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Sample records for sea life microbes

  1. Life Redefined: Microbes Built with Arsenic

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Sam (SLAC and Felisa Wolfe-Simon, NASA and U.S. Geological Survey)

    2011-03-22

    Life can survive in many harsh environments, from extreme heat to the presence of deadly chemicals. However, life as we know it has always been based on the same six elements -- carbon, oxygen, nitrogen, hydrogen, sulfur and phosphorus. Now it appears that even this rule has an exception. In the saline and poisonous environment of Mono Lake, researchers have found a bacterium that can grow by incorporating arsenic into its structure in place of phosphorus. X-ray images taken at SLAC's synchrotron light source reveal that this microbe may even use arsenic as a building block for DNA. Please join us as we describe this discovery, which rewrites the textbook description of how living cells work.

  2. Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

    Science.gov (United States)

    Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

    2016-02-01

    Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

  3. The high life: Transport of microbes in the atmosphere

    Science.gov (United States)

    Smith, David J.; Griffin, Dale W.; Jaffe, Daniel A.

    2011-07-01

    Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating animals or the hydrological cycle, but transport by wind may be the most common way microbes spread. General awareness of airborne microbes predates the science of microbiology. People took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur's quest to disprove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experiments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil.

  4. Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

    Science.gov (United States)

    Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

    2017-10-03

    Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

  5. Evolution, human-microbe interactions, and life history plasticity.

    Science.gov (United States)

    Rook, Graham; Bäckhed, Fredrik; Levin, Bruce R; McFall-Ngai, Margaret J; McLean, Angela R

    2017-07-29

    A bacterium was once a component of the ancestor of all eukaryotic cells, and much of the human genome originated in microorganisms. Today, all vertebrates harbour large communities of microorganisms (microbiota), particularly in the gut, and at least 20% of the small molecules in human blood are products of the microbiota. Changing human lifestyles and medical practices are disturbing the content and diversity of the microbiota, while simultaneously reducing our exposures to the so-called old infections and to organisms from the natural environment with which human beings co-evolved. Meanwhile, population growth is increasing the exposure of human beings to novel pathogens, particularly the crowd infections that were not part of our evolutionary history. Thus some microbes have co-evolved with human beings and play crucial roles in our physiology and metabolism, whereas others are entirely intrusive. Human metabolism is therefore a tug-of-war between managing beneficial microbes, excluding detrimental ones, and channelling as much energy as is available into other essential functions (eg, growth, maintenance, reproduction). This tug-of-war shapes the passage of each individual through life history decision nodes (eg, how fast to grow, when to mature, and how long to live). Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Life under the Microscope: Children's Ideas about Microbes

    Science.gov (United States)

    Allen, Michael; Bridle, Georgina; Briten, Elizabeth

    2015-01-01

    Microbes (by definition) are tiny living things that are only visible through a microscope and include bacteria, viruses, fungi, and protoctists (mainly single-celled life forms such as amoebae and algae). Although people are familiar with the effects of microbes, such as infectious disease and food spoilage, because of their lack of visibility,…

  7. Potential impact of global climate change on benthic deep-sea microbes.

    Science.gov (United States)

    Danovaro, Roberto; Corinaldesi, Cinzia; Dell'Anno, Antonio; Rastelli, Eugenio

    2017-12-15

    Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus)

    Science.gov (United States)

    Jiang, Yan; Wang, Yingeng; Mai, Kangsen; Zhang, Zheng; Liao, Meijie; Rong, Xiaojun

    2015-10-01

    The effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus) were compared to select the optimal fermentation strain in this study. Saccharomgces cerevisae, Candida utilis, Bacillus subtilis and Geotrichum candidum were independently added into the experimental compound feed, while only saline was mixed with the control feed. The fermentation treatments were inoculated with 10% seed solution under the condition of 25°C and 70% water content, which lasted for 5 days to elucidate the optimal microbe strain for fermenting effect. Physicochemical indexes and sensorial characteristics were measured per day during the fermentation. The indexes included dry matter recovery (DMR), crude protein (CP), the percentage of amino acid nitrogen to total nitrogen (AA-N/tN), the percentage of ammonia nitrogen to total nitrogen (NH3-N/tN), and the ratio of fermentation strains and vibrios to the total microbes, color, smell and viscosity. The results showed that DMR, CP and AA-N/tN of the S. cerevisae group reached the highest level on day 3, but the ratio of fermentation strain was second to C. utilis group. In addition, its NH3-N/tN and the ratio of vibrios were maintained at low levels, and the sensory evaluation score including smell, color and viscosity was the highest in S. cerevisae group on day 3. Therefore, S. cerevisae could be the optimal strain for the feed fermentation for sea cucumber. This research developed a new production method of fermentation feed for sea cucumber.

  9. Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea.

    Science.gov (United States)

    Yu, Tiantian; Li, Meng; Niu, Mingyang; Fan, Xibei; Liang, Wenyue; Wang, Fengping

    2018-01-01

    In marine sediments, microorganisms are known to play important roles in nitrogen cycling; however, the composition and quantity of microbes taking part in each process of nitrogen cycling are currently unclear. In this study, two different types of marine sediment samples (shallow bay and deep-sea sediments) in the South China Sea (SCS) were selected to investigate the microbial community involved in nitrogen cycling. The abundance and composition of prokaryotes and seven key functional genes involved in five processes of the nitrogen cycle [nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox)] were presented. The results showed that a higher abundance of denitrifiers was detected in shallow bay sediments, while a higher abundance of microbes involved in ammonia oxidation, anammox, and DNRA was found in the deep-sea sediments. Moreover, phylogenetic differentiation of bacterial amoA, nirS, nosZ, and nrfA sequences between the two types of sediments was also presented, suggesting environmental selection of microbes with the same geochemical functions but varying physiological properties.

  10. Molecular Phylogeny Of Microbes In The Deep-Sea Sediments From Tropical West Pacific Warm Pool

    Science.gov (United States)

    Wang, F.; Xiao, X.; Wang, P.

    2005-12-01

    The presence and phylogeny of bacteria and archaea in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1cm-, 3cm-, 6cm-, 10cm-, 12cm- layer) of the 12-cm sediment core of WP-0 were checked and compared. The microbial diversity in the five deep-sea sediments were similar as revealed by denaturing gradient gel electrophoresis, and all of them contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. The composition of methylotrophs including methanotrophs, sulfate reducing bacteria in the WP-0 sediment core were further investigated by molecular marker based analysis of mxaF, pmoA, dsrAB, specific anoxic methane oxidation archaeal and sulfate reducing bacterial 16S rRNA genes. From MxaF amino acid sequence analysis, it was demonstrated that microbes belonging to α - Proteobacteria most related to Hyphomicrobium and Methylobacterium were dominant aerobic methylotrophs in this deep-sea sediment; and small percentage of type II methanotrophs affiliating closest to Methylocystis and Methylosinus were also detected in this environment. mxaF quantitative PCR results showed that in the west Pacific WP sediment there existed around 3× 10 4-5 methylotrophs per gram sediment, 10-100 times more than that in samples collected from several other deep-sea Pacific sediment sample, but about 10 times less than that present in samples collected from rice and flower garden soil. Diverse groups of novel archaea (named as WPA), not belonging to any known archaeal lineages were checked out. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. Possible sulfate reducing bacterial related with Desulfotomaculum, Desulfacinum, Desulfomonile and Desulfanuticus were also detected in our study. The vertical distributions of WPA

  11. The extreme environments and their microbes as models for extraterrestrial life

    Science.gov (United States)

    Seckbach, J.; Oren, A.; Chela-Flores, J.

    2008-09-01

    Life exists almost everywhere on Earth. Presence of liquid water is a prerequisite for life (Oren, 2008). Living organisms are not only found in `normal' habitats (from the anthropocentric view). Many types, especially of microorganisms, not only tolerate harsh environmental conditions, but even thive in them. Such organisms that resist very harsh physical and chemical conditions in their habitats are termed `extremophiles'. Some extremophilic microorganisms are able to overcome more than one type of extreme conditions in their environment. For example, some `polyextremophiles' grow under hundreds of atmospheres of hydrostatic pressure (barophiles) and at very low, or alternatively at very high temperatures. In many hot springs there are acido-thermophiles that tolerate elevated temperatures and very low pH levels (e.g. the Cyanidium caldarium group, see Seckbach 1994). Members of Cyanidium are able to thrive in pure CO2, a condition not tolerated by most algae (Seckbach et al., 1970). Some thermophilic Archaea grow at temperatures up to 1130C and possibly even higher. In the Arctic and Antarctic regions and in the permafrost region in Siberia there are cold-loving microorganisms (psychrophiles) which are able to grow at -200C. Many types of Bacteria and Archaea tolerate extreme dryness, and spores of Bacillus and relatives that have been encapsulated within salt crystals may have survived in a dormant state for thousands and even millions of years, and still can be revived today. Other extremophiles tolerate salt concentrations up to saturation. Halophilic microorganisms such as found in the Dead Sea or in the Great Salt Lake have developed different strategies to cope with the high osmotic pressure of their environment. Some (e.g. the unicellular green alga Dunaliella salina) balance the salts in their medium by accumulating organic compounds such as glycerol. Others (halophilic Archaea of the order Halobacteriales, as well as a few representatives of the

  12. The sea - landfill or sphere of life

    International Nuclear Information System (INIS)

    Haury, H.J.; Koller, U.; Assmann, G.

    1990-01-01

    The Environmental Information Agency held its third seminar for journalists, entitled 'The sea - landfill or sphere of life' in Hamburg on July 18, 1989. Some 40 journalists - radio journalists and journalists from the staff of dailies and the technical press - took the opportunity to listen for a day to short lectures on selected subjects and submit their questions concerning sea pollution to scientists of diverse disciplines. (orig.) [de

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

    KAUST Repository

    Wang, Yong; Cao, Huiluo; Zhang, Guishan; Bougouffa, Salim; Lee, On On; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan

    2013-01-01

    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

  14. Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp Ortholog Data detail Data name Ortholog DOI 10.18908/lsdba.nbdc01181-010.V002 V...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

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

    Science.gov (United States)

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

    2016-08-01

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

  16. Earth analogs for Martian life - Microbes in evaporites, a new model system for life on Mars

    Science.gov (United States)

    Rothschild, Lynn J.

    1990-01-01

    It is suggested that 'oases' in which life forms may persist on Mars could occur, by analogy with terrestrial cases, in (1) rocks, as known in endolithic microorganisms, (2) polar ice caps, as seen in snow and ice algae, and (3) volcanic regions, as witnessed in the chemoautotrophs which live in ocean-floor hydrothermal vents. Microorganisms, moreover, have been known to survive in salt crystals, and it has even been shown that organisms can metabolize while encrusted in evaporites. Evaporites which may occur on Mars would be able to attenuate UV light, while remaining more transparent to the 400-700 nm radiation useful in photosynthesis. Suggestions are made for the selection of Martian exobiological investigation sites.

  17. 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.

  18. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  19. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  20. BRC - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...table). Data file File name: brc.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/brc.ta...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

  1. SRA - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e following table). Data file File name: sra.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/L...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us SRA - MicrobeDB.jp | LSDB Archive ...

  2. Disease - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...File name: disease.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/...iption Download License Update History of This Database Site Policy | Contact Us Disease - MicrobeDB.jp | LSDB Archive ...

  3. Soil mineralogy and microbes determine forest life history strategy and carbon cycling in humid tropical forests

    Science.gov (United States)

    Soong, J.; Verbruggen, E.; Peñuelas, J.; Janssens, I. A.; Grau, O.

    2017-12-01

    Tropical forests account for over one third of global terrestrial gross primary productivity and cycle more C than any other ecosystem on Earth. However, we still lack a mechanistic understanding of how such high productivity is maintained on the old, highly weathered and phosphorus depleted soils in the tropics. We hypothesized that heterogeneity in soil texture, mineralogy and microbial community composition may be the major drivers of differences in soil C storage and P limitation across tropical forests. We sampled 12 forest sites across a 200 km transect in the humid neo-tropics of French Guiana that varied in soil texture, precipitation and mineralogy. We found that soil texture was a major driver of soil carbon stocks and forest life history strategy, where sandy forests have lower soil C stocks, slower turnover and decomposition and a more closed nutrient cycle while clayey forests have higher soil C stocks, faster turnover and a more leaky nutrient cycle (using natural abundance stable isotope evidence). We found that although the presence of Al and Fe oxides in the clayey soils occludes soil organic matter and P, a greater abundance of arbuscular mycorrhizal fungi help forests to access occluded P in clayey soils fueling higher turnover and faster decomposition rates. Evidence from a laboratory incubation of tropical soils with nutrient additions further demonstrates the de-coupling of microbial P demands from C:N limitations providing further evidence for the need to examine microbial stoichiometry to explain C cycling in the P-limited tropics. We argue that microbial community composition and physiological demands, constrained within the limitations of soil mineralogical reactivity, largely controls nutrient and C cycling in tropical forest soils. Together our observational field study and laboratory incubation provide a unique dataset to shed light on the mineralogical and microbial controls on C and nutrient cycling in tropical soils. By integrating

  4. Diversity and distribution of microbes in deep-sea sub-vent systems, using newly designed in situ growth chambers

    Science.gov (United States)

    Higashi, Y.; Sunamura, M.; Utsumi, M.; Urabe, T.; Maruyama, A.

