in the face of environmental changes. Here, we used the artificial cohort method to examine the effects of temperature, body size, and chlorophyll concentration (a proxy for food) on weight-specific growth rates for copepod communities in the East China Sea. Specifically, we tested the hypothesis that copepod community growth rates can be described by the metabolic theory of ecology (MTE), linking spatio-temporal variation of copepod growth rate with temperature and their body size. Our results generally agree with predictions made by the MTE and demonstrate that weight-specific growth rates of copepod communities in our study area are positively related with temperature and negatively related to body size. However, the regression coefficients of body size do not approach the theoretical predictions. Furthermore, we find that the deviation from the MTE predictions may be partly attributed to the effect of food availability (which is not explicitly accounted for by the MTE). In addition, significant difference in the coefficients of temperature and body size exists among taxonomic groups. Our results suggest that considering the effects of food limitation and taxonomy is necessary to better understand copepod growth rates under in situ conditions, and such effects on the MTE-based predictions need further investigation.

  5. Copepod community growth rates in relation to body size, temperature, and food availability in the East China Sea: a test of metabolic theory of ecology

    Directory of Open Access Journals (Sweden)

    K. Y. Lin

    2013-03-01

    Full Text Available Zooplankton play an essential role in marine food webs, and understanding how community-level growth rates of zooplankton vary in the field is critical for predicting how marine ecosystem function may vary in the face of environmental changes. Here, we used the artificial cohort method to examine the effects of temperature, body size, and chlorophyll concentration (a proxy for food on weight-specific growth rates for copepod communities in the East China Sea. Specifically, we tested the hypothesis that copepod community growth rates can be described by the metabolic theory of ecology (MTE, linking spatio-temporal variation of copepod growth rate with temperature and their body size. Our results generally agree with predictions made by the MTE and demonstrate that weight-specific growth rates of copepod communities in our study area are positively related with temperature and negatively related to body size. However, the regression coefficients of body size do not approach the theoretical predictions. Furthermore, we find that the deviation from the MTE predictions may be partly attributed to the effect of food availability (which is not explicitly accounted for by the MTE. In addition, significant difference in the coefficients of temperature and body size exists among taxonomic groups. Our results suggest that considering the effects of food limitation and taxonomy is necessary to better understand copepod growth rates under in situ conditions, and such effects on the MTE-based predictions need further investigation.

  6. Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.

    Science.gov (United States)

    Erkel, Christoph; Kube, Michael; Reinhardt, Richard; Liesack, Werner

    2006-07-21

    Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere. PMID:16857943

  7. Changes of Key Enzymes in Sucrose Metabol ism of Flue-cured Tobacco in Different Ecological Regions%不同生态区烤烟蔗糖代谢关键酶活性的变化

    Institute of Scientific and Technical Information of China (English)

    任竹; 赵会纳; 曾陨涛; 元野; 韦成才; 冯小芽; 冯先情; 李伟鹏; 雷波

    2014-01-01

    为了解不同生态区与烤烟蔗糖代谢关键酶活性变化的差异,采集关键生产时期K326的烟样,对不同生态区烟叶的蔗糖代谢关键酶活性进行测定与分析。结果表明:淀粉酶(AMS)、蔗糖合成酶(SS)与不同生态区之间和不同生长时期间的差异均达到极显著水平,生态区与生长时期的交互作用对淀粉酶(AMS)、蔗糖磷酸合成酶(SPS)、蔗糖合成酶(SS)活性的影响均达极显著水平。%In order to explore the changes of key enzymes in sucrose metabolism of flue-cured tobacco in different ecological regions,the key enzymes activity in sucrose metabolism of K326 flue-cured tobacco collected in key production period from different ecological regions was detected and analyzed.Results:the difference of AMS and SS in different ecological region and growth stage reached extremely significant level.The interaction of ecological region and growth stage had very significant influence on AMS,SPS and SS.

  8. Patterns of ^(15)N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS

    OpenAIRE

    Orphan, Victoria J; Turk, Kendra A.; Green, Abigail M.; House, Christopher H.

    2009-01-01

    Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary i...

  9. Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors.

    Science.gov (United States)

    Duardo-Sánchez, Aliuska; Munteanu, Cristian R; Riera-Fernández, Pablo; López-Díaz, Antonio; Pazos, Alejandro; González-Díaz, Humberto

    2014-01-27

    The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order k(th) (W(k)). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the W(k)(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated W

  10. [Ecology and ecologies].

    Science.gov (United States)

    Valera, Luca

    2011-01-01

    Ecology (from the Greek words οιχοσ, "house" and λογια "study of") is the science of the "house", since it studies the environments where we live. There are three main ways of thinking about Ecology: Ecology as the study of interactions (between humans and the environment, between humans and living beings, between all living beings, etc.), Ecology as the statistical study of interactions, Ecology as a faith, or rather as a science that requires a metaphysical view. The history of Ecology shows us how this view was released by the label of "folk sense" to gain the epistemological status of science, a science that strives to be interdisciplinary. So, the aim of Ecology is to study, through a scientific methodology, the whole natural world, answering to very different questions, that arise from several fields (Economics, Biology, Sociology, Philosophy, etc.). The plurality of issues that Ecology has to face led, during the Twentieth-century, to branch off in several different "ecologies". As a result, each one of these new approaches chose as its own field a more limited and specific portion of reality.

  11. The ecology of coral-microbe interactions

    OpenAIRE

    Marhaver, Kristen Laura

    2010-01-01

    At every moment, a tropical reef coral interacts with millions of microbial organisms from tens of thousands of different species. Among these viruses, bacteria, archaea, dinoflagellates, and protists are cooperative symbionts as well as pathogens and parasites. Each interaction between a coral and a microscopic organism has ecological consequences for the coral community. In this dissertation, I show that juveniles of the Caribbean coral Montastraea faveolata suffer distance-dependent mortal...

  12. Widespread Disulfide Bonding in Proteins from Thermophilic Archaea

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    Julien Jorda

    2011-01-01

    Full Text Available Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.

  13. An ecological analysis of the herbivory-elicited JA burst and its metabolism: plant memory processes and predictions of the moving target model.

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    William Stork

    Full Text Available BACKGROUND: Rapid herbivore-induced jasmonic acid (JA accumulation is known to mediate many induced defense responses in vascular plants, but little is known about how JA bursts are metabolized and modified in response to repeated elicitations, are propagated throughout elicited leaves, or how they directly influence herbivores. METHODOLOGY/PRINCIPAL FINDINGS: We found the JA burst in a native population of Nicotiana attenuata to be highly robust despite environmental variation and we examined the JA bursts produced by repeated elicitations with Manduca sexta oral secretions (OS at whole- and within-leaf spatial scales. Surprisingly, a 2(nd OS-elicitation suppressed an expected JA burst at both spatial scales, but subsequent elicitations caused more rapid JA accumulation in elicited tissue. The baseline of induced JA/JA-Ile increased with number of elicitations in discrete intervals. Large veins constrained the spatial spread of JA bursts, leading to heterogeneity within elicited leaves. 1(st-instar M. sexta larvae were repelled by elicitations and changed feeding sites. JA conjugated with isoleucine (JA-Ile translates elicitations into defense production (e.g., TPIs, but conjugation efficiency varied among sectors and depended on NaWRKY3/6 transcription factors. Elicited TPI activity correlated strongly with the heterogeneity of JA/JA-Ile accumulations after a single elicitation, but not repeated elicitations. CONCLUSIONS/SIGNIFICANCE: Ecologically informed scaling of leaf elicitation reveals the contribution of repeated herbivory events to the formation of plant memory of herbivory and the causes and importance of heterogeneity in induced defense responses. Leaf vasculature, in addition to transmitting long-distance damage cues, creates heterogeneity in JA bursts within attacked leaves that may be difficult for an attacking herbivore to predict. Such unpredictability is a central tenet of the Moving Target Model of defense, which posits that

  14. Classification of Bacteria and Archaea: past, present and future.

    Science.gov (United States)

    Schleifer, Karl Heinz

    2009-12-01

    The late 19th century was the beginning of bacterial taxonomy and bacteria were classified on the basis of phenotypic markers. The distinction of prokaryotes and eukaryotes was introduced in the 1960s. Numerical taxonomy improved phenotypic identification but provided little information on the phylogenetic relationships of prokaryotes. Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977. The current classification of Bacteria and Archaea is based on an operational-based model, the so-called polyphasic approach, comprised of phenotypic, chemotaxonomic and genotypic data, as well as phylogenetic information. The provisional status Candidatus has been established for describing uncultured prokaryotic cells for which their phylogenetic relationship has been determined and their authenticity revealed by in situ probing. The ultimate goal is to achieve a theory-based classification system based on a phylogenetic/evolutionary concept. However, there are currently two contradictory opinions about the future classification of Bacteria and Archaea. A group of mostly molecular biologists posits that the yet-unclear effect of gene flow, in particular lateral gene transfer, makes the line of descent difficult, if not impossible, to describe. However, even in the face of genomic fluidity it seems that the typical geno- and phenotypic characteristics of a taxon are still maintained, and are sufficient for reliable classification and identification of Bacteria and Archaea. There are many well-defined genotypic clusters that are congruent with known species delineated by polyphasic approaches. Comparative sequence analysis of certain core genes, including rRNA genes, may be useful for the characterization of higher taxa, whereas various character genes may be suitable as phylogenetic markers for the delineation of lower taxa. Nevertheless, there may still be

  15. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    OpenAIRE

    Vidya eDe Gannes; Gaius eEudoxie; Dyer, David H.; William James Hickey

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  16. Stable Carbon Isotope Fractionation by Methylotrophic Methanogenic Archaea

    OpenAIRE

    Penger, Jörn; Conrad, Ralf; Blaser, Martin

    2012-01-01

    In natural environments methane is usually produced by aceticlastic and hydrogenotrophic methanogenic archaea. However, some methanogens can use C1 compounds such as methanol as the substrate. To determine the contributions of individual substrates to methane production, the stable-isotope values of the substrates and the released methane are often used. Additional information can be obtained by using selective inhibitors (e.g., methyl fluoride, a selective inhibitor of acetoclastic methanoge...

  17. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  18. Carotenoid Production by Halophilic Archaea Under Different Culture Conditions.

    Science.gov (United States)

    Calegari-Santos, Rossana; Diogo, Ricardo Alexandre; Fontana, José Domingos; Bonfim, Tania Maria Bordin

    2016-05-01

    Carotenoids are pigments that may be used as colorants and antioxidants in food, pharmaceutical, and cosmetic industries. Since they also benefit human health, great efforts have been undertaken to search for natural sources of carotenoids, including microbial ones. The optimization of culture conditions to increase carotenoid yield is one of the strategies used to minimize the high cost of carotenoid production by microorganisms. Halophilic archaea are capable of producing carotenoids according to culture conditions. Their main carotenoid is bacterioruberin with 50 carbon atoms. In fact, the carotenoid has important biological functions since it acts as cell membrane reinforcement and it protects the microorganism against DNA damaging agents. Moreover, carotenoid extracts from halophilic archaea have shown high antioxidant capacity. Therefore, current review summarizes the effect of different culture conditions such as salt and carbon source concentrations in the medium, light incidence, and oxygen tension on carotenoid production by halophilic archaea and the strategies such as optimization methodology and two-stage cultivation already used to increase the carotenoid yield of these microorganisms. PMID:26750123

  19. Metabolism of hyperthermophiles.

    Science.gov (United States)

    Schönheit, P; Schäfer, T

    1995-01-01

    Hyperthermophiles are characterized by a temperature optimum for growth between 80 and 110°C. They are considered to represent the most ancient phenotype of living organisms and thus their metabolic design might reflect the situation at an early stage of evolution. Their modes of metabolism are diverse and include chemolithoautotrophic and chemoorganoheterotrophic. No extant phototrophic hyperthermophiles are known. Lithotrophic energy metabolism is mostly anaerobic or microaerophilic and based on the oxidation of H2 or S coupled to the reduction of S, SO inf4 (sup2-) , CO2 and NO inf3 (sup-) but rarely to O2. the substrates are derived from volcanic activities in hyperthermophilic habitats. The lithotrophic energy metabolism of hyperthermophiles appears to be similar to that of mesophiles. Autotrophic CO2 fixation proceeds via the reductive citric acid cycle, considered to be one of the first metabolic cycles, and via the reductive acetyl-CoA/carbon monoxide dehydrogenase pathway. The Calvin cycle has not been found in hyperthermophiles (or any Archaea). Organotrophic metabolism mainly involves peptides and sugars as substrates, which are either oxidized to CO2 by external electron acceptors or fermented to acetate and other products. Sugar catabolism in hyperthermophiles involves non-phosphorylated versions of the Entner-Doudoroff pathway and modified versions of the Embden-Meyerhof pathway. The 'classical' Embden-Meyerhof pathway is present in hyperthermophilic Bacteria (Thermotoga) but not in Archaea. All hyperthermophiles (and Archaea) tested so far utilize pyruvate:ferredoxin oxidoreductase for acetyl-CoA formation from pyruvate. Acetyl-CoA oxidation in anaerobic sulphur-reducing and aerobic hyperthermophiles proceeds via the citric acid cycle; in the hyperthermophilic sulphate-reducer Archaeoglobus an oxidative acetyl-CoA/carbon monoxide dehydrogenase pathway is operative. Acetate formation from acetyl-CoA in Archaea, including hyperthermophiles, is

  20. The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under Hops (Humulus lupulus

    Directory of Open Access Journals (Sweden)

    Karolina Oszust

    2014-06-01

    Full Text Available The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential. Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a ecological based on the use of probiotic preparations and organic fertilization (b conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP of PCR ammonia monooxygenase α-subunit (amoA gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application.

  1. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Kozubal, Mark; Romine, Margaret F.; Jennings, Ryan; Jay, Z.; Tringe, Susannah G.; Rusch, Douglas B.; Beam, Jake; McCue, Lee Ann; Inskeep, William P.

    2013-03-01

    Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicate that the replicate assemblies represent a new phylum-level lineage referred to here as 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I CO dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogues active in YNP today.

  2. METABOLISM OF SULFATE-REDUCING PROKARYOTES

    NARCIS (Netherlands)

    HANSEN, TA

    1994-01-01

    Dissimilatory sulfate reduction is carried out by a heterogeneous group of bacteria and archaea that occur in environments with temperatures up to 105 degrees C. As a group together they have the capacity to metabolize a wide variety of compounds ranging from hydrogen via typical organic fermentatio

  3. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids.

    Science.gov (United States)

    Hoedt, Emily C; Cuív, Páraic Ó; Evans, Paul N; Smith, Wendy J M; McSweeney, Chris S; Denman, Stuart E; Morrison, Mark

    2016-10-01

    The Australian macropodids (kangaroos and wallabies) possess a distinctive foregut microbiota that contributes to their reduced methane emissions. However, methanogenic archaea are present within the macropodid foregut, although there is scant understanding of these microbes. Here, an isolate taxonomically assigned to the Methanosphaera genus (Methanosphaera sp. WGK6) was recovered from the anterior sacciform forestomach contents of a Western grey kangaroo (Macropus fuliginosus). Like the human gut isolate Methanosphaera stadtmanae DSMZ 3091(T), strain WGK6 is a methylotroph with no capacity for autotrophic growth. In contrast, though with the human isolate, strain WGK6 was found to utilize ethanol to support growth, but principally as a source of reducing power. Both the WGK6 and DSMZ 3091(T) genomes are very similar in terms of their size, synteny and G:C content. However, the WGK6 genome was found to encode contiguous genes encoding putative alcohol and aldehyde dehydrogenases, which are absent from the DSMZ 3091(T) genome. Interestingly, homologs of these genes are present in the genomes for several other members of the Methanobacteriales. In WGK6, these genes are cotranscribed under both growth conditions, and we propose the two genes provide a plausible explanation for the ability of WGK6 to utilize ethanol for methanol reduction to methane. Furthermore, our in vitro studies suggest that ethanol supports a greater cell yield per mol of methane formed compared to hydrogen-dependent growth. Taken together, this expansion in metabolic versatility can explain the persistence of these archaea in the kangaroo foregut, and their abundance in these 'low-methane-emitting' herbivores. PMID:27022996

  4. The Co-Distribution of Nitrifying Archaea and Diazotrophic Bacteria in Geothermal Springs

    Science.gov (United States)

    Hamilton, T. L.; Jewell, T. N. M.; de la Torre, J. R.; Boyd, E. S.

    2014-12-01

    Microbial processes that regulate availability of nutrients play key roles in shaping community composition. All life requires fixed nitrogen (N), and its bioavailability is what often limits ecosystem productivity. Biological nitrogen fixation, or the reduction of dinitrogen (N2) to ammonia (NH3), is a keystone process in N limited ecosystems, providing nitrogen for members of the community. N2 fixing organisms likely represent a 'bottom up control' on the structure of communities that develop in N limited environments. N2 fixation is catalyzed by a limited number of metabolically diverse bacteria and some methanogenic archaea and occurs in a variety of physically and geochemically diverse environments. Nitrification, or the sequential oxidation of NH4+ to nitrite (NO2-) and ultimately nitrate (NO3-), is catalyzed by several lineages of Proteobacteria at temperatures of < 62°C and by members of the Thaumarcheota at temperatures up to 90°C. Nitrification can thus be considered a 'top down control' on the structure of communities that develop in N limited environments. Our research in Yellowstone National Park (YNP) reveals a strong correspondence between the distribution of ammonia oxidizing archaea (AOA) and nitrogen fixing aquificae (NFA) in nitrogen-limited geothermal hot springs over large environmental gradients. Based on the physiology of AOA and NFA, we propose that the strong co-distributional pattern results from interspecies interactions, namely competition for bioavailable ammonia. Our recent work has shown that in springs where the niche dimension of AOA and NFA overlap (e.g., Perpetual Spouter; pH 7.1, 86.4°C), the dissimilar affinities for NH4 result in AOA metabolism maintaining a low NH4(T) pool and selecting for inclusion of NFA during the assembly of these communities. Here, we examine in situ physiological interactions of AOA and NFA, tracking changes in transcript levels of key genes involved in nitrogen metabolism and carbon fixation of

  5. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2014-01-01

    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.

  6. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

    Directory of Open Access Journals (Sweden)

    Rika E Anderson

    Full Text Available The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.

  7. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2014-01-01

    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities. PMID:25279954

  8. Archaea in metazoan diets: implications for food webs and biogeochemical cycling

    OpenAIRE

    Andrew R Thurber; Levin, Lisa A.; Orphan, Victoria J.; Marlow, Jeffrey J.

    2012-01-01

    Although the importance of trophic linkages, including ‘top-down forcing’, on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary sour...

  9. Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork

    OpenAIRE

    Grogan, Dennis W.

    2015-01-01

    Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but re...

  10. Exploring the diversity of extremely halophilic archaea in food-grade salts

    OpenAIRE

    Henriet, O.; Fourmentin, J.; Delincé, B.; Mahillon, J

    2014-01-01

    Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony...

  11. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Science.gov (United States)

    Löscher, C. R.; Kock, A.; Könneke, M.; LaRoche, J.; Bange, H. W.; Schmitz, R. A.

    2012-07-01

    The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA) were detectable throughout the water column of the eastern tropical North Atlantic (ETNA) and eastern tropical South Pacific (ETSP) Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.

  12. Administrative Ecology

    Science.gov (United States)

    McGarity, Augustus C., III; Maulding, Wanda

    2007-01-01

    This article discusses how all four facets of administrative ecology help dispel the claims about the "impossibility" of the superintendency. These are personal ecology, professional ecology, organizational ecology, and community ecology. Using today's superintendency as an administrative platform, current literature describes a preponderance of…

  13. The effects of space relevant environmental factors on halophilic Archaea

    Science.gov (United States)

    Leuko, Stefan; Moeller, Ralf; Rettberg, Petra

    Within the last 50 years, space technology has provided tools for transporting terrestrial (microbial) life beyond Earth's protective shield in order to study its responses to selected conditions of space. Microorganisms are ubiquitous and can be found in almost every environment on Earth. They thrive and survive in a broad spectrum of environments and are true masters in adapting to rapidly changing external conditions. Although microorganisms cannot actively grow under the harsh conditions of outer space or other known planets, some microorganisms might be able to survive for a time in space or other planets as dormant, inactive spores or in similar desiccation-resistant resting states, e.g., enclosed in halite crystals or biofilms. Halite crystals are the realm of halophilic Archaea as they have adapted to life at extreme salt concentrations. They can stay entrapped in such crystals for millions of years without losing viability and therefore the family Halobacteriaceae belongs to the group of microorganisms which may survive space travel or may even be found on other planets. Several members of this family have been utilized in space relevant experiments where they were exposed to detrimental environmental conditions such as UV-C radiation, vacuum, temperature cycles (+60(°) C and -25(°) C) and heavy iron bombardment (150 MeV He, 500 MeV Ar and 500 MeV Fe ions). The viability was evaluated by colony forming unit (cfu) counts as well as with the LIFE/DEAD kit. Results revealed that UV-C radiation (up to 1.000 J/m (2) ) has a considerable effect on the viability, whereas the other tested parameters inflict little damage onto the organisms. Repair of UV-C inflicted damage is efficient and several DNA damage repair genes are up-regulated following exposure. Halophilic archaea display a strong resistance against heavy iron bombardment, with dosages of up to 2.000 Gy 500 MeV Fe ions needed to establish a visible effect on the vitality. Genomic integrity after

  14. Purine biosynthesis in archaea: variations on a theme

    Directory of Open Access Journals (Sweden)

    Brown Anne M

    2011-12-01

    Full Text Available Abstract Background The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains. Results We searched the Integrated Microbial Genome system (IMG for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function. Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified. Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected or Enzyme Commission (E. C. numbers (57 proteins, 7.7%. There were also 57 proteins (7.7% assigned overly generic names and 78 proteins (10.6% without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified. Conclusions The patchy distribution of purine biosynthetic genes in archaea is

  15. CRISPR loci reveal networks of gene exchange in archaea

    Directory of Open Access Journals (Sweden)

    Brodt Avital

    2011-12-01

    Full Text Available Abstract Background CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. Results Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. Open peer review This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten

  16. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

    DEFF Research Database (Denmark)

    Lange, M.; Ahring, Birgitte Kiær

    2001-01-01

    Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict ...

  17. Intact polar lipids of ammonia-oxidizing Archaea: Structural diversity anapplication inmolecular ecology

    NARCIS (Netherlands)

    Pitcher, A.

    2011-01-01

    Non-extremophilic Crenarchaeota are ubiquitous, and comprise a major component of the microbial assemblages in many modern-day systems. Several studies have analyzed glycerol dialkyl glycerol tetraether (GDGT) membrane lipids synthesized by Crenarchaeota to interpret the presence, distribution, and

  18. New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches.

    Science.gov (United States)

    Ding, Jing; Ding, Zhao-Wei; Fu, Liang; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

    2015-11-01

    The significance of ANME-2d in methane sink in the environment has been overlooked, and there was no any study evaluating the distribution of ANME-2d in the environment. New primers were thus needed to be designed for following research. In this paper, a pair of primers (DP397F and DP569R) was designed to quantify ANME-2d. The specificity and amplification efficiency of this primer pair were acceptable. PCR amplification of another pair of primers (DP142F and DP779R) generated a single, bright targeted band from the enrichment sample, but yielded faint, multiple bands from the environmental samples. Nested PCR was conducted using the primers DP142F/DP779R in the first round and DP142F/DP569R in the second round, which generated a bright targeted band. Further phylogenetic analysis showed that these targeted bands were ANME-2d-related sequences. Real-time PCR showed that the copies of the 16s ribosomal RNA gene of ANME-2d in these samples ranged from 3.72 × 10(4) to 2.30 × 10(5) copies μg(-1) DNA, indicating that the percentage of ANME-2d was greatest in a polluted river sample and least in a rice paddy sample. These results demonstrate that the newly developed real-time PCR primers could sufficiently quantify ANME-2d and that nested PCR with an appropriate combination of the new primers could successfully detect ANME-2d in environmental samples; the latter finding suggests that ANME-2d may spread in environments. PMID:26300291

  19. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

    Science.gov (United States)

    McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

    2012-03-01

    Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

  20. Intact polar lipids of ammonia-oxidizing Archaea: structural diversity application in molecular ecology

    NARCIS (Netherlands)

    Pitcher, A.M.

    2011-01-01

    Non-extremophilic Crenarchaeota are ubiquitous, and comprise a major component of the microbial assemblages in many modern-day systems. Several studies have analyzed glycerol dialkyl glycerol tetraether (GDGT) membrane lipids synthesized by non-extremophilic Crenarchaeota to interpret the presence,

  1. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Löscher

    2012-07-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O.

    Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the eastern tropical North Atlantic (ETNA and eastern tropical South Pacific (ETSP Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved

  2. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Loescher

    2012-02-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O which occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been described to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the Eastern Tropical North Atlantic (ETNA and Eastern Tropical South Pacific Oceans (ETSP. Particularly in the ETNA, maxima in abundance and expression of archaeal amoA genes correlated with the N2O maximum and the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen

  3. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil.

    Directory of Open Access Journals (Sweden)

    Anne Daebeler

    Full Text Available The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH(3F caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH(3F (v/v. The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis, remained stable over a wide range of CH(3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH(3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH(3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.

  4. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    Science.gov (United States)

    Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A; Kjeldsen, Kasper U; Jørgensen, Bo B; Plugge, Caroline M

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

  5. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    Directory of Open Access Journals (Sweden)

    Derya eOzuolmez

    2015-05-01

    Full Text Available Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744, a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

  6. Eubacteria and Archaea community of simultaneous methanogenesis and denitrification granular sludge

    Institute of Scientific and Technical Information of China (English)

    SUN Yujiao; ZUO Jiane; CHEN Lili; WANG Yong

    2008-01-01

    Based on the successful performance of a lab-scale upflow anaerobic sludge blanket (UASB) reactor with the capacity of simultaneous methanogenesis and denitrification (SMD), the specific phylogenetic groups and community structure of microbes in the SMD granule in the UASB reactor were investigated by the construction of the Eubacteria and Archaea 16S rDNA clone libraries, fragment length polymorphism, and sequence blast. Real time quantitative-polymerase chain reaction (RTQ-PCR) technique was used to quantify the contents of Eubacteria and Archaea in the SMD granule. The contents of some special predominant methanogens were also investigated. The results indicated that the Methanosaeta and Methanobacteria were the predominant methanogens in all Archaea in the SMD granule, with contents of 71. 59% and 22. 73% in all 88 random Archaea clones, respectively. The diversity of Eubacteria was much more complex than that of Archaea. The low GC positive gram bacteria and Б-Protebacteria were the main predominant Eubacteria species in SMD granule, their contents were 49. 62% and 12. 03% in all 133 random Eubacteria clones respectively. The results of RTQ-PCR indicated that the content of Archaea was less than Eubacteria, the Archaea content in total microorganisms in SMD granule was about 27. 6%.

  7. Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells

    Directory of Open Access Journals (Sweden)

    Fang Liu

    2011-01-01

    Full Text Available Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.

  8. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    Science.gov (United States)

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S.; Schouten, Stefan; Rijpstra, W. Irene C.; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, SangHoon; Madsen, Eugene L.; Rhee, Sung-Keun

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes. PMID:27339136

  9. Identification of a glycolytic regulon in the Archaea Pyrococcus and Thermococcus

    NARCIS (Netherlands)

    Werken, van de H.J.G.; Verhees, C.H.; Akerboom, A.P.; Vos, de W.M.; Oost, van der J.