    2004-12-01

    Subsurface of deep-sea hydrothermal vent environments is one of the most difficult fields on the Earth to approach and collect reliable samples for microbiological study. In our Archaean Park project, we developed in situ incubation instruments to directly collect microbes from sub-vent fields through a drilled borehole. After excavation using a portable submarine driller (BMS) around deep-sea hydrothermal vents in the Suiyo Seamount on the Izu-Bonin Arc (2001, 2002) and the South Mariana (2003), microbial diversity was examined in samples collected from the boreholes, as well as natural vents, using catheter- and column-type in situ growth chambers. In the catheter samples collected from the Suiyo Seamount, several novel phylotypes of microbial SSU rRNA genes were assigned within epsilon-Proteobacteria and hyperthermophile-related Euryarchaea groups. The former novel epsilon group (SSSV-BE1) was also detected in the South Mariana, but they only appeared in the catheter samples collected just below the venting seafloor. These suggest that the group must be significant in warm, shallow and microaerobic sub-vent layers over the sea, at least in the northwest Pacific Ocean. The column-type in situ growth chamber was specially designed for creating and maintaining physico-chemical gradients in a ca. 40-cm-long column situated on an active vent. In Suiyo Seamount samples (vent temp.: ca. 30-100 degree C), a unique vertical profile was found in the diversity of Archaea. At the column bottom, most of the clones were assigned to be members within the lithoautotrophic thermophilic Ignicoccus, while heterotrophic thermophilic Thermococcus were abundant at the column top. Similar vertical profile has also been appeared in the column samples from the South Mariana. Further quantitative population analysis is now under going using these samples. Our approach to the sub-vent biosphere by the combination of drilling and in situ incubation is almost sure to give us important clues

  5. License - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp License License to Use This Database Last updated : 2017/06/29 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database... Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, yo

  6. Ontology - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available gzip) consists of some directories (see the following table). Data file File name: ontology....tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/ontology.tar.gz File size: 9...he NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. O...ples Data item Description ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes). onto...logy/meo/meo_fma_mapping.ttl An ontology mapping files t

  7. Life in Darwin's dust: intercontinental transport and survival of microbes in the nineteenth century.

    Science.gov (United States)

    Gorbushina, Anna A; Kort, Renate; Schulte, Anette; Lazarus, David; Schnetger, Bernhard; Brumsack, Hans-Jürgen; Broughton, William J; Favet, Jocelyne

    2007-12-01

    Charles Darwin, like others before him, collected aeolian dust over the Atlantic Ocean and sent it to Christian Gottfried Ehrenberg in Berlin. Ehrenberg's collection is now housed in the Museum of Natural History and contains specimens that were gathered at the onset of the Industrial Revolution. Geochemical analyses of this resource indicated that dust collected over the Atlantic in 1838 originated from the Western Sahara, while molecular-microbiological methods demonstrated the presence of many viable microbes. Older samples sent to Ehrenberg from Barbados almost two centuries ago also contained numbers of cultivable bacteria and fungi. Many diverse ascomycetes, and eubacteria were found. Scanning electron microscopy and cultivation suggested that Bacillus megaterium, a common soil bacterium, was attached to historic sand grains, and it was inoculated onto dry sand along with a non-spore-forming control, the Gram-negative soil bacterium Rhizobium sp. NGR234. On sand B. megaterium quickly developed spores, which survived for extended periods and even though the numbers of NGR234 steadily declined, they were still considerable after months of incubation. Thus, microbes that adhere to Saharan dust can live for centuries and easily survive transport across the Atlantic.

  8. Effectiveness of beneficial plant-microbe interactions under hypobaric and hypoxic conditions in an advanced life support system

    Science.gov (United States)

    MacIntyre, Olathe; Stasiak, Michael; Cottenie, Karl; Trevors, Jack; Dixon, Mike

    An assembled microbial community in the hydroponics solution of an advanced life support system may improve plant performance and productivity in three ways: (1) exclusion of plant pathogens from the initial community, (2) resistance to infection, and (3) plant-growth promotion. However, the plant production area is likely to have a hypobaric (low pressure) and hypoxic (low oxygen) atmosphere to reduce structural mass and atmosphere leakage, and these conditions may alter plant-microbe interactions. Plant performance and productivity of radish (Raphanus sativus L. cv. Cherry Bomb II) grown under hypobaric and hypoxic conditions were investigated at the University of Guelph's Controlled Environment Systems Research Facility. Changes in the microbial communities that routinely colonized the re-circulated nutrient solution, roots, and leaves of radishes in these experiments were quantified in terms of similarity in community composition, abundance of bacteria, and community diversity before and after exposure to hypobaric and hypoxic conditions relative to communities maintained at ambient growth conditions. The microbial succession was affected by extreme hypoxia (2 kPa oxygen partial pressure) while hypobaria as low as 10 kPa total pressure had little effect on microbial ecology. There were no correlations found between the physiological profile of these unintentional microbial communities and radish growth. The effects of hypobaric and hypoxic conditions on specific plant-microbe interactions need to be determined before beneficial gnotobiotic communities can be developed for use in space. The bacterial strains Tal 629 of Bradyrhizobium japonicum and WCS417 of Pseudomonas fluorescens, and the plant pathogen Fusarium oxysporum f. sp. raphani will be used in future experiments. B. japonicum Tal 629 promotes radish growth in hydroponics systems and P. fluorescens WCS417 induces systemic resistance to fusarium wilt (F. oxysporum f. sp. raphani) in radish under ambient

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

    Science.gov (United States)

    Grosch, Eugene G; Hazen, Robert M

    2015-10-01

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

  10. The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond.

    Science.gov (United States)

    Röling, Wilfred F M; Aerts, Joost W; Patty, C H Lucas; ten Kate, Inge Loes; Ehrenfreund, Pascale; Direito, Susana O L

    2015-06-01

    The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most promising for exploration. We review relevant mineral-biomarker and mineral-microbe interactions. The local mineralogy on a particular planet reflects its past and current environmental conditions and allows a habitability assessment by comparison with life under extreme conditions on Earth. The type of mineral significantly influences the potential abundances and types of biomarkers and microorganisms containing these biomarkers. The strong adsorptive power of some minerals aids in the preservation of biomarkers and may have been important in the origin of life. On the other hand, this strong adsorption as well as oxidizing properties of minerals can interfere with efficient extraction and detection of biomarkers. Differences in mechanisms of adsorption and in properties of minerals and biomarkers suggest that it will be difficult to design a single extraction procedure for a wide range of biomarkers. While on Mars samples can be used for direct detection of biomarkers such as nucleic acids, amino acids, and lipids, on other planetary bodies remote spectrometric detection of biosignatures has to be relied upon. The interpretation of spectral signatures of photosynthesis can also be affected by local mineralogy. We identify current gaps in our knowledge and indicate how they may be filled to improve the chances of detecting biomarkers on Mars and beyond.

  11. Effects of Simulated Eutrophication and Overfishing on Coral Reef Invertebrates, Algae and Microbes in the Red Sea

    OpenAIRE

    Jessen, Christian

    2013-01-01

    Besides the main climate change consequences, ocean warming and acidification, local disturbances such as overfishing and eutrophication are major threats to coral reefs worldwide. Despite its relatively healthy coral reefs that are increasingly faced with growing coastal development, the Red Sea is highly under-investigated, particularly outside the Gulf of Aqaba. This thesis therefore aims to contribute to the understanding of eutrophication and overfishing effects on Red Sea coral reefs by...

  12. Diversity and distribution of eukaryotic microbes in and around a brine pool adjacent to the Thuwal cold seeps in the Red Sea

    KAUST Repository

    Wang, Yong

    2014-02-04

    A hypoxic/suboxic brine pool at a depth of about 850 m was discovered near the Thuwal cold seeps in the Red Sea. Filled with high concentrations of hydrogen sulfide and ammonia, such a brine pool might limit the spread of eukaryotic organisms. Here, we compared the communities of the eukaryotic microbes in a microbial mat, sediments and water samples distributed in 7 sites within and adjacent to the brine pool. Taxonomic classification of the pyrosequenced 18S rRNA amplicon reads showed that fungi highly similar to the species identified along the Arabic coast were almost ubiquitous in the water and sediment samples, supporting their wide distribution in various environments. The microbial mat displayed the highest species diversity and contained grazers and a considerable percentage of unclassified species. Phylogeny-based methods revealed novel lineages representing a majority of the reads from the interface between the sea water and brine pool. Phylogenetic relationships with more reference sequences suggest that the lineages were affiliated with novel Alveolata and Euglenozoa inhabiting the interface where chemosynthetic prokaryotes are highly proliferative due to the strong chemocline and halocline. The brine sediments harbored abundant species highly similar to invertebrate gregarine parasites identified in different oxygen-depleted sediments. Therefore, the present findings support the uniqueness of some microbial eukaryotic groups in this cold seep brine system. 2014 Wang, Zhang, Cao, Shek, Tian, Wong, Batang, Al-suwailem and Qian.

  13. Noise-proof bubbles to protect sea life

    International Nuclear Information System (INIS)

    Deboutte, G.

    2012-01-01

    The construction of wind turbines in shallow sea might jeopardize the life of mammals living nearby. The wave sound generated by each hammer impact to drive the pillars deep in the sea bottom can reach up to 200 decibels at 750 m away from the construction site. Repeated noises at this sound level is thought to be damaging for audition systems of sea mammals. The German authorities have launched a 4-year long program to find efficient technical solutions to damp sound waves. Various techniques have been tested in the Baltic sea and it appears that most techniques are efficient but some seem more relevant like the bubble curtain in which air bubbles generated around the site disturb the propagation of sound waves, or the balloon curtain in which air balloons plays the role of the bubbles, or the network of vertical pipes set around the construction site, or the sound-proofed sheath set around the pillar and hammer. (A.C.)

  14. Emerging Methods and Systems for Observing Life in the Sea

    Science.gov (United States)

    Chavez, F.; Pearlman, J.; Simmons, S. E.

    2016-12-01

    There is a growing need for observations of life in the sea at time and space scales consistent with those made for physical and chemical parameters. International programs such as the Global Ocean Observing System (GOOS) and Marine Biodiversity Observation Networks (MBON) are making the case for expanded biological observations and working diligently to prioritize essential variables. Here we review past, present and emerging systems and methods for observing life in the sea from the perspective of maintaining continuous observations over long time periods. Methods that rely on ships with instrumentation and over-the-side sample collections will need to be supplemented and eventually replaced with those based from autonomous platforms. Ship-based optical and acoustic instruments are being reduced in size and power for deployment on moorings and autonomous vehicles. In parallel a new generation of low power, improved resolution sensors are being developed. Animal bio-logging is evolving with new, smaller and more sophisticated tags being developed. New genomic methods, capable of assessing multiple trophic levels from a single water sample, are emerging. Autonomous devices for genomic sample collection are being miniaturized and adapted to autonomous vehicles. The required processing schemes and methods for these emerging data collections are being developed in parallel with the instrumentation. An evolving challenge will be the integration of information from these disparate methods given that each provides their own unique view of life in the sea.

  15. How deep-sea wood falls sustain chemosynthetic life.

    Directory of Open Access Journals (Sweden)

    Christina Bienhold

    Full Text Available Large organic food falls to the deep sea--such as whale carcasses and wood logs--are known to serve as stepping stones for the dispersal of highly adapted chemosynthetic organisms inhabiting hot vents and cold seeps. Here we investigated the biogeochemical and microbiological processes leading to the development of sulfidic niches by deploying wood colonization experiments at a depth of 1690 m in the Eastern Mediterranean for one year. Wood-boring bivalves of the genus Xylophaga played a key role in the degradation of the wood logs, facilitating the development of anoxic zones and anaerobic microbial processes such as sulfate reduction. Fauna and bacteria associated with the wood included types reported from other deep-sea habitats including chemosynthetic ecosystems, confirming the potential role of large organic food falls as biodiversity hot spots and stepping stones for vent and seep communities. Specific bacterial communities developed on and around the wood falls within one year and were distinct from freshly submerged wood and background sediments. These included sulfate-reducing and cellulolytic bacterial taxa, which are likely to play an important role in the utilization of wood by chemosynthetic life and other deep-sea animals.