    2006-01-01

    The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, so

  10. Physiological ecology of Mediterranean blue tits (Parus caeruleus L.): effects of ectoparasites (Protocalliphora spp.) and food abundance on metabolic capacity of nestlings.

    Science.gov (United States)

    Simon, Aurélie; Thomas, Don; Blondel, Jacques; Perret, Philippe; Lambrechts, Marcel M

    2004-01-01

    The consequences of nest ectoparasites, such as Protocalliphora larvae, on nestling birds have been the subject of numerous studies. Despite observed reductions in mass and hematocrit of chicks from parasitized nests, no studies have found any effect of Protocalliphora on nestling survival, suggesting that fitness consequences of Protocalliphora are either weak or occur after fledging. From experiments on the metabolic performance of chicks, we found that parasitized chicks suffer from reduced thermogenic and metabolic capacities as a result of decreased mass and hematocrit. Hence, Protocalliphora may potentially affect nestling survival after fledging, when energetically costly activities such as flight and moult are undertaken. Previous studies have demonstrated an increase in parental feeding rate to compensate for the detrimental consequences of parasite infestation. We tested whether parasite effects on nestling aerobic capacity were dependent on food availability during the feeding period. Measures of caterpillar densities and experimental manipulations of parasite loads allowed us to investigate relationships among host, parasite, and environment. A positive relationship between chick aerobic and thermogenic performances and caterpillar density suggests that negative effects of parasitism may be offset by increased food availability. This study provides the first measurement of the effects of an ectoparasite on metabolic competence in wild birds and documentation of the effect of food availability on ectoparasite virulence using a quantitative measure of food abundance. PMID:15286922

  11. Picoheterotroph (Bacteria and Archaea biomass distribution in the global ocean

    Directory of Open Access Journals (Sweden)

    M. R. Landry

    2012-09-01

    Full Text Available We compiled a database of 39 766 data points consisting of flow cytometric and microscopical measurements of picoheterotroph abundance, including both Bacteria and Archaea. After gridding with 1° spacing, the database covers 1.3% of the ocean surface. There are data covering all ocean basins and depths except the Southern Hemisphere below 350 m or from April until June. The average picoheterotroph biomass is 3.9 ± 3.6 μg C l−1 with a 20-fold decrease between the surface and the deep sea. We estimate a total ocean inventory of about 1.3 × 1029 picoheterotroph cells. Surprisingly, the abundance in the coastal regions is the same as at the same depths in the open ocean. Using an average of published open ocean measurements for the conversion from abundance to carbon biomass of 9.1 fg cell−1, we calculate a picoheterotroph carbon inventory of about 1.2 Pg C. The main source of uncertainty in this inventory is the conversion factor from abundance to biomass. Picoheterotroph biomass is ~2 times higher in the tropics than in the polar oceans. doi:10.1594/PANGAEA.779142

  12. Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

    Science.gov (United States)

    Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

    1997-07-01

    Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

  13. A First Analysis of Metallome Biosignatures of Hyperthermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Vyllinniskii Cameron

    2012-01-01

    Full Text Available To date, no experimental data has been reported for the metallome of hyperthermophilic microorganisms although their metal requirements for growth are known to be unique. Here, experiments were conducted to determine (i cellular trace metal concentrations of the hyperthermophilic Archaea Methanococcus jannaschii and Pyrococcus furiosus, and (ii a first estimate of the metallome for these hyperthermophilic species via ICP-MS. The metal contents of these cells were compared to parallel experiments using the mesophilic bacterium Escherichia coli grown under aerobic and anaerobic conditions. Fe and Zn were typically the most abundant metals in cells. Metal concentrations for E. coli grown aerobically decreased in the order Fe > Zn > Cu > Mo > Ni > W > Co. In contrast, M. jannaschii and P. furiosus show almost the reverse pattern with elevated Ni, Co, and W concentrations. Of the three organisms, a biosignature is potentially demonstrated for the methanogen M. jannaschii that may, in part, be related to the metallome requirements of methanogenesis. The bioavailability of trace metals more than likely has varied through time. If hyperthermophiles are very ancient, then the trace metal patterns observed here may begin to provide some insights regarding Earth's earliest cells and in turn, early Earth chemistry.

  14. Involvement of thermophilic archaea in the biocorrosion of oil pipelines.

    Science.gov (United States)

    Davidova, Irene A; Duncan, Kathleen E; Perez-Ibarra, B Monica; Suflita, Joseph M

    2012-07-01

    Two thermophilic archaea, strain PK and strain MG, were isolated from a culture enriched at 80°C from the inner surface material of a hot oil pipeline. Strain PK could ferment complex organic nitrogen sources (e.g. yeast extract, peptone, tryptone) and was able to reduce elemental sulfur (S°), Fe(3+) and Mn(4+) . Phylogenetic analysis revealed that the organism belonged to the order Thermococcales. Incubations of this strain with elemental iron (Fe°) resulted in the abiotic formation of ferrous iron and the accumulation of volatile fatty acids during yeast extract fermentation. The other isolate, strain MG, was a H(2) :CO(2) -utilizing methanogen, phylogenetically affiliated with the genus Methanothermobacter family. Co-cultures of the strains grew as aggregates that produced CH(4) without exogenous H(2) amendment. The co-culture produced the same suite but greater concentrations of fatty acids from yeast extract than did strain PK alone. Thus, the physiological characteristics of organisms both alone and in combination could conceivably contribute to pipeline corrosion. The Thermococcus strain PK could reduce elemental sulfur to sulfide, produce fatty acids and reduce ferric iron. The hydrogenotrophic methanogen strain MG enhanced fatty acid production by fermentative organisms but could not couple the dissolution Fe° with the consumption of water-derived H(2) like other methanogens.

  15. Growth and Methane Oxidation Rates of Anaerobic Methanotrophic Archaea in a Continuous-Flow Bioreactor

    OpenAIRE

    Peter R. Girguis; Orphan, Victoria J; Hallam, Steven J.; DeLong, Edward F

    2003-01-01

    Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that...

  16. Bridging domains : a comparison between information processing in Archaea and Eukarya

    OpenAIRE

    Koning, de, H.

    2015-01-01

    Bridging Domains A Comparison between Information Processing in Archaea and Eukarya Studying Information Processing Living cells evolved complex systems to handle the flow of information both accurately and efficiently. These systems are highly comparable between the three domains of life: eukaryotes, bacteria and archaea. The central components of replication, transcription, aminoacylation, and translation are found in every living cell known today, with only relatively small deviations, des...

  17. Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2014-03-01

    Full Text Available Ammonia-oxidizingarchaea (AOA and ammonia-oxidizing bacteria (AOB play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasechain reaction PCR(qPCR combined with the terminal restrictionfragment length polymorphism(T-RFLP were employed to characterize the abundance, diversity, and communitystructure of the AOA and AOB in 32 freshwater sediments. AOA and AOB wereubiquitous in all sediments, and archaeal amoA far outnumbered bacterial amoA inmost sediments with lower organic matters. The abundance of AOA and AOB did notvary with the freshwater ecological type (macrophyte dominated region and algaedominated region. Based on  the T-RFLP of an amoA gene, this research found that organicmatters in pore water rather than other factors affect the AOA communitystructure in sediments, while the AOB were not significantly different in thefreshwater sediments. Phylogenetic analysis showed that all archaeal amoAsequences fell within either the Crenarchaeotal Group (CG I.1b or the CGI.1asubgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira. The data obtained inthis study elucidates the role of ammonia-oxidizing archaea andammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

  18. Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation

    Directory of Open Access Journals (Sweden)

    Janosch eSchirmack

    2015-03-01

    Full Text Available Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g. permafrost environments, desert soils and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 %wt of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats

  19. Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation.

    Science.gov (United States)

    Schirmack, Janosch; Alawi, Mashal; Wagner, Dirk

    2015-01-01

    Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g., permafrost environments, desert soils, and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs (MRAs) on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 wt% of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats on Earth

  20. Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment.

    Directory of Open Access Journals (Sweden)

    Davi Pedroni Barreto

    Full Text Available The study of of the distribution of microorganisms through space (and time allows evaluation of biogeographic patterns, like the species-area index (z. Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism targeting mcrA (coding for a subunit of methyl-coenzyme M reductase and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.

  1. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

    Directory of Open Access Journals (Sweden)

    B. Orcutt

    2008-11-01

    Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

  2. Ecological Economics

    OpenAIRE

    Martínez Alier, Joan

    2001-01-01

    Ecological economics is a relatively new interdisciplinary field concerned with the relationship between economic systems and the biological and physical world. This article covers the following topics: A discussion of views on whether ecological economics is just a field or approach within economics or a new ÒtransdisciplinaryÓ field in its own right; Origin of the name of the field; Core common principles of ecological economics; Comparison with environmental economics; Applications; Histor...

  3. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    Directory of Open Access Journals (Sweden)

    Vidya eDe Gannes

    2012-07-01

    Full Text Available Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, coffee hulls, which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase and the finished product (mature phase. The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (groub I.1b, in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have signifcant effects on its performanc as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities with nitrification in these systems.

  4. Human metabolism and ecological transfer of radioactive caesium: Comparative studies of Chernobyl debris and nuclear weapons fallout, in Southern Sweden and in Bryansk, Russia

    Science.gov (United States)

    Raaf, Christopher Leopold

    The whole-body content of radiocaesium was measured in a South-Swedish urban group of people residing in the city of Lund (55.7°N, 13.2°E) between 1960 and 1994. The results from the survey have been analysed in order to estimate the ecological half-time, Teff,eco, of fallout radiocaesium and the aggregate transfer from ground deposition to man in the region. After 1987, the biological half-times, Ts, of 137Cs and 40K in man were also determined in the reference group through whole-body content measurements in combination with 24-hour urine sampling. Relationships between 24-hour urinary excretion and body burden of 137Cs in the group together with data from the literature were then applied to urine samples collected in 1994 and 1995 from adult subjects living in the highly contaminated region of Bryansk, Russia, in order to estimate their average body burden of 137Cs. The equivalent biological half-time for 137Cs in females of the Lund reference group was, on average (+/-1 WSE), 66 +/- 3 d, which agrees with other findings, whereas the value for the males, 81 +/- 4 d, was, on average, significantly lower than what is found in the literature. This is partly explained by the elevated mean age and relatively low mean body muscle mass of the males investigated in the group during the post-Chernobyl study period. The effective ecological half-time for 137Cs from Chernobyl was found to be 1.8 +/- 0.2 y. The aggregate transfer of 137Cs from deposition to mean activity concentration in man was estimated to be 1.7 Bq kg-1/kBq m-2. These vales may be compared with an effective ecological half-time of 1.3 years found in the reference group in the 1960s, and an aggregate transfer factor of 9.8 Bq kg-1/kBq m-2. The average committed effective dose from ingested 137Cs Chernobyl fallout in the study group was estimated to be 0.02 mSv and from the nuclear weapons fallout to 0.20 mSv. The estimates of whole-body content of 137Cs in the Russian subjects obtained through

  5. In-vitro archaeacidal activity of biocides against human-associated archaea.

    Directory of Open Access Journals (Sweden)

    Saber Khelaifia

    Full Text Available BACKGROUND: Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea. METHODOLOGY: The minimal archaeacidal concentration (MAC of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arboriphilicus, Methanosphaera stadtmanae, Methanomassiliicoccus luminyensis and two environmental methanogens Methanobacterium beijingense and Methanosaeta concilii by using a serial dilution technique in Hungates tubes. PRINCIPAL FINDINGS: MAC of squalamine derivative S1 was 0.05 mg/L against M. smithii strains, M. oralis, M. arboriphilicus, M. concilii and M. beijingense whereas MAC of squalamine and derivatives S2-S12 varied from 0.5 to 5 mg/L. For M. stadtmanae and M. luminyensis, MAC of derivative S1 was 0.1 mg/L and varied from 1 to ≥ 10 mg/L for squalamine and its parent derivatives S2-S12. Under the same experimental conditions, chlorhexidine and peracetic acid lead to a MAC of 0.2 and 1.5 mg/L, respectively against all tested archaea. CONCLUSIONS/SIGNIFICANCE: Squalamine derivative S1 exhibited a 10-200 higher archaeacidal activity than other tested squalamine derivatives, on the majority of human-associated archaea. As previously reported and due to their week corrosivity and their wide spectrum of antibacterial and antifungal properties, squalamine and more precisely derivative S1 appear as promising compounds to be further tested for the decontamination of medical devices contaminated by human-associated archaea.

  6. Ecological stability in response to warming

    NARCIS (Netherlands)

    Fussmann, Katarina E.; Schwarzmueller, Florian; Brose, Ulrich; Jousset, Alexandre; Rall, Bjoern C.

    2014-01-01

    That species' biological rates including metabolism, growth and feeding scale with temperature is well established from warming experiments(1). The interactive influence of these changes on population dynamics, however, remains uncertain. As a result, uncertainty about ecological stability in respon

  7. Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics.

    Science.gov (United States)

    Pakpour, Sepideh; Scott, James A; Turvey, Stuart E; Brook, Jeffrey R; Takaro, Timothy K; Sears, Malcolm R; Klironomos, John

    2016-08-01

    Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments. PMID:27098176

  8. Exploring the diversity of extremely halophilic archaea in food-grade salts.

    Science.gov (United States)

    Henriet, Olivier; Fourmentin, Jeanne; Delincé, Bruno; Mahillon, Jacques

    2014-11-17

    Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony counts reached more than 10(5)CFU per gram in three salts. All archaeal isolates identified by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar occurrence. The number of distinct genera per salt ranged from 21 to 27. Halorubrum had a significant contribution to the archaeal diversity in seven salts; this correlates with its frequent occurrence in crystallization ponds. On the contrary, Haloquadratum walsbyi, the halophilic archaea most commonly found in solar salterns, was a minor actor of the food-grade salt diversity. Our results indicate that the occurrence and diversity of viable halophilic archaea in salt can be important, while their fate in the gastrointestinal tract after ingestion remains largely unknown. PMID:25217724

  9. Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork

    Directory of Open Access Journals (Sweden)

    Dennis W. Grogan

    2015-01-01

    Full Text Available Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.

  10. Exploring the diversity of extremely halophilic archaea in food-grade salts.

    Science.gov (United States)

    Henriet, Olivier; Fourmentin, Jeanne; Delincé, Bruno; Mahillon, Jacques

    2014-11-17

    Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony counts reached more than 10(5)CFU per gram in three salts. All archaeal isolates identified by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar occurrence. The number of distinct genera per salt ranged from 21 to 27. Halorubrum had a significant contribution to the archaeal diversity in seven salts; this correlates with its frequent occurrence in crystallization ponds. On the contrary, Haloquadratum walsbyi, the halophilic archaea most commonly found in solar salterns, was a minor actor of the food-grade salt diversity. Our results indicate that the occurrence and diversity of viable halophilic archaea in salt can be important, while their fate in the gastrointestinal tract after ingestion remains largely unknown.

  11. Human metabolism and ecological transfer of radioactive caesium. Comparative studies of Chernobyl debris and nuclear weapons fallout, in southern Sweden and in Bryansk, Russia

    Energy Technology Data Exchange (ETDEWEB)

    Raeaef, C.L

    2000-05-01

    The whole-body content of radiocaesium was measured in a South Swedish urban group of people residing in the city of Lund between 1960 and 1994. The results from the survey have been analysed in order to estimate the ecological half time, T{sub eff,eco} of fallout radiocaesium, and the aggregate transfer from ground deposition to man in the region. After 1987, the biological half times, T{sub e} of {sup 137}Cs and {sup 40}K in man were also determined in the reference group through whole-body content measurements in combination with 24-hour urine sampling. Relationships between 24-hour urinary excretion and body burden of {sup 137}Cs in the group together with data from the literature were then applied to urine samples collected in 1994 and 1995 from adult subjects living in the highly contaminated region of Bryansk, Russia, in order to estimate their average body burden of {sup 137}Cs. The equivalent biological half-time for {sup 137}Cs in females of the Lund reference group was, on average 66{+-}3 d, which agrees with other findings, whereas the value for the males, 81{+-}4 d, was, on average, significantly lower than what is found in the literature. This is partly explained by the elevated mean age and relatively low mean body muscle mass of the males investigated. The {sup 137}Cs from nuclear weapons tests in the 1950s and 1960s still gave a significant contribution to the total {sup 137}Cs levels in man during the post-Chernobyl study period (1987-1994). About 10% of the peak post-Chernobyl concentration level of {sup 137}Cs (3.5-4 Bq/kg) in 1987, was attributed to pre-Chernobyl {sup 137}Cs. The effective ecological half-time for {sup 137}Cs from Chernobyl was found to be 1.8{+-}0.2 y. The time-integrated aggregate transfer of {sup 137}Cs from ground deposition to mean activity concentration in man was estimated to be 0.4 Bq/kg/kBq/m{sup 2}. These values may be compared with an effective ecological half-time of 1.3 years found in the Lund reference group in

  12. The TrmB family: a versatile group of transcriptional regulators in Archaea.

    Science.gov (United States)

    Gindner, Antonia; Hausner, Winfried; Thomm, Michael

    2014-09-01

    Microbes are organisms which are well adapted to their habitat. Their survival depends on the regulation of gene expression levels in response to environmental signals. The most important step in regulation of gene expression takes place at the transcriptional level. This regulation is intriguing in Archaea because the eu-karyotic-like transcription apparatus is modulated by bacterial-like transcription regulators. The transcriptional regulator of mal operon (TrmB) family is well known as a very large group of regulators in Archaea with more than 250 members to date. One special feature of these regulators is that some of them can act as repressor, some as activator and others as both repressor and activator. This review gives a short updated overview of the TrmB family and their regulatory patterns in different Archaea as a lot of new data have been published on this topic since the last review from 2008.

  13. Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea

    Science.gov (United States)

    Charlesworth, James C.; Burns, Brendan P.

    2015-01-01

    Archaea are an understudied domain of life often found in “extreme” environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. In this review we will discuss the diversity of small molecules, both peptide and nonpeptide, produced by archaea and their potential biotechnological applications. PMID:26504428

  14. Archaea in metazoan diets: implications for food webs and biogeochemical cycling

    Science.gov (United States)

    Thurber, Andrew R; Levin, Lisa A; Orphan, Victoria J; Marlow, Jeffrey J

    2012-01-01

    Although the importance of trophic linkages, including ‘top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ13C=−92±4‰ polar lipids −116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as ‘archivory'. PMID:22402398

  15. Cognitive ecology.

    Science.gov (United States)

    Hutchins, Edwin

    2010-10-01

    Cognitive ecology is the study of cognitive phenomena in context. In particular, it points to the web of mutual dependence among the elements of a cognitive ecosystem. At least three fields were taking a deeply ecological approach to cognition 30 years ago: Gibson's ecological psychology, Bateson's ecology of mind, and Soviet cultural-historical activity theory. The ideas developed in those projects have now found a place in modern views of embodied, situated, distributed cognition. As cognitive theory continues to shift from units of analysis defined by inherent properties of the elements to units defined in terms of dynamic patterns of correlation across elements, the study of cognitive ecosystems will become an increasingly important part of cognitive science.

  16. Community Ecology

    CERN Document Server

    1988-01-01

    This book presents the proceedings of a workshop on community ecology organized at Davis, in April, 1986, sponsored by the Sloan Foundation. There have been several recent symposia on community ecology (Strong et. al., 1984, Diamond and Case, 1987) which have covered a wide range of topics. The goal of the workshop at Davis was more narrow: to explore the role of scale in developing a theoretical approach to understanding communities. There are a number of aspects of scale that enter into attempts to understand ecological communities. One of the most basic is organizational scale. Should community ecology proceed by building up from population biology? This question and its ramifications are stressed throughout the book and explored in the first chapter by Simon Levin. Notions of scale have long been important in understanding physical systems. Thus, in understanding the interactions of organisms with their physical environment, questions of scale become paramount. These more physical questions illustrate the...

  17. Ecological Modernization

    NARCIS (Netherlands)

    Mol, A.P.J.

    2006-01-01

    The Encyclopedia of Globalization provides a thorough understanding of the theoretical underpinnings of globalization as well as the various historical and analytical interpretations. Consisting of over 400 entries, coverage includes key cultural, ecological, economic, geographical, historical, poli

  18. Ecological shortage

    International Nuclear Information System (INIS)

    The Meadows study (Limits to Growth) has made the environmental problem popular, but it has reduced the ecological problem to one of population and raw materials, leaving the conditions of social organisation and developmental policy out of consideration. This means that in spite of the repeated moral appeals, developing countries are left to their natural fate while fear and resignation are spread in the industrial nations. The present study tries to contradict this trend in consideration of interdependences in ecological development. (orig.)

  19. Stress response of methanogenic archaea from Siberian permafrost compared to methanogens from non-permafrost habitats

    OpenAIRE

    Daria Morozova; Dirk Wagner;  

    2007-01-01

    We examined the survival potential of methanogenic archaea exposed to different environmental stress conditions such as low temperature (down to 78.5 °C), high salinity (up to 6 M NaCl), starvation (up to 3 months), long-term freezing (up to 2 years), desiccation (up to 25 days) and oxygen exposure (up to 72 hours). The experiments were conducted with microbial populations of methanogenic archaea from Siberian permafrost and were complemented by experiments on well-studied methanogens from no...

  20. Metabolomics in chemical ecology.

    Science.gov (United States)

    Kuhlisch, Constanze; Pohnert, Georg

    2015-07-01

    Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.

  1. The effects of various land reclamation scenarios on the succession of soil Bacteria, Archaea, and fungi over the short and long term

    Directory of Open Access Journals (Sweden)

    Junjian eLi

    2016-03-01

    Full Text Available Ecological restoration of mining areas has mainly focused on the succession dynamics of vegetation and the fate of microbial communities remains poorly understood. We examined changes in soil characteristics and plant and microbial communities with increasing reclamation period in an open coal mine. Bacterial, archaeal and fungal communities were assessed by tag-encoded 454 pyrosequencing. At the phylum level, Proteobacteria, Crenarchaeota, and Ascomycota had the highest detected relative abundance within bacteria, archaea, and fungi, respectively. Partial regressions and canonical correspondence analysis demonstrated that vegetation played a major role in bacterial and archaeal diversity and assemblies, and soil characteristics, especially nitrogen, were important for fungal diversity and assemblies. Spearman rank correlation indicated that bacterial and archaeal communities showed synergistic succession with plants; whereas, fungal communities showed no such pattern. Overall, our data suggest that there are different drivers of bacterial, archaeal and fungal succession during secondary succession in a reclaimed open mine.

  2. Gene Expression in Archaea: Studies of Transcriptional Promoters, Messenger RNA Processing, and Five Prime Untranslated Regions in "Methanocaldococcus Jannashchii"

    Science.gov (United States)

    Zhang, Jian

    2009-01-01

    Gene expression in Archaea is less understood than those in Bacteria and Eucarya. In general, three steps are involved in gene expression--transcription, RNA processing, and translation. To expand our knowledge of these processes in Archaea, I have studied transcriptional promoters, messenger RNA processing, and 5'-untranslated regions in…

  3. Massive Expansion of Marine Archaea During The Early Albian Oceanic Anoxic Event 1B

    Science.gov (United States)

    Kuypers, M. M.; Kuypers, M. M.; Blokker, P.; Erbacher, J.; Kinkel, H.; Pancost, R. D.; Pancost, R. D.; Schouten, S.; Sinninghe Damsté, J. S.

    2001-12-01

    Oceanic anoxic events (OAEs), periods of globally enhanced burial of organic matter (OM) in the marine realm, played an important role in the mid-Cretaceous `greenhouse climate' by effectively reducing atmospheric carbon dioxide concentrations. It is generally believed that these OAEs were caused either by decreased remineralisation or increased production of phytoplanktonic OM. Here we show that enhanced organic carbon (OC) burial during the early Albian OAE1b (~112 My) was caused by a different process. Combined biogeochemical and stable carbon isotopic analyses indicate that black shales from this period contain up to 80% of OC derived from archaea. Archaea-derived isoprenoidal tetraether membrane lipids and free and macromolecularly bound isoprenoid alkanes are abundantly present in these black shales. More specifically the presence of certain ether lipids (cyclic biphytane tetraethers) indicates representatives of the pelagic archaea. To the best of our knowledge this is the earliest fossil evidence for marine planktonic archaea, extending their geological record by more than 60 million years. The diversity of archaeal lipids recovered from the OAE1b black shales suggests that they derive from a multitude of archaeal species. However, the specific 13C enrichment of all such lipids indicates a common `heavy' (13C-rich) carbon source for the archaea and/or a common pathway of carbon-fixation with a reduced 13C fractionation effect compared to the Calvin cycle used by algae, cyanobacteria and higher plants. The large differences (up to 12%) in 13C/12C ratios between the algal biomarkers and the much more abundant archaeal molecular fossils suggest that the latter were not living heterotrophically on photoautotrophic biomass. It seems likely that the archaea present during OAE1b used a chemical energy source (possibly ammonium) for carbon fixation since photoautotrophy within the domain of the Archaea is restricted to only a few species from hypersaline

  4. Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event

    DEFF Research Database (Denmark)

    Kuypers, M.M.M.; Blokker, P.; Erbacher, J.;

    2001-01-01

    Biogeochemical and stable carbon isotopic analysis of black-shale sequences deposited during an Albian oceanic anoxic event (∼112 million years ago) indicate that up to 80 weight percent of sedimentary organic carbon is derived from marine, nonthermophilic archaea. The carbon-13 content of archae...

  5. Role of multiprotein bridging factor 1 in archaea: bridging the domains?

    NARCIS (Netherlands)

    Koning, de B.; Blombach, F.; Wu Hao,; Brouns, S.J.J.; Oost, van der J.

    2009-01-01

    MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge bet

  6. Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano.

    Science.gov (United States)

    Dorador, Cristina; Vila, Irma; Remonsellez, Francisco; Imhoff, Johannes F; Witzel, Karl-Paul

    2010-08-01

    Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83-96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 x 10(4) and site H6: 1.37 x 10(4) microS cm(-1)) and in one of the water samples (freshwater from site H0: 607 muS cm(-1)). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

  7. Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora▿

    OpenAIRE

    Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

    2008-01-01

    Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.

  8. Bacteria and Archaea in acidic environments and a key to morphological identification

    Science.gov (United States)

    Robbins, E.I.

    2000-01-01

    Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

  9. UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili

    NARCIS (Netherlands)

    Ajon, Malgorzata; Froels, Sabrina; van Wolferen, Marleen; Stoecker, Kilian; Teichmann, Daniela; Driessen, Arnold J. M.; Grogan, Dennis W.; Albers, Sonja-Verena; Schleper, Christa; Ajon, Małgorzata

    2011-01-01

    Archaea, like bacteria and eukaryotes, contain proteins involved in various mechanisms of DNA repair, highlighting the importance of these processes for all forms of life. Species of the order Sulfolobales of hyperthermophilic crenarchaeota are equipped with a strongly UV-inducible type IV pilus sys

  10. A virus of hyperthermophilic archaea with a unique architecture among DNA viruses

    NARCIS (Netherlands)

    Rensen, E.I.; Mochizuki, T,; Quemin, E.R. J.; Schouten, S.; Krupovica, M.; Prangishvili, D.

    2016-01-01

    Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Her

  11. Murein and pseudomurein cell wall binding domains of bacteria and archaea-a comparative view

    NARCIS (Netherlands)

    Visweswaran, Ganesh Ram R.; Dijkstra, Bauke W.; Kok, Jan

    2011-01-01

    The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and a

  12. Bridging domains : a comparison between information processing in Archaea and Eukarya

    NARCIS (Netherlands)

    Koning, de B.

    2015-01-01

    Bridging Domains A Comparison between Information Processing in Archaea and Eukarya

    Studying Information Processing Living cells evolved complex systems to handle the flow of information both accurately and efficiently.

  13. Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species

    NARCIS (Netherlands)

    van der Maarel, MJEC; Sprenger, W; Haanstra, R; Forney, LJ

    1999-01-01

    A methanogen-specific nested PCR approach was used to detect methanogenic archaea in seawater particles of the North Sea and the feces and the digestive tract of flounder (Platichthys flesus), a fish found in the North Sea. A number of 16S rDNA sequences with 97.6-99.5% similarity to Methanococcoide

  14. Diversity of membrane transport proteins for vitamins in bacteria and archaea

    NARCIS (Netherlands)

    Jähme, Michael; Slotboom, Dirk Jan

    2014-01-01

    BACKGROUND: All organisms use cofactors to extend the catalytic capacities of proteins. Many bacteria and archaea can synthesize cofactors from primary metabolites, but there are also prokaryotes that do not have the complete biosynthetic pathways for all essential cofactors. These organisms are dep

  15. Bacteria, not archaea, restore nitrification in a zinc-contaminated soil

    NARCIS (Netherlands)

    Mertens, J.; Broos, K.; Wakelin, S.A.; Kowalchuk, G.A.; Springael, D.; Smolders, E.

    2009-01-01

    Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of - and -proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of am

  16. Survival of Halophilic Archaea in the Stratosphere as a Mars Analog: A Transcriptomic Approach

    Science.gov (United States)

    DasSarma, S.; DasSarma, P.; Laye, V.; Harvey, J.; Reid, C.; Shultz, J.; Yarborough, A.; Lamb, A.; Koske-Phillips, A.; Herbst, A.; Molina, F.; Grah, O.; Phillips, T.

    2016-05-01

    On Earth, halophilic Archaea tolerate multiple extreme conditions similar to those on Mars. In order to study their survival, we launched live cultures into Earth’s stratosphere on helium balloons. The effects on survival and transcriptomes were interrogated in the lab.

  17. Exploring the ecophysiology of anaerobic communities of methanotrophic archaea and sulfate-reducing bacteria

    NARCIS (Netherlands)

    Timmers, P.H.A.

    2015-01-01

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is a widespread occurring process in anoxic marine sediments. The process is performed by ANaerobic MEthane oxidizing archaea (ANME) and associated sulfate reducing bacteria (SRB). The ANME presumably oxidize methane through reve

  18. Information Ecology

    DEFF Research Database (Denmark)

    Christiansen, Ellen Tove

    2006-01-01

    in the 1960ties, and chosen here because it integrates cultural and psychological trajectories in a theory of living settings. The pedagogical-didactical paradigm comprises three distinct information ecologies, named after their intended outcome: the problem-setting, the exploration-setting, and the fit......The paper describes a pedagogical didactical paradigm for teaching student-designers how to deal with context issues. Form/context-relationships are conceptualized as information ecologies and described as behavioral settings using a key concept developed by social psychologist R.A. Baker......-setting. It is specified how context issues can be treated within each of these information ecologies. The paper concludes by discussing the outcome of applying this paradigm with respect to the student-designers’ competence as reflective practitioners....

  19. Apparent Minimum Free Energy Requirements for Methanogenic Archaea and Sulfate-Reducing Bacteria in an Anoxic Marine Sediment

    Science.gov (United States)

    Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.; DeVincenzi, Don (Technical Monitor)

    2000-01-01

    Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).

  20. ECOLOGICAL EDUCATION

    Directory of Open Access Journals (Sweden)

    GABRIELA GYONGY MIHUT

    2011-04-01

    Full Text Available While in most emerging and developing countries, the population has a lower ecological footprint in the developed countries have a larger footprint.There is also an alarming contrast between a person perception of her liability for damages to its environment and its actual size. These misconceptions may have their source in the absence of awareness of risks from climate change, culture or religion.The purpose of this study is to analyze the situation at the international and Romanian level and to draw attention on the necessity of un ecological education.

  1. Central Metabolic Pathways of Hyperthermophiles: Important Clues on how Metabolism Gives Rise to Life

    Science.gov (United States)

    Ronimus, R. S.; Morgan, H. W.

    2004-06-01

    Vital clues on life's origins within the galaxy exist here on present day Earth. Life is currently divided into the three domains Bacteria, Archaea and Eukarya based on the phylogeny of small ribosomal subunit RNA (16S/18S) gene sequences. The domains are presumed to share a ``last universal common ancestor'' (LUCA). Hyperthermophilic bacteria and archaea, which are able to thrive at 80^{circ}C or higher, dominate the bottom of the tree of life and are thus suggested to be the least evolved, or most ``ancient''. Geochemical data indicates that life first appeared on Earth approximately 3.8 billion years ago in a hot environment. Due to these considerations, hyperthermophiles represent the most appropriate microorganisms to investigate the origins of metabolism. The central biochemical pathway of gluconeogenesis/glycolysis (the Embden-Meyerhof pathway) which produces six carbon sugars from three carbon compounds is present in all organisms and can provide important hints concerning the early development of metabolism. Significantly, there are a number of striking deviations from the textbook canonical reaction sequence that are found, particularly in hyperthermophilic archaea. In this paper the phylogenetic istribution of enzymes of the pathway is detailed; overall, the distribution pattern provides strong evidence for the pathway to have developed from the bottom-up.

  2. Heme metabolism in stress regulation and protein production: from Cinderella to a key player

    DEFF Research Database (Denmark)

    Martínez, J. L.; Petranovic, D.; Nielsen, Jens

    2016-01-01

    Heme biosynthesis is a highly conserved pathway which is present in all kingdoms, from Archaea to higher organisms such as plants and mammals. The heme molecule acts as a prosthetic group for different proteins and enzymes involved in energy metabolism and reactions involved in electron transfer....

  3. [Microbial metabolism in typical flooded paddy soils ].

    Science.gov (United States)

    Cai, Yuanfeng; Wu, Yucheng; Wang, Shuwei; Yan, Xiaoyuan; Zhu, Yongguan; Jia, Zhongjun

    2014-09-01

    [OBJECTIVE] The object of this study is to reveal the composition of active microorganism and their metabolic activities in flooded paddy soils with long-term fertilization ( Mineral nitrogen, phosphorus, and potassium, NPK) and without fertilizer (Control check, CK) by environmental transcriptomics. [METHODS] Flooded soil microcosms were incubated in the laboratory for two weeks, then total RNA were extracted from the soil for transcriptome sequencing. Resulting fastq files were uploaded to the Metagenomics Analysis Server (MG-RAST) for taxonomic analysis, gene annotation and function classification. [RESULTS] Transcripts from diverse active microorganism, including bacteria ( > 95% ) , archaea, eukaryotes and viruses, were detected in both flooded paddy soils of CK and NPK treatments. Most of the transcripts (active genes) of bacteria and archaea were derived from Proteobacteria (more than 50% of total bacterial transcripts) and Thaumarchaaeota (about 70% of total archaeal transcripts ) respectively in both treatments. Transcriptional activity of Acidobacteria in NPK treatment paddy soil was significantly higher than that in CK treatment paddy soil. As for other phyla of bacteria and archaea, there were no significant differences of transcriptional activity of them between CK and NPK treatment paddy soils. The highest expressed gene in both CK and NPK treatment paddy soils is ABC transporter encoding gene which related to the transmembrane transport of substances. Based on gene function category of COG (Clusters of Orthologous Genes), Subsystem and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, we found that the main metabolic activities of microorganisms in both CK and NPK treatment paddy soils were related to energy production and conversion, carbohydrate metabolism, protein metabolism and amino acid metabolism, and the dominant KEGG pathways were oxidative phosphorylation and aminoacyl-tRNA biosynthesis. [ CONCLUSION] Composition of active

  4. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

    Directory of Open Access Journals (Sweden)

    B. Orcutt

    2008-05-01

    Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

  5. Bacterial motility in the sea and its ecological implications

    DEFF Research Database (Denmark)

    Grossart, Hans-Peter; Riemann, Lasse; Azam, F.

    2001-01-01

    Motility could be an important adaptation of heterotrophic bacteria and archaea, and it may have ecological and biogeochemical implications. However, the limited observations so far show that only a small fraction (=10%) of bacteria is motile. We report a systematic 10 mo long field study off...... the coast of La Jolla, California, as well as a mesocosm study to examine bacterial motility and its relationship to environmental variables. Dark-field microscopy revealed periods of sustained low (fall and winter, bacteria (% motile......). Bacteria in natural seawater did not swim constantly nor at constant speeds; over 40% swam bacteria...

  6. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

    OpenAIRE

    Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W.; Prosser, James I.; Gubry-Rangin, Cécile

    2015-01-01

    Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylog...

  7. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

    Science.gov (United States)

    Evans, Paul N; Parks, Donovan H; Chadwick, Grayson L; Robbins, Steven J; Orphan, Victoria J; Golding, Suzanne D; Tyson, Gene W

    2015-10-23

    Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota. PMID:26494757

  8. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

    Science.gov (United States)

    Evans, Paul N; Parks, Donovan H; Chadwick, Grayson L; Robbins, Steven J; Orphan, Victoria J; Golding, Suzanne D; Tyson, Gene W

    2015-10-23

    Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.

  9. Ecological macroeconomics

    DEFF Research Database (Denmark)

    Røpke, Inge

    2013-01-01

    of the economy could go hand in hand with increased employment. These ideas were not reflected much in actual policies, and – despite some green elements – the subsequent economic upturn was driven first of all by consumption, and in several affluent countries, fueled by credit expansion. The current revival...... on how to reconcile environmental and social concerns. Based on this broad variety of pieces in a jigsaw puzzle, a new ecological macroeconomics is emerging, but the contours are still vague. This chapter seeks to outline some of this topography and to add a few pieces of its own by highlighting the need...... to shift resources from consumption to investment and describing the role of consumer-citizens in such a change. The chapter starts by identifying the problems and challenges for an ecological macroeconomics. The next section outlines some of the shortcomings of traditional macroeconomics...

  10. ECOLOGICAL EDUCATION

    OpenAIRE

    GABRIELA GYONGY MIHUT

    2011-01-01

    While in most emerging and developing countries, the population has a lower ecological footprint in the developed countries have a larger footprint.There is also an alarming contrast between a person perception of her liability for damages to its environment and its actual size. These misconceptions may have their source in the absence of awareness of risks from climate change, culture or religion.The purpose of this study is to analyze the situation at the international and Romanian level an...

  11. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...... biogeochemical processes are carried exclusively by bacteria. * Bacteria play an important role in all types of habitats including some that cannot support eukaryotic life....

  12. The Divergence and Natural Selection of Autocatalytic Primordial Metabolic Systems

    Science.gov (United States)

    Marakushev, Sergey A.; Belonogova, Ol'ga V.

    2013-06-01

    The diversity of the central metabolism of modern organisms is caused by the existence of a few metabolic modules, combination of which produces multiple metabolic pathways. This paper analyzes biomimetically reconstructed coupled autocatalytic cycles as the basis of ancestral metabolic systems. The mechanism for natural selection and evolution in autocatalytic chemical systems may be affected by natural homeostatic parameters such as ambient chemical potentials, temperature, and pressure. Competition between separate parts of an autocatalytic network with positive-plus-negative feedback resulted in the formation of primordial autotrophic, mixotrophic, and heterotrophic metabolic systems. This work examined the last common ancestor of a set of coupled metabolic cycles in a population of protocells. Physical-chemical properties of these cycles determined the main principles of natural selection for the ancestral Bacteria and Archaea taxa.

  13. Genome sequencing of methanogenic Archaea Methanosarcina mazei TUC01 strain isolated from an Amazonian Flooded Area

    Science.gov (United States)

    Baraúna, R. A.; Graças, D. A.; Ramos, R. T.; Carneiro, A. R.; Lopes, T. S.; Lima, A. R.; Zahlouth, R. L.; Pellizari, V. H.; Silva, A.

    2013-05-01

    Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order. This species is known for its broad catabolic range among methanogens and is widespread throughout diverse environments. The draft genome of a strain cultivated from the sediment of the Tucuruí hydroelectric power station, the fourth largest hydroelectric dam in the world, is described here. Approximately 80% of methane is produced by biogenic sources, such as methanogenic archaea from M. mazei species. Although the methanogenesis pathway is well known, some aspects of the core genome, genome evolution and shared genes are still unclear. A sediment sample from the Tucuruí hydropower station reservoir was inoculated in mineral media supplemented with acetate and methanol. This media was maintained in an H2:CO2 (80:20) atmosphere to enrich and cultivate M. mazei. The enrichment was conducted at 30°C under standard anaerobic conditions. After several molecular and cellular analyses, total DNA was extracted from a non-pure culture of M. mazei, amplified using phi29 DNA polymerase (BioLabs) and finally used as a source template for genome sequencing. The draft genome was obtained after two rounds of sequencing. First, the genome was sequenced using a SOLiD System V3 with a mate-paired library, which yielded 24,405,103 and 24,399,268 reads (50 bp) for the R3 and F3 tags, respectively. The second round of sequencing was performed using the SOLiD 5500 XL platform with a mate-paired library, resulting in a total of 113,588,848 reads (60 bp) for each tag (F3 and R3). All reads obtained by this procedure were filtered using Quality Assessment software, whereby reads with an average quality score below Phred 20 were removed. Velvet and Edena were used to assemble the reads, and Simplifier was used to remove the redundant sequences. After this, a total of 16,811 contigs were obtained. M. mazei GO1 (AE008384) genome was used to map the contigs and generate the scaffolds. We used the

  14. One-carbon metabolism in acetogenic and sulfate-reducing bacteria

    OpenAIRE

    Visser, M.

    2015-01-01

    ABSTRACT One-carbon metabolism in acetogenic and sulfate-reducing bacteria Life on earth is sustained by the constant cycling of six essential elements: oxygen, hydrogen, nitrogen, sulfur, phosphorous, and carbon. The continuous cycling of these elements is due to geo-chemical processes and the combined metabolism of all life on earth. Microorganisms like bacteria and archaea play a major role in this. This is also true for the carbon cycle. In this cycle carbon dioxide and methane are two im...

  15. Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2007-01-01

    -specific microbial community distinct from that of unvegetated sediment and (ii) that aquatic macrophytes have an impact on abundance and activity of nitrifying and denitrifying bacteria in freshwater sediment. The goal of this study was to test these hypotheses for the key functional group for coupled nitrification......AMMONIA-OXIDIZING ARCHAEA AND BACTERIA IN THE RHIZOSPHERE OF FRESHWATER MACROPHYTES Martina Herrmann and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia dortmanna release oxygen from...... measurements revealed clear differences in ammonia oxidation rates. The diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was assessed using the ammonia monooxygenase (amoA) gene as functional marker. Both AOA and AOB could be detected in the rhizosphere of all three plant...

  16. Do the maximum sizes, ages and patterns of growth of three reef-dwelling labrid species at two latitudes differ in a manner conforming to the metabolic theory of ecology?

    Science.gov (United States)

    Lek, E; Fairclough, D V; Hall, N G; Hesp, S A; Potter, I C

    2012-11-01

    The size and age data and patterns of growth of three abundant, reef-dwelling and protogynous labrid species (Coris auricularis, Notolabrus parilus and Ophthalmolepis lineolata) in waters off Perth at c. 32° S and in the warmer waters of the Jurien Bay Marine Park (JBMP) at c. 30° S on the lower west coast of Australia are compared. Using data for the top 10% of values and a randomization procedure, the maximum total length (L(T) ) and mass of each species and the maximum age of the first two species were estimated to be significantly greater off Perth than in the JBMP (all P 0.05). These latitudinal trends, thus, typically conform to those frequently exhibited by fish species and the predictions of the metabolic theory of ecology (MTE). While, in terms of mass, the instantaneous growth rates of each species were similar at both latitudes during early life, they were greater at the higher latitude throughout the remainder and thus much of life, which is broadly consistent with the MTE. When expressed in terms of L(T), however, instantaneous growth rates did not exhibit consistent latitudinal trends across all three species. The above trends with mass, together with those for reproductive variables, demonstrate that a greater amount of energy is directed into somatic growth and gonadal development by each of these species at the higher latitude. The consistency of the direction of the latitudinal trends for maximum body size and age and pattern of growth across all three species implies that each species is responding in a similar manner to differences between the environmental characteristics, such as temperature, at those two latitudes. The individual maximum L(T), mass and age and pattern of growth of O. lineolata at a higher and thus cooler latitude on the eastern Australian coast are consistent with the latitudinal trends exhibited by those characteristics for this species in the two western Australian localities. The implications of using mass rather than

  17. The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea

    OpenAIRE

    Mongodin, E. F.; Nelson, K. E.; Daugherty, S; DeBoy, R. T.; Wister, J.; Khouri, H; Weidman, J.; Walsh, D.A.; Papke, R. T.; Sanchez Perez, G.; Sharma, A K; Nesbø, C L; Macleod, D; Bapteste, E; Doolittle, W F

    2005-01-01

    Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes produc...

  18. Survival of Methanogenic Archaea from Siberian Permafrost under Simulated Martian Thermal Conditions

    OpenAIRE

    Daria Morozova; D. Möhlmann; Dirk Wagner

    2007-01-01

    Since ESA mission Mars Express determined water on Mars, a fundamental requirement for life, as well as the presence of CH4 in the Martian atmosphere, which could only have originated from active volcanism or from biological sources, it is obviously that microbial life could still exist on Mars, for example in the form of subsurface lithoautotrophic ecosystems, which are also exist in permafrost regions on Earth. Present work deals with the resistance investigation of methanogenic archaea fro...

  19. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

    OpenAIRE

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  20. Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant

    OpenAIRE

    Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

    2012-01-01

    Background The activated sludge process is one of the most widely used methods for treatment of wastewater and the microbial community composition in the sludge is important for the process operation. While the bacterial communities have been characterized in various activated sludge systems little is known about archaeal communities in activated sludge. The diversity and dynamics of the Archaea community in a full-scale activated sludge wastewater treatment plant were investigated by fluores...

  1. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes.

    Science.gov (United States)

    Régnier, Mireille; Chassignet, Philippe

    2016-01-01

    Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences.

  2. Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

    OpenAIRE

    Christian Hoffmann; Serena Dollive; Stephanie Grunberg; Jun De Chen; Hongzhe Li; Wu, Gary D.; Lewis, James D.; Bushman, Frederic D.

    2013-01-01

    Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi w...

  3. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes.

    Science.gov (United States)

    Régnier, Mireille; Chassignet, Philippe

    2016-01-01

    Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences. PMID:27376057

  4. Detection of Ammonia-Oxidizing Archaea in Fish Processing Effluent Treatment Plants

    OpenAIRE

    Devivaraprasad Reddy, A.; Subrahmanyam, Gangavarapu; Shivani Kallappa, Girisha; Karunasagar, Iddya; Karunasagar, Indrani

    2014-01-01

    Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of t...

  5. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat

    OpenAIRE

    Biller, Steven J.; Mosier, Annika C.; Wells, George F.; Francis, Christopher A.

    2012-01-01

    Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 800...

  6. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil

    OpenAIRE

    Serrano, P; Hermelink, A.; Lasch, P.; de Vera, J.-P.; König, N.; Burckhardt, O.; Wagner, D.

    2015-01-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the 25 production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the diffe...

  7. Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems.

    Science.gov (United States)

    Danovaro, Roberto; Molari, Massimiliano; Corinaldesi, Cinzia; Dell'Anno, Antonio

    2016-04-01

    Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes. PMID:27386507

  8. Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda.

    Directory of Open Access Journals (Sweden)

    Vladimír Šustr

    Full Text Available Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE. The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.

  9. Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda).

    Science.gov (United States)

    Šustr, Vladimír; Chroňáková, Alica; Semanová, Stanislava; Tajovský, Karel; Šimek, Miloslav

    2014-01-01

    Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.

  10. A review of acquired thermotolerance, heat shock proteins, and molecular chaperones in archaea

    Energy Technology Data Exchange (ETDEWEB)

    Trent, J.D.

    1996-05-01

    Acquired thermotolerance, the associated synthesis of heat-shock proteins (HSPs) under stress conditions, and the role of HSPs as molecular chaperones under normal growth conditions have been studied extensively in eukaryotes and bacteria, whereas research in these areas in archaea is only beginning. All organisms have evolved a variety of strategies for coping with high-temperature stress, and among these strategies is the increased synthesis of HSPs. The facts that both high temperatures and chemical stresses induce the HSPs and that some of the HSPs recognize and bind to unfolded proteins in vitro have led to the theory that the function of HSPs is to prevent protein aggregation in vivo. The facts that some HSPs are abundant under normal growth conditions and that they assist in protein folding in vitro have led to the theory that they assist protein folding in vivo; in this role, they are referred to as molecular chaperones. The limited research on acquired thermotolerance, HSPs, and molecular chaperones in archaea, particularly the hyperthermophilic archaea, suggests that these extremophiles provide a new perspective in these areas of research, both because they are members of a separate phylogenetic domain and because they have evolved to live under extreme conditions.

  11. Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages.

    Science.gov (United States)

    Shi, Yu; Huang, Zhou; Han, Shuai; Fan, Shuo; Yang, Hong

    2015-08-01

    Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites.

  12. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

    Directory of Open Access Journals (Sweden)

    Christian Hoffmann

    Full Text Available Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

  13. Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil

    Science.gov (United States)

    Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.; Murphy, Daniel V.

    2015-06-01

    Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.

  14. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

    Science.gov (United States)

    Woese, C R; Kandler, O; Wheelis, M L

    1990-06-01

    Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea. PMID:2112744

  15. Reassembling ecologies

    OpenAIRE

    Justesen, Lise; Mouritsen, Jan; Tryggestad, Kjell

    2011-01-01

    In its general form, stakeholder theory posits an extension of the ecology. It claims that there are other stakes and interests than those posited by shareholder value theory (Freeman et al. 2004; Jensen and Sandström 2011), and some stakeholder theory proponents argue that the natural environment is also to be considered as a stakeholder (Driscoll and Starik 2004; Norton 2007). It is a positive claim – there are more stakes and interests – and a moral one – we should look towards more intere...

  16. Ecological Economics

    Science.gov (United States)

    Common, Michael; Stagl, Sigrid

    2005-10-01

    Taking as its starting point the interdependence of the economy and the natural environment, this book provides a comprehensive introduction to the emerging field of ecological economics. The authors, who have written extensively on the economics of sustainability, build on insights from both mainstream economics and ecological sciences. Part I explores the interdependence of the modern economy and its environment, while Part II focuses mainly on the economy and on economics. Part III looks at how national governments set policy targets and the instruments used to pursue those targets. Part IV examines international trade and institutions, and two major global threats to sustainability - climate change and biodiversity loss. Assuming no prior knowledge of economics, this textbook is well suited for use on interdisciplinary environmental science and management courses. It has extensive student-friendly features including discussion questions and exercises, keyword highlighting, real-world illustrations, further reading and website addresses. A comprehensive introduction to a developing field which will interest students from science, economics and management backgrounds A global approach to the problems of sustainability and sustainable development, issues which are increasingly prominent in political debate and policy making Filled with student-friendly features including focus areas for each chapter, keyword highlighting, real-world illustrations, discussion questions and exercises, further reading and website addresses

  17. Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.

    Directory of Open Access Journals (Sweden)

    Seiya Watanabe

    Full Text Available Proline racemase (ProR is a member of the pyridoxal 5'-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE, which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372 from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR. This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241 and natural ProR (phenylalanine. The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline, and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.

  18. Scaling metabolic rate fluctuations

    OpenAIRE

    Labra, Fabio A.; Marquet, Pablo A.; Bozinovic, Francisco

    2007-01-01

    Complex ecological and economic systems show fluctuations in macroscopic quantities such as exchange rates, size of companies or populations that follow non-Gaussian tent-shaped probability distributions of growth rates with power-law decay, which suggests that fluctuations in complex systems may be governed by universal mechanisms, independent of particular details and idiosyncrasies. We propose here that metabolic rate within individual organisms may be considered as an example of an emerge...

  19. Metabolic acidosis

    Science.gov (United States)

    Acidosis - metabolic ... Metabolic acidosis occurs when the body produces too much acid. It can also occur when the kidneys are not ... the body. There are several types of metabolic acidosis. Diabetic acidosis develops when acidic substances, known as ...

  20. Associative patterns among anaerobic fungi, methanogenic archaea and bacterial communities in response to changes in diet and age in the rumen of dairy cows

    Directory of Open Access Journals (Sweden)

    Sanjay eKumar

    2015-07-01

    Full Text Available The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF, protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation and multiparous (≥ second lactation cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n=5 and multiparous (n=5 cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index revealed the effect of diet (P < 0.01 on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05. Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet whereas, Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to

  1. Ecological Ethics

    International Nuclear Information System (INIS)

    Deborah Oughton started with a view of the work in progress by the ICRP TG 94 on ethics, from the historical context and the principles-based ethics in RP, to continue with an overview of the ethical theories and with the main area of elaboration which concerns the common values, to conclude with considerations about the implementation in different area such as biomedicine, nuclear safety and workers, ecological aspects, and environmental health and society. By reading again the ICRP and IAEA publications on the ethical aspects in the protection of environment from the effects of ionizing radiation, the presentation covers the various and different cultures within the history of environmental ethics, the perception of Nature and the theories of environmental ethics, in particular by focusing on anthropocentrism, biocentrism and ecocentrism, as philosophical worldwide views, and on conservation, biodiversity, sustainability, environmental justice and human dignity, as primary principles of environmental protection. The influence of western Christianity, with a view of man dominating over every creeping thing on earth, and of the non-western ideas, the human perception of Nature has been analyzed and discussed to conclude that, in reality then, the anthropocentrism, biocentrism and ecocentrism, as reflected in many cultures and religions, they all support the need to protect the environment and to recognise and preserve the diversity. Three challenges were then discussed in the presentation: the ecosystem approach and ecological economics, for example in the case of Fukushima by asking what is the economic cost of marine contamination; the ecosystem changes with attention to what harms, as in the case of the environment in the contaminated areas around Chernobyl; and the environmental consequences of remediation, which can be considered a source of controversy for environmental ethics and policy

  2. Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing

    Institute of Scientific and Technical Information of China (English)

    HUO Yingyi; CHENG Hong; Anton F Post; WANG Chunsheng; JIANG Xiawei; PAN Jie; WU Min; XU Xuewei

    2015-01-01

    Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16S rRNA based PCR method. Proteobacteria and MGI Thaumarch-aeota dominated the bacterial and archaeal 16S rRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer (HGT) events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93a, belonging to MGI Thaumarch-aeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

  3. Ecological stability of landscape - ecological infrastructure - ecological management

    International Nuclear Information System (INIS)

    The Field Workshop 'Ecological Stability of Landscape - Ecological Infrastructure - Ecological Management' was held within a State Environmental Programme financed by the Federal Committee for the Environment. The objectives of the workshop were to present Czech and Slovak approaches to the ecological stability of the landscape by means of examples of some case studies in the field, and to exchange ideas, theoretical knowledge and practical experience on implementing the concept of ecological infrastructure in landscape management. Out of 19 papers contained in the proceedings, 3 items were inputted to the INIS system. (Z.S.)