  16. How Deep-Sea Wood Falls Sustain Chemosynthetic Life

    Science.gov (United States)

    Bienhold, Christina; Pop Ristova, Petra; Wenzhöfer, Frank; Dittmar, Thorsten; Boetius, Antje

    2013-01-01

    Large organic food falls to the deep sea – such as whale carcasses and wood logs – are known to serve as stepping stones for the dispersal of highly adapted chemosynthetic organisms inhabiting hot vents and cold seeps. Here we investigated the biogeochemical and microbiological processes leading to the development of sulfidic niches by deploying wood colonization experiments at a depth of 1690 m in the Eastern Mediterranean for one year. Wood-boring bivalves of the genus Xylophaga played a key role in the degradation of the wood logs, facilitating the development of anoxic zones and anaerobic microbial processes such as sulfate reduction. Fauna and bacteria associated with the wood included types reported from other deep-sea habitats including chemosynthetic ecosystems, confirming the potential role of large organic food falls as biodiversity hot spots and stepping stones for vent and seep communities. Specific bacterial communities developed on and around the wood falls within one year and were distinct from freshly submerged wood and background sediments. These included sulfate-reducing and cellulolytic bacterial taxa, which are likely to play an important role in the utilization of wood by chemosynthetic life and other deep-sea animals. PMID:23301092

  17. The significance of microbe-mineral-biomarker interactions in the detection of life on Mars and beyond

    NARCIS (Netherlands)

    Röling, Wilfred F M; Aerts, Joost W.; Patty, C. H Lucas; Ten Kate, Inge Loes; Ehrenfreund, Pascale; Direito, Susana O L

    The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most

  18. The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond.

    NARCIS (Netherlands)

    Roling, W.F.M.; Aerts, J.W.; Patty, C.H.L.; ten Kate, I.L.; Ehrenfreund, P.; Direito, S.O.

    2015-01-01

    The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most

  19. Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity.

    Science.gov (United States)

    Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

    2018-01-01

    Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile

  20. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

    Energy Technology Data Exchange (ETDEWEB)

    Salinero, Kennan Kellaris; Keller, Keith; Feil, William S.; Feil, Helene; Trong, Stephan; Di Bartolo, Genevieve; Lapidus, Alla

    2008-11-17

    Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. The a priori prediction that the D. aromatica genome would contain previously characterized 'central' enzymes involved in anaerobic aromatic degradation proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzyl succinyl synthase (bssABC) genes (responsible for formate addition to toluene) and the central benzoylCoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex with the somewhat rare exosortase (epsH), is also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and nitrogen fixation (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively). Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial

  1. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

    Directory of Open Access Journals (Sweden)

    Feil Helene

    2009-08-01

    Full Text Available Abstract Background Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. Results The a priori prediction that the D. aromatica genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (bssABC genes (responsible for fumarate addition to toluene and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively. Conclusion Analysis of the D. aromatica genome indicates there is much to be

  2. Playing Sport In The Stormy Sea Of Street Life | Human | African ...

    African Journals Online (AJOL)

    Currently, there are many street children in South Africa (SA). They have been robbed from the safe harbour of family life and on a daily basis experience the stormy sea of street life. Society has an obligation to intervene in the lives of these street children through, for example, quality education, basic health services and ...

  3. Studies on the structure and function of intestinal microbes of surgeonfishes in the central Red Sea with a focus on the giant bacteria Epulopiscium spp.

    KAUST Repository

    Miyake, Sou

    2015-05-01

    The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

  4. MEMS and the microbe

    NARCIS (Netherlands)

    Ingham, C.J.; Vlieg, J.E.T.V.H.

    2008-01-01

    In recent years, relatively simple MEMS fabrications have helped accelerate our knowledge of the microbial cell. Current progress and challenges in the application of lab-on-a-chip devices to the viable microbe are reviewed. Furthermore, the degree to which microbiologists are becoming the engineers

  5. Meet the Microbes through the Microbe World Activities with Microbe the Magnificent and Mighty Microbe.

    Science.gov (United States)

    Frame, Kathy, Ed.; Ryan, Karen, Ed.

    The activities presented in this book are the product of the Community Outreach Initiative of the Microbial Literacy Collaborative (MLC). This activity book presents a balanced view of microbes, their benefits, and the diseases they cause. Each activity starts with an interesting introductory statement and includes goals, activity time, time to…

  6. Life on wood - the carnivorous deep-sea mussel Idas argenteus (Bathymodiolinae, Mytilidae, Bivalvia

    DEFF Research Database (Denmark)

    Ockelmann, Kurt W.; Dinesen, Grete E.

    2011-01-01

    to an ephemeral habitat in the deep sea of both species are described herein. Although larviphagi is known to occur in some filter-feeding bivalves, Idas argenteus is the first mytilid known to be specifically adapted to a carnivorous life. Further, it is argued that the modifications of I. argenteus with regard...... to its shell development, alimentary system, gill anatomy and life habits provide important clues to the evolution of the Bathymodiolinae....

  7. Early life developmental effects of marine persistent organic pollutants on the sea urchin Psammechinus miliaris

    NARCIS (Netherlands)

    Drs Anselmo, H.M.R.; Koerting, L.; Devito, S.; Berg, van den J.H.J.; Dubbeldam, M.; Kwadijk, C.J.A.F.; Murk, A.J.

    2011-01-01

    A new 16-day echinoid early life stage (ELS) bioassay was developed to allow for prolonged observation of possible adverse effects during embryogenesis and larval development of the sea urchin Psammechinus miliaris. Subsequently, the newly developed bioassay was applied to study the effects of key

  8. Molecular ecology of aquatic microbes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  9. Textiles and Microbes

    Science.gov (United States)

    Freney, Jean; Renaud, François N. R.

    Microbes can be carried by and even multiply on textiles. The first real, premeditated, microbiological warfare happened in 1763, during the Anglo-French wars in North America, when Native American emissaries were given blankets or handkerchiefs contaminated with smallpox. Thus, a small epidemic started and spread rapidly, causing considerable damage to the rank and file of the Native Americans. Nowadays, it could be said that textiles could be vectors of infections in hospitals or communities. The making of antimicrobial textiles could prevent them from becoming a reservoir of microbes in the transmission of infections and in cases of voluntary contamination in a terrorist threat for example. However, methods have to show that textiles are really active and do not attack the cutaneous flora they are in contact with. In this chapter, the role of textiles in the transmission of infections is summarized and the main characteristics of antimicrobial textiles are described.

  10. Oceanic fronts in the Sargasso Sea control the early life and drift of Atlantic eels

    DEFF Research Database (Denmark)

    Munk, Peter; Hansen, Michael Møller; Maas, Gregory E.

    2010-01-01

    Anguillid freshwater eels show remarkable life histories. In the Atlantic, the European eel (Anguilla anguilla) and American eel (Anguilla rostrata) undertake extensive migrations to spawn in the oceanic Sargasso Sea, and subsequently the offspring drift to foraging areas in Europe and North......, during a field expedition to the eel spawning sites in the Sargasso Sea, we carried out a wide range of dedicated bio-physical studies across areas of eel larval distribution. Our findings suggest a key role of oceanic frontal processes, retaining eel larvae within a zone of enhanced feeding conditions...

  11. The Lampedusa Disaster: How to Prevent Further Loss of Life at Sea?

    Directory of Open Access Journals (Sweden)

    Jasmine Coppens

    2013-12-01

    Full Text Available Lampedusa – an Italian island barely 70 miles from northern Africa and 100 miles from Malta – has become a gateway to Europe for migrants. In some seasons, boats filled with asylum seekers arrive almost daily. However, yearly, hundreds of people die trying to cross the Mediterranean Sea. This paper will deal with the obligations of States towards seaborne migrants, the question of why so many people die near Lampedusa and the possible solutions in order to prevent further loss of life at sea.

  12. Life history variation in Barents Sea fish: implications for sensitivity to fishing in a changing environment.

    Science.gov (United States)

    Wiedmann, Magnus A; Primicerio, Raul; Dolgov, Andrey; Ottesen, Camilla A M; Aschan, Michaela

    2014-09-01

    Under exploitation and environmental change, it is essential to assess the sensitivity and vulnerability of marine ecosystems to such stress. A species' response to stress depends on its life history. Sensitivity to harvesting is related to the life history "fast-slow" continuum, where "slow" species (i.e., large, long lived, and late maturing) are expected to be more sensitive to fishing than "fast" ones. We analyze life history traits variation for all common fish species in the Barents Sea and rank fishes along fast-slow gradients obtained by ordination analyses. In addition, we integrate species' fast-slow ranks with ecosystem survey data for the period 2004-2009, to assess life history variation at the community level in space and time. Arctic fishes were smaller, had shorter life spans, earlier maturation, larger offspring, and lower fecundity than boreal ones. Arctic fishes could thus be considered faster than the boreal species, even when body size was corrected for. Phylogenetically related species possessed similar life histories. Early in the study period, we found a strong spatial gradient, where members of fish assemblages in the southwestern Barents Sea displayed slower life histories than in the northeast. However, in later, warmer years, the gradient weakened caused by a northward movement of boreal species. As a consequence, the northeast experienced increasing proportions of slower fish species. This study is a step toward integrating life history traits in ecosystem-based areal management. On the basis of life history traits, we assess the fish sensitivity to fishing, at the species and community level. We show that climate warming promotes a borealization of fish assemblages in the northeast, associated with slower life histories in that area. The biology of Arctic species is still poorly known, and boreal species that now establish in the Arctic are fishery sensitive, which calls for cautious ecosystem management of these areas.

  13. General Concerns Life-Cycle Design of Economical Ice-Resistant Structures in the Bohai Sea

    Directory of Open Access Journals (Sweden)

    Zhang Da-yong

    2017-08-01

    Full Text Available In China, the oil and natural gas resources of Bohai Bay are mainly marginal oil fields. It is necessary to build both iceresistant and economical offshore platforms. However, there are many risks during the life cycle of offshore platforms due to the imperfect preliminary design for the Bohai Sea economical ice-resistant structures. As a result, the whole life-cycle design should be considered, including plan, design, construction, management and maintenance design. Based on the demand of existing codes and research of the basic design, structural ice-resistant performance and the reasonable management and maintenance, the life-cycle design theory is discussed. It was concluded that the life-cycle cost-effective optimum design proposed will lead to a minimum risk.

  14. Ecological suicide in microbes.

    Science.gov (United States)

    Ratzke, Christoph; Denk, Jonas; Gore, Jeff

    2018-05-01

    The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution.

  15. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

    .... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

  16. Microbe-microbe interactions in mixed culture food fermentations

    NARCIS (Netherlands)

    Smid, E.J.; Lacroix, C.

    2013-01-01

    Most known natural and industrial food fermentation processes are driven by either simple or complex communities of microorganisms. Obviously, these fermenting microbes will not only interact with the fermentable substrate but also with each other. These microbe–microbe interactions are complex but

  17. Mining with microbes

    International Nuclear Information System (INIS)

    Rawlings., D.E.; Silver, S.

    1995-01-01

    Microbes are playing increasingly important roles in commercial mining operations, where they are being used in the open-quotes bioleachingclose quotes of copper, uranium, and gold ores. Direct leaching is when microbial metabolism changes the redox state of the metal being harvested, rendering it more soluble. Indirect leaching includes redox chemistry of other metal cations that are then coupled in chemical oxidation or reduction of the harvested metal ion and microbial attack upon and solubilization of the mineral matrix in which the metal is physically embedded. In addition, bacterial cells are used to detoxify the waste cyanide solution from gold-mining operations and as open-quotes absorbantsclose quotes of the mineral cations. Bacterial cells may replace activated carbon or alternative biomass. With an increasing understanding of microbial physiology, biochemistry and molecular genetics, rational approaches to improving these microbial activities become possible. 40 refs., 3 figs

  18. Radiation induced pesticidal microbes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ki Yup; Lee, Y. K.; Kim, J. S.; Kim, J. K.; Lee, S. J.; Lim, D. S

    2001-01-01

    To isolate pesticidal microbes against plant pathogenic fungi, 4 strains of bacteria(K1. K3, K4, YS1) were isolated from mushroom compost and hot spring. K4, K1, K3, YS1 strain showed wide antifungal spectrum and high antifungal activities against 12 kinds of fungi. Specific proteins and the specific transcribed genes were found from the YS1 and its radiation-induced mutants. And knock-out mutants of antifungal activity were derived by transposon mutagenesis. From these knock-out mutants, the antifungal activity related genes and its modification by gamma-ray radiation are going to be studied. These results suggested that radiation could be an useful tool for the induction of functional mutants.