  4. Public aquaria as long-term enrichments for investigating planktonic Archaea

    Science.gov (United States)

    Goldenstein, Nadine I.; Warren, Courtney E.; Lipp, Julius S.; Pagani, Mark; Hinrichs, Kai-Uwe

    2016-04-01

    The most abundant group of planktonic Archaea , the so-called Thaumarchaeota, represents 20% of all marine planktonic microorganisms (Karner et al., 2001) and their energy efficient performance of nitrification makes them key players in the global nitrogen- and carbon-cycle (Könneke et al., 2014). Furthermore, planktonic Archaea are considered to be the major producers of specific microbial membrane lipids that are extensively used as paleoproxies in marine climate research (Schouten et al., 2002). Therefore, assessing the parameters controlling the distribution of Archaea in the marine water column is crucial for studies of modern and past marine environments. Although diverse studies utilizing DNA- and biomarker-based approaches have constrained the turnover and distribution of marine Archaea, the environmental factors affecting their abundance and activity (e.g., Wuchter et al., 2006; Bale et al., 2013) are still poorly understood. Further, previous surveys, using enrichment cultivation and pure culture experiments, provided valuable information on adaptation of planktonic Archaea to changes of parameters affecting growth conditions, such as temperature, salinity and growth stage (Elling et al., 2014, 2015). Hence, we know that planktonic Archaea directly adapt their membranes to changing growth conditions, but also that environmental selection for individual phylogenetic groups of these organisms is also reflected in the membrane lipid pool. Extending these studies, this project further aims at constraining the environmental parameters controlling archaeal abundance in the marine environment. Public aquaria, which are comparable to perfectly monitored long-term enrichment cultures, are optimal sampling sites for this task. A comprehensive set of 120 water and substrate samples from fresh, marine and brackish systems exhibiting diverse conditions was selected from 15 public aquaria at the east and west coast of the USA. These samples were examined for their

  5. Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.

    Science.gov (United States)

    Petitjean, Céline; Deschamps, Philippe; López-García, Purificación; Moreira, David

    2015-01-01

    The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome. PMID:25527841

  6. Ecological perspectives on synthetic biology: insights from microbial population biology

    OpenAIRE

    Ana E. Escalante; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent member...

  7. Diversity, dynamics and activity of mesophilic Archaea in stratified feshwater lakes. Implications in biogeochemical cycles

    OpenAIRE

    Llirós Dupré, Marc

    2010-01-01

    Aquesta tesi doctoral va estudiar la diversitat (riquesa i abundància), la distribució i la dinàmica de les comunitats planctòniques d'Archaea presents a diferents llacs estratificats temperats d'aigua dolça per aportar evidencies sobre la seva distribució i la seva possible activitat en aquests ecosistemes en relació als cicles biogeoquímics presents en els mateixos. Es varen estudiar dos estanyols d'origen càrstic (l'Estanyol del Vilar durant cinc anys consecutius (2001-2005) i l'Estanyol d...

  8. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China

    Science.gov (United States)

    Liu, D. Y.; Ding, W. X.; Jia, Z. J.; Cai, Z. C.

    2011-02-01

    Methane (CH4) emissions from natural wetland ecosystems exhibit large spatial variability at regional, national, and global levels related to temperature, water table, plant type and methanogenic archaea etc. To understand the underlying factors that induce spatial differences in CH4 emissions, and the relationship between the population of methanogenic archaea and CH4 production potential in natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical soil profiles sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjiang marsh in the cold temperate zone, and the Ruoergai peatland in the Qinghai-Tibetan Plateau in the alpine climate zone. The top soil layer had the highest population of methanogens (1.07-8.29 × 109 cells g-1 soil) in all wetlands except the Ruoergai peatland and exhibited the maximum CH4 production potential measured at the mean in situ summer temperature. There is a significant logarithmic correlation between the abundance of methanogenic archaea and the soil organic carbon (R2 = 0.72, P nitrogen concentrations (R2 = 0.76, P affect the population of methanogens in wetland ecosystems. While the CH4 production potential is not significantly related to methanogen population (R2 = 0.01, P > 0.05, n = 13), it is related to the dissolved organic carbon concentration (R2 = 0.31, P = 0.05, n = 13). This suggests that the methanogen population might be not an effective index for predicting the CH4 production in wetland ecosystems. The CH4 production rate of the top soil layer increases with increasing latitude, from 273.64 μg CH4 kg-1 soil d-1 in the Poyang wetland to 664.59 μg CH4 kg-1 soil d-1 in the Carex lasiocarpa marsh of the Sanjiang Plain. We conclude that CH4 production potential in the freshwater wetlands of Eastern China is mainly affected by the supply of methanogenic substrates rather than temperature; in contrast

  9. Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil

    OpenAIRE

    Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.; Murphy, Daniel V.

    2015-01-01

    Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, an...

  10. Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus

    Directory of Open Access Journals (Sweden)

    Müller Judith

    2009-03-01

    Full Text Available Abstract Background Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. Results Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a photophobic responses were measured by a computer-based cell tracking system b flagellar rotational bias was determined by dark-field microscopy, and c chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea

  11. Sound Ecologies

    Directory of Open Access Journals (Sweden)

    Michelle Duffy

    2010-02-01

    Full Text Available Discussions about what constitutes ‘the rural’ invariably focus on notions of spatial location – of inhabiting spaces apart from that of the metropolitan. Deeply embedded in our images of what it means to be Australian, nonetheless our intellectual framing of ‘the rural’ as something outback and beyond has significant implications for our relations with these spaces. The relatively recent phenomenon of sea- and tree-changes has struck many unawares, and not simply because a good latté is so hard to find. Although a frivolous remark, such an apparent lack does shift our focus to a bodily scale of the rural; how is rural place re/made through our experiences of it? This article originates out of on-going research that explores the practice of listening and sound and the ways in which the body can draw attention to the intuitive, emotional, and psychoanalytical processes of subjectivity and place-making. Drawing on Nigel Thrift’s concept of an ecology of place, I suggest that contemporary heightened concerns with regards to loss and lack in rural Australia has led to a nascent emotional economy – one in which individual and intimate connections to the rural require a rethinking of how we live community and belonging. In such a terrain, what does it mean to be rural?

  12. Interdisciplinary Pathways for Urban Metabolism Research

    Science.gov (United States)

    Newell, J. P.

    2011-12-01

    With its rapid rise as a metaphor to express coupled natural-human systems in cities, the concept of urban metabolism is evolving into a series of relatively distinct research frameworks amongst various disciplines, with varying definitions, theories, models, and emphases. In industrial ecology, housed primarily within the disciplinary domain of engineering, urban metabolism research has focused on quantifying material and energy flows into, within, and out of cities, using methodologies such as material flow analysis and life cycle assessment. In the field of urban ecology, which is strongly influenced by ecology and urban planning, research focus has been placed on understanding and modeling the complex patterns and processes of human-ecological systems within urban areas. Finally, in political ecology, closely aligned with human geography and anthropology, scholars theorize about the interwoven knots of social and natural processes, material flows, and spatial structures that form the urban metabolism. This paper offers three potential interdisciplinary urban metabolism research tracks that might integrate elements of these three "ecologies," thereby bridging engineering and the social and physical sciences. First, it presents the idea of infrastructure ecology, which explores the complex, emergent interdependencies between gray (water and wastewater, transportation, etc) and green (e.g. parks, greenways) infrastructure systems, as nested within a broader socio-economic context. For cities to be sustainable and resilient over time-space, the theory follows, these is a need to understand and redesign these infrastructure linkages. Second, there is the concept of an urban-scale carbon metabolism model which integrates consumption-based material flow analysis (including goods, water, and materials), with the carbon sink and source dynamics of the built environment (e.g. buildings, etc) and urban ecosystems. Finally, there is the political ecology of the material

  13. The information science of microbial ecology.

    Science.gov (United States)

    Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

    2016-06-01

    A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation.

  14. Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.

    Science.gov (United States)

    Martin del Campo, Martha; Camacho, Rosa M; Mateos-Díaz, Juan C; Müller-Santos, Marcelo; Córdova, Jesus; Rodríguez, Jorge A

    2015-11-01

    Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.

  15. Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid.

    Directory of Open Access Journals (Sweden)

    Salla T Jaakkola

    Full Text Available Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38-41 million years ago rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11-14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6-8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.

  16. Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.

    Directory of Open Access Journals (Sweden)

    Feng-Jie Sun

    2008-03-01

    Full Text Available Transfer RNAs (tRNAs are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.

  17. The Function of Gas Vesicles in Halophilic Archaea and Bacteria: Theories and Experimental Evidence

    Directory of Open Access Journals (Sweden)

    Aharon Oren

    2012-12-01

    Full Text Available A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp. possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of gas vesicles in Hbt. salinarum and Hfx. mediterranei and the regulation of their formation. Different functions were suggested for gas vesicle synthesis: buoying cells towards oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells optimally for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (for the Archaea and dispersal of endospores (for the anaerobic spore-forming Bacteria. Except for Hqr. walsbyi which abounds in saltern crystallizer brines, gas-vacuolate halophiles are not among the dominant life forms in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies failed to provide clear evidence for their possible function. This paper summarizes the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms.

  18. Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.

    Science.gov (United States)

    Martin del Campo, Martha; Camacho, Rosa M; Mateos-Díaz, Juan C; Müller-Santos, Marcelo; Córdova, Jesus; Rodríguez, Jorge A

    2015-11-01

    Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production. PMID:26369647

  19. Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.

    Science.gov (United States)

    van de Werken, Harmen J G; Verhees, Corné H; Akerboom, Jasper; de Vos, Willem M; van der Oost, John

    2006-07-01

    The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, some of which catalyze unique conversions. Moreover, the enzymes appear not to be regulated allosterically, but rather at transcriptional level. To elucidate details of the gene expression control, the transcription initiation sites of the glycolytic genes in Pyrococcus furiosus have been mapped by primer extension analysis and the obtained promoter sequences have been compared with upstream regions of non-glycolytic genes. Apart from consensus sequences for the general transcription factors (TATA-box and BRE) this analysis revealed the presence of a potential transcription factor binding site (TATCAC-N(5)-GTGATA) in glycolytic and starch utilizing promoters of P. furiosus and several thermococcal species. The absence of this inverted repeat in Pyrococcus abyssi and Pyrococcus horikoshii probably reflects that their reduced catabolic capacity does not require this regulatory system. Moreover, this phyletic pattern revealed a TrmB-like regulator (PF0124 and TK1769) which may be involved in recognizing the repeat. This Thermococcales glycolytic regulon, with more than 20 genes, is the largest regulon that has yet been described for Archaea.

  20. Enhanced abundance and diversity of ammonia-oxidizing Archaea in the Pearl River estuary

    Science.gov (United States)

    Xie, W.; Zhang, C. L.; Wang, P.; Zhou, X.; Guo, W.

    2014-12-01

    Thaumarchaeota are recently recognized as an important group of Archaea that can perform aerobic oxidation of ammonia in a wide range of environments. The goal of this study was to evaluate changes in abundance and diversity of planktonic ammonia-oxidizing Archaea (e.g., Thaumarchaeota) along a salinity gradient from the lower Pearl River to the northern South China Sea. Quantitative PCR and sequencing of total archaeal 16S rRNA gene and the archaeal amoA gene were performed on suspended particulate organic matter collected in different seasons from the freshwater to the ocean water. Total amoA gene copies and relative abundance of Thaumarchaeota all peaked in the estuary where salinity ranged between 4.5‰ and 26.7‰. The diversity of archaeal amoA gene was also highest in the estuary. Seasonality and SiO32- appear to be two major factors affecting the distribution of subclusters of archaeal amoA genes. For example, Nitrosopumilus subcluster 7.1 was most abundant in winter in fresh water, whereas Nitrososphaera were more abundant in summer. Samples collected from the area around Wanshan Island, which is located at the outermost part of the Pearl River estuary, had high abundance of unclassified archaeal amoA genes, suggesting some new groups of Thaumarchaeota might inhabit this water body. Overall, the high abundance and diversity of Thaumarchaeota in the Pearl River estuary may indicate enhanced role of AOA in nitrogen cycle in this dynamic ecosystem.

  1. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: fengyg@qibebt.ac.cn [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  2. Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean.

    Science.gov (United States)

    Rosenwasser, Shilo; Ziv, Carmit; Creveld, Shiri Graff van; Vardi, Assaf

    2016-10-01

    Marine viruses are considered to be major ecological, evolutionary, and biogeochemical drivers of the marine environment, responsible for nutrient recycling and determining species composition. Viruses can re-shape their host's metabolic network during infection, generating the virocell-a unique metabolic state that supports their specific requirement. Here we discuss the concept of 'virocell metabolism' and its formation by rewiring of host-encoded metabolic networks, or by introducing virus-encoded auxiliary metabolic genes which provide the virocell with novel metabolic capabilities. The ecological role of marine viruses is commonly assessed by their relative abundance and phylogenetic diversity, lacking the ability to assess the dynamics of active viral infection. The new ability to define a unique metabolic state of the virocell will expand the current virion-centric approaches in order to quantify the impact of marine viruses on microbial food webs.

  3. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China

    Directory of Open Access Journals (Sweden)

    D. Y. Liu

    2011-02-01

    Full Text Available Methane (CH4 emissions from natural wetland ecosystems exhibit large spatial variability at regional, national, and global levels related to temperature, water table, plant type and methanogenic archaea etc. To understand the underlying factors that induce spatial differences in CH4 emissions, and the relationship between the population of methanogenic archaea and CH4 production potential in natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical soil profiles sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjiang marsh in the cold temperate zone, and the Ruoergai peatland in the Qinghai-Tibetan Plateau in the alpine climate zone. The top soil layer had the highest population of methanogens (1.07–8.29 × 109 cells g−1 soil in all wetlands except the Ruoergai peatland and exhibited the maximum CH4 production potential measured at the mean in situ summer temperature. There is a significant logarithmic correlation between the abundance of methanogenic archaea and the soil organic carbon (R2 = 0.72, P < 0.001, n = 13 and between the abundance of methanogenic archaea and the total nitrogen concentrations (R2 = 0.76, P < 0.001, n = 13 in wetland soils. This indicates that the amount of soil organic carbon may affect the population of methanogens in wetland ecosystems. While the CH4 production potential is not significantly related to methanogen population (R2 = 0.01, P > 0.05, n = 13, it is related to the dissolved organic carbon concentration (R2 = 0.31, P = 0.05, n = 13. This suggests that the methanogen population might be not an effective index for predicting the CH4 production in wetland

  4. Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.

    Science.gov (United States)

    Rosselló-Móra, Ramon

    2012-02-01

    Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material. PMID:21958017

  5. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

    OpenAIRE

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L.; McDermott, Timothy R.; Macur, Richard E.; Inskeep, William P.; Nealson, Kenneth H

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surf...

  6. High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.

    Directory of Open Access Journals (Sweden)

    Curtis J Hayden

    Full Text Available Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA and bacteria (AOB in 9 high-altitude lakes (2289-3160 m in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2 = 0.32, p<0.1, whereas AOA abundance was inversely correlated with lake elevation (r(2 = 0.43, p<0.05. We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

  7. Metabolic Disorders

    Science.gov (United States)

    ... as your liver, muscles, and body fat. A metabolic disorder occurs when abnormal chemical reactions in your body ... that produce the energy. You can develop a metabolic disorder when some organs, such as your liver or ...

  8. Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent red sea brine pools

    KAUST Repository

    Wang, Yong

    2013-04-29

    In the Red Sea, two neighboring deep-sea brine pools, Atlantis II and Discovery, have been studied extensively, and the results have shown that the temperature and concentrations of metal and methane in Atlantis II have increased over the past decades. Therefore, we investigated changes in the microbial community and metabolic pathways. Here, we compared the metagenomes of the two pools to each other and to those of deep-sea water samples. Archaea were generally absent in the Atlantis II metagenome; Bacteria in the metagenome were typically heterotrophic and depended on aromatic compounds and other extracellular organic carbon compounds as indicated by enrichment of the related metabolic pathways. In contrast, autotrophic Archaea capable of CO2 fixation and methane oxidation were identified in Discovery but not in Atlantis II. Our results suggest that hydrothermal conditions and metal precipitation in the Atlantis II pool have resulted in elimination of the autotrophic community and methanogens.

  9. A strong response to selection on mass-independent maximal metabolic rate without a correlated response in basal metabolic rate

    DEFF Research Database (Denmark)

    Wone, B W M; Madsen, Per; Donovan, E R;

    2015-01-01

    Metabolic rates are correlated with many aspects of ecology, but how selection on different aspects of metabolic rates affects their mutual evolution is poorly understood. Using laboratory mice, we artificially selected for high maximal mass-independent metabolic rate (MMR) without direct selecti...

  10. Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China, a subtropical maritime zone

    Institute of Scientific and Technical Information of China (English)

    Zhixin Li; Wenbiao Jin; Zhaoyun Liang; Yangyang Yue; Junhong Lv

    2013-01-01

    Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments.However,little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district.To understand the abundance,diversity,and distribution of AOA in Pearl River Delta of China in response to various habitats,the archaeal amoA genes in soil,marine,river,lake,hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries.Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades,i.e.,estuary sediment,marine water/sediment,soil,hot spring and Cluster 1.Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation.The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature,pH,total organic carbon,total nitrogen and dissolved oxygen variables.Assessing AOA amoA gene copy numbers,ranging from 6.84 × 106 to 9.45 × 107 copies/g in dry soil/sediment,and 6.06 × 106 to 2.41 × 107 copies/L in water samples,were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude.However,AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples.Overall,these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge.The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters.New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.

  11. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

    NARCIS (Netherlands)

    Sauder, L.A.; Peterse, F.; Schouten, S.; Neufeld, J.D.

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidiz

  12. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

    NARCIS (Netherlands)

    Pitcher, A.; Villanueva, L.; Hopmans, E.C.; Schouten, S.; Reichart, G.J.; Sinninghe Damsté, J.S.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists;

  13. RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China ▿ †

    OpenAIRE

    Jiang, Hongchen; Huang, Qiuyuan; DONG, HAILIANG; WANG, Peng; Wang, Fengping; Li, Wenjun; Zhang, Chuanlun

    2010-01-01

    Using RNA-based techniques and hot spring samples collected from Yunnan Province, China, we show that the amoA gene of aerobic ammonia-oxidizing archaea can be transcribed at temperatures higher than 74°C and up to 94°C, suggesting that archaeal nitrification can potentially occur at near boiling temperatures.

  14. The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium

    NARCIS (Netherlands)

    Santos, dos A.B.; Cervantes, F.J.; Madrid, de M.P.; Bok, de F.A.M.; Stams, A.J.M.; Lier, van J.B.

    2006-01-01

    The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium was studied. Additionally, the effects of different electron-donating substrates and the redox mediator riboflavin on dye reduction were assessed by using either a methanoge

  15. Growth of anaerobic methane oxidizing archaea and sulfate reducing bacteria in a high pressure membrane-capsule bioreactor

    NARCIS (Netherlands)

    Timmers, P.H.A.; Gieteling, J.; Widjaja-Greefkes, H.C.A.; Plugge, C.M.; Stams, A.J.M.; Lens, P.N.L.; Meulepas, R.J.W.

    2015-01-01

    Anaerobic methane oxidizing communities of archaea (ANME) and sulfate reducing bacteria (SRB) grow slowly, which limits physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated sulfate

  16. Genetic analysis of the br gene in halophilic archaea isolated from Xinjiang region, China

    Institute of Scientific and Technical Information of China (English)

    Xiaohong XU; Min WU; Huibin ZHANG; Zhihu LIU

    2008-01-01

    Some novel members of extremely halophilic archaea, strains AJ 11, AJ 12 and AJ 13, were isolated from the Aularz Lake located in the Altun Mountain National Nature Reserve of Xinjiang, Uygur Autonomous Region in China. Partial DNA fragments encoding a bacteriorho-dopsin (BR), as well as for 16S rRNA of isolated strains, were amplified by PCR and their DNA sequences were determined subsequently. On the basis of homology and phylogenetic analysis of the 16S rDNA, we thought that the isolated strains forming a microbiological population are the members of the genus Natrinema. The results of genetic analysis, such as GC content, transition/transver-sion (Ti/Tv) rate ratios and synonymous substitution rates (Ks) indicate that the br fragments, with a high level of genetic divergence, are faced with both purifying selection and bias mutation pressure. The study provides the basis for use of species and BR proteins resources.

  17. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea

    DEFF Research Database (Denmark)

    Treusch, Alexander H; Kletzin, Arnulf; Raddatz, Guenter;

    2004-01-01

    of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages. The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively......Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total...... covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments...

  18. The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome

    Institute of Scientific and Technical Information of China (English)

    FENG Yanjing; CHI Shan; LIU Cui; CHEN Shengping; YU Jun; WANG Xumin; LIU Tao

    2014-01-01

    Phosphomannomutase (PMM;EC 5.4.2.8) is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project (OneKP) in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.

  19. Characterising the CRISPR immune system in Archaea using genome sequence analysis

    DEFF Research Database (Denmark)

    Shah, Shiraz Ali

    Archaea, a group of microorganisms distinct from bacteria and eukaryotes, are equipped with an adaptive immune system called the CRISPR system, which relies on an RNA interference mechanism to combat invading viruses and plasmids. Using a genome sequence analysis approach, the four components...... of archaeal genomic CRISPR loci were analysed, namely, repeats, spacers, leaders and cas genes. Based on analysis of spacer sequences it was predicted that the immune system combats viruses and plasmids by targeting their DNA. Furthermore, analysis of repeats, leaders and cas genes revealed that CRISPR...... systems exist as distinct families which have key differences between themselves. Closely related organisms were seen harbouring different CRISPR systems, while some distantly related species carried similar systems, indicating frequent horizontal exchange. Moreover, it was found that cas genes of Type I...

  20. Fishery by-product as a nutrient source for bacteria and archaea growth media.

    Science.gov (United States)

    Martone, Celina B; Pérez Borla, Olinda; Sánchez, Jorge J

    2005-02-01

    A highly soluble fish protein hydrolysates (FPH) with an 80% protein (peptide size between 1.5 and 20 kDa) and a low free amino acid content was obtained from hake (Merluccius hubssi) filleting waste [Lat. Am. Appl. Res. 30 (2000) 241]. Assays with Halobacterium salinarum, Escherichia coli, Bacillus subtilis and Staphylococcus epidermidis were performed in order to test that FPH as nutrient source for archaea and eubacteria culture media. Cell growth was evaluated by plate count, and by monitoring turbidity and nucleic acids content in liquid cultures. Neither cell growth nor generation times resulting from control and FPH cultures exhibited statistically significant differences at alpha: 0.05 suggesting that FPH can be used as an alternative substrate for microorganism cultural purposes. PMID:15474942

  1. Synthesis, Production, and Biotechnological Applications of Exopolysaccharides and Polyhydroxyalkanoates by Archaea

    Directory of Open Access Journals (Sweden)

    Annarita Poli

    2011-01-01

    Full Text Available Extreme environments, generally characterized by atypical temperatures, pH, pressure, salinity, toxicity, and radiation levels, are inhabited by various microorganisms specifically adapted to these particular conditions, called extremophiles. Among these, the microorganisms belonging to the Archaea domain are of significant biotechnological importance as their biopolymers possess unique properties that offer insights into their biology and evolution. Particular attention has been devoted to two main types of biopolymers produced by such peculiar microorganisms, that is, the extracellular polysaccharides (EPSs, considered as a protection against desiccation and predation, and the endocellular polyhydroxyalkanoates (PHAs that provide an internal reserve of carbon and energy. Here, we report the composition, biosynthesis, and production of EPSs and PHAs by different archaeal species.

  2. Vertical stratification of bacteria and archaea in sediments of a boreal stratified humic lake

    Science.gov (United States)

    Rissanen, Antti J.; Mpamah, Promise; Peura, Sari; Taipale, Sami; Biasi, Christina; Nykänen, Hannu

    2015-04-01

    Boreal stratified humic lakes, with steep redox gradients in the water column and in the sediment, are important sources of methane (CH4) to the atmosphere. CH4 flux from these lakes is largely controlled by the balance between CH4-production (methanogenesis), which takes place in the organic rich sediment and in the deepest water layers, and CH4-consumption (methanotrophy), which takes place mainly in the water column. While there is already some published information on the activity, diversity and community structure of bacteria in the water columns of these lakes, such information on sediment microbial communities is very scarce. This study aims to characterize the vertical variation patterns in the diversity and the structure of microbial communities in sediment of a boreal stratified lake. Particular focus is on microbes with the potential to contribute to methanogenesis (fermentative bacteria and methanogenic archaea) and to methanotrophy (methanotrophic bacteria and archaea). Two sediment cores (26 cm deep), collected from the deepest point (~6 m) of a small boreal stratified lake during winter-stratification, were divided into depth sections of 1 to 2 cm for analyses. Communities were studied from DNA extracted from sediment samples by next-generation sequencing (Ion Torrent) of polymerase chain reaction (PCR) - amplified bacterial and archaeal 16S rRNA gene amplicons. The abundance of methanogenic archaea was also specifically studied by quantitative-PCR of methyl coenzyme-M reductase gene (mcrA) amplicons. Furthermore, the community structure and the abundance of bacteria were studied by phospholipid fatty acid (PLFA) analysis. Dominant potential fermentative bacteria belonged to families Syntrophaceae, Clostridiaceae and Peptostreptococcaceae. There were considerable differences in the vertical distribution among these groups. The relative abundance of Syntrophaceae started to increase from the sediment surface, peaked at depth layer from 5 to 10 cm (up

  3. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.

    Directory of Open Access Journals (Sweden)

    Yuejian Mao

    Full Text Available Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR and diversity (barcoded pyrosequencing of key functional genes (nifH, bacterial/archaeal amoA and nosZ and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop, in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA not bacteria (AOB, indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

  4. Uranium association with halophilic and non-halophilic bacteria and archaea

    Energy Technology Data Exchange (ETDEWEB)

    Francis, A.J.; Gillow, J.B.; Dodge, C.J. [Brookhaven National Lab., Upton, NY (United States); Harris, R.; Beveridge, T.J. [Univ. of Guelph, ON (Canada); Papenguth, H.W. [Sandia National Labs., Albuquerque, NM (United States)

    2004-07-01

    We determined the association of uranium with bacteria isolated from the Waste Isolation Pilot Plant (WIPP), Carlsbad, New Mexico, and compared this with known strains of halophilic and non-halophilic bacteria and archaea. Examination of the cultures by transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS) showed uranium accumulation extracellularly and/or intracellularly to a varying degree. In Pseudomonas fluorescens and Bacillus subtilis uranium was associated with the cell surface and in the latter it was present as irregularly shaped grains. In Halobacterium halobium, the only archeon studied here, uranium was present as dense deposits and with Haloanaerobium praevalens as spikey deposits. Halomonas sp. isolated from the WIPP site accumulated uranium both extracellularly on the cell surface and intracellularly as electron-dense discrete granules. Extended X-ray absorption fine structure (EXAFS) analysis of uranium with the halophilic and non-halophilic bacteria and archaea showed that the uranium present in whole cells was bonded to an average of 2.4 {+-} 0.7 phosphoryl groups at a distance of 3.65 {+-} 0.03 Aa. Comparison of whole cells of Halomonas sp. with the cell wall fragments of lysed cells showed the presence of a uranium bidentate complex at 2.91 {+-} 0.03 Aa with the carboxylate group on the cell wall, and uranyl hydroxide with U-U interaction at 3.71 {+-} 0.03 Aa due to adsorption or precipitation reactions; no U-P interaction was observed. Addition of uranium to the cell lysate of Halomonas sp. resulted in the precipitation of uranium due to the inorganic phosphate produced by the cells. These results show that the phosphates released from bacteria bind a significant amount of uranium. However, the bacterially immobilized uranium was readily solubilized by bicarbonate with concurrent release of phosphate into solution. (orig.)