  19. Radiation induced pesticidal microbes

    International Nuclear Information System (INIS)

    Kim, Ki Yup; Lee, Y. K.; Kim, J. S.; Kim, J. K.; Lee, S. J.; Lim, D. S.

    2001-01-01

    To isolate pesticidal microbes against plant pathogenic fungi, 4 strains of bacteria(K1. K3, K4, YS1) were isolated from mushroom compost and hot spring. K4, K1, K3, YS1 strain showed wide antifungal spectrum and high antifungal activities against 12 kinds of fungi. Specific proteins and the specific transcribed genes were found from the YS1 and its radiation-induced mutants. And knock-out mutants of antifungal activity were derived by transposon mutagenesis. From these knock-out mutants, the antifungal activity related genes and its modification by gamma-ray radiation are going to be studied. These results suggested that radiation could be an useful tool for the induction of functional mutants

  20. Microbe Phobia and Kitchen Microbiology.

    Science.gov (United States)

    Williams, Robert P.; Gillen, Alan L.

    1991-01-01

    The authors present an exercise designed to help students overcome the misconception that most microbes make people sick. The activity helps students of all ages understand the important benefits of microbes such as in making bread, soy sauce, cheese, and wine. The role of microorganisms in processing cocoa and coffee and growing plants is also…

  1. The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

    Science.gov (United States)

    Shaaban, Heba; Westfall, David A; Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E

    2018-01-05

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes' characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY-Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism's taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

  2. Borders of life: lessons from Microbiology of deep-sea hydrothermal vents

    Science.gov (United States)

    Prieur, D.

    Thirty years ago, the deep-sea was known as a low density biotope due to coldness, darkness and famine-like conditions. The discovery of deep-sea hydrothermal vents in the Eastern Pacific in 1977 and the associated black smokers in 1979 considerably changed our views about life on Earth. For the first time, an ecosystem almost independent (at least for tens of years) of solar nergy was discovered. Besides the spectacular and unexpected communities of invertebrates based on symbiotic associations with chemo-litho-autotrophic bacteria, prokaryotic communities associated with high temperature black smokers fascinated microbiologists of extreme environments. Within mineral structures where temperature gradients may fluctuate from ambient seawater temperatures (2°C) up to 350°C, thermophilic (optimal growth above 60°C) and hyperthermophilic (optimal growth above 80°C) microorganisms thrived under very severe conditions due to elevated hydrostatic pressure, toxic compounds or strong ionizing radiations. These organisms belong to both domains of Bacteria and Archaea and live aerobically but mostly anaerobically, using a variety of inorganic and organic carbon sources, and a variety of electron donnors and acceptors as well. The most thermophilic organism known on Earth was isolated from a mid-Atlantic-Ridge hydrotermal vent: Pyrolobus fumarii grows optimally at 110°c and its upper temperature limit for life is 113°C. Such an organism survived to autoclaving conditions currently used for sterilization procedures. Many other hyperthermophilic organisms were isolated and described, including fermenters, sulphate and sulphur reducers, hydrogen oxidizers, nitrate reducers, methanogens, etc. Although most of anaerobes are killed when exposed to oxygen, several deep-sea hyperthermophiles appeared to survive to both oxygen and starvation exposures, indicating that they probably can colonize rather distant environments Because of elevated hydrostatic pressure that exists at

  3. The microbe capture experiment in space: Fluorescence microscopic detection of microbes captured by aerogel

    Science.gov (United States)

    Sugino, Tomohiro; Yokobori, Shin-Ichi; Yang, Yinjie; Kawaguchi, Yuko; Okudaira, Kyoko; Tabata, Makoto; Kawai, Hideyuki; Hasegawa, Sunao; Yamagishi, Akihiko

    Microbes have been collected at the altitude up to about 70 km in the sampling experiment done by several groups[1]. We have also collected high altitude microbes, by using an airplane and balloons[2][3][4][5]. We collected new deinococcal strain (Deinococcus aetherius and Deinococ-cus aerius) and several strains of spore-forming bacilli from stratosphere[2][4][5]. However, microbe sampling in space has never been reported. On the other hand, "Panspermia" hy-pothesis, where terrestrial life is originated from outside of Earth, has been proposed[6][7][8][9]. Recent report suggesting existence of the possible microbe fossils in the meteorite of Mars origin opened the serious debate on the possibility of migration of life embedded in meteorites (and cosmic dusts)[10][11]. If we were able to find terrestrial microbes in space, it would suggest that the terrestrial life can travel between astronomical bodies. We proposed a mission "Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments" to examine possible inter-planetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module of the International Space Station (ISS)[12]. Two of six sub themes in this mission are directly related to interplanetary migration of microbes. One is the direct capturing experi-ment of microbes (probably within the particles such as clay) in space by the exposed ultra-low density aerogel. Another is the exposure experiment to examine survivability of the microbes in harsh space environment. They will tell us the possibility of interplanetary migration of microbes (life) from Earth to outside of Earth (or vise versa). In this report, we will report whether aerogel that have been used for the collection of space debris and cosmic dusts can be used for microbe sampling in space. We will discuss how captured particles by aerogel can be detected with DNA-specific fluorescent dye, and how to distinguish microbes from other mate-rials (i.e. aerogel and

  4. Oceans, microbes, and global climate change

    OpenAIRE

    Danovaro, Roberto

    2016-01-01

    Sea-surface warming, sea-ice melting and related freshening, changes in circulation and mixing regimes, and ocean acidification induced by the present climate changes are modifying marine ecosystem structure and function and have the potential to alter the cycling of carbon and nutrients in surface oceans. Changing climate has direct and indirect consequences on marine life and on microbial components. Prokaryotes (Bacteria and Archaea), viruses and other microbial life forms are impacted by ...

  5. Biofuels from microbes

    Energy Technology Data Exchange (ETDEWEB)

    Antoni, D. [Technische Univ. Muenchen, Freising-Weihenstephan (Germany). Inst. of Resource and Energy Technology; Zverlov, V.V.; Schwarz, W.H. [Technische Univ. Muenchen, Freising-Weihenstephan (Germany). Dept. of Microbiology

    2007-11-15

    Today, biomass covers about 10% of the world's primary energy demand. Against a backdrop of rising crude oil prices, depletion of resources, political instability in producing countries and environmental challenges, besides efficiency and intelligent use, only biomass has the potential to replace the supply of an energy hungry civilisation. Plant biomass is an abundant and renewable source of energy-rich carbohydrates which can be efficiently converted by microbes into biofuels, of which, only bioethanol is produced on an industrial scale today. Biomethane is produced on a large scale, but is not yet utilised for transportation. Biobutanol is on the agenda of several companies and may be used in the near future as a supplement for gasoline, diesel and kerosene, as well as contributing to the partially biological production of butyl-t-butylether, BTBE as does bioethanol today with ETBE. Biohydrogen, biomethanol and microbially made biodiesel still require further development. This paper reviews microbially made biofuels which have potential to replace our present day fuels, either alone, by blending, or by chemical conversion. It also summarises the history of biofuels and provides insight into the actual production in various countries, reviewing their policies and adaptivity to the energy challenges of foreseeable future. (orig.)

  6. Life cycle and spring phenology of Temora longicornis in the Baltic Sea

    DEFF Research Database (Denmark)

    Dutz, Jörg; Mohrholz, V.; van Beusekom, J. E. E.

    2010-01-01

    The seasonal variation in abundance, biomass and vertical distribution of nauplii and copepodites of Temora longicornis in the Bornholm Basin was studied from March 2002 to May 2003 to understand the overwintering, spring development and life cycle of this species in the Baltic Sea. The analysis...... of the life cycle by means of stage structure, copepodite length and stage duration revealed that T. longicornis produced 5 to 6 generations yr–1. The species overwintered in low abundance as an active, slowly developing generation with adults appearing from February/March onwards. The onset of the spring...... bloom in April triggered reproduction and initiated the first spring generation (G1) with a strong rise in nauplii abundance. The stock biomass increased in May with the occurrence of the copepodites of G1 and remained high during the succeeding generations G2 and G3 until August. The stock...

  7. Where the Wild Microbes Are: Education and Outreach on Sub-Seafloor Microbes

    Science.gov (United States)

    Cooper, S. K.; Kurtz, K.; Orcutt, B.; Strong, L.; Collins, J.; Feagan, A.

    2014-12-01

    Sub-seafloor microbiology has the power to spark the imaginations of children, students and the general public with its mysterious nature, cutting-edge research, and connections to the search for extraterrestrial life. These factors have been utilized to create a number of educational and outreach products to bring subsurface microbes to non-scientist audiences in creative and innovative ways. The Adopt a Microbe curriculum for middle school students provides hands-on activities and investigations for students to learn about microbes and the on-going research about them, and provides opportunities to connect with active expeditions. A new series of videos engages non-scientists with stories about research expeditions and the scientists themselves. A poster and associated activities explore the nature of science using a microbiologist and her research as examples. A new e-book for young children will engage them with age-appropriate text and illustrations. These projects are multidisciplinary, involve science and engineering practices, are available to all audiences and provide examples of high level and meaningful partnerships between scientists and educators and the kinds of products that can result. Subseafloor microbiology projects such as these, aimed at K-12 students and the general public, have the potential to entice the interest of the next generation of microbe scientists and increase general awareness of this important science.

  8. Life under Climate Change Scenarios: Sea Urchins’ Cellular Mechanisms for Reproductive Success

    Directory of Open Access Journals (Sweden)

    Desislava Bögner

    2016-03-01

    Full Text Available Ocean Acidification (OA represents a major field of research and increased efforts are being made to elucidate its repercussions on biota. Species survival is ensured by successful reproduction, which may be threatened under detrimental environmental conditions, such as OA acting in synergy with other climate change related stressors. Achieving successful gametogenesis, fertilization, and the development of larvae into healthy juveniles and adults is crucial for the perpetuation of species and, thus, ecosystems’ functionality. The considerable vulnerability of the abovementioned developmental stages to the adverse conditions that future OA may impose has been shown in many species, including sea urchins which are commonly used due to the feasibility of their maintenance in captivity and the great amount of gametes that a mature adult is able to produce. In the present review, the latest knowledge about the impact of OA on various stages of the life cycle of sea urchins is summarized with remarks on the possible impact of other stressors. The cellular physiology of the gametes before, at fertilization and, at early development, is extensively described with a focus on the complex enzymatic machinery and the intracellular pH (pHi and Ca2+ homeostasis for their vulnerability when facing adverse conditions such as acidification, temperature variations, or hypoxia.

  9. Amphidromy in shrimps: a life cycle between rivers and the sea

    Directory of Open Access Journals (Sweden)

    Raymond T Bauer

    2013-09-01

    Full Text Available Amphidromy is a diadromous life history pattern, common in tropical and subtropical freshwater caridean shrimps, in which adults live, breed and spawn small-sized embryos in freshwater but have extended larval development (ELD in marine waters. Most completely freshwater species spawn large embryos with either direct or abbreviated larval development (ALD. An important benefit of amphidromy is dispersal among river systems via marine larvae, which increases their access to alternative habitats. Thus, amphidromous species have much broader geographic distributions than closely related completely freshwater ones with ALD. ALD and freshwater ELD species appear to have evolved from amphidromous species with marine ancestors. Delivery of larvae to the sea in many amphidromous species is accomplished by upstream hatching and river drift of larvae to the sea. In other species, the females themselves apparently migrate down to marine waters to spawn. After development, the postlarvae must find a river mouth and migrate upstream to the adult habitat. Migrations occur at night, with juveniles swimming or crawling along the river or stream bank. Larvae are released during the wet or flood season of the year, while juvenile migrations take place during the dry or low-flow season. Both larval downstream and juvenile upstream movements are disrupted by human impacts such as dams and other forms of river control. Although much progress has been made in understanding the evolution and ecology of amphidromy, research is still needed on all aspects of shrimp amphidromy, especially in Latin America with its diverse freshwater shrimp fauna.