  5. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea.

    Science.gov (United States)

    Chun, Jongsik; Rainey, Fred A

    2014-02-01

    The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12,000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11,000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

  6. The Role of Tetraether Lipid Composition in the Adaptation of Thermophilic Archaea to Acidity

    Directory of Open Access Journals (Sweden)

    Eric eBoyd

    2013-04-01

    Full Text Available Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park (YNP, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings, the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly

  7. Origin and evolution of metabolic pathways

    Science.gov (United States)

    Fani, Renato; Fondi, Marco

    2009-03-01

    The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less-dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Among these gene elongations, gene and operon duplications undoubtedly played a major role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence giving rise to new genes coding for new metabolic abilities. Gene duplication has been invoked in the different schemes proposed to explain why and how the extant metabolic pathways have arisen and shaped. Both the analysis of completely sequenced genomes and directed evolution experiments strongly support one of them, i.e. the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis and nitrogen fixation, suggested that other different hypothesis, i.e. the retrograde hypothesis or the semi-enzymatic theory, may account for the arisal of some metabolic routes.

  8. SPATIAL AND TEMPORAL VARIABILITY AND DRIVERS OF NET ECOSYSTEM METABOLISM IN WESTERN GULF OF MEXICO ESTUARIES

    Science.gov (United States)

    Net ecosystem metabolism (NEM) is becoming a commonly used ecological indicator of estuarine ecosystem metabolic rates. Estuarine ecosystem processes are spatially and temporally variable, but the corresponding variability in NEM has not been properly assessed. Spatial and temp...

  9. Taoism and Deep Ecology.

    Science.gov (United States)

    Sylvan, Richard; Bennett, David

    1988-01-01

    Contrasted are the philosophies of Deep Ecology and ancient Chinese. Discusses the cosmology, morality, lifestyle, views of power, politics, and environmental philosophies of each. Concludes that Deep Ecology could gain much from Taoism. (CW)

  10. EcologicOther_ELT

    Data.gov (United States)

    Vermont Center for Geographic Information — The EcologicOther_ELT (Ecological Land Type) data layer was developed by the Green Mountain National Forest in the early 1980's from aerial photography. Using...

  11. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Kateryna V Zhalnina

    Full Text Available The activity of ammonia-oxidizing archaea (AOA leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

  12. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism....... The aim of this article is to provide knowledge of nucleotide metabolism and its regulation to facilitate interpretation of data arising from genetics, proteomics, and transcriptomics in connection with biotechnological processes and beyond....

  13. Assessment of hydrogen metabolism in commercial anaerobic digesters.

    Science.gov (United States)

    Kern, Tobias; Theiss, Juliane; Röske, Kerstin; Rother, Michael

    2016-05-01

    Degradation of biomass in the absence of exogenous electron acceptors via anaerobic digestion involves a syntrophic association of a plethora of anaerobic microorganisms. The commercial application of this process is the large-scale production of biogas from renewable feedstock as an alternative to fossil fuels. After hydrolysis of polymers, monomers are fermented to short-chain fatty acids and alcohols, which are further oxidized to acetate. Carbon dioxide, molecular hydrogen (H2), and acetate generated during the process are converted to methane by methanogenic archaea. Since many of the metabolic pathways as well as the syntrophic interactions and dependencies during anaerobic digestion involve formation, utilization, or transfer of H2, its metabolism and the methanogenic population were assessed in various samples from three commercial biogas plants. Addition of H2 significantly increased the rate of methane formation, which suggested that hydrogenotrophic methanogenesis is not a rate-limiting step during biogas formation. Methanoculleus and Methanosarcina appeared to numerically dominate the archaeal population of the three digesters, but their proportion and the Bacteria-to-Archaea ratio did not correlate with the methane productivity. Instead, hydrogenase activity in cell-free extracts from digester sludge correlated with methane productivity in a positive fashion. Since most microorganisms involved in biogas formation contain this activity, it approximates the overall anaerobic metabolic activity and may, thus, be suitable for monitoring biogas reactor performance. PMID:26995607

  14. Ecological, Pedagogical, Public Rhetoric

    Science.gov (United States)

    Rivers, Nathaniel A.; Weber, Ryan P.

    2011-01-01

    Public rhetoric pedagogy can benefit from an ecological perspective that sees change as advocated not through a single document but through multiple mundane and monumental texts. This article summarizes various approaches to rhetorical ecology, offers an ecological read of the Montgomery bus boycotts, and concludes with pedagogical insights on a…

  15. Enrichment of Thermophilic Ammonia-Oxidizing Archaea from an Alkaline Hot Spring in the Great Basin, USA

    Science.gov (United States)

    Zhang, C.; Huang, Z.; Jiang, H.; Wiegel, J.; Li, W.; Dong, H.

    2010-12-01

    One of the major advances in the nitrogen cycle is the recent discovery of ammonia oxidation by archaea. While culture-independent studies have revealed occurrence of ammonia-oxidizing archaea (AOA) in nearly every surface niche on earth, most of these microorganisms have resisted isolation and so far only a few species have been identified. The Great Basin contains numerous hot springs, which are characterized by moderately high temperature (40-65 degree C) and circumneutral or alkaline pH. Unique thermophilic archaea have been identified based on molecular DNA and lipid biomarkers; some of which may be ammonia oxidizers. This study aims to isolate some of these archaea from a California hot spring that has pH around 9.0 and temperature around 42 degree C. Mat material was collected from the spring and transported on ice to the laboratory. A synthetic medium (SCM-5) was inoculated with the mat material and the culture was incubated under varying temperature (35-65 degree C) and pH (7.0-10.0) conditions using antibiotics to suppress bacterial growth. Growth of the culture was monitored by microscopy, decrease in ammonium and increase in nitrite, and increases in Crenarchaeota and AOA abundances over time. Clone libraries were constructed to compare archaeal community structures before and after the enrichment experiment. Temperature and pH profiles indicated that the culture grew optimally at pH 9.0 and temperature 45 degree C, which are consistent with the geochemical conditions of the natural environment. Phylogenetic analysis showed that the final OTU was distantly related to all known hyperthermophilic archaea. Analysis of the amoA genes showed two OTUs in the final culture; one of them was closely related to Candidatus Nitrososphaera gargensis. However, the enrichment culture always contained bacteria and attempts to separate them from archaea have failed. This highlights the difficulty in bringing AOA into pure culture and suggests that some of the AOA may

  16. Philosophy of ecology

    CERN Document Server

    Brown, Bryson; Peacock, Kent A

    2011-01-01

    The most pressing problems facing humanity today - over-population, energy shortages, climate change, soil erosion, species extinctions, the risk of epidemic disease, the threat of warfare that could destroy all the hard-won gains of civilization, and even the recent fibrillations of the stock market - are all ecological or have a large ecological component. in this volume philosophers turn their attention to understanding the science of ecology and its huge implications for the human project. To get the application of ecology to policy or other practical concerns right, humanity needs a clear and disinterested philosophical understanding of ecology which can help identify the practical lessons of science. Conversely, the urgent practical demands humanity faces today cannot help but direct scientific and philosophical investigation toward the basis of those ecological challenges that threaten human survival. This book will help to fuel the timely renaissance of interest in philosophy of ecology that is now oc...

  17. Plant Terpenoids: Biosynthesis and Ecological Functions

    Institute of Scientific and Technical Information of China (English)

    Ai-Xia Cheng; Yong-Gen Lou; Ying-Bo Mao; Shan Lu; Ling-Jian Wang; Xiao-Ya Chen

    2007-01-01

    Among plant secondary metabolites terpenoids are a structurally most diverse group; they function as phytoalexins in plant direct defense, or as signals in indirect defense responses which involves herbivores and their natural enemies. In recent years, more and more attention has been paid to the investigation of the ecological role of plant terpenoids. The biosynthesis pathways of monoterpenes, sesquiterpenes, and diterpenes include the synthesis of C5 precursor isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), the synthesis of the immediate diphosphate precursors, and the formation of the diverse terpenoids. Terpene synthases (TPSs) play a key role in volatile terpene synthesis. By expression of the TPS genes, significant achievements have been made on metabolic engineering to increase terpenoid production. This review mainly summarizes the recent research progress in elucidating the ecological role of terpenoids and characterization of the enzymes involved in the terpenoid biosynthesis. Spatial and temporal regulations of terpenoids metabolism are also discussed.

  18. Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

    Directory of Open Access Journals (Sweden)

    Pride David T

    2008-09-01

    Full Text Available Abstract Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC, where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of

  19. Extremely halophilic archaea from ancient salt sediments and their possible survival in halite fluid inclusions

    Science.gov (United States)

    Stan-Lotter, H.; Fendrihan, S.; Gerbl, F. W.; Dornmayr-Pfaffenhuemer, M.; Frethem, C.

    2008-09-01

    Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, marine solar salterns and alkaline salt lakes; they have also been isolated from ancient subsurface salt sediments of great geological age (195-280 million years) and some of those strains were described as novel species (1). The cells survived perhaps while being enclosed within small fluid inclusions in the halite. The characterization of subsurface microbial life is of astrobiological relevance since extraterrestrial halite has been detected and since microbial life on Mars, if existent, may have retreated into the subsurface. We attempted to simulate the embedding process of extremely halophilic archaea and to analyse any cellular changes which might occur. When enclosing haloarchaea in laboratory grown halite, cells accumulated preferentially in fluid inclusions, as could be demonstrated by pre-staining with fluorescent dyes. With increased time of embedding, rod-shaped cells of Halobacterium salinarum strains were found to assume roundish morphologies. Upon dissolution of the salt crystals, these spheres were stable and viable for months when kept in buffers containing 4 M NaCl. Scanning electron microscopy (SEM) following fixation with glutaraldehyde suggested a potentially gradual transformation from rods to spheres. This notion was supported by fluorescence microscopy of Halobacterium cells, following embedding in halite and staining with SYTO 9. One-dimensional protein patterns of rods and spheres, following SDS polyacrylamide gel electrophoresis, were similar except that the S-layer protein appeared reduced by about 15 - 20 % in spheres. The reddish-orange pigmentation of spheres was much lighter compared to that of rod-shaped cells, suggesting lowered concentrations of carotenoids; this was confirmed by extraction and spectrometry of pigments. The data suggested that Halobacterium cells are capable of forming specific

  20. Eukaryotic versus prokaryotic marine picoplankton ecology.

    Science.gov (United States)

    Massana, Ramon; Logares, Ramiro

    2013-05-01

    Marine microorganisms contribute markedly to global biomass and ecosystem function. They include a diverse collection of organisms differing in cell size and in evolutionary history. In particular, microbes within the picoplankton are similar in size but belong to two drastically different cellular plans, the prokaryotes and the eukaryotes. Compared with larger organisms, prokaryotes and picoeukaryotes share ecological features, such as high specific activity, large and constant abundances, and high dispersal potential. Still, there are some aspects where their different cell organization influences their ecological performance. First, prokaryotes have a huge metabolic versatility and are involved in all biogeochemical cycles, whereas picoeukaryotes are metabolically less flexible but can exploit diverse predatory life strategies due to their phagocytic capacity. Second, sexual reproduction is absent in prokaryotes but may be present in picoeukaryotes, thus determining different evolutionary diversification dynamics and making species limits clearer in picoeukaryotes. Finally, it is plausible that picoeukaryotes are less flexible to enter a reversible state of low metabolic activity, thus picoeukaryote assemblages may have fewer rare species and may be less resilient to environmental change. In summary, lumping together pico-sized microbes may be convenient for some ecological studies, but it is also important to keep in mind their differences.

  1. What is dental ecology?

    Science.gov (United States)

    Cuozzo, Frank P; Sauther, Michelle L

    2012-06-01

    Teeth have long been used as indicators of primate ecology. Early work focused on the links between dental morphology, diet, and behavior, with more recent years emphasizing dental wear, microstructure, development, and biogeochemistry, to understand primate ecology. Our study of Lemur catta at the Beza Mahafaly Special Reserve, Madagascar, has revealed an unusual pattern of severe tooth wear and frequent tooth loss, primarily the result of consuming a fallback food for which these primates are not dentally adapted. Interpreting these data was only possible by combining our areas of expertise (dental anatomy [FC] and primate ecology [MS]). By integrating theoretical, methodological, and applied aspects of both areas of research, we adopted the term "dental ecology"-defined as the broad study of how teeth respond to the environment. Specifically, we view dental ecology as an interpretive framework using teeth as a vehicle for understanding an organism's ecology, which builds upon earlier work, but creates a new synthesis of anatomy and ecology that is only possible with detailed knowledge of living primates. This framework includes (1) identifying patterns of dental pathology and tooth use-wear, within the context of feeding ecology, behavior, habitat variation, and anthropogenic change, (2) assessing ways in which dental development and biogeochemical signals can reflect habitat, environmental change and/or stress, and (3) how dental microstructure and macro-morphology are adapted to, and reflect feeding ecology. Here we define dental ecology, provide a short summary of the development of this perspective, and place our new work into this context.

  2. Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.

    Directory of Open Access Journals (Sweden)

    Zhu Chen

    Full Text Available The Grain to Green Project (GGP is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L. or shrubs (Caragana korshinskii Kom.. In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.. A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.

  3. Influence of niche differentiation on the abundance of methanogenic archaea and methane production potential in natural wetland ecosystems across China

    OpenAIRE

    D. Liu; Ding, W.; Jia, Z; Cai, Z.

    2010-01-01

    Methane (CH4) emissions from natural wetland ecosystems exhibit large spatial variability. To understand the underlying factors that induce differences in CH4 emissions from natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical profile soils sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjia...

  4. Rapid and dissimilar response of ammonia oxidising archaea and bacteria to nitrogen and water amendment in two temperate forest soils

    OpenAIRE

    Szukics, Ute; Hackl, Evelyn; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela

    2011-01-01

    Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental ...

  5. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

    OpenAIRE

    Sauder, L.A.; Peterse, F.; Schouten, S; Neufeld, J. D.

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creat...

  6. Review article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders

    OpenAIRE

    Gottlieb, K.; Wacher, V.; Sliman, J.; Pimentel, M. (collab.)

    2015-01-01

    Summary Background Observational studies show a strong association between delayed intestinal transit and the production of methane. Experimental data suggest a direct inhibitory activity of methane on the colonic and ileal smooth muscle and a possible role for methane as a gasotransmitter. Archaea are the only confirmed biological sources of methane in nature and Methanobrevibacter smithii is the predominant methanogen in the human intestine. Aim To review the biosynthesis and composition of...

  7. Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems

    OpenAIRE

    Najjari, Afef; Mostafa S Elshahed; Cherif, Ameur; Youssef, Noha H.

    2015-01-01

    We examined the diversity and community structure of members of the halophilic Archaea (class Halobacteria) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examin...

  8. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

    OpenAIRE

    Pitcher, A.; Villanueva, L; Hopmans, E.C.; Schouten, S.; G. J. Reichart; Sinninghe Damsté, J.S.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of ...

  9. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

    OpenAIRE

    Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei; He, Ji-Zheng

    2011-01-01

    Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA...

  10. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    OpenAIRE

    Bustamante, Mauricio; Verdejo, Valentina; Zúñiga, Catalina; Espinosa, Fernanda; Orlando, Julieta; Carú, Margarita

    2012-01-01

    Water availability is the main limiting factor in arid soils; however, few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcos...

  11. Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil▿

    OpenAIRE

    Kelly, John J.; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S.

    2011-01-01

    The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically dige...

  12. Distribution of Ammonia-Oxidizing Archaea and Bacteria in the Surface Sediments of Matsushima Bay in Relation to Environmental Variables

    OpenAIRE

    Sakami, Tomoko

    2011-01-01

    Ammonia oxidization is the first and a rate-limiting step of nitrification, which is often a critical process in nitrogen removal from estuarine and coastal environments. To clarify the correlation of environmental conditions with the distribution of ammonia oxidizers in organic matter-rich coastal sediments, ammonia-oxidizing archaea (AOA) and bacteria (AOB) ammonia monooxygenase alpha subunit gene (amoA) abundance was determined in sediments of Matsushima Bay located in northeast Japan. The...

  13. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    OpenAIRE

    JulietaOrlando

    2012-01-01

    Water availability is the main limiting factor in arid soils; however few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosm...

  14. Metabolic encephalopathies.

    Science.gov (United States)

    Angel, Michael J; Young, G Bryan

    2011-11-01

    Kinnier Wilson coined the term metabolic encephalopathy to describe a clinical state of global cerebral dysfunction induced by systemic stress that can vary in clinical presentation from mild executive dysfunction to deep coma with decerebrate posturing; the causes are numerous. Some mechanisms by which cerebral dysfunction occurs in metabolic encephalopathies include focal or global cerebral edema, alterations in transmitter function, the accumulation of uncleared toxic metabolites, postcapillary venule vasogenic edema, and energy failure. This article focuses on common causes of metabolic encephalopathy, and reviews common causes, clinical presentations and, where relevant, management.

  15. The X-ray Crystal Structure of RNA Polymerase from Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Hirata,A.; Klein, B.; Murakami, K.

    2008-01-01

    The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits3, 4. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 Angstroms resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 Angstroms ) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron-sulphur (Fe-S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.

  16. General trends in selectively driven codon usage biases in the domain archaea.

    Science.gov (United States)

    Iriarte, Andrés; Jara, Eugenio; Leytón, Lucía; Diana, Leticia; Musto, Héctor

    2014-10-01

    Since the advent of rapid techniques for sequencing DNA in the mid 70's, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain.

  17. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

    KAUST Repository

    Kyrpides, Nikos C.

    2014-08-05

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet\\'s most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet\\'s genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  18. A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.

    Science.gov (United States)

    Rensen, Elena Ilka; Mochizuki, Tomohiro; Quemin, Emmanuelle; Schouten, Stefan; Krupovic, Mart; Prangishvili, David

    2016-03-01

    Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.

  19. A review of ammonia-oxidizing bacteria and archaea in Chinese soils

    Directory of Open Access Journals (Sweden)

    Ji-Zheng eHe

    2012-08-01

    Full Text Available Ammonia (NH3 oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB and ammonia oxidizing archaea (AOA in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizer in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N2O emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.

  20. Isolation and characterization of halophilic bacteria and archaea from salt ponds in Hangu Saltworks, Tianjin, China

    Science.gov (United States)

    Deng, Yuangao; Xu, Gaochao; Sui, Liying

    2015-07-01

    A total of 26 isolates were obtained from solar salt ponds of different salinities (100, 150, 200, and 250) in Hangu Saltworks Co. Ltd., Tianjin, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that five bacteria genera Halomonas, Salinicoccus, Oceanobacillus, Gracibacillus, and Salimicrobium and one archaea genera Halorubrum were present. The genus Halomonas was predominant with eight strains distributed in a salinity range of 100-200, followed by Halorubrum with six strains in salinity 250. Based on the genus and original sampling salinity, eight bacterial and two archaeal isolates were selected for further morphological, physiological, and biochemical characterization. All of the bacterial strains were moderately halophilic with the optimal salinity for growth being either 50 or 100, while two archaeal strains were extremely halophilic with an optimal growth salinity of 200. Additionally, we put forth strain SM.200-5 as a new candidate Salimicrobium species based on the phylogenic analysis of the 16S rRNA gene sequence and its biochemical characteristics when compared with known related species.

  1. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Science.gov (United States)

    Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter

    2014-08-01

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  2. Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans.

    Science.gov (United States)

    Bhattacharyya, Anish; Majumder, Niladri Shekhar; Basak, Pijush; Mukherji, Shayantan; Roy, Debojyoti; Nag, Sudip; Haldar, Anwesha; Chattopadhyay, Dhrubajyoti; Mitra, Suparna; Bhattacharyya, Maitree; Ghosh, Abhrajyoti

    2015-01-01

    Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions. PMID:26346219

  3. Role of Mn2+ and Compatible Solutes in the Radiation Resistance of Thermophilic Bacteria and Archaea

    Directory of Open Access Journals (Sweden)

    Kimberly M. Webb

    2012-01-01

    Full Text Available Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.

  4. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    Science.gov (United States)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  5. Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms.

    Science.gov (United States)

    Zhang, Yan; Chen, Lujun; Dai, Tianjiao; Sun, Renhua; Wen, Donghui

    2015-08-01

    Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones. PMID:25797330

  6. Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

    Science.gov (United States)

    Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

    2016-08-01

    Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions. PMID:27037935

  7. Potential production of nitrous oxide by archaea in the eastern Tropical North Atlantic Ocean

    Science.gov (United States)

    Loescher, C.; Kock, A.; Bange, H.; Laroche, J.

    2009-04-01

    The greenhouse gas nitrous oxide (N2O) is mainly produced by the processes of nitrification and denitrification. In order to identify the major formation pathway in the eastern tropical North Atlantic Ocean, measurements of dissolved nitrous oxide along vertical profiles were made during a cruise in February 2007. Identification of possible producing organsims took place by DNA and RNA analysis. The present oxygen concentrations, as well as the absence of transcripts of the denitrification key genes nirS/K and nosZ indicate, that N2O formation did not take place via denitrification. However, a positive correlation of N2O with nitrate, as well as excess N2O with the apparent oxygen utilization, suggest that nitrification is the major formation pathway in the study area. Detection of amoA, the key gene for the oxidation of ammonia approved this observation. It was found, that transcripts of amoA deriving from archaea were found throughout the water column, whereas transcripts of bacterial amoA could not be detected. Therefore, a production of N2O via archaeal nitrification is suggested.

  8. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Directory of Open Access Journals (Sweden)

    Nikos C Kyrpides

    2014-08-01

    Full Text Available Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance. However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000. This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  9. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

    Science.gov (United States)

    Marusenko, Yevgeniy; Garcia-Pichel, Ferran; Hall, Sharon J

    2015-02-01

    In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability. PMID:25764551

  10. Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans

    Directory of Open Access Journals (Sweden)

    Anish Bhattacharyya

    2015-01-01

    Full Text Available Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani. The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea compared to station (Dhulibhashani with nearly pristine environment (dominated by methanogens. It is indicated that sediment archaeal community patterns were influenced by environmental conditions.

  11. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

    Science.gov (United States)

    Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

    2016-01-01

    Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota. PMID:26140533

  12. ADP-bildende Acetyl-CoA Synthetasen aus hyperthermophilen Archaea: Molekularbiologische und biochemische Charakterisierung von neuartigen Enzymen der Acetat-Bildung und ATP-Synthese

    OpenAIRE

    Musfeldt, Meike

    2001-01-01

    Keine deutschsprachige Zusammenfassung vorhanden. Acetyl-CoA synthetase (ADP-forming) (ADP-ACS) represents a novel enzyme of acetate formation and energy conservation (acetyl-CoA + ADP + Pi -> acetate + ATP + CoA) in Archaea and eukaryotic protists. The only characterized ADP-ACS in Archaea, two isoenzymes from the hyperthermophile Pyrococcus furiosus, constitute 145 kDa heterotetramers (a2, b2). By using the N-terminal amino acid sequences of both subunits, which are located at different ...

  13. Genome-wide comparison of ferritin family from Archaea, Bacteria, Eukarya, and Viruses: its distribution, characteristic motif, and phylogenetic relationship

    Science.gov (United States)

    Bai, Lina; Xie, Ting; Hu, Qingqing; Deng, Changyan; Zheng, Rong; Chen, Wanping

    2015-10-01

    Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.

  14. A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life

    Directory of Open Access Journals (Sweden)

    Arshan Nasir

    2014-01-01

    Full Text Available The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.

  15. Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution.

    Science.gov (United States)

    Smyshlyaev, Georgy; Voigt, Franka; Blinov, Alexander; Barabas, Orsolya; Novikova, Olga

    2013-12-10

    Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons. PMID:24277848

  16. Germination ecology in orchids

    OpenAIRE

    TĚŠITELOVÁ, Tamara

    2009-01-01

    Germination ecology of four Epipactis species (E. albensis, E. atrorubens, E. helleborine, E. purpurata) was studied. Habitat preferences of adult plants were analyzed using phytosociological relevés from the Czech Phytosociological Database. A field experiment was carried out to determine course of germination of Epipactis seeds sown in different habitat types. Relationship between ecological preferences and germination ecology, and spatial aspects of seed dispersal and seedling recruitment ...

  17. Development of Ecological Buildings

    Directory of Open Access Journals (Sweden)

    Andrius Keizikas

    2011-04-01

    Full Text Available The article presents research on ecological buildings and their influence on the constructional sphere. The aim of the paper is to reveal the essence of ecological architecture showing substantial progress and its potential to stimulate architectural and technological growth. The article also describes relations between the ideas of ecological buildings and the ‘passive house’ concepts and aspects of development as well as describes the possibilities of improving building sustainability and energy efficiency. Article in Lithuanian

  18. Between Design and Ecology

    DEFF Research Database (Denmark)

    Bjørn, Mona Chor

    such vegetation, based on concepts and theories in plant community ecology. If these communities are based on local forbs there is a continuum in anthropogenic intervention from designed and intensively maintained to semi-natural herbaceous vegetation. Results from a large field experiment show that, after three...... colonised by grasses and eventually woody species. This thesis adds useful basic knowledge in plant community ecology and species-specific growth, which are relevant to research and planning in landscape architecture and ecology....