  10. Life Cycle Assessments of Manure Management Techniques for the Baltic Sea Regions

    DEFF Research Database (Denmark)

    Hamelin, Lorie; Baky, A; Cano-Bernal, J

    The report summarizes the key results of the consequential life cycle assessments (LCAs) carried out for a variety of manure management techniques over the Baltic Sea Regions (BSR). For all manure management technologies assessed, the environmental impacts (in terms of potential to global warming......, acidification of aquatic & terrestrial systems as well as phosphorus and nitrogen enrichment) are evaluated along the whole “manure management chain”, quantified and compared to the applying reference manure management system. The LCA results presented in this report cover 4 main manure types (dairy cow slurry....... Assessed separation technologies include concentration technologies, state-of-the-art decanter centrifuge and source-separation technologies. The energy production technologies addressed consist of thermal gasification, incineration and anaerobic digestion (for which a myriad of carbon co...

  11. A molecular study of microbe transfer between distant environments.

    Science.gov (United States)

    Hooper, Sean D; Raes, Jeroen; Foerstner, Konrad U; Harrington, Eoghan D; Dalevi, Daniel; Bork, Peer

    2008-07-09

    Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.

  12. A molecular study of microbe transfer between distant environments.

    Directory of Open Access Journals (Sweden)

    Sean D Hooper

    Full Text Available BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. METHODOLOGY: By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. CONCLUSIONS: Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.

  13. Impacts of Global Warming and Sea Level Rise on Service Life of Chloride-Exposed Concrete Structures

    Directory of Open Access Journals (Sweden)

    Xiao-Jian Gao

    2017-03-01

    Full Text Available Global warming will increase the rate of chloride ingress and the rate of steel corrosion of concrete structures. Furthermore, in coastal (atmospheric marine zones, sea level rise will reduce the distance of concrete structures from the coast and increase the surface chloride content. This study proposes a probabilistic model for analyzing the effects of global warming and sea level rise on the service life of coastal concrete structures. First, in the corrosion initiation stage, an improved chloride diffusion model is proposed to determine chloride concentration. The Monte Carlo method is employed to calculate the service life in the corrosion initiation stage; Second, in the corrosion propagation stage, a numerical model is proposed to calculate the rate of corrosion, probability of corrosion cracking, and service life. Third, overall service life is determined as the sum of service life in the corrosion initiation and corrosion propagation stages. After considering the impacts of global warming and sea level rise, the analysis results show that for concrete structures having a service life of 50 years, the service life decreases by about 5%.

  14. Biology and life cycles of pelagic tunicates in the Lazarev Sea, Southern Ocean

    Science.gov (United States)

    Pakhomov, E. A.; Dubischar, C. D.; Hunt, B. P. V.; Strass, V.; Cisewski, B.; Siegel, V.; von Harbou, L.; Gurney, L.; Kitchener, J.; Bathmann, U.

    2011-07-01

    Four grid surveys were carried out in the top 200 m layer of the Lazarev Sea during fall 2004, summer 2005-06, winter 2006 and summer 2007-08 onboard the R.V. Polarstern as a part of the German SO-GLOBEC. The distribution, abundance and biology of two species of salps, Salpa thompsoni and Ihlea racovitzai, were investigated. With the exception of fall 2004, I. racovitzai dominated the salp community although being represented by low densities (<20 ind. 1000 m -3). S. thompsoni was scarce during the summers of 2005-06 and 2007-08 and almost absent from the region during winter 2006. Nevertheless, it was modestly numerous during fall 2004 reaching densities of up to 33 ind. 1000 m -3 in the south-western stations of the grid. The data on the seasonal population structure and life cycle of I. racovitzai showed that this species followed the generalized pattern typical of S. thompsoni, i.e. sexual/asexual reproduction and spawning during fall. I. racovitzai densities were the lowest during summer, increased during fall and peaked in during winter. Numerous offspring were produced by I. racovitzai during fall, just before the area became ice-covered. Conversely, S. thompsoni was not able to complete its life cycle in the Lazarev Sea, with a high occurrence of stage X (unfertilized) aggregates present. Highest S. thompsoni densities in summer and fall, and its disappearance in winter are indicative of a population of the expatriate origin that is sustained by advection.

  15. Sensitivity of Calanus spp. copepods to environmental changes in the North Sea using life-stage structured models

    DEFF Research Database (Denmark)

    Maar, Marie; Møller, Eva Friis; Gürkan, Zeren

    2013-01-01

    Sea because it allows them to utilize the spring bloom more efficiently and independently of the timing and amount of oceanic inflow. The combination of lower temperatures, higher overwintering and oceanic inflow simulating the situation in the 1960s largely favoured C. finmarchicus and their relative......, overwintering and oceanic inflow in the North Sea. Life-stage structured models are validated against CPR data and vertical distributions north of the Dogger Bank in the North Sea for the reference year 2005. The model shows that 1) ± 2°C changes from the current level mainly influence the seasonal patterns...... and not the relative occurrence of the two species, 2) changes due to oceanic inflow mainly appeared in the northern and southern part of the North Sea connected to the NE Atlantic and not in the central part and 3) the abundance of Calanus species were very sensitive to the degree of overwintering within the North...

  16. Proteomic profiles reveal age-related changes in coelomic fluid of sea urchin species with different life spans.

    Science.gov (United States)

    Bodnar, Andrea

    2013-05-01

    Sea urchins have a different life history from humans and traditional model organisms used to study the process of aging. Sea urchins grow indeterminately, reproduce throughout their life span and some species have been shown to exhibit negligible senescence with no increase in mortality rate at advanced ages. Despite these properties, different species of sea urchins are reported to have very different natural life spans providing a unique model to investigate cellular mechanisms underlying life span determination and negligible senescence. To gain insight into the biological changes that accompany aging in these animals, proteomic profiles were examined in coelomic fluid from young and old sea urchins of three species with different life spans: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate life span. The proteomic profiles of cell-free coelomic fluid were complex with many proteins exhibiting different forms and extensive post-translational modifications. Approximately 20% of the protein spots on 2-D gels showed more than two-fold change with age in each of the species. Changes that are consistent with age in all three species may prove to be useful biomarkers for age-determination for these commercially fished marine invertebrates and also may provide clues to mechanisms of negligible senescence. Among the proteins that change with age, the ectodomain of low-density lipoprotein receptor-related protein 4 (LRP4) was significantly increased in the coelomic fluid of all three sea urchin species suggesting that the Wnt signaling pathway should be further investigated for its role in negligible senescence. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Principles of Plant-Microbe Interactions - Microbes for Sustainable Agriculture

    Science.gov (United States)

    Crops lack resistance to many soilborne pathogens and rely on antagonistic microbes recruited from the soil microbiome to protect their roots. Disease-suppressive soils, the best examples of microbial-based defense, are soils in which a pathogen does not establish or persist, establishes but causes ...

  18. Biofilms for Babies: Introducing Microbes and Biofilms to Preschool-Aged Children

    Directory of Open Access Journals (Sweden)

    Jillian M. Couto

    2017-05-01

    Full Text Available Microbes are beneficial to life on our planet as they facilitate natural processes such as global nutrient cycling in our environment. This article details a 30-minute activity to introduce pre-school children ranging from 3 to 5 years of age to microbes and biofilms in the natural environment.

  19. Sensitivity to UV radiation in early life stages of the Mediterranean sea urchin Sphaerechinus granularis (Lamarck)

    Energy Technology Data Exchange (ETDEWEB)

    Nahon, Sarah [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Castro Porras, Viviana A. [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Pruski, Audrey M. [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Charles, Francois [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France)], E-mail: charles@obs-banyuls.fr

    2009-03-01

    The sea urchin Sphaerechinus granularis was used to investigate the impact of relevant levels of UV-B radiation on the early life stages of a common Mediterranean free spawning benthic species. Sperm, eggs and embryos were exposed to a range of UV radiation doses. The resulting endpoints were evaluated in terms of fertilisation success, development and survival rates. Above a weighted UV radiation dose of 0.0029 kJ m{sup -2}, fertilisation capability of irradiated sperm decreased rapidly. The exposure of the eggs to 0.0175 kJ m{sup -2} and more led to delayed and inhibited development with ensuing embryonic morphological abnormalities. One-day old larvae remained strongly sensitive to UV radiation as shown by the 50% decrease of the larval survival rate for a dose of 0.025 kJ m{sup -2} UVR. The elevated sensitivity of embryos to experimental UVR went along with a lack of significant amount of sunscreen compounds (e.g., mycosporine-like amino acids) in the eggs. The present results demonstrated that gamete viability and embryonic development may be significantly impaired by solar UV radiation in S. granularis, compromising in this way the reproduction of the species. Unless adaptive behavioural reproductive strategies exist, the influence of ambient UV radiation appears as a selective force for population dynamics of broadcast spawners in the shallow benthic Mediterranean environment.

  20. Sensitivity to UV radiation in early life stages of the Mediterranean sea urchin Sphaerechinus granularis (Lamarck)

    International Nuclear Information System (INIS)

    Nahon, Sarah; Castro Porras, Viviana A.; Pruski, Audrey M.; Charles, Francois

    2009-01-01

    The sea urchin Sphaerechinus granularis was used to investigate the impact of relevant levels of UV-B radiation on the early life stages of a common Mediterranean free spawning benthic species. Sperm, eggs and embryos were exposed to a range of UV radiation doses. The resulting endpoints were evaluated in terms of fertilisation success, development and survival rates. Above a weighted UV radiation dose of 0.0029 kJ m -2 , fertilisation capability of irradiated sperm decreased rapidly. The exposure of the eggs to 0.0175 kJ m -2 and more led to delayed and inhibited development with ensuing embryonic morphological abnormalities. One-day old larvae remained strongly sensitive to UV radiation as shown by the 50% decrease of the larval survival rate for a dose of 0.025 kJ m -2 UVR. The elevated sensitivity of embryos to experimental UVR went along with a lack of significant amount of sunscreen compounds (e.g., mycosporine-like amino acids) in the eggs. The present results demonstrated that gamete viability and embryonic development may be significantly impaired by solar UV radiation in S. granularis, compromising in this way the reproduction of the species. Unless adaptive behavioural reproductive strategies exist, the influence of ambient UV radiation appears as a selective force for population dynamics of broadcast spawners in the shallow benthic Mediterranean environment

  1. The effect of CO2 injection in the sea on the marine life

    International Nuclear Information System (INIS)

    Magnesen, T.

    1993-02-01

    In the literature it is shown that aquatic organisms are very sensitive to changes in the pH value. Exposure to a lower pH value than what is normal for the animals, may lead to distinct effects in the reproduction, growth and survival. Harmful effects may arise by a reduction of only 0.2 pH units. The effects increase by increasing the pH reduction, and by increasing the exposure time. It is pointed out in the report that the data basis is small, and that only a few long term and life cycle studies have been performed. The background material of the report shows that injection of CO 2 into the sea will create a bottom stream with pH values between 4.5 and 6.5. These values are much lower than the normal pH value of seawater, and much lower than the limit value for harmful effects. For this reason, harmful effects on the bottom fauna may be expected. 57 refs., 3 figs., 2 tabs

  2. TANPOPO: Microbe and micrometeoroid capture experiments on International Space Station.

    Science.gov (United States)

    Yamagishi, Akihiko; Kobayashi, Kensei; Yano, Hajime; Yokobori, Shinichi; Hashimoto, Hirofumi; Kawai, Hideyuki; Yamashita, Masamichi

    There is a long history of the microbe-collection experiments at high altitude. Microbes have been collected using balloons, aircraft and meteorological rockets from 1936 to 1976. Spore forming fungi and Bacilli, and Micrococci have been isolated in these experiments. It is not clear how high do microbes go up. If the microbes might have been present even at higher altitudes, the fact would endorse the possibility of interplanetary migration of life. TANPOPO, dandelion, is the name of a grass whose seeds with floss are spread by the wind. We propose the analyses of interplanetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module (JEM) of the International Space Station (ISS). Ultra low-density aerogel will be used to capture micrometeoroid and debris. Particles captured by aerogel will be used for several analyses after the initial inspection of the gel and tracks. Careful analysis of the tracks in the aerogel will provide the size and velocity dependence of debris flux. The particles will be analyzed for mineralogical, organic and microbiological characteristics. Aerogels are ready for production in Japan. Aerogels and trays are space proven. All the analytical techniques are ready. The Tanpopo mission was accepted as a candidate experiments on Exposed Facility of ISS-JEM.

  3. Heavy rare earth elements affect early life stages in Paracentrotus lividus and Arbacia lixula sea urchins

    International Nuclear Information System (INIS)

    Oral, Rahime; Pagano, Giovanni; Siciliano, Antonietta; Gravina, Maria; Palumbo, Anna; Castellano, Immacolata; Migliaccio, Oriana; Thomas, Philippe J.; Guida, Marco; Tommasi, Franca; Trifuoggi, Marco

    2017-01-01

    Background: Heavy rare earth elements (HREEs) have been scarcely studied for their toxicity, in spite of their applications in several technologies. Thus HREEs require timely investigations for their adverse health effects. Methods: Paracentrotus lividus and Arbacia lixula embryos and sperm were exposed to trichloride salts of five HREEs (Dy, Ho, Er, Yb and Lu) and to Ce(III) as a light REE (LREE) reference to evaluate: 1) developmental defects (% DD) in HREE-exposed larvae or in the offspring of HREE-exposed sperm; 2) mitotic anomalies; 3) fertilization success; and 4) reactive oxygen species (ROS) formation, and nitric oxide (NO) and malondialdehyde (MDA) levels. Nominal HREE concentrations were confirmed by inductively coupled plasma mass spectrometry (ICP-MS). Results: HREEs induced concentration-related DD increases in P. lividus and A. lixula larvae, ranging from no significant DD increase at 10 −7 M HREEs up to ≅100% DD at 10 −5 M HREE. Larvae exposed to 10 −5 M Ce(III) resulted in less severe DD rates compared to HREEs. Decreased mitotic activity and increased aberration rates were found in HREE-exposed P. lividus embryos. Significant increases in ROS formation and NO levels were found both in HREE-exposed and in Ce(III) embryos, whereas only Ce(III), but not HREEs resulted in significant increase in MDA levels. Sperm exposure to HREEs (10 −5 –10 −4 M) resulted in a concentration-related decrease in fertilization success along with increase in offspring damage. These effects were significantly enhanced for Dy(III), Ho(III), Er(III) and Yb(III), compared to Lu(III) and to Ce(III). Conclusion: HREE-associated toxicity affected embryogenesis, fertilization, cytogenetic and redox endpoints showing different toxicities of tested HREEs. - Highlights: • Different toxicities were exerted by five tested HREEs on sea urchin early life stages. • Sea urchin embryos and sperm were sensitive to HREE levels ranging from 1 to 100 μM, according to

  4. Heavy rare earth elements affect early life stages in Paracentrotus lividus and Arbacia lixula sea urchins

    Energy Technology Data Exchange (ETDEWEB)

    Oral, Rahime [Ege University, Faculty of Fisheries, TR-35100 Bornova, İzmir (Turkey); Pagano, Giovanni, E-mail: gbpagano@tin.it [“Federico II” University of Naples, Department of Chemical Sciences, I-80126 Naples (Italy); Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples (Italy); Siciliano, Antonietta; Gravina, Maria [“Federico II” University of Naples, Department of Biology, I-80126 Naples (Italy); Palumbo, Anna; Castellano, Immacolata; Migliaccio, Oriana [Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples (Italy); Thomas, Philippe J. [Environment and Climate Change Canada, Science & Technology Branch, National Wildlife Research Center – Carleton University, Ottawa, Ontario, Canada K1A 0H3 (Canada); Guida, Marco [“Federico II” University of Naples, Department of Biology, I-80126 Naples (Italy); Tommasi, Franca [University of Bari, Department of Biology, Bari (Italy); Trifuoggi, Marco [“Federico II” University of Naples, Department of Chemical Sciences, I-80126 Naples (Italy)

    2017-04-15

    Background: Heavy rare earth elements (HREEs) have been scarcely studied for their toxicity, in spite of their applications in several technologies. Thus HREEs require timely investigations for their adverse health effects. Methods: Paracentrotus lividus and Arbacia lixula embryos and sperm were exposed to trichloride salts of five HREEs (Dy, Ho, Er, Yb and Lu) and to Ce(III) as a light REE (LREE) reference to evaluate: 1) developmental defects (% DD) in HREE-exposed larvae or in the offspring of HREE-exposed sperm; 2) mitotic anomalies; 3) fertilization success; and 4) reactive oxygen species (ROS) formation, and nitric oxide (NO) and malondialdehyde (MDA) levels. Nominal HREE concentrations were confirmed by inductively coupled plasma mass spectrometry (ICP-MS). Results: HREEs induced concentration-related DD increases in P. lividus and A. lixula larvae, ranging from no significant DD increase at 10{sup −7} M HREEs up to ≅100% DD at 10{sup −5} M HREE. Larvae exposed to 10{sup −5} M Ce(III) resulted in less severe DD rates compared to HREEs. Decreased mitotic activity and increased aberration rates were found in HREE-exposed P. lividus embryos. Significant increases in ROS formation and NO levels were found both in HREE-exposed and in Ce(III) embryos, whereas only Ce(III), but not HREEs resulted in significant increase in MDA levels. Sperm exposure to HREEs (10{sup −5}–10{sup −4} M) resulted in a concentration-related decrease in fertilization success along with increase in offspring damage. These effects were significantly enhanced for Dy(III), Ho(III), Er(III) and Yb(III), compared to Lu(III) and to Ce(III). Conclusion: HREE-associated toxicity affected embryogenesis, fertilization, cytogenetic and redox endpoints showing different toxicities of tested HREEs. - Highlights: • Different toxicities were exerted by five tested HREEs on sea urchin early life stages. • Sea urchin embryos and sperm were sensitive to HREE levels ranging from 1 to 100

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

    KAUST Repository

    Rö thig, Till; Yum, Lauren; Kremb, Stephan Georg; Roik, Anna Krystyna; Voolstra, Christian R.

    2017-01-01

    Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed

  6. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development.

    Science.gov (United States)

    Bing, XiaoLi; Gerlach, Joseph; Loeb, Gregory; Buchon, Nicolas

    2018-03-20

    Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions. IMPORTANCE Animals are commonly associated with specific microbes, which play important roles in host development and fitness. However, little information about the function of microbes has been available for the important invasive pest Drosophila suzukii , also known as Spotted

  7. Growth Rates of Microbes in the Oceans.

    Science.gov (United States)

    Kirchman, David L

    2016-01-01

    A microbe's growth rate helps to set its ecological success and its contribution to food web dynamics and biogeochemical processes. Growth rates at the community level are constrained by biomass and trophic interactions among bacteria, phytoplankton, and their grazers. Phytoplankton growth rates are approximately 1 d(-1), whereas most heterotrophic bacteria grow slowly, close to 0.1 d(-1); only a few taxa can grow ten times as fast. Data from 16S rRNA and other approaches are used to speculate about the growth rate and the life history strategy of SAR11, the most abundant clade of heterotrophic bacteria in the oceans. These strategies are also explored using genomic data. Although the methods and data are imperfect, the available data can be used to set limits on growth rates and thus on the timescale for changes in the composition and structure of microbial communities.

  8. Life cycle assessment of different sea cucumber ( Apostichopus japonicus Selenka) farming systems

    Science.gov (United States)

    Wang, Guodong; Dong, Shuanglin; Tian, Xiangli; Gao, Qinfeng; Wang, Fang; Xu, Kefeng

    2015-12-01

    The life cycle assessment was employed to evaluate the environmental impacts of three farming systems (indoor intensive, semi-intensive and extensive systems) of sea cucumber living near Qingdao, China, which can effectively overcome the interference of inaccurate background parameters caused by the diversity of economic level and environment in different regions. Six indicators entailing global warming potential (1.86E + 04, 3.45E + 03, 2.36E + 02), eutrophication potential (6.65E + 01, -1.24E + 02, -1.65E + 02), acidification potential (1.93E + 02, 4.33E + 01, 1.30E + 00), photochemical oxidant formation potential (2.35E-01, 5.46E -02, 2.53E-03), human toxicity potential (2.47E + 00, 6.08E-01, 4.91E + 00) and energy use (3.36E + 05, 1.27E + 04, 1.48E + 03) were introduced in the current study. It was found that all environmental indicators in the indoor intensive farming system were much higher than those in semi-intensive and extensive farming systems because of the dominant role of energy input, while energy input also contributed as the leading cause factor for most of the indicators in the semi-intensive farming system. Yet in the extensive farming system, infrastructure materials played a major role. Through a comprehensive comparison of the three farming systems, it was concluded that income per unit area of indoor intensive farming system was much higher than those of semi-intensive and extensive farming systems. However, the extensive farming system was the most sustainable one. Moreover, adequate measures were proposed, respectively, to improve the environmental sustainability of each farming system in the present study.

  9. The influence of environmental conditions on early life stages of flounder (Platichthys flesus) in the central Baltic Sea

    Science.gov (United States)

    Ustups, Didzis; Müller-Karulis, Bärbel; Bergstrom, Ulf; Makarchouk, Andrej; Sics, Ivo

    2013-01-01

    Flounder (Platichthys flesus) is a temperate marine fish that is well adapted to the brackish waters of the Baltic Sea. There are two sympatric flounder populations in the Baltic Sea, pelagic and demersal spawners, which differ in their spawning habitat and egg characteristics. In the present study, pelagic spawning flounder of the central Baltic Sea was studied. We examined whether variations in hydrological regime can explain fluctuations in flounder early life stages that have occurred over the past 30 years (1970-2005). Using generalized additive modeling to explain the abundance of flounder eggs and larvae in a Latvian ichthyoplankton dataset, we evaluate the hypothesis that the available reproductive volume, defined as the water column with dissolved oxygen larger than 1 ml/l and salinity between 10.6 and 12 PSU, affects the survival of flounder ichthyoplankton and determines recruitment success. Both reproductive volume and spawning stock biomass were significant factors determining flounder ichthyoplankton abundance. Different measures of water temperature did not contribute significantly to the variability of eggs or larvae. However, recruitment did not correlate to the supply of larvae. The findings presented in this study on the relationship between flounder reproduction, spawning stock biomass and reproductive volume, as well as the lack of correlation to recruitment, are valuable for the understanding of flounder ecology in the Baltic Sea, and for developing the management of the species.

  10. NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

    OpenAIRE

    Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

    2015-01-01

    Background Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host...

  11. NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

    Science.gov (United States)

    Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

    2015-05-17

    Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

  12. 15 CFR 971.701 - Criteria for safety of life and property at sea.

    Science.gov (United States)

    2010-01-01

    ... REGULATIONS OF THE ENVIRONMENTAL DATA SERVICE DEEP SEABED MINING REGULATIONS FOR COMMERCIAL RECOVERY PERMITS... (pursuant to § 971.205(a)). United States flag vessels are under United States jurisdiction on the high seas...

  13. 15 CFR 970.801 - Criteria for safety of life and property at sea.

    Science.gov (United States)

    2010-01-01

    ... REGULATIONS OF THE ENVIRONMENTAL DATA SERVICE DEEP SEABED MINING REGULATIONS FOR EXPLORATION LICENSES Safety... jurisdiction on the high seas and subject to domestic enforcement procedures. With respect to foreign flag...

  14. Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea

    KAUST Repository

    Pascual, Marta

    2017-05-10

    Marine species can demonstrate strong genetic differentiation and population structure despite the hypothesis of open seas and high connectivity. Some suggested drivers causing the genetic breaks are oceanographic barriers and the species\\' biology. We assessed the relevance of seven major oceanographic fronts on species connectivity while considering their dispersal capacity and life strategy.We systematically reviewed the scientific articles reporting population genetic differentiation along the Mediterranean Sea and across the Atlantic-Mediterranean transition. We retained those considering at least one sampling locality at each side of an oceanographic front, and at least two localities with no-front between them to correctly assess the effect of the front. To estimate the impact of life history characteristics affecting connectivity we considered the planktonic larval duration (PLD) and adult life strategy.Oceanographic barriers in the Mediterranean Sea seem to reduce gene flow globally; however, this effect is not homogeneous considering the life history traits of the species. The effect of the oceanographic fronts reduces gene flow in highly mobile species with PLD larger than 2-4 weeks. Benthic sessile species and/or with short PLD (< 2 weeks) have more significant genetic breaks between localities than species with higher motility; however, genetic differentiation occurs independently of the presence of a front.Genetic connectivity is important for populations to recover from anthropogenic or natural impacts. We show that species with low mobility, mostly habitat-formers, have high genetic differentiation but low gene flow reduction mediated by the front, therefore, considering the importance of these species, we emphasize the vulnerability of the Mediterranean ecosystems and the necessity of protection strategies based on the whole ecosystem.

  15. Host-Microbe Interactions in Microgravity: Assessment and Implications

    Directory of Open Access Journals (Sweden)

    Jamie S. Foster

    2014-05-01

    Full Text Available Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

  16. Host-microbe interactions in microgravity: assessment and implications.

    Science.gov (United States)

    Foster, Jamie S; Wheeler, Raymond M; Pamphile, Regine

    2014-05-26

    Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

  17. Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

    Science.gov (United States)

    Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

    2003-01-01

    We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

  18. Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism.