  19. The ecological economics: An ecological economics

    International Nuclear Information System (INIS)

    Ecological Economics arise as a scientific discipline aimed to integrate concepts of economics, ecology, thermodynamics, ethic and other natural and social sciences in order to incorporate a biophysical and integrated perspective of the inter dependences between economies and environment, from a plural conception and a methodology beyond disciplines. Ecological Economics studies the black box of economic processes usually excluded of the traditional economics: thermodynamics and ecology. Although it is relatively a new field of study, it has been strengthening its theoretical framework with scientific basis and analytic principles that lead to its identification as a new discipline that show a whole new paradigm. The scope of this article is to show the conceptual and methodological bases, the main founders, approaches and central debates of this new discipline. This brief introduction is a preamble to the papers of the meeting Ecological Economics: a perspective for Colombia included in this number, that took place on September 22 - 27 of 2007, at the National University of Colombia at Bogota. During tree days national and international experts, professors, researchers, workers of environmental sector and people interested on environmental issues joined together to know the conceptual and methodological achievements reached of this discipline; as well as to analyse and evaluate the environmental problems of the country, from the systemic, interdisciplinary and general perspective that it promotes

  20. Metabolic syndrome

    Directory of Open Access Journals (Sweden)

    Gogia Atul

    2006-02-01

    Full Text Available The Metabolic syndrome is a widely prevalent and multi-factorial disorder. The syndrome has been given several names, including- the metabolic syndrome, the insulin resistance syndrome, the plurimetabolic syndrome, and the deadly quartet. With the formulation of NCEP/ATP III guidelines, some uniformity and standardization has occurred in the definition of metabolic syndrome and has been very useful for epidemiological purposes. The mechanisms underlying the metabolic syndrome are not fully known; however resistance to insulin stimulated glucose uptake seems to modify biochemical responses in a way that predisposes to metabolic risk factors. The clinical relevance of the metabolic syndrome is related to its role in the development of cardiovascular disease. Management of the metabolic syndrome involves patient-education and intervention at various levels. Weight reduction is one of the main stays of treatment. In this article we comprehensively discuss this syndrome- the epidemiology, pathogenesis, clinical relevance and management. The need to do a comprehensive review of this particular syndrome has arisen in view of the ever increasing incidence of this entitiy. Soon, metabolic syndrome will overtake cigarette smoking as the number one risk factor for heart disease among the US population. Hardly any issue of any primary care medical journal can be opened without encountering an article on type 2 diabetes, dyslipidemia or hypertension. It is rare to see type 2 diabetes, dyslipidemia, obesity or hypertension in isolation. Insulin resistance and resulting hyperinsulinemia have been implicated in the development of glucose intolerance (and progression to type 2 diabetes, hypertriglyceridemia, hypertension, polycystic ovary yndrome, hypercoagulability and vascular inflammation, as well as the eventual development of atherosclerotic cardiovascular disease manifested as myocardial infarction, stroke and myriad end organ diseases. Conversely

  1. Lipid Metabolism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008393 Effects of angiotensin Ⅱ type 1 receptor blocker on triglyceride metabolism in the liver: experiment with Zucker fatty rats. RAN Jianmin(冉建民), et al. Dept Endocrinol, Guangzhou Red Cross Hosp, 4th Hosp Med Coll, Jinan Univ, Guangzhou 510220. Natl Med J China 2008;88(22):1557-1561. Objective To investigate the effects of angiotensin receptor blocker (ARB) on triglyceride (TG) metabolism and mechanism thereof.

  2. Chemical ecology of fungi.

    Science.gov (United States)

    Spiteller, Peter

    2015-07-01

    Fungi are widespread in nature and have conquered nearly every ecological niche. Fungi occur not only in terrestrial but also in freshwater and marine environments. Moreover, fungi are known as a rich source of secondary metabolites. Despite these facts, the ecological role of many of these metabolites is still unknown and the chemical ecology of fungi has not been investigated systematically so far. This review intends to present examples of the various chemical interactions of fungi with other fungi, plants, bacteria and animals and to give an overview of the current knowledge of fungal chemical ecology.

  3. Animal metabolism

    International Nuclear Information System (INIS)

    Studies on placental transport included the following: clearance of tritiated water as a baseline measurement for transport of materials across perfused placentas; transport of organic and inorganic mercury across the perfused placenta of the guinea pig in late gestation; and transport of cadmium across the perfused placenta of the guinea pig in late gestation. Studies on cadmium absorption and metabolism included the following: intestinal absorption and retention of cadmium in neonatal rats; uptake and distribution of an oral dose of cadmium in postweanling male and female, iron-deficient and normal rats; postnatal viability and growth in rat pups after oral cadmium administration during gestation; and the effect of calcium and phosphorus on the absorption and toxicity of cadmium. Studies on gastrointestinal absorption and mineral metabolism included: uptake and distribution of orally administered plutonium complex compounds in male mice; gastrointestinal absorption of 144Ce in the newborn mouse, rat, and pig; and gastrointestinal absorption of 95Nb by rats of different ages. Studies on iodine metabolism included the following: influence of thyroid status and thiocyanate on iodine metabolism in the bovine; effects of simulated fallout radiation on iodine metabolism in dairy cattle; and effects of feeding iodine binding agents on iodine metabolism in the calf

  4. Scaling of Metabolic Scaling within Physical Limits

    Directory of Open Access Journals (Sweden)

    Douglas S. Glazier

    2014-10-01

    Full Text Available Both the slope and elevation of scaling relationships between log metabolic rate and log body size vary taxonomically and in relation to physiological or developmental state, ecological lifestyle and environmental conditions. Here I discuss how the recently proposed metabolic-level boundaries hypothesis (MLBH provides a useful conceptual framework for explaining and predicting much, but not all of this variation. This hypothesis is based on three major assumptions: (1 various processes related to body volume and surface area exert state-dependent effects on the scaling slope for metabolic rate in relation to body mass; (2 the elevation and slope of metabolic scaling relationships are linked; and (3 both intrinsic (anatomical, biochemical and physiological and extrinsic (ecological factors can affect metabolic scaling. According to the MLBH, the diversity of metabolic scaling relationships occurs within physical boundary limits related to body volume and surface area. Within these limits, specific metabolic scaling slopes can be predicted from the metabolic level (or scaling elevation of a species or group of species. In essence, metabolic scaling itself scales with metabolic level, which is in turn contingent on various intrinsic and extrinsic conditions operating in physiological or evolutionary time. The MLBH represents a “meta-mechanism” or collection of multiple, specific mechanisms that have contingent, state-dependent effects. As such, the MLBH is Darwinian in approach (the theory of natural selection is also meta-mechanistic, in contrast to currently influential metabolic scaling theory that is Newtonian in approach (i.e., based on unitary deterministic laws. Furthermore, the MLBH can be viewed as part of a more general theory that includes other mechanisms that may also affect metabolic scaling.

  5. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

    Science.gov (United States)

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-05-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  6. Metabolism of oligosaccharides and starch in lactobacilli: a review

    Directory of Open Access Journals (Sweden)

    Michael eGänzle

    2012-09-01

    Full Text Available Oligosaccharides, compounds that are composed of 2 – 10 monosaccharide residues, are major carbohydrate sources in habitats populated by lactobacilli. Moreover, oligosaccharide metabolism is essential for ecological fitness of lactobacilli. Disaccharide metabolism by lactobacilli is well understood; however, few data on the metabolism of higher oligosaccharides are available. Research on the ecology of intestinal microbiota as well as the commercial application of prebiotics has shifted the interest from (digestible disaccharides to (indigestible higher oligosaccharides. This review provides an overview on oligosaccharide metabolism in lactobacilli. Emphasis is placed on maltodextrins, isomalto-oligosaccharides, fructo-oligosaccharides, galacto-oligosaccharides, and raffinose-family oligosaccharides. Starch is also considered. Metabolism is discussed on the basis of metabolic studies related to oligosaccharide metabolism, information on the cellular location and substrate specificity of carbohydrate transport systems, glycosyl hydrolases and phorphorylases, and the presence of metabolic genes in genomes of 28 strains of lactobacilli. Metabolic pathways for disaccharide metabolism often also enable the metabolism of tri- and tetrasaccharides. However, with the exception of amylase and levansucrase, metabolic enzymes for oligosaccharide conversion are intracellular and oligosaccharide metabolism is limited by transport. This general restriction to intracellular glycosyl hydrolases differentiates lactobacilli from other bacteria that adapted to intestinal habitats, particularly Bifidobacterium spp.

  7. Public goods and metabolic strategies.

    Science.gov (United States)

    Bachmann, Herwig; Bruggeman, Frank J; Molenaar, Douwe; Branco Dos Santos, Filipe; Teusink, Bas

    2016-06-01

    Microbial growth can be characterized by a limited set of macroscopic parameters such as growth rate, biomass yield and substrate affinity. Different culturing protocols for laboratory evolution have been developed to select mutant strains that have one specific macroscopic growth parameter improved. Some of those mutant strains display tradeoffs between growth parameters and changed metabolic strategies, for example, a shift from respiration to fermentation. Here we discuss recent studies suggesting that metabolic strategies and growth parameter tradeoffs originate from a common set of physicochemical and cellular constraints, associated with the allocation of intracellular resources over biosynthetic processes, mostly protein synthesis. This knowledge will give insight in ecological and biological concepts and can be used for metabolic and evolutionary engineering strategies.

  8. Microbial Diversity and Ecology in the Interfaces of the Deep-sea Anoxic Brine Pools in the Red Sea

    KAUST Repository

    Hikmawan, Tyas I.

    2015-05-01

    Deep-sea anoxic brine pools are one of the most extreme ecosystems on Earth, which are characterized by drastic changes in salinity, temperature, and oxygen concentration. The interface between the brine and overlaying seawater represents a boundary of oxic-anoxic layer and a steep gradient of redox potential that would initiate favorable conditions for divergent metabolic activities, mainly methanogenesis and sulfate reduction. This study aimed to investigate the diversity of Bacteria, particularly sulfate-reducing communities, and their ecological roles in the interfaces of five geochemically distinct brine pools in the Red Sea. Performing a comprehensive study would enable us to understand the significant role of the microbial groups in local geochemical cycles. Therefore, we combined culture-dependent approach and molecular methods, such as 454 pyrosequencing of 16S rRNA gene, phylogenetic analysis of functional marker gene encoding for the alpha subunits of dissimilatory sulfite reductase (dsrA), and single-cell genomic analysis to address these issues. Community analysis based on 16S rRNA gene sequences demonstrated high bacterial diversity and domination of Bacteria over Archaea in most locations. In the hot and multilayered Atlantis II Deep, the bacterial communities were stratified and hardly overlapped. Meanwhile in the colder brine pools, sulfatereducing Deltaproteobacteria were the most prominent bacterial groups inhabiting the interfaces. Corresponding to the bacterial community profile, the analysis of dsrA gene sequences revealed collectively high diversity of sulfate-reducing communities. Desulfatiglans-like dsrA was the prevalent group and conserved across the Red Sea brine pools. In addition to the molecular studies, more than thirty bacterial strains were successfully isolated and remarkably were found to be cytotoxic against the cancer cell lines. However, none of them were sulfate reducers. Thus, a single-cell genomic analysis was used to study

  9. Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.

    Science.gov (United States)

    Todor, Horia; Sharma, Kriti; Pittman, Adrianne M C; Schmid, Amy K

    2013-10-01

    Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.

  10. Protein–DNA binding dynamics predict transcriptional response to nutrients in archaea

    Science.gov (United States)

    Todor, Horia; Sharma, Kriti; Pittman, Adrianne M. C.; Schmid, Amy K.

    2013-01-01

    Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators. PMID:23892291

  11. Biosemiotics and ecological monitoring

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio

    2001-01-01

    of the qualitative and relational aspects that can only be grasped by considering the semiotic networks operative in complex ecological and cultural systems. In this paper, it is suggested that a biosemiotic approach to ecology may prove useful for the modelling process, which in turn will allow the construction...

  12. Complex adaptive systems ecology

    DEFF Research Database (Denmark)

    Sommerlund, Julie

    2003-01-01

    In the following, I will analyze two articles called Complex Adaptive Systems EcologyI & II (Molin & Molin, 1997 & 2000). The CASE-articles are some of the more quirkyarticles that have come out of the Molecular Microbial Ecology Group - a groupwhere I am currently making observational studies...

  13. Terrestrial Ecology Guide.

    Science.gov (United States)

    Morrison, James W., Ed.; Hall, James A., Ed.

    This collection of study units focuses on the study of the ecology of land habitats. Considered are such topics as map reading, field techniques, forest ecosystem, birds, insects, small mammals, soils, plant ecology, preparation of terrariums, air pollution, photography, and essentials of an environmental studies program. Each unit contains…

  14. Quantitative plant ecology

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2014-01-01

    This e-book is written in the Wolfram' CDF format (download free CDF player from Wolfram.com) The objective of this e-book is to introduce the population ecological concepts for measuring and predicting the ecological success of plant species. This will be done by focusing on the measurement......, will not be covered in this e-book....

  15. Ecological analyses and applications

    International Nuclear Information System (INIS)

    Progress is reported on the following: assessment of nuclear power plants; ecological analysis of uranium mining, milling, and fuel fabrication; environmental impact statements concerning uranium enrichment facilities; site evaluations for storage of radioactive wastes; ecological analysis of geothermal energy development; enhanced oil recovery; environmental monitoring plan for modular integrated utility systems; and fossil energy environmental project

  16. Dynamics in artifact ecologies

    DEFF Research Database (Denmark)

    Bødker, Susanne; Klokmose, Clemens Nylandsted

    2012-01-01

    artifacts influence the use of others. Understanding this interplay becomes more and more essential for interaction design as our artifact ecologies grow. This paper continues a recent discourse on artifact ecologies. Through interviews with iPhone users, we demonstrate that relationships between artifacts...

  17. Island Ecology in Bermuda.

    Science.gov (United States)

    Wulff, Barry L.; And Others

    1981-01-01

    Reports on an island ecology course offered by Eastern Connecticut State College providing opportunities for students to study the ecology and natural history of organisms found in a variety of subtropical habitats in Bermuda. Explains student selection criteria, trip preparation, evaluation criteria, daily programs, and habitats studied on the…

  18. RADIOECOLOGY AND ECOLOGICAL IMMUNOLOGY

    Directory of Open Access Journals (Sweden)

    V. M. Shubik

    2009-01-01

    Full Text Available The author's investigations results are presented in comparing with literary materials concerning the application of principles and methods of ecological immunology for solving radioecological questions. The data on characteristic of immunity and health of human population affected with radiation factors of the environment is given as well as animals' population state as the links offood ecological chains.

  19. Ecological production certification and the consumer ecological wants evolution

    OpenAIRE

    Chaikin, O.

    2013-01-01

    Article deals with the problem of modern tendency of the consumers ecological wants evolution development. The place of ecological certification in consumer evolutionary ecological want satisfaction under sustainable development condition bounds have been researched

  20. Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils.

    Science.gov (United States)

    Jung, Man-Young; Well, Reinhard; Min, Deullae; Giesemann, Anette; Park, Soo-Je; Kim, Jong-Geol; Kim, So-Jeong; Rhee, Sung-Keun

    2014-05-01

    N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA. PMID:24225887

  1. Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

    Science.gov (United States)

    Bagchi, Samik; Vlaeminck, Siegfried E; Sauder, Laura A; Mosquera, Mariela; Neufeld, Josh D; Boon, Nico

    2014-01-01

    Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

  2. Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

    Directory of Open Access Journals (Sweden)

    Samik Bagchi

    Full Text Available Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA, as opposed to ammonia-oxidizing bacteria (AOB, were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR for bacterial and thaumarchaeal ammonia monooxygenase (amoA genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS based on denaturing gradient gel electrophoresis (DGGE fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater

  3. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.

    Science.gov (United States)

    Li, Hu; Weng, Bo-Sen; Huang, Fu-Yi; Su, Jian-Qiang; Yang, Xiao-Ru

    2015-07-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity. PMID:25744648

  4. Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

    KAUST Repository

    Bagchi, Samik

    2014-12-05

    Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

  5. Predictive systems ecology.

    Science.gov (United States)

    Evans, Matthew R; Bithell, Mike; Cornell, Stephen J; Dall, Sasha R X; Díaz, Sandra; Emmott, Stephen; Ernande, Bruno; Grimm, Volker; Hodgson, David J; Lewis, Simon L; Mace, Georgina M; Morecroft, Michael; Moustakas, Aristides; Murphy, Eugene; Newbold, Tim; Norris, K J; Petchey, Owen; Smith, Matthew; Travis, Justin M J; Benton, Tim G

    2013-11-22

    Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the properties and behaviour of ecological systems. We discuss the necessary and desirable features of predictive systems ecology models. There are places where predictive systems ecology is already being practised and we summarize a range of terrestrial and marine examples. Significant challenges remain but we suggest that ecology would benefit both as a scientific discipline and increase its impact in society if it were to embrace the need to become more predictive.

  6. 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

  7. Metabolic microspheres

    Science.gov (United States)

    Fox, Sidney W.

    1980-08-01

    A systematic review of catalytic activities in thermal proteinoids and microspheres aggregated therefrom yields some new inferences on the origins and evolution of metabolism. Experiments suggest that, instead of being inert, protocells were already biochemically and cytophysically competent. The emergence and refinement of metabolism ab initio is thus partly traced conceptually. When the principle of molecular self-instruction, as of amino acids in peptide synthesis, is taken into account as a concomitant of natural selection, an expanded theory of organismic evolution, including saltations, emerges.

  8. Education in ecology

    International Nuclear Information System (INIS)

    It is not enough to convey knowledge, insights and attitudes if education in ecology is to have fruitful effects. Space and opportunity for action and creativity must be provided in addition. This includes personal consumer habits (eating, transport, hygiene, leisure activities etc.); an individual workplace - in this case school - that can be shaped according to ecological needs. Beyond this, ecological maturation should not be confined to, but should transcend school, for instance in youth groups, citizens' committees, political parties. If school does not inspire action - including action outside school -then education in ecology could be smothered by the Midas effect, where all life is reduced to material, to the curriculum in this case. This book presents ecological projects that have been tried at schools. They aim at an education in ecology that is oriented to the pupil and open to experience. They could be an incentive for colleagues to conduct similar projects at their schools. The projects work from the pupils' own experience and aim at concrete action and activities in his or her own environment. They should encourage teachers to venture outside the classroom with the pupils and teach ecology where it takes place. (orig.)

  9. Metabolic Syndrome

    Science.gov (United States)

    ... If you already have metabolic syndrome, making these healthy lifestyle choices can help reduce your risk of heart disease and other health problems. If lifestyle changes alone can’t control your ... to help. Maintain a healthy weight Your doctor can measure your body mass ...

  10. Metabolic syndrome

    Institute of Scientific and Technical Information of China (English)

    Charles Shaeffer

    2004-01-01

    @@ The emergence of cardiac disease as the number one world-wide cause of death justifies efforts to identify individuals at higher risk for preventive therapy. The metabolic syndrome, originally described by Reaven, 1 has been associated with higher cardiovascular disease risk. 2 Type Ⅱ diabetes is also a frequent sequela. 3

  11. Metabolic Syndrome

    Science.gov (United States)

    Metabolic syndrome is a group of conditions that put you at risk for heart disease and diabetes. These conditions are High blood pressure High blood glucose, or blood sugar, levels High levels of triglycerides, a type of fat, in your blood Low ...

  12. Quantitative plant ecology

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2014-01-01

    This e-book is written in the Wolfram' CDF format (download free CDF player from Wolfram.com) The objective of this e-book is to introduce the population ecological concepts for measuring and predicting the ecological success of plant species. This will be done by focusing on the measurement and...... statistical modelling of plant species abundance and the relevant ecological processes that control species abundance. The focus on statistical modelling and likelihood function based methods also means that more algorithm based methods, e.g. ordination techniques and boosted regression tress, will not be...

  13. Quantitative plant ecology

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2014-01-01

    This e-book is written in the Wolfram' CDF format (download free CDF player from Wolfram.com) The objective of this e-book is to introduce the population ecological concepts for measuring and predicting the ecological success of plant species. This will be done by focusing on the measurement...... and statistical modelling of plant species abundance and the relevant ecological processes that control species abundance. The focus on statistical modelling and likelihood function based methods also means that more algorithm based methods, e.g. ordination techniques and boosted regression tress...

  14. [Parasitism and ecological parasitology].

    Science.gov (United States)

    Balashov, Iu S

    2011-01-01

    Parasitism as one of the life modes is a general biological phenomenon and is a characteristic of all viruses, many taxa of bacteria, fungi, protists, metaphytes, and metazoans. Zooparasitology is focused on studies of parasitic animals, particularly, on their taxonomy, anatomy, life cycles, host-parasite relations, biocoenotic connections, and evolution. Ecological parasitology is a component of ecology, as the scientific study of the relation of living organisms with each other and their surroundings. In the present paper, critical analysis of the problems, main postulates, and terminology of the modern ecological parasitology is given.

  15. New perspectives in benthic deep-sea microbial ecology

    Directory of Open Access Journals (Sweden)

    Cinzia eCorinaldesi

    2015-03-01

    Full Text Available Deep-sea ecosystems represent the largest and most remote biome of the biosphere. They play a fundamental role in global biogeochemical cycles and their functions allow existence of life on our planet. In the last 20 years enormous progress has been made in the investigation of deep-sea microbes, but the knowledge of the microbial ecology of the soft bottoms (representing >90% of the deep-sea floor surface is still very limited. Deep-sea sediments host the largest fractions of Bacteria, Archaea and viruses on Earth, and potentially, a high diversity. At the same time, available results from metagenomics suggest that a large fraction of microbial taxa is completely unknown to science. Estimating the diversity of deep-sea benthic microbes and understanding their functions are some of the challenges of absolute priority, not only for deep-sea microbial ecology, but also for the entire research field of life sciences. The achievement of these goals, given the importance of the deep-sea microbial life for the functioning of the global biosphere, will open new perspectives for the comprehension of adaptation processes to the impact of global changes.

  16. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization.

    Science.gov (United States)

    DeLong, E F; Taylor, L T; Marsh, T L; Preston, C M

    1999-12-01

    Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled oligonucleotide probes often is undetectable above background fluorescence in many cells. To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide probes to identify and enumerate marine planktonic archaea and bacteria. The approach greatly enhanced the sensitivity and applicability of FISH with seawater samples, allowing confident identification and enumeration of planktonic cells to ocean depths of 3,400 m. Quantitative whole-cell hybridization experiments using these probes accounted for 90 to 100% of the total 4',6-diamidino-2-phenylindole (DAPI)-stained cells in most samples. As predicted in a previous study (R. Massana, A. E. Murray, C. M. Preston, and E. F. DeLong, Appl. Environ. Microbiol. 63:50-56, 1997), group I and II marine archaea predominate in different zones in the water column, with maximal cell densities of 10(5)/ml. The high cell densities of archaea, extending from surface waters to abyssal depths, suggest that they represent a large and significant fraction of the total picoplankton biomass in coastal ocean waters. The data also show that the vast majority of planktonic prokaryotes contain significant numbers of ribosomes, rendering them easily detectable with polyribonucleotide probes. These results imply that the majority of planktonic cells visualized by DAPI do not represent lysed cells or "ghosts," as was suggested in a previous report. PMID:10584017

  17. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    Directory of Open Access Journals (Sweden)

    S. Chen

    2015-10-01

    Full Text Available The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N–NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g−1 h−1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g−1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell−1 h−1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  18. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    Science.gov (United States)

    Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

    2015-10-01

    The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  19. Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China

    OpenAIRE

    Jin, Tao; ZHANG, Tong; Lin YE; Lee, On On; Wong, Yue Him; Qian, Pei Yuan

    2011-01-01

    The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28...

  20. Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria▿ †

    OpenAIRE

    Park, Byoung-Joon; Park, Soo-Je; Yoon, Dae-No; Schouten, Stefan; Sinninghe Damsté, Jaap S.; Rhee, Sung-Keun

    2010-01-01

    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichmen...

  1. Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea.

    Directory of Open Access Journals (Sweden)

    Mariam Brenneis

    2007-12-01

    Full Text Available The basal transcription apparatus of archaea is well characterized. However, much less is known about the mechanisms of transcription termination and translation initation. Recently, experimental determination of the 5'-ends of ten transcripts from Pyrobaculum aerophilum revealed that these are devoid of a 5'-UTR. Bioinformatic analysis indicated that many transcripts of other archaeal species might also be leaderless. The 5'-ends and 3'-ends of 40 transcripts of two haloarchaeal species, Halobacterium salinarum and Haloferax volcanii, have been determined. They were used to characterize the lengths of 5'-UTRs and 3'-UTRs and to deduce consensus sequence-elements for transcription and translation. The experimental approach was complemented with a bioinformatics analysis of the H. salinarum genome sequence. Furthermore, the influence of selected 5'-UTRs and 3'-UTRs on transcript stability and translational efficiency in vivo was characterized using a newly established reporter gene system, gene fusions, and real-time PCR. Consensus sequences for basal promoter elements could be refined and a novel element was discovered. A consensus motif probably important for transcriptional termination was established. All 40 haloarchaeal transcripts analyzed had a 3'-UTR (average size 57 nt, and their 3'-ends were not posttranscriptionally modified. Experimental data and genome analyses revealed that the majority of haloarchaeal transcripts are leaderless, indicating that this is the predominant mode for translation initiation in haloarchaea. Surprisingly, the 5'-UTRs of most leadered transcripts did not contain a Shine-Dalgarno (SD sequence. A genome analysis indicated that less than 10% of all genes are preceded by a SD sequence and even most proximal genes in operons lack a SD sequence. Seven different leadered transcripts devoid of a SD sequence were efficiently translated in vivo, including artificial 5'-UTRs of random sequences. Thus, an interaction of

  2. Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group

    Directory of Open Access Journals (Sweden)

    Christa eSchleper

    2012-06-01

    Full Text Available Ammonia-oxidising archaea (AOA have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with groupI.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of sixteen fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, five were fully sequenced, four of which grouped with the soil/I.1b (Nitrososphaera- lineage and one with marine/I.1a (Nitrosopumilus- lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologues in currently available marine thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta- genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of thaumarchaeota.

  3. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

    Science.gov (United States)

    Alves, Ricardo J. E.; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M.; Schleper, Christa; Urich, Tim

    2014-05-01

    The functioning of Arctic soil ecosystems is crucially important for global climate, although basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and therefore it is particularly important to gain a better understanding of the microbial populations catalyzing transformations that influence N bioavailability. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils from Svalbard were analyzed through a polyphasic approach, including determination of gross nitrification rates through a 15N pool dilution method, qualitative and quantitative analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) populations based on the functional marker gene amoA (encoding the ammonia monooxygenase subunit A), and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils, and outnumbered AOB by 1 to 3 orders of magnitude in most others. AOA showed a great overall phylogenetic diversity that was differentially distributed across soil ecosystems, and exhibited an uneven population composition that reflected the dominance of a single AOA phylotype in each population. Moreover, AOA populations showed a multifactorial association with the soil properties, which reflected an overall distribution associated with tundra type and with several physico-chemical parameters combined, namely pH and soil moisture and N contents (i.e., NO3- and dissolved organic N). Remarkably, the different gross in situ and potential nitrification rates between soils were associated with distinct AOA phylogenetic clades, suggesting differences in their nitrifying potential, both under the native NH3 conditions and as a response to higher NH3 availability. This was further supported by the selective enrichment of two AOA clades that exhibited

  4. Green Turtle Trophic Ecology

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — SWFSC is currently conducting a study of green sea turtle (Chelonia mydas) trophic ecology in the eastern Pacific. Tissue samples and stable carbon and stable...

  5. Urban Sound Ecologies

    DEFF Research Database (Denmark)

    Groth, Sanne Krogh; Samson, Kristine

    2013-01-01

    of the 1970s while developing them into recent definitions of ecology in urban studies. Finally, we unfold our framing of urban sound ecologies with three case analyses: a sound intervention in Berlin, a symphony for wind instruments in Copenhagen and a video walk in a former railway station in Kassel......Within recent years, there has been a renewed focus on sound in urban environments. From sound installations in public space to sound festivals in alternative settings, we find a common interest in sound art relating to the urban environment. Artworks or interventions presented in such contexts...... share the characteristics of site specificity. However, this article will consider the artwork in a broader context by re-examining how sound installations relate to the urban environment. For that purpose, this article brings together ecology terms from acoustic ecology of the sound theories...

  6. Market Squid Ecology Dataset

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains ecological information collected on the major adult spawning and juvenile habitats of market squid off California and the US Pacific...