    Science.gov (United States)

    Kemen, Ariane C; Agler, Matthew T; Kemen, Eric

    2015-06-01

    Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host-pathogen-microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  19. Cooperation and cheating in microbes

    Science.gov (United States)

    Gore, Jeff

    2011-03-01

    Understanding the cooperative and competitive dynamics within and between species is a central challenge in evolutionary biology. Microbial model systems represent a unique opportunity to experimentally test fundamental theories regarding the evolution of cooperative behaviors. In this talk I will describe our experiments probing cooperation in microbes. In particular, I will compare the cooperative growth of yeast in sucrose and the cooperative inactivation of antibiotics by bacteria. In both cases we find that cheater strains---which don't contribute to the public welfare---are able to take advantage of the cooperator strains. However, this ability of cheaters to out-compete cooperators occurs only when cheaters are present at low frequency, thus leading to steady-state coexistence. These microbial experiments provide fresh insight into the evolutionary origin of cooperation.

  20. Chemosynthesis in deep-sea red-clay: Linking concepts to probable martian life

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; Mourya, B.S.; Mamatha, S.S.; Khadge, N.H.; LokaBharathi, P.A.

    of microbial biogeochemistry are used in the pres- ent deep-sea analogue studies and would be imple- mented for actual Martian soil samples in future: Microbial abundance in terms of total counts » Diversity of culture dependent and independent Chemos... soils done earlier by Viking I robots [5, Bianciardi et. al, 2012

  1. Research progress and application prospect of radiation-resistant prokaryotic microbe

    International Nuclear Information System (INIS)

    Wang Wei; Zhu Jing; Zhang Zhidong; Tang Qiyong; Chen Ming

    2013-01-01

    Radiation-resistant microbe is becoming the research hotspot because of its special life phenomenon and physiological mechanism. Radiation-resistant bacteria are one kind of the most studied radiation-resistant microbe. This article summarized some aspects of the research on radiation-resistant bacteria, including the radiation resistant bacteria resources, and discussed its potential application prospects in the environmental engineering, biotechnology, human health, military and space et al. (authors)

  2. Shifting patterns of nitrogen excretion and amino acid catabolism capacity during the life cycle of the sea lamprey (Petromyzon marinus).

    Science.gov (United States)

    Wilkie, Michael P; Claude, Jaime F; Cockshutt, Amanda; Holmes, John A; Wang, Yuxiang S; Youson, John H; Walsh, Patrick J

    2006-01-01

    The jawless fish, the sea lamprey (Petromyzon marinus), spends part of its life as a burrow-dwelling, suspension-feeding larva (ammocoete) before undergoing a metamorphosis into a free swimming, parasitic juvenile that feeds on the blood of fishes. We predicted that animals in this juvenile, parasitic stage have a great capacity for catabolizing amino acids when large quantities of protein-rich blood are ingested. The sixfold to 20-fold greater ammonia excretion rates (J(Amm)) in postmetamorphic (nonfeeding) and parasitic lampreys compared with ammocoetes suggested that basal rates of amino acid catabolism increased following metamorphosis. This was likely due to a greater basal amino acid catabolizing capacity in which there was a sixfold higher hepatic glutamate dehydrogenase (GDH) activity in parasitic lampreys compared with ammocoetes. Immunoblotting also revealed that GDH quantity was 10-fold and threefold greater in parasitic lampreys than in ammocoetes and upstream migrant lampreys, respectively. Higher hepatic alanine and aspartate aminotransferase activities in the parasitic lampreys also suggested an enhanced amino acid catabolizing capacity in this life stage. In contrast to parasitic lampreys, the twofold larger free amino acid pool in the muscle of upstream migrant lampreys confirmed that this period of natural starvation is accompanied by a prominent proteolysis. Carbamoyl phosphate synthetase III was detected at low levels in the liver of parasitic and upstream migrant lampreys, but there was no evidence of extrahepatic (muscle, intestine) urea production via the ornithine urea cycle. However, detection of arginase activity and high concentrations of arginine in the liver at all life stages examined infers that arginine hydrolysis is an important source of urea. We conclude that metamorphosis is accompanied by a metabolic reorganization that increases the capacity of parasitic sea lampreys to catabolize intermittently large amino acid loads arising

  3. Extreme longevity in a deep-sea vestimentiferan tubeworm and its implications for the evolution of life history strategies

    Science.gov (United States)

    Durkin, Alanna; Fisher, Charles R.; Cordes, Erik E.

    2017-08-01

    The deep sea is home to many species that have longer life spans than their shallow-water counterparts. This trend is primarily related to the decline in metabolic rates with temperature as depth increases. However, at bathyal depths, the cold-seep vestimentiferan tubeworm species Lamellibrachia luymesi and Seepiophila jonesi reach extremely old ages beyond what is predicted by the simple scaling of life span with body size and temperature. Here, we use individual-based models based on in situ growth rates to show that another species of cold-seep tubeworm found in the Gulf of Mexico, Escarpia laminata, also has an extraordinarily long life span, regularly achieving ages of 100-200 years with some individuals older than 300 years. The distribution of results from individual simulations as well as whole population simulations involving mortality and recruitment rates support these age estimates. The low 0.67% mortality rate measurements from collected populations of E. laminata are similar to mortality rates in L. luymesi and S. jonesi and play a role in evolution of the long life span of cold-seep tubeworms. These results support longevity theory, which states that in the absence of extrinsic mortality threats, natural selection will select for individuals that senesce slower and reproduce continually into their old age.

  4. Making Marine Noise Pollution Impacts Heard: The Case of Cetaceans in the North Sea within Life Cycle Impact Assessment

    Directory of Open Access Journals (Sweden)

    Heleen Middel

    2017-06-01

    Full Text Available Oceans represent more than 95% of the world’s biosphere and are among the richest sources of biodiversity on Earth. However, human activities such as shipping and construction of marine infrastructure pose a threat to the quality of marine ecosystems. Due to the dependence of most marine animals on sound for their communication, foraging, protection, and ultimately their survival, the effects of noise pollution from human activities are of growing concern. Life cycle assessment (LCA can play a role in the understanding of how potential environmental impacts are related to industrial processes. However, noise pollution impacts on marine ecosystems have not yet been taken into account. This paper presents a first approach for the integration of noise impacts on marine ecosystems into the LCA framework by developing characterization factors (CF for the North Sea. Noise pollution triggers a large variety of impact pathways, but as a starting point and proof-of-concept we assessed impacts on the avoidance behaviour of cetaceans due to pile-driving during the construction of offshore windfarms in the North Sea. Our approach regards the impact of avoidance behaviour as a temporary loss of habitat, and assumes a temporary loss of all individuals within that habitat from the total regional population. This was verified with an existing model that assessed the population-level effect of noise pollution on harbour porpoises (Phocoena phocoena in the North Sea. We expanded our CF to also include other cetacean species and tested it in a case study of the construction of an offshore windfarm (Prinses Amalia wind park. The total impact of noise pollution was in the same order of magnitude as impacts on other ecosystems from freshwater eutrophication, freshwater ecotoxicity, terrestrial acidification, and terrestrial ecotoxicity. Although there are still many improvements to be made to this approach, it provides a basis for the implementation of noise

  5. Effects of microbes on the immune system

    National Research Council Canada - National Science Library

    Fujinami, Robert S; Cunningham, Madeleine W

    2000-01-01

    .... The book synthesizes recent discoveries on the various mechanisms by which microbes subvert the immune response and on the role of these immunologic mechanisms in the pathogenesis of infectious diseases...

  6. A global census of marine microbes

    Digital Repository Service at National Institute of Oceanography (India)

    Amaral-Zettler, L.; Artigas, L.F.; Baross, J.; LokaBharathi, P.A; Boetius, A; Chandramohan, D.; Herndl, G.; Kogure, K.; Neal, P.; Pedros-Alio, C.; Ramette, A; Schouten, S.; Stal, L.; Thessen, A; De Leeuw, J.; Sogin, M.

    In this chapter we provide a brief history of what is known about marine microbial diversity, summarize our achievements in performing a global census of marine microbes, and reflect on the questions and priorities for the future of the marine...

  7. Microbes safely, effectively bioremediate oil field pits

    International Nuclear Information System (INIS)

    Shaw, B.; Block, C.S.; Mills, C.H.

    1995-01-01

    Natural and augmented bioremediation provides a safe, environmental, fast, and effective solution for removing hydrocarbon stains from soil. In 1992, Amoco sponsored a study with six bioremediation companies, which evaluated 14 different techniques. From this study, Amoco continued using Environmental Protection Co.'s (EPC) microbes for bioremediating more than 145 sites near Farmington, NM. EPC's microbes proved effective on various types of hydrocarbon molecules found in petroleum stained soils from heavy crude and paraffin to volatiles such as BTEX (benzene, toluene, ethylbenzene, xylene) compounds. Controlled laboratory tests have shown that these microbes can digest the hydrocarbon molecules with or without free oxygen present. It is believed that this adaptation gives these microbes their resilience. The paper describes the bioremediation process, environmental advantages, in situ and ex situ bioremediation, goals of bioremediation, temperature effects, time, cost, and example sites that were treated

  8. Comparative anatomy and histology of developmental and parasitic stages in the life cycle of the lined sea anemone Edwardsiella lineata.

    Science.gov (United States)

    Reitzel, Adam M; Daly, Marymegan; Sullivan, James C; Finnerty, John R

    2009-02-01

    The evolution of parasitism is often accompanied by profound changes to the developmental program. However, relatively few studies have directly examined the developmental evolution of parasitic species from free-living ancestors. The lined sea anemone Edwardsiella lineata is a relatively recently evolved parasite for which closely related free-living outgroups are known, including the starlet sea anemone Nematostella vectensis. The larva of E. lineata parasitizes the ctenophore Mnemiopsis leidyi, and, once embedded in its host, the anemone assumes a novel vermiform body plan. That we might begin to understand how the developmental program of this species has been transformed during the evolution of parasitism, we characterized the gross anatomy, histology, and cnidom of the parasitic stage, post-parasitic larval stage, and adult stage of the E. lineata life cycle. The distinct parasitic stage of the life cycle differs from the post-parasitic larva with respect to overall shape, external ciliation, cnida frequency, and tissue architecture. The parasitic stage and planula both contain holotrichs, a type of cnida not previously reported in Edwardsiidae. The internal morphology of the post-parasitic planula is extremely similar to the adult morphology, with a complete set of mesenterial tissue and musculature despite this stage having little external differentiation. Finally, we observed 2 previously undocumented aspects of asexual reproduction in E. lineata: (1) the parasitic stage undergoes transverse fission via physal pinching, the first report of asexual reproduction in a pre-adult stage in the Edwardsiidae; and (2) the juvenile polyp undergoes transverse fission via polarity reversal, the first time this form of fission has been reported in E. lineata.

  9. From traits to life-history strategies: Deconstructing fish community composition across European seas

    DEFF Research Database (Denmark)

    Pécuchet, Lauréne; Lindegren, Martin; Hidalgo, Manuel

    2017-01-01

    The life history of a species is determined by trade-offs between growth, survival and reproduction to maximize fitness in a given environment. Following a theoretical model, we investigate whether the composition of marine fish communities can be understood in terms of a set of lifehistory...

  10. Transgenerational plasticity in the sea: context-dependent maternal effects across the life history.

    Science.gov (United States)

    Marshall, Dustin J

    2008-02-01

    Maternal effects can have dramatic influences on the phenotype of offspring. Maternal effects can act as a conduit by which the maternal environment negatively affects offspring fitness, but they can also buffer offspring from environmental change by altering the phenotype of offspring according to local environmental conditions and as such, are a form of transgenerational plasticity. The benefits of maternal effects can be highly context dependent, increasing performance in one life-history stage but reducing it in another. While maternal effects are increasingly well understood in terrestrial systems, studies in the marine environment are typically restricted to a single, early life-history stage. Here, I examine the role of maternal effects across the life history of the bryozoan Bugula neritina. I exposed maternal colonies to a common pollution stress (copper) in the laboratory and then placed them in the field for one week to brood offspring. I then examined the resistance of offspring to copper from toxicant-exposed and toxicant-naïve mothers and found that offspring from toxicant-exposed mothers were larger, more dispersive, and more resistant to copper stress than offspring from naïve mothers. However, maternal exposure history had pervasive, negative effects on the post-metamorphic performance (particularly survival) of offspring: offspring from toxicant-exposed mothers had poorer performance after six weeks in the field, especially when facing high levels of intraspecific competition. Maternal experience can have complex effects on offspring phenotype, enhancing performance in one life-history stage while decreasing performance in another. The context-dependent costs and benefits associated with maternally derived pollution resistance may account for why such resistance is induced rather than continually expressed: mothers must balance the benefits of producing pollution-resistant larvae with the costs of producing poorer performing adults (in the

  11. Genetic engineering microbes for bioremediation/ biorecovery of uranium

    International Nuclear Information System (INIS)

    Apte, S.K.; Rao, A.S.; Appukuttan, D.; Nilgiriwala, K.S.; Acharya, C.

    2005-01-01

    Bioremediation (both bioremoval and biorecovery) of metals is considered a feasible, economic and eco-friendly alternative to chemical methods of metal extraction, particularly when the metal concentration is very low. Scanty distribution along with poor ore quality makes biomining of uranium an attractive preposition. Biosorption, bioprecipitation or bioaccumulation of uranium, aided by recombinant DNA technology, offer a promising technology for recovery of uranium from acidic or alkaline nuclear waste, tailings or from sea-water. Genetic engineering of bacteria, with a gene encoding an acid phosphatase, has yielded strains that can bioprecipitate uranium from very low concentrations at acidic-neutral pH, in a relatively short time. Organisms overproducing alkaline phosphatase have been selected for uranium precipitation from alkaline waste. Such abilities have now been transferred to the radioresistant microbe Deinococcus radiodurans to facilitate in situ bioremediation of nuclear waste, with some success. Sulfate-reducing bacteria are being characterized for bioremediation of uranium in tailings with the dual objective of uranium precipitation and reduction of sulfate to sulphide. Certain marine cyanobacteria have shown promise for uranium biosorption to extracellular polysaccharides, and intracellular accumulation involving metal sequestering metallothionin proteins. Future work is aimed at understanding the genetic basis of these abilities and to engineer them into suitable organisms subsequently. As photosynthetic, nitrogen-fixing microbes, which are considerably resistant to ionizing radiations, cyanobacteria hold considerable potential for bioremediation of nuclear waste. (author)

  12. Nautilus pompilius life history and demographics at the Osprey Reef Seamount, Coral Sea, Australia.

    Directory of Open Access Journals (Sweden)

    Andrew J Dunstan

    Full Text Available Nautiloids are the subject of speculation as to their threatened status arising from the impacts of targeted fishing for the ornamental shell market. Life history knowledge is essential to understand the susceptibility of this group to overfishing and to the instigation of management frameworks. This study provides a comprehensive insight into the life of Nautilus in the wild. At Osprey Reef from 1998-2008, trapping for Nautilus was conducted on 354 occasions, with 2460 individuals of one species, Nautilus pompilius, captured and 247 individuals recaptured. Baited remote underwater video systems (BRUVS were deployed on 15 occasions and six remotely operated vehicle (ROV dives from 100-800 m were conducted to record Nautilus presence and behavior. Maturity, sex and size data were recorded, while measurements of recaptured individuals allowed estimation of growth rates to maturity, and longevity beyond maturity. We found sexual dimorphism in size at maturity (males: 131.9±SD = 2.6 mm; females: 118.9±7.5 mm shell diameter in a population dominated by mature individuals (58%. Mean growth rates of 15 immature recaptured animals were 0.061±0.023 mm day(-1 resulting in an estimate of around 15.5 years to maturation. Recaptures of mature animals after five years provide evidence of a lifespan exceeding 20 years. Juvenile Nautilus pompilius feeding behavior was recorded for the first time within the same depth range (200-610 m as adults. Our results provide strong evidence of a K-selected life history for Nautilus from a detailed study of a 'closed' wild population. In conjunction with population size and density estimates established for the Osprey Reef Nautilus, this work allows calculations for sustainable catch and provides mechanisms to extrapolate these findings to other extant nautiloid populations (Nautilus and Allonautilus spp. throughout the Indo-Pacific.

  13. Life-history responses to changing temperature and salinity of the Baltic Sea copepod Eurytemora affinis.

    Science.gov (United States)

    Karlsson, Konrad; Puiac, Simona; Winder, Monika

    2018-01-01

    To understand the effects of predicted warming and changing salinity of marine ecosystems, it is important to have a good knowledge of species vulnerability and their capacity to adapt to environmental changes. In spring and autumn of 2014, we conducted common garden experiments to investigate how different populations of the copepod Eurytemora affinis from the Baltic Sea respond to varying temperatures and salinity conditions. Copepods were collected in the Stockholm archipelago, Bothnian Bay, and Gulf of Riga (latitude, longitude: 58°48.19', 17°37.52'; 65°10.14', 23°14.41'; 58°21.67', 24°30.83'). Using individuals with known family structure, we investigated within population variation of the reaction norm (genotype and salinity interaction) as a means to measure adaptive capacity. Our main finding was that low salinity has a detrimental effect on development time, the additive effects of high temperature and low salinity have a negative effect on survival, and their interaction has a negative effect on hatching success. We observed no variation in survival and development within populations, and all genotypes had similar reaction norms with higher survival and faster development in higher salinities. This suggests that there is no single genotype that performs better in low salinity or high salinity; instead, the best genotype in any given salinity is best in all salinities. Genotypes with fast development time also had higher survival compared to slow developing genotypes at all salinities. Our results suggest that E. affinis can tolerate close to freshwater conditions also in high temperatures, but with a significant reduction in fitness.

  14. Exploring Archaeal Communities And Genomes Across Five Deep-Sea Brine Lakes Of The Red Sea With A Focus On Methanogens

    KAUST Repository

    Guan, Yue

    2015-12-15

    The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

  15. Preliminary Investigation on the Use of Allyi Isothiocyanate to Increase the Shelf-Life of Gilthead Sea Bream (Sparus Aurata) Fillets.

    Science.gov (United States)

    Giarratana, Filippo; Crinò, Chiara; Muscolino, Daniele; Beninati, Chiara; Ziino, Graziella; Giuffrida, Alessandro; Panebianco, Antonio

    2015-06-30

    The aim of this work is to evaluate the activity of allyl isothiocyanate (AITC) against fish spoilage bacteria (specific spoilage organisms; SSOs) as well as its possible use in gilthead sea bream ( Sparus aurata ) fillets to extend their shelf-life. In this regard, in vitro tests are carried out in order to evaluate the inhibitory activity of AITC and its vapours on several strains of SSOs. The AITC effect on the shelf-life of sea bream fillets was made by putting them in plastic trays hermetically closed with the addition AITC. Microbiological and sensorial evaluations were made on fish fillets during storage. Treated fillets maintained microbial populations at a significantly lower level compared with the control samples during storage, showing better sensorial characteristics. Therefore, the use of AITC's vapours seems to be a new and interesting alternative way to increase fish product shelf-life.

  16. MicrobeWorld Radio and Communications Initiative

    Energy Technology Data Exchange (ETDEWEB)

    Barbara Hyde

    2006-11-22

    MicrobeWorld is a 90-second feature broadcast daily on more than 90 public radio stations and available from several sources as a podcast, including www.microbeworld.org. The feature has a strong focus on the use and adapatbility of microbes as alternative sources of energy, in bioremediation, their role in climate, and especially the many benefits and scientific advances that have resulting from decoding microbial genomes. These audio features are permanantly archived on an educational outreach site, microbeworld.org, where they are linked to the National Science Education Standards. They are also being used by instructors at all levels to introduce students to the multiple roles and potential of microbes, including a pilot curriculum program for middle-school students in New York.

  17. Life-history traits of the long-nosed skate Dipturus oxyrinchus, from the central western Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    Antonello Mulas

    2015-11-01

    Full Text Available Skates are often considered vulnerable to overfishing because of their peculiar life cycle characteristics rendering them susceptible to overexploitation. In this regard, life-history traits of a by-catch species, the long-nosed skate Dipturus oxyrinchus (Linnaeus, 1758 from Sardinian waters, were investigated. The age, growth and reproduction were studied using 706 specimens sampled during experimental and commercial hauls (depths 76-671 metres. Females (10.4-117.5 cm in total length, TL attained larger sizes than males (14.5-99.5 cm TL. To evaluate the growth, a subsample of 130 individuals (76 females and 54 males was employed. The age was estimated through the annuli counts on sectioned vertebral centra. A high ageing reproducibility and precision was obtained (Index of Average Percent Error=6.56; %CV=8.9. Four models were applied on length at age data: the von Bertalanffy (VBGF, the Exponential, the Gompertz and the Logistic functions. According to the Akaike’s Information Criterion, the Gompertz model (L∞=127.5±4.9 cm; k=0.14±0.009; inflection point=3.97 y-1±0.9 provided the best fitting curve, showing a higher growth rate and a lower L∞ than what obtained with the VBGF (L∞=144.4±11.5 cm; k=0.08±0.001; t0=-1.09±0.23. The oldest female and male were 17 (115.5 cm TL and 15 years (96 cm TL, respectively. Lengths at maturity were 103.5 cm (14 years for females and 91 cm (12.1 years for males corresponding to 88 and 91.5% of the maximum observed length, respectively. The monthly evolution of maturity stages highlighted an extended reproductive cycle with spawning females and active males almost over the year, as confirmed by the Gonado-somatic Index. Ovarian fecundity reached a maximum of 26 yolked follicles. Given the relative abundance in Sardinian seas, we hope that these results will prove useful for the implementation of basic management measures in order to ensure the sustainability of catches of this species, particularly

  18. Red Sea as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-01-01

    King-Abdullah University of Science and Technology (KAUST) is located on the shores of the Red Sea in Saudi Arabia. The Red Sea is well known for its unique environment, harboring various microbes capable of surviving in salty brines. We collected

  19. Sea Legs

    Science.gov (United States)

    Macdonald, Kenneth C.

    Forty-foot, storm-swept seas, Spitzbergen polar bears roaming vast expanses of Arctic ice, furtive exchanges of forbidden manuscripts in Cold War Moscow, the New York city fashion scene, diving in mini-subs to the sea floor hot srings, life with the astronauts, romance and heartbreak, and invading the last bastions of male exclusivity: all are present in this fast-moving, non-fiction account of one woman' fascinating adventures in the world of marine geology and oceanography.

  20. Psychrophiles and astrobiology: microbial life of frozen worlds

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2003-01-01

    Most bodies of our Solar System are "Frozen Worlds" where the prevailing surface temperature remains at or below freezing. On Earth there are vast permanently frozen regions of permafrost, polar ice sheets, and glaciers and the deep oceans and deep-sea marine sediments have remained at 2 - 4°C for eons. Psychrophilic and psychrotrophic microbiota that inhabit these regimes provide analogs for microbial life that might inhabit ice sheets and permafrost of Mars, comets, or the ice/water interfaces or sediments deep beneath the icy crusts of Europa, Callisto, or Ganymede. Cryopreserved micro-organisms can remain viable (in a deep anabiotic state) for millions of years frozen in permafrost and ice. Psychrophilic and psychrotrophic (cold-loving) microbes can carry out metabolic processes in water films and brine, acidic, or alkaline chanels in permafrost or ice at temperatures far below 0°C. These microbes of the cryosphere help define the thermal and temporal limits of life on Earth and may provide clues to where and how to search for evidence of life elsewhere in the Cosmos. Astrobiologists at the NASA Marshall Space Flight Center have collected microbial extremophiles from the Pleistocene ice wedges and frozen thermokarst ponds from the Fox Permafrost Tunnel of Alaska. Microbes have also been isolated from samples of Magellanic Penguin guano from Patagonia; deep-sea marine muds near hydrothermal vents; snow and permafrost from Siberia, and deep ice cores, ice-bubble and cryoconite rocks of the Central Antarctic Ice Sheet. These samples have yielded microbial extremophiles representing a wide variety of anaerobic bacteria and archaea. These microbes have been isolated, cultured, characterized and analyzed by phylogenetic and genomic methods. Images were obtained by Phase Contrast, Environmental, Field Emission Scanning and Transmission Electron Microscopes to study the ultra-microstructure and elemental distribution in the composition of these micro-organisms. We

  1. First Foods and Gut Microbes

    DEFF Research Database (Denmark)

    Laursen, Martin Frederik; Bahl, Martin Iain; Michaelsen, Kim F.

    2017-01-01

    The establishment of the human gut microbiota in early life has been associated with later health and disease. During the 1st months after birth, the microbial composition in the gut is known to be affected by the mode of delivery, use of antibiotics, geographical location and type of feeding...... of this window is currently debated, but it likely coincides with the complementary feeding period, marking the gradual transition from milk- based infant feeding to family diet usually occurring between 6 and 24 months. Furthermore, the 'first 1000 days,' i.e., the period from conception until age 2 years...... microbiota development. This perspective paper summarizes the currently very few studies addressing the effects of complementary diet on gut microbiota, and highlights the recent finding that transition to family foods greatly impacts the development of gut microbial diversity. Further, we discuss potential...

  2. Activity of R(+) limonene on the maximum growth rate