  7. Ecological Sections of Minnesota

    Data.gov (United States)

    Minnesota Department of Natural Resources — This coverage provides information for the second level of the Ecological Classification System. The boundaries of the polygons of this coverage were derived from...

  8. Urban Sound Ecologies

    DEFF Research Database (Denmark)

    Groth, Sanne Krogh; Samson, Kristine

    2013-01-01

    Within recent years, there has been a renewed focus on sound in urban environments. From sound installations in public space to sound festivals in alternative settings, we find a common interest in sound art relating to the urban environment. Artworks or interventions presented in such contexts...... share the characteristics of site specificity. However, this article will consider the artwork in a broader context by re-examining how sound installations relate to the urban environment. For that purpose, this article brings together ecology terms from acoustic ecology of the sound theories of the...... 1970s while developing them into recent definitions of ecology in urban studies. Finally, we unfold our framing of urban sound ecologies with three case analyses: a sound intervention in Berlin, a symphony for wind instruments in Copenhagen and a video walk in a former railway station in Kassel. The...

  9. Ecological Provinces of Minnesota

    Data.gov (United States)

    Minnesota Department of Natural Resources — This coverage provides information for the first level of the Ecological Classification System. The boundaries of the polygons of this coverage were derived from...

  10. Ecological Subsections of Minnesota

    Data.gov (United States)

    Minnesota Department of Natural Resources — This coverage provides information for the third level of the Ecological Classification System. The boundaries of the polygons of this coverage were derived from...

  11. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

    NARCIS (Netherlands)

    Daebeler, A.; Gansen, M.; Frenzel, P.

    2013-01-01

    The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly

  12. Developments in numerical ecology

    Energy Technology Data Exchange (ETDEWEB)

    Legendre, P.; Legendre, L.

    1987-01-01

    From earlier ecological studies it has become apparent that simple univariate or bivariate statistics are often inappropriate, and that multivariate statistical analyses must be applied. Despite several difficulties arising from the application of multivariate methods, community ecology has acquired a mathematical framework, with three consequences: it can develop as an exact science; it can be applied operationally as a computer-assisted science to the solution of environmental problems; and it can exchange information with other disciplines using the language of mathematics.

  13. Ecological Succession Model

    OpenAIRE

    Lanchier, Nicolas

    2003-01-01

    We introduce a new interacting particle system intended to model an example of ecological succession involving two species: the bracken and the european beech. The objective is to exhibit phase transitions by proving that there exist three possible evolutions of the system to distinct ecological balances. More precisely, the whole population may die out, the european beech may conquer the bracken, and coexistence of both species may occur.

  14. Ecological Perspectives in HCI

    DEFF Research Database (Denmark)

    Blevis, Eli; Bødker, Susanne; Flach, John;

    The aim of the workshop is to provide a forum for researchers and practitioners to discuss the present and future of ecological perspectives in HCI. The participants will reflect on the current uses and interpretations of “ecology” and related concepts in the field. The workshop will assess...... the potential of ecological perspectives in HCI for supporting rich and meaningful analysis, as well as innovative design, of interactive technologies in real-life contexts...

  15. ECOLOGICAL WEED MANAGEMENT

    OpenAIRE

    Radicetti, Emanuele

    2012-01-01

    Nowadays there is much concern over environmental and human health impacts on weed management practices which has led agricultural producers and scientists in many countries to seek innovative strategies for weed control. As weed management systems are being developed, ecological knowledge will become more and more important and the complexity of weed management must be considered. Therefore understanding weed-crop ecology will lead to more effective weed prevention, management, and control t...

  16. (International meetings on ecology)

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, D.L.; Garten, C.T. Jr.; Turner, M.G.

    1990-09-25

    the travelers attended the Fifth International Congress of Ecology (INTECOL) in Yokohama, Japan, and two presented invited papers and chaired symposia. One traveler also attended the OJI International Seminar in Gifu, Japan and the Fukuoka Symposium on Theoretical Ecology in Fukuoka, Japan and presented invited papers. At these scientific gatherings, a large number of symposia and specific presentations were relevant to current research at Oak Ridge National Laboratory (ORNL), especially in the areas of landscape dynamics, plant physiology, and aquatic ecosystems.

  17. Microbial Ecology of Lake Kivu

    OpenAIRE

    Llirós, Marc; Descy, Jean-Pierre; Libert, Xavier; Morana, Cédric; Schmitz, Mélodie; Wimba, Louisette; Nzavuga-Izere, Angélique; García-Armisen, Tamara; Borrego, Carles; Servais, Pierre; Darchambeau, François

    2012-01-01

    We review available data on archaea, bacteria and small eukaryotes in an attempt to provide a general picture of microbial diversity, abundances and microbe-driven processes in Lake Kivu surface and intermediate waters (ca. 0–100 m). The various water layers present contrasting physical and chemical properties and harbour very different microbial communities supported by the vertical redox structure. For instance, we found a clear vertical segregation of archaeal and bacterial assemblages bet...

  18. The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

    Directory of Open Access Journals (Sweden)

    Stefan Spring

    2010-01-01

    Full Text Available Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

  19. Urban ecology and its Importance

    Institute of Scientific and Technical Information of China (English)

    艾玛诺

    2015-01-01

    With the development of ecological problems are becoming more and more serious people pay more and more attention on ecological city,, this paper analyzes the sources of city ecological problems from the angle of the city planning, to explore the feasible measures to solve or al eviate the increasingly serious ecological problems.

  20. Diversity and Distribution of Archaea Community along a Stratigraphic Permafrost Profile from Qinghai-Tibetan Plateau, China

    Directory of Open Access Journals (Sweden)

    Shiping Wei

    2014-01-01

    Full Text Available Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.

  1. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

    Science.gov (United States)

    Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

    2015-12-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature. PMID:26499486

  2. Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes

    Directory of Open Access Journals (Sweden)

    Tim Soderberg

    2005-01-01

    Full Text Available A phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (PPP, the ribulose monophosphate (RuMP pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the PPP genes in archaea. Genomic and biochemical evidence suggests that three archaeal species (Methanocaldococcus jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium produce ribose-5-phosphate via the nonoxidative PPP (NOPPP, whereas nine species apparently lack an NOPPP but may employ a reverse RuMP pathway for pentose synthesis. One species (Halobacterium sp. NRC-1 lacks both the NOPPP and the RuMP pathway but may possess a modified oxidative PPP (OPPP, the details of which are not yet known. The presence of transketolase in several archaeal species that are missing the other two NOPPP genes can be explained by the existence of differing requirements for erythrose-4-phosphate (E4P among archaea: six species use transketolase to make E4P as a precursor to aromatic amino acids, six species apparently have an alternate biosynthetic pathway and may not require the ability to make E4P, and one species (Pyrococcus horikoshii probably does not synthesize aromatic amino acids at all.

  3. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    Science.gov (United States)

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems. PMID:26125322

  4. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter;

    2003-01-01

    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  5. Defining and measuring ecological specialization

    OpenAIRE

    Devictor, Vincent; Clavel, Joanne; Julliard, Romain; Lavergne, Sébastien; Mouillot, David; Thuiller, Wilfried; Venail, Patrick; Villéger, Sébastien; Mouquet, Nicolas

    2010-01-01

    1.  Ecological specialization is one of the main concepts in ecology and conservation. However, this concept has become highly context-dependent and is now obscured by the great variability of existing definitions and methods used to characterize ecological specialization. 2.  In this study, we clarify this concept by reviewing the strengths and limitations of different approaches commonly used to define and measure ecological specialization. We first show that ecological specialization can e...

  6. Fermentation Enhancement of Methanogenic Archaea Consortia from an Illinois Basin Coalbed via DOL Emulsion Nutrition

    OpenAIRE

    Xiao, Dong; Peng, Su-Ping; Wang, En-Yuan

    2015-01-01

    Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nu...

  7. Editorial: Pedagogical Media Ecologies

    Directory of Open Access Journals (Sweden)

    Dorothee M. Meister

    2014-07-01

    Full Text Available From educational gaming through portable e-readers to cell phones, media are interpenetrating educational spaces and activities. Accordingly, understanding media in environmental or ecological terms has become increasingly important for education internationally. In North America, for example, the centenary of McLuhan’s birth has focused attention on approaches to media – whether oral, textual, electronic or digital– as a kind of environment in which education takes place. In parts of Europe, the so-called mediatic turn – following on the linguistic and iconic turns – has similarly emphasized the role of media as a condition for the possibility of educational activities and programs. With a few exceptions1 the papers in this special issue were first presented at the conference «Educational Media Ecologies: International Perspectives» which took place at the University of Paderborn, Germany, on March 27–28, 2012.2 The event was an interdisciplinary and transatlantic endeavor to bring together a wide range of perspectives on various issues relevant to educational media ecologies,3 and on related debates on mediation, medialization, mediatization, and mediality.4 The purpose of this volume, like the conference, is to foster and deepen international dialogue in the area of educational media. Areas of research and scholarship relevant to this dialogue include educational media, media literacy, educational philosophy, and media and cultural studies. The contributions, described below, put conceptual issues as well as social practices and applications at the center of the debate. Klaus Rummler opens the issue by clarifying the concept of ecology itself. Referencing a range of work over the past 50 years, Rummler describes how ecological models have been cast in sociological, semiotic, cultural, mediatic and other terms, and he explains the implications of these various perspectives for the study of educational contexts. Rummler also

  8. Urban sound ecologies

    Directory of Open Access Journals (Sweden)

    Sanne Krogh Groth

    2013-12-01

    Full Text Available Within recent years, there has been a renewed focus on sound in urban environments. From sound installations in public space to sound festivals in alternative settings, we find a common interest in sound art relating to the urban environment. Artworks or interventions presented in such contexts share the characteristics of site specificity. However, this article will consider the artwork in a broader context by re-examining how sound installations relate to the urban environment. For that purpose, this article brings together ecology terms from acoustic ecology of the sound theories of the 1970s while developing them into recent definitions of ecology in urban studies. Finally, we unfold our framing of urban sound ecologies with three case analyses: a sound intervention in Berlin, a symphony for wind instruments in Copenhagen and a video walk in a former railway station in Kassel. The article concludes that the ways in which recent sound installations work with urban ecologies vary. While two of the examples blend into the urban environment, the other transfers the concert format and its mode of listening to urban space. Last, and in accordance with recent soundscape research, we point to how artists working with new information and media technologies create inventive ways of inserting sound and image into urban environments.

  9. ECOLOGICAL ECONOMICS VS ECONOMIC(AL ECOLOGY

    Directory of Open Access Journals (Sweden)

    G. Kharlamova

    2015-10-01

    Full Text Available Currently world faces the dilemma – ecological economy or economic(al ecology. The researchers produce hundreds of surveys on the topic. However the analyses of recent most cited simulations had shown the diversity of results. Thus, for some states the Kuznets environmental curve has place, for others – no. Same could be said about different years for the same state. It provokes the necessity of drawing new group analyses to reveal the tendencies and relationships between economic and environmental factors. Most flexible and mirror factor of environmental sustainability is the volume of CO2 emissions. The econometric analysis was used for detecting the economic impact on this indicator at the global level and in the spectra of group of states depending on their income. The hypothesis of the existence of environmental Kuznets curve for the analysed data is rejected. Real GDP per capita impact on carbon dioxide emissions is considered only at the global level. The impact of openness of the economy is weak. Rejection happened also to the hypothesis that for the developed countries there is a reverse dependence between the environmental pollution and economic openness. Indicator “energy consumption per capita” impacts on greenhouse gas emissions only in countries with high income. Whereby it should be noted that the more developed a country is, the more elastic is this influence. These results have a potential usage for environmental policy regulation and climate strategy.

  10. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

    DEFF Research Database (Denmark)

    Inskeep, William P; Jay, Zackary J; Herrgard, Markus;

    2013-01-01

    Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high......-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.......4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and...

  11. Coevolutionary ecological economics

    Energy Technology Data Exchange (ETDEWEB)

    Kallis, Giorgos [ICREA Researcher, ICTA, Universidad Autonoma de Barcelona, ETSE, QC/3095, 08193 Bellatera, Barcelona (Spain); Norgaard, Richard B. [Energy and Resources Group, University of California at Berkeley, 310 Barrows Hall, Berkeley, CA, 94720-3050 (United States)

    2010-02-15

    This paper maps a coevolutionary research agenda for ecological economics. At an epistemological level coevolution offers a powerful logic for transcending environmental and social determinisms and developing a cross-disciplinary approach in the study of socio-ecological systems. We identify four consistent stories emerging out of coevolutionary studies in ecological economics, concerning: environmental degradation and development failure in peripheral regions; the lock-in of unsustainable production-consumption patterns; the vicious cycle between human efforts to control undesirable micro-organisms and the evolution of these organisms; and the adaptive advantages of other-regarding, cooperative behaviors and institutions. We identify challenges in the conceptualization of coevolutionary relationships in relation to: the interaction between different hierarchical levels of evolution; the role of space and social power; uneven rates of change and crises. We conclude with the political implications of a coevolutionary perspective based on the premises of pragmatism. (author)

  12. Application of ecological mapping

    International Nuclear Information System (INIS)

    The US Fish and Wildlife Service has initiated the production of a comprehensive ecological inventory map series for use as a major new planning tool. Important species data along with special land use designations are displayed on 1:250,000 scale topographic base maps. Sets of maps have been published for the Atlantic and Pacific coastal areas of the United States. Preparation of a map set for the Gulf of Mexico is underway at the present time. Potential application of ecological inventory map series information to a typical land disposal facility could occur during the narrowing of the number of possible disposal sites, the design of potential disposal site studies of ecological resources, the preparation of the environmental report, and the regulatory review of license applications. 3 figures, 3 tables

  13. Size-energy relationships in ecological communities.

    Directory of Open Access Journals (Sweden)

    Brent J Sewall

    Full Text Available Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights

  14. EcoLogic Reader

    OpenAIRE

    Šeikienė, Nijolė

    2008-01-01

    Mokymo priemonė skirta aplinkos apsaugos studijų programos studentams. Ją sudaro abėcėliniai tekstų rinkinėliai, atrinkta ir paryškinta specialybinė leksika bei įvairūs įtvirtinamieji pratimai. Knygos pabaigoje spausdinami testai ir tekstai geresniam žodyno suvokimui bei turtinimui. Medžiaga atspindi šiandienines aktualijas, ji gali būti naudinga kiekvienam, norinčiam pagilinti anglų kalbos žinias ekologine tematika. The EcoLogic Reader is an educational book for students of ecology. It pr...

  15. Ecological Communities by Design

    Energy Technology Data Exchange (ETDEWEB)

    Fredrickson, Jim K.

    2015-06-25

    In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions. Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species. Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels. However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities.

  16. Ecology of gelatious plankton

    DEFF Research Database (Denmark)

    Jaspers, Cornelia

    as a result of this invasion and its ecological and economic impacts. In 2005, when M. leidyi was sighted in Northern Europe for the first time, similar consequences were feared. The aim of my PhD project was to understand the potential impact of M. leidyi on the Baltic Sea ecosystem and constrains on its...... in high and intermediate saline areas in Northern Europe. While the ecological impact of M. leidyi in the central Baltic appears to be limited concern, the environment in other European waters should be more favourable to their populations. In these areas, it is suggested that M. leidyi constitutes...

  17. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    Science.gov (United States)

    Case, David H.

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  18. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

    Science.gov (United States)

    Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  19. Manipulatiaon of Biofilm Microbial Ecology

    Energy Technology Data Exchange (ETDEWEB)

    Burkhalter, R.; Macnaughton, S.J.; Palmer, R.J.; Smith, C.A.; Whitaker, K.W.; White, D.C.; Zinn, M.; kirkegaard, R.

    1998-08-09

    The Biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms by generated. The most effective monitoring of biofilm formation, succession and desquamation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in the distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  20. Manipulation of Biofilm Microbial Ecology

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

    1998-08-15

    The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  1. An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea

    Directory of Open Access Journals (Sweden)

    Hauryliuk Vasili

    2011-01-01

    Full Text Available Abstract Background SelB is the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. In archaea, only a subset of methanogens utilizes selenocysteine and encodes archaeal SelB (aSelB. A SelB-like (aSelBL homolog has previously been identified in an archaeon that does not encode selenosysteine, and has been proposed to be a pyrrolysyl-tRNA-specific elongation factor (EF-Pyl. However, elongation factor EF-Tu is capable of binding archaeal Pyl-tRNA in bacteria, suggesting the archaeal ortholog EF1A may also be capable of delivering Pyl-tRNA to the ribosome without the need of a specialized factor. Results We have phylogenetically characterized the aSelB and aSelBL families in archaea. We find the distribution of aSelBL to be wider than both selenocysteine and pyrrolysine usage. The aSelBLs also lack the carboxy terminal domain usually involved in recognition of the selenocysteine insertion sequence in the target mRNA. While most aSelBL-encoding archaea are methanogenic Euryarchaea, we also find aSelBL representatives in Sulfolobales and Thermoproteales of Crenarchaea, and in the recently identified phylum Thaumarchaea, suggesting that aSelBL evolution has involved horizontal gene transfer and/or parallel loss. Severe disruption of the GTPase domain suggests that some family members may employ a hitherto unknown mechanism of nucleotide hydrolysis, or have lost their GTPase ability altogether. However, patterns of sequence conservation indicate that aSelBL is still capable of binding the ribosome and aminoacyl-tRNA. Conclusions Although it is closely related to SelB, aSelBL appears unlikely to either bind selenocysteinyl-tRNA or function as a classical GTP hydrolyzing elongation factor. We propose that following duplication of aSelB, the resultant aSelBL was recruited for binding another aminoacyl-tRNA. In bacteria, aminoacylation with selenocysteine is essential for efficient thermodynamic coupling of SelB binding to t

  2. The development of ecological tourism and ecological civilization construction

    Institute of Scientific and Technical Information of China (English)

    张波

    2014-01-01

    This passage shows us the characters of ecology tourism and reveals the problems in the modern tourism , emphasises that we should develop ecology tourism and make a link between them, then leads to Sustainable Development.

  3. Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism.

    Science.gov (United States)

    Grein, Fabian; Ramos, Ana Raquel; Venceslau, Sofia S; Pereira, Inês A C

    2013-02-01

    Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron-sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. PMID:22982583

  4. Ecology in Urban Education.

    Science.gov (United States)

    Johnson, Letitia K.; Ryan, Michael

    In this course guide to the teaching of urban ecology, six learning activities on the following topics are outlined: (1) city location and growth; (2) an in-depth study of New Orleans; (3) city shape and structure; (4) size and spacing of cities; (5) cities with special functions; (6) local community study. Educational objectives for each activity…

  5. Education for industrial ecology.

    OpenAIRE

    Starr, C

    1992-01-01

    The societal issues relevant to the subject of industrial ecology call for the participation of broadly educated engineers who can integrate their technology with the social, political, environmental, and economic aspects of its applications. This increase in the responsibility of traditional engineering to include the end-use, obsolescence, and disposition of technical products signals a new era for engineering education.

  6. Towards ecological autarky

    OpenAIRE

    Dartel, Michel van; Nigten, Anne

    2014-01-01

    While the notion of autarky is often contested in terms of feasibility and desirability, art and design projects that deal with autarky seem to moreover suggest positive socio-cultural and ecological effects of autarkic living. A social network model of autarky is introduced to unify these seemingly opposing views.

  7. Towards ecological autarky

    NARCIS (Netherlands)

    Dartel, Michel van; Nigten, Anne

    2014-01-01

    While the notion of autarky is often contested in terms of feasibility and desirability, art and design projects that deal with autarky seem to moreover suggest positive socio-cultural and ecological effects of autarkic living. A social network model of autarky is introduced to unify these seemingly

  8. THE AUTOIMMUNE ECOLOGY.

    Directory of Open Access Journals (Sweden)

    Juan-Manuel eAnaya

    2016-04-01

    Full Text Available Autoimmune diseases (ADs represent a heterogeneous group of disorders that affect specific target organs or multiple organ systems. These conditions share common immunopathogenic mechanisms (i.e., the autoimmune tautology, which explain the clinical similarities they have among them as well as their familial clustering (i.e., coaggregation. As part of the autoimmune tautology, the influence of environmental exposure on the risk of developing ADs is paramount (i.e., the autoimmune ecology. In fact, environment, more than genetics, shapes immune system. Autoimmune ecology is akin to exposome, that is all the exposures - internal and external - across the lifespan, interacting with hereditary factors (both genetics and epigenetics to favor or protect against autoimmunity and its outcomes. Herein we provide an overview of the autoimmune ecology, focusing on the immune response to environmental agents in general, and microbiota, cigarette smoking, alcohol and coffee consumption, socioeconomic status, gender and sex hormones, vitamin D, organic solvents and vaccines in particular. Inclusion of the autoimmune ecology in disease etiology and health will improve the way personalized medicine is currently conceived and applied.

  9. Marine and Island Ecology.

    Science.gov (United States)

    Stephens, Lawrence J.; And Others

    1988-01-01

    Describes an ecology course which provides students with an opportunity to observe aquatic and terrestrial life in the Bahamas. States that students learn scientific methodology by measuring physical and chemical aspects of the island habitats. Provides information on the island, course description and objectives, transportation, facilities, and…

  10. Aspects of Marine Ecology.

    Science.gov (United States)

    Awkerman, Gary L.

    This publication is designed for use in standard science curricula to develop oceanologic manifestations of certain science topics. Included are teacher guides, student activities, and demonstrations to impart ocean science understanding, specifically, aspects of marine ecology, to high school students. The course objectives include the ability of…

  11. Biodiversity in Benthic Ecology

    DEFF Research Database (Denmark)

    Friberg, Nikolai; Carl, J. D.

    Foreword: This proceeding is based on a set of papers presented at the second Nordic Benthological Meeting held in Silkeborg, November 13-14, 1997. The main theme of the meeting was biodiversity in benthic ecology and the majority of contributions touch on this subject. In addition, the proceeding...

  12. Ecology and Human Destiny.

    Science.gov (United States)

    Haught, John F.

    1999-01-01

    Examines eschatology as the heart of Christian faith, suggesting that an appreciation of an eschatological interpretation of the cosmos enables acceptance of nature's transience and a grounding for an ecological ethic. Maintains that recent scientific developments present a promising, rather than pessimistic, picture of the universe. Holds that…

  13. Revitalizing ecological capital

    NARCIS (Netherlands)

    Swagemakers, P.; Wiskerke, J.S.C.

    2011-01-01

    The modernization of agricultural food production has diminished and is diminishing the sustainable use of the local natural resource base, resulting in the fragmentation of landscapes and the decline of biodiversity. In this paper we analyze the revitalization of ecological capital, which provides

  14. Challenges of ecological restoration

    DEFF Research Database (Denmark)

    Halme, Panu; Allen, Katherine A.; Aunins, Ainars;

    2013-01-01

    The alarming rate of ecosystem degradation has raised the need for ecological restoration throughout different biomes and continents. North European forests may appear as one of the least vulnerable ecosystems from a global perspective, since forest cover is not rapidly decreasing and many ecosys...

  15. The Autoimmune Ecology.

    Science.gov (United States)

    Anaya, Juan-Manuel; Ramirez-Santana, Carolina; Alzate, Maria A; Molano-Gonzalez, Nicolas; Rojas-Villarraga, Adriana

    2016-01-01

    Autoimmune diseases (ADs) represent a heterogeneous group of disorders that affect specific target organs or multiple organ systems. These conditions share common immunopathogenic mechanisms (i.e., the autoimmune tautology), which explain the clinical similarities they have among them as well as their familial clustering (i.e., coaggregation). As part of the autoimmune tautology, the influence of environmental exposure on the risk of developing ADs is paramount (i.e., the autoimmune ecology). In fact, environment, more than genetics, shapes immune system. Autoimmune ecology is akin to exposome, that is all the exposures - internal and external - across the lifespan, interacting with hereditary factors (both genetics and epigenetics) to favor or protect against autoimmunity and its outcomes. Herein, we provide an overview of the autoimmune ecology, focusing on the immune response to environmental agents in general, and microbiota, cigarette smoking, alcohol and coffee consumption, socioeconomic status (SES), gender and sex hormones, vitamin D, organic solvents, and vaccines in particular. Inclusion of the autoimmune ecology in disease etiology and health will improve the way personalized medicine is currently conceived and applied.

  16. Ecological stability in response to warming

    Science.gov (United States)

    Fussmann, Katarina E.; Schwarzmüller, Florian; Brose, Ulrich; Jousset, Alexandre; Rall, Björn C.

    2014-03-01

    That species’ biological rates including metabolism, growth and feeding scale with temperature is well established from warming experiments. The interactive influence of these changes on population dynamics, however, remains uncertain. As a result, uncertainty about ecological stability in response under warming remains correspondingly high. In previous studies, severe consumer extinction waves in warmed microcosms were explained in terms of warming-induced destabilization of population oscillations. Here, we show that warming stabilizes predator-prey dynamics at the risk of predator extinction. Our results are based on meta-analyses of a global database of temperature effects on metabolic and feeding rates and maximum population size that includes species of different phylogenetic groups and ecosystem types. To unravel population-level consequences we parameterized a bioenergetic predator-prey model and simulated warming effects within ecological, non-evolutionary timescales. In contrast to previous studies, we find that warming stabilized population oscillations up to a threshold temperature, which is true for most of the possible parameter combinations. Beyond the threshold level, warming caused predator extinction due to starvation. Predictions were tested in a microbial predator-prey system. Together, our results indicate a major change in how we expect climate change to alter natural ecosystems: warming should increase population stability while undermining species diversity.

  17. Metabolic Flexibility of Sulfate Reducing Bacteria

    Directory of Open Access Journals (Sweden)

    Caroline M. Plugge

    2011-05-01

    Full Text Available Dissimilatory sulfate-reducing prokaryotes (SRB are a very diverse group of anaerobic bacteria that are omnipresent in nature and play an imperative role in the global cycling of carbon and sulfur. In anoxic marine sediments sulfate reduction accounts for up to 50% of the entire organic mineralization in coastal and shelf ecosystems where sulfate diffuses several meters deep into the sediment. As a consequence, SRB would be expected in the sulfate-containing upper sediment layers, whereas methanogenic Archaea would be expected to succeed in the deeper sulfate-depleted layers of the sediment. Where sediments are high in organic matter, sulfate is depleted at shallow sediment depths, and biogenic methane production will occur. In the absence of sulfate, many SRB ferment organic acids and alcohols, producing hydrogen, acetate, and carbon dioxide, and may even rely on hydrogen- and acetate-scavenging methanogens to convert organic compounds to methane. SRB can establish two different life styles, and these can be termed as sulfidogenic and acetogenic, hydrogenogenic metabolism. The advantage of having different metabolic capabilities is that it raises the chance of survival in environments when electron acceptors become depleted. In marine sediments, SRB and methanogens do not compete but rather complement each other in the degradation of organic matter.Also in freshwater ecosystems with sulfate concentrations of only 10-200 μM, sulfate is consumed efficiently within the top several cm of the sediments. Here, many of the δ-Proteobacteria present have the genetic machinery to perform dissimilatory sulfate reduction, yet they have an acetogenic, hydrogenogenic way of life.In this review we evaluate the physiology and metabolic mode of SRB in relation with their environment.

  18. Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

    Science.gov (United States)

    Wang, Chen; Uversky, Vladimir N; Kurgan, Lukasz

    2016-05-01

    Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. PMID:27037624

  19. Valuation of ecological resources

    Energy Technology Data Exchange (ETDEWEB)

    Scott, M.J.; Bilyard, G.R.; Link, S.O.; Ricci, P.F.; Seely, H.E.; Ulibarri, C.A.; Westerdahl, H.E.

    1995-04-01

    Ecological resources are resources that have functional value to ecosystems. Frequently, these functions are overlooked in terms of the value they provide to humans. Environmental economics is in search of an appropriate analysis framework for such resources. In such a framework, it is essential to distinguish between two related subsets of information: (1) ecological processes that have intrinsic value to natural ecosystems; and (2) ecological functions that are values by humans. The present study addresses these concerns by identifying a habitat that is being displaced by development, and by measuring the human and ecological values associated with the ecological resources in that habitat. It is also essential to determine which functions are mutually exclusive and which are, in effect, complementary or products of joint production. The authors apply several resource valuation tools, including contingent valuation methodology (CVM), travel cost methodology (TCM), and hedonic damage-pricing (HDP). One way to derive upper-limit values for more difficult-to-value functions is through the use of human analogs, because human-engineered systems are relatively inefficient at supplying the desired services when compared with natural systems. Where data on the relative efficiencies of natural systems and human analogs exist, it is possible to adjust the costs of providing the human analog by the relative efficiency of the natural system to obtain a more realistic value of the function under consideration. The authors demonstrate this approach in an environmental economic case study of the environmental services rendered by shrub-steppe habitats of Benton County, Washington State.

  20. Nutrition, ecology and nutritional ecology: towardan integrated framework

    DEFF Research Database (Denmark)

    Raubenheimer, David; Simpson, Steven J.; Mayntz, David

    2009-01-01

    1. The science of nutritional ecology spans a wide range of fields, including ecology, nutrition, behaviour, morphology, physiology, life history and evolutionary biology. But does nutritional ecology have a unique theoretical framework and research program and thus qualify as a field of research...

  1. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.

    Science.gov (United States)

    Bolduc, Benjamin; Shaughnessy, Daniel P; Wolf, Yuri I; Koonin, Eugene V; Roberto, Francisco F; Young, Mark

    2012-05-01

    There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.

  2. RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

    Directory of Open Access Journals (Sweden)

    Henning Seedorf

    2014-08-01

    Full Text Available Methane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion efficiency, it is essential that methanogens can be identified and taxonomically classified with high accuracy. Currently available taxonomic frameworks offer only limited resolution beyond the genus level for taxonomic assignments of sequence data stemming from high throughput sequencing technologies. Therefore, we have developed a QIIME-compatible database (DB designed for species-level taxonomic assignment of 16S rRNA gene amplicon data targeting methanogenic archaea from the rumen, and from animal and human intestinal tracts. Called RIM-DB (Rumen and Intestinal Methanogen-DB, it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders. The taxonomy encompasses the recently-proposed seventh order of methanogens, the Methanomassiliicoccales, and allows differentiation between defined groups within this order. Sequence reads from rumen contents from a range of ruminant-diet combinations were taxonomically assigned using RIM-DB, Greengenes and SILVA. This comparison clearly showed that taxonomic assignments with RIM-DB resulted in the most detailed assignment, and only RIM-DB taxonomic assignments allowed methanogens to be distinguished taxonomically at the species level. RIM-DB complements the use of comprehensive databases such as Greengenes and SILVA for community structure analysis of methanogens from the rumen and other intestinal environments, and allows identification of target species for methane mitigation strategies.

  3. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    Directory of Open Access Journals (Sweden)

    Mauricio eBustamante

    2012-08-01

    Full Text Available Water availability is the main limiting factor in arid soils; however few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB and archaea (AOA from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosms (p<0.001. This stimulation of net nitrification by water addition was inhibited by acetylene addition at 100 Pa. The composition of AOA and AOB assemblages from the soils microcosms was determined by clone sequencing of amoA genes (A-amoA and B-amoA, respectively, and the 16S rRNA genes specific for β-proteobacteria (beta-amo. Sequencing of beta-amo genes has revealed representatives of Nitrosomonas and Nitrosospira while B-amoA clones consisted only of Nitrosospira sequences. Furthermore, all clones from the archaeal amoA gene library (A-amoA were related to ‘mesophilic Crenarchaeota’ sequences (actually, reclassified as the phylum Thaumarchaeota. The effect of water availability on both microbial assemblages structure was determined by T-RFLP profiles using the genetic markers amoA for archaea, and beta-amo for bacteria. While AOA showed fluctuations in some T-RFs, AOB structure remained unchanged by water pulses. The relative abundance of AOA and AOB was estimated by the Most Probable Number coupled to Polymerase Chain Reaction (MPN-PCR assay. AOB was the predominant guild in this soil and higher soil water content did not affect their abundance, in contrast to AOA, which slightly increased under these conditions. Therefore, these results suggest that water addition to these semiarid soil microcosms could favor archaeal contribution to ammonium oxidation.

  4. Shrinking body size as an ecological response to climate change

    Science.gov (United States)

    Sheridan, Jennifer A.; Bickford, David

    2011-11-01

    Determining how climate change will affect global ecology and ecosystem services is one of the next important frontiers in environmental science. Many species already exhibit smaller sizes as a result of climate change and many others are likely to shrink in response to continued climate change, following fundamental ecological and metabolic rules. This could negatively impact both crop plants and protein sources such as fish that are important for human nutrition. Furthermore, heterogeneity in response is likely to upset ecosystem balances. We discuss future research directions to better understand the trend and help ameliorate the trophic cascades and loss of biodiversity that will probably result from continued decreases in organism size.

  5. The redoubtable ecological periodic table

    Science.gov (United States)

    Ecological periodic tables are repositories of reliable information on quantitative, predictably recurring (periodic) habitat–community patterns and their uncertainty, scaling and transferability. Their reliability derives from their grounding in sound ecological principle...

  6. Sources and significance of variation in basal, summit and maximal metabolic rates in birds

    Directory of Open Access Journals (Sweden)

    Andrew E. MCKECHNIE, David L. SWANSON

    2010-12-01

    Full Text Available The rates at which birds use energy may have profound effects on fitness, thereby influencing physiology, behavior, ecology and evolution. Comparisons of standardized metabolic rates (e.g., lower and upper limits of metabolic power output present a method for elucidating the effects of ecological and evolutionary factors on the interface between physiology and life history in birds. In this paper we review variation in avian metabolic rates [basal metabolic rate (BMR; minimum normothermic metabolic rate, summit metabolic rate (Msum; maximal thermoregulatory metabolic rate, and maximal metabolic rate (MMR; maximal exercise metabolic rate], the factors associated with this variation, the evidence for functional links between these metabolic traits, and the ecological and evolutionary significance of avian metabolic diversity. Both lower and upper limits to metabolic power production are phenotypically flexible traits, and vary in association with numerous ecological and evolutionary factors. For both inter- and intraspecific comparisons, lower and upper limits to metabolic power production are generally upregulated in response to energetically demanding conditions and downregulated when energetic demands are relaxed, or under conditions of energetic scarcity. Positive correlations have been documented between BMR, Msum and MMR in some, but not all studies on birds, providing partial support for the idea of a functional link between lower and upper limits to metabolic power production, but more intraspecific studies are needed to determine the robustness of this conclusion. Correlations between BMR and field metabolic rate (or daily energy expenditure, in birds are variable, suggesting that the linkage between these traits is subject to behavioral adjustment, and studies of the relationship between field and maximal metabolic rates are lacking. Our understanding of avian metabolic diversity would benefit from future studies of: (1 the functional

  7. Rumen microbial communities influence metabolic phenotypes in lambs

    DEFF Research Database (Denmark)

    Morgavi, Diego P.; Rahahao-Paris, Estelle; Popova, Milka;

    2015-01-01

    and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted...... the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult...... sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure...

  8. Fermentation enhancement of methanogenic archaea consortia from an Illinois basin coalbed via DOL emulsion nutrition.

    Science.gov (United States)

    Xiao, Dong; Peng, Su-Ping; Wang, En-Yuan

    2015-01-01

    Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate. PMID:25884952

  9. Fermentation enhancement of methanogenic archaea consortia from an Illinois basin coalbed via DOL emulsion nutrition.

    Directory of Open Access Journals (Sweden)

    Dong Xiao

    Full Text Available Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate.

  10. Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources.

    Science.gov (United States)

    Cerqueda-García, Daniel; Falcón, Luisa I

    2016-08-01

    Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter. PMID:27324427

  11. Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources.

    Science.gov (United States)

    Cerqueda-García, Daniel; Falcón, Luisa I

    2016-08-01

    Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter.

  12. Hanford Site Ecological Quality Profile

    Energy Technology Data Exchange (ETDEWEB)

    Bilyard, Gordon R.; Sackschewsky, Michael R.; Tzemos, Spyridon

    2002-02-17

    This report reviews the ecological quality profile methodology and results for the Hanford Site. It covers critical ecological assets and terrestrial resources, those in Columbia River corridor and those threatened and engdangered, as well as hazards and risks to terrestrial resources. The features of a base habitat value profile are explained, as are hazard and ecological quality profiles.

  13. Blueberries and Metabolic Syndrome

    Science.gov (United States)

    Metabolic Syndrome is a cluster of metabolic disorders that increase the risk of cardiovascular diseases. Type 2 diabetes, elevated blood pressure, and atherogenic dyslipidemia are among the metabolic alterations that predispose the individual to several adverse cardiovascular complications. The hea...

  14. Carbohydrate Metabolism Disorders

    Science.gov (United States)

    ... you eat. Food is made up of proteins, carbohydrates, and fats. Chemicals in your digestive system (enzymes) ... metabolic disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. ...

  15. Ecological recovery in ERA

    DEFF Research Database (Denmark)

    EFSA Scientific Committee (Scientific Committee); Topping, Christopher John

    2016-01-01

    recognises the importance of more integrated ERAs considering both the local and landscape scales, as well as the possible co-occurrence of multiple potential stressors that fall under the remit of EFSA, which are important when addressing ecological recovery. In this scientific opinion, the Scientific...... Committee gathered scientific knowledge on the potential for the recovery of non-target organisms for the further development of ERA. Current EFSA guidance documents and opinions were reviewed on how ecological recovery is addressed in ERA schemes. In addition, this scientific opinion is based on expert...... knowledge and data retrieved from the literature. Finally, the information presented in this opinion was reviewed by experts from the relevant EFSA Panels, European risk assessment bodies and through an open consultation requesting input from stakeholders. A conceptual framework was developed to address...

  16. Socio-Ecological Innovation

    DEFF Research Database (Denmark)

    Edgeman, Rick; Eskildsen, Jacob Kjær

    is part of the enterprise cultural fabric, is foundational to enterprise strategy, and contributes to the financial security of the enterprise. Innovation for Sustainability is innovation that is specifically targeted to address ecological and / or societal considerations. That is, Innovation......Socio‐Ecological Innovation or SEI is innovation resulting from strategic integration of sustainable innovation and innovation for sustainability. In particular SEI is regarded as critical to organizations intent on progressing toward Sustainable Enterprise Excellence (SEE) and, indeed, progressing...... toward the asymptotic goal of becoming a continuously relevant and responsible organization (CR2O). Sustainable Innovation is something that is attained only when innovation in an enterprise is regular, systematic, and systemic to the endeavors of the enterprise itself – that is – Sustainable Innovation...

  17. Chasing Ecological Interactions

    Science.gov (United States)

    2016-01-01

    Basic research on biodiversity has concentrated on individual species—naming new species, studying distribution patterns, and analyzing their evolutionary relationships. Yet biodiversity is more than a collection of individual species; it is the combination of biological entities and processes that support life on Earth. To understand biodiversity we must catalog it, but we must also assess the ways species interact with other species to provide functional support for the Tree of Life. Ecological interactions may be lost well before the species involved in those interactions go extinct; their ecological functions disappear even though they remain. Here, I address the challenges in studying the functional aspects of species interactions and how basic research is helping us address the fast-paced extinction of species due to human activities. PMID:27631692

  18. Fundamental ecology is fundamental.

    Science.gov (United States)

    Courchamp, Franck; Dunne, Jennifer A; Le Maho, Yvon; May, Robert M; Thébaud, Christophe; Hochberg, Michael E

    2015-01-01

    The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research in the light of potential applications. This includes the understanding of our environment, for intellectual, economical, social, and political reasons, and as a major source of innovation. We contend that we should focus less on short-term, objective-driven research and more on creativity and exploratory analyses, quantitatively estimate the benefits of fundamental research for society, and better explain the nature and importance of fundamental ecology to students, politicians, decision makers, and the general public. Our perspective and underlying arguments should also apply to evolutionary biology and to many of the other biological and physical sciences.

  19. Editorial: Pedagogical Media Ecologies

    Directory of Open Access Journals (Sweden)

    Dorothee M. Meister

    2014-07-01

    Full Text Available From educational gaming through portable e-readers to cell phones, media are interpenetrating educational spaces and activities. Accordingly, understanding media in environmental or ecological terms has become increasingly important for education internationally. In North America, for example, the centenary of McLuhan’s birth has focused attention on approaches to media – whether oral, textual, electronic or digital– as a kind of environment in which education takes place. In parts of Europe, the so-called mediatic turn – following on the linguistic and iconic turns – has similarly emphasized the role of media as a condition for the possibility of educational activities and programs. With a few exceptions1 the papers in this special issue were first presented at the conference «Educational Media Ecologies: International Perspectives» which took place at the University of Paderborn, Germany, on March 27–28, 2012.2 The event was an interdisciplinary and transatlantic endeavor to bring together a wide range of perspectives on various issues relevant to educational media ecologies,3 and on related debates on mediation, medialization, mediatization, and mediality.4 The purpose of this volume, like the conference, is to foster and deepen international dialogue in the area of educational media. Areas of research and scholarship relevant to this dialogue include educational media, media literacy, educational philosophy, and media and cultural studies. The contributions, described below, put conceptual issues as well as social practices and applications at the center of the debate. Klaus Rummler opens the issue by clarifying the concept of ecology itself. Referencing a range of work over the past 50 years, Rummler describes how ecological models have been cast in sociological, semiotic, cultural, mediatic and other terms, and he explains the implications of these various perspectives for the study of educational contexts. Rummler also

  20. To the Ecological Aesthetics

    Institute of Scientific and Technical Information of China (English)

    王秀青

    2014-01-01

    Landscape design is one of the space form and space environment comprehensive planning and design, to im-prove the quality of urban environment, quality of life and urban landscape level play a very important role.It is expounded in this article based on the value of landscape ecological aesthetics under the background of productive landscape, discusses the"bigfoot aesthetics"innovative application in modern landscape design and new thinking.

  1. "Ecologically Sustainable Tourism Management"

    OpenAIRE

    Christine Lim; Michael McAleer

    2003-01-01

    One of the primary challenges facing ecotourism management is to establish a profitable and ecologically sustainable industry, while simultaneously achieving a satisfying experience for visitors and raising standards of living in the host community. This paper analyses the management practices and challenges faced by two ecotourism attractions on the Gold Coast in Queensland, Australia, namely Couran Cove Island Resort and Boondall Wetlands Reserve. As an ecotourism-based resort on one of the...

  2. Ecologically Sustainable Tourism Management

    OpenAIRE

    Lim, Christine; Michael, McAleer

    2003-01-01

    One of the primary challenges facing ecotourism management is to establish a profitable and ecologically sustainable industry, while simultaneously achieving a satisfying experience for visitors and raising standards of living in the host community. This paper analyses the management practices and challenges faced by two ecotourism attractions on the Gold Coast in Queensland, Australia, namely Couran Cove Island Resort and Boondall Wetlands Reserve. As an ecotourism-based resort on one of the...

  3. Ecologism in Interior Design

    OpenAIRE

    Ruizhou Liu; Yunkai Xu

    2008-01-01

    With the progress of our mankind, great changes have taken place in economy as well as our society, so have the natural environment and ecological system in which we live. Nowadays, we are faced with decreasing natural environment, forest, species, clean water, air and cultivable land. In addition, some urgent issues such as global warming, exhausted energy and widespread rubbish force us to reflect on our future life style. In this situation, interior designers are expected to introduce ecol...

  4. Environmental and Ecological Challenges

    OpenAIRE

    Sauter, E. J.

    2014-01-01

    Abstract: Title: “Environmental and Ecological Challenges” The Arctic faces rapid changes in the context of global warming. This presentation recaps the most important processes and physical boundary conditions relevant for the development of Arctic shipping. It is common sense that the changes observed in the Arctic are not created locally but globally. Vice versa the will affect back global processes. Globalism includes the Arctic in both directions. However, as an area of extreme cli...

  5. Powering Ecological Futures

    DEFF Research Database (Denmark)

    Witzke, Anne Sophie; Schick, Lea

    2011-01-01

    This paper riffs off from Peter Sloterdijk’s important concept of ‘air-condition’ and Bruno Latour’s influential idea about ‘ecologizing’, which establish a theoretical framework to discuss the engagement of digital art in environmental problems. Looking at two projects – Nuage Vert by the duo He......He and Natural Fuse by Haque Design – the article argues that digital art can articulate the complexity and ambiguities of an ecological futur...

  6. To the Ecological Aesthetics

    Institute of Scientific and Technical Information of China (English)

    王秀青

    2014-01-01

    Landscape design is one of the space form and space environment comprehensive planning and design, to im- prove the quality of urban environment, quality of life and urban landscape level play a very important role.It is expounded in this article based on the value of landscape ecological aesthetics under the background of productive landscape, discusses the "bigfoot aesthetics" innovative application in modern landscape design and new thinking.

  7. Groundwater ecology literature review

    OpenAIRE

    Maurice, L.

    2009-01-01

    Groundwater ecology is the study of ecosystems that occur in the subsurface within groundwater. Groundwater often contains a diverse range of organisms, and those that live in groundwater and generally do not live above the ground surface are called Stygobites. Stygobites species come from several different taxonomic groups of animals. Many animals found in groundwater are Crustaceans (Copepoda, Ostracoda, Amphipoda, Isopoda, Syncarida, Cladocera) but species of Oligocheata and...

  8. Toward an Agathocentric Ecology

    Directory of Open Access Journals (Sweden)

    Erazim Kohák

    2007-04-01

    Full Text Available I should like to submit to you a simple, basic thesis--that what we are accustomed to calling the "ecological crisis" is not a product of a conflict between human needs and the needs of nature but of a flawed perception of what our needs in truth are. It is, I believe, a crisis of our humanity rather than one of nature or technology, and so requires not only technological but also humanistic answers.

  9. Terrestrial Ecology Section

    International Nuclear Information System (INIS)

    Progress is reported on the following research projects: ecological effects of air pollutants from coal combustion; gaseous diffusion plants as a source of atmospheric fluoride; atmospheric emission and plant uptake of Hg from agricultural soils near the Almaden Hg mine; Walker Branch Watershed; carbon allocation in deciduous forest trees; scaled soil hydraulic properties and water budget modeling; measured and simulated plant-water relations of yellow poplar; foliar nitrogen translocation in eastern forest species; Environmental Research Park; and forest resource management

  10. Editorial: Pedagogical Media Ecologies

    OpenAIRE

    Dorothee M. Meister; Theo Hug; Friesen Norm

    2014-01-01

    From educational gaming through portable e-readers to cell phones, media are interpenetrating educational spaces and activities. Accordingly, understanding media in environmental or ecological terms has become increasingly important for education internationally. In North America, for example, the centenary of McLuhan’s birth has focused attention on approaches to media – whether oral, textual, electronic or digital– as a kind of environment in which education takes place. In parts of Europe,...

  11. Ecological planning: A review

    Science.gov (United States)

    Steiner, Frederick; Brooks, Kenneth

    1981-11-01

    Beginning with the passage of the National Environmental Policy Act in 1969, the federal government of the United States has enacted numerous pieces of legislation intended to protect or conserve the environment. Other national governments have also enacted environmental legislation during the past two decades. State and local governments have also adopted policies concerned with environmental planning and management. Multiple laws and overlapping governmental agency responsibilities have confused development and resource management efforts. A comprehensive methodology that integrates the legal mandates and the agency missions into a common and unified framework is needed. Ecological planning offers such a method. Application of the method allows planners and resource managers to better understand the nature and character of the land and/or resource and therefore make better decisions about its appropriate use or management. The steps taken in an ecological planning process—1) goal setting, 2) inventory and analysis of data, 3) suitability analysis, 4) developing alternatives, 5) implementation, 6) administration, and 7) evaluation—are outlined and explained. Hand-drawn overlays and computer programs as techniques for handling ecological planning information are compared. Observations and suggestions for further research are offered.

  12. Resilience Through Ecological Network

    Directory of Open Access Journals (Sweden)

    Grazia Brunetta

    2014-05-01

    Full Text Available The paper explores the strategic role that urban biodiversity and ecosystem services management, natural infrastructure and adaptive governance approaches can play in making our economies and societies more resilient and in linking human societies and the natural environment. Resilience – a concept that entered the debate on urban governance – means the ability of urban systems, considered as linear-systems, to react to external disturbances by returning to some socio-ecological equilibrium steady-state by overcoming a crisis period (Gunderson & al. 2010, Newman & al. 2009. In this view, green infrastructures can assume a strategic role in restoring and enhancing the ecological and environmental livability in urban areas. Starting from the International and European context, the paper discusses innovative programs and interdisciplinary projects and practices (some cases in Turin Metropolitan Area to demonstrate how green infrastructures can increase the adaptive capacity of urban systems in term of resilience. They can contribute to increase the ability of European cities to adapt to climate change and to reduce their ecological footprints, to enhance security and life quality.

  13. European ecological networks and greenways

    DEFF Research Database (Denmark)

    Kristiansen, Ib; Jongman, Rob H.G.; Kulvik, Mart

    2004-01-01

    In the context of European integration, networks are becoming increasingly important in both social and ecological sense. Since the beginning of the 1990s, societal and scientific exchanges are being restructured as the conceptual approaches towards new nature conservation strategies have been...... renewed. Within the framework of nature conservation, the notion of an ecological network has become increasingly important. Throughout Europe, regional and national approaches are in different phases of development, which are all based on recent landscape ecological principles. Ecological networks....... This complex interaction between cultural and natural features results in quite different ways for the elaboration of ecological networks and greenways....

  14. Ecology for a changing earth

    International Nuclear Information System (INIS)

    To forecast the ecological impact of global change, research initiatives are needed on the explicit role of humans in ecological systems, and on how ecological processes functioning at different spatial and temporal scales are coupled. Furthermore, to synthesize the results of ecological research for Congress, policymakers, and the general public, a new agency, called the United States Ecological Survey (USES) is urgently required. Also, a national commitment to environmental health, as exemplified by establishing a National Institutes of the Environment (NIE), should be a goal

  15. Bioreporters in microbial ecology

    NARCIS (Netherlands)

    Leveau, J.H.J.; Lindow, S.E.

    2002-01-01

    Bioreporters are effective research tools for gaining an understanding of a microbe's perception of the world. Fitted with a fusion of an environmentally responsive promoter to a suitable reporter gene, a bacterial or fungal bioreporter is able to communicate its metabolic or transcriptional behavio

  16. Research on Ecological Civilization Evaluation Index System

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Ecological civilization, which refers to the harmonious development of man and the nature, has the connotation of the ecological material civilization, ecological consciousness civilization, ecological institutional civilization and ecological behavior civilization. The research on ecological civilization evaluation index system is important in that it can provide the guidance for the construction of ecological civilization, and besides it can improve public recognition of the importance of ecological civil...

  17. Recombination does not hinder formation or detection of ecological species of Synechococcus inhabiting a hot spring cyanobacterial mat

    Directory of Open Access Journals (Sweden)

    Melanie Crystal Melendrez

    2016-01-01

    Full Text Available Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B´ of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B´ lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B´ lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes, and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal

  18. Statistical ecology comes of age.

    Science.gov (United States)

    Gimenez, Olivier; Buckland, Stephen T; Morgan, Byron J T; Bez, Nicolas; Bertrand, Sophie; Choquet, Rémi; Dray, Stéphane; Etienne, Marie-Pierre; Fewster, Rachel; Gosselin, Frédéric; Mérigot, Bastien; Monestiez, Pascal; Morales, Juan M; Mortier, Frédéric; Munoz, François; Ovaskainen, Otso; Pavoine, Sandrine; Pradel, Roger; Schurr, Frank M; Thomas, Len; Thuiller, Wilfried; Trenkel, Verena; de Valpine, Perry; Rexstad, Eric

    2014-12-01

    The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1-4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.

  19. Influence of niche differentiation on the abundance of methanogenic archaea and methane production potential in natural wetland ecosystems across China

    Directory of Open Access Journals (Sweden)

    D. Liu

    2010-10-01

    Full Text Available Methane (CH4 emissions from natural wetland ecosystems exhibit large spatial variability. To understand the underlying factors that induce differences in CH4 emissions from natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical profile soils sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjiang marsh in the cold temperate zone, and the Ruoergai peatland in the Qinghai-Tibetan Plateau. The top soil layer had the highest population of methanogens (1.07−8.29×109 cells g−1 soil in all wetlands except the Ruoergai peatland and exhibited the maximum CH4 production potential measured at the mean in situ summer temperature. There is a significant logarithmic correlation between the abundance of methanogenic archaea and the soil organic carbon (R2=0.718, P<0.001, n=13 and between the abundance of methanogenic archaea and the total nitrogen concentrations (R2=0.758, P<0.001, n=13 in wetland soils. This indicates that the amount of soil organic carbon may affect the population of methanogens in wetland ecosystems. While the CH4 production potential is not significantly related to methanogen population (R2=0.011, P>0.05, n=13, it is related to the dissolved organic carbon concentration (R2=0.305, P=0.05, n=13. This suggests that the methanogen population is not an effective index for predicting the CH4 production in wetland ecosystems. The CH4 production rate of the top soil layer increases with increasing latitude, from 274 μg CH4 kg−1 soil d−1 in the Poyang wetland to 665 μg CH4 kg−1 soil d−1 in the Carex lasiocarpa

  20. The metabolism and biotechnological application of betaine in microorganism.

    Science.gov (United States)

    Zou, Huibin; Chen, Ningning; Shi, Mengxun; Xian, Mo; Song, Yimin; Liu, Junhong

    2016-05-01

    Glycine betaine (betaine) is widely distributed in nature and can be found in many microorganisms, including bacteria, archaea, and fungi. Due to its particular functions, many microorganisms utilize betaine as a functional chemical and have evolved different metabolic pathways for the biosynthesis and catabolism of betaine. As in animals and plants, the principle role of betaine is to protect microbial cells against drought, osmotic stress, and temperature stress. In addition, the role of betaine in methyl group metabolism has been observed in a variety of microorganisms. Recent studies have shown that betaine supplementation can improve the performance of microbial strains used for the fermentation of lactate, ethanol, lysine, pyruvate, and vitamin B12, during which betaine can act as stress protectant or methyl donor for the biosynthesis of structurally complex compounds. In this review, we summarize the transport, synthesis, catabolism, and functions of betaine in microorganisms and discuss potential engineering strategies that employ betaine as a methyl donor for the biosynthesis of complex secondary metabolites such as a variety of vitamins, coenzymes, and antibiotics. In conclusion, the biocompatibility, C/N ratio, abundance, and comprehensive metabolic information of betaine collectively indicate that this molecule has great potential for broad applications in microbial biotechnology. PMID:27005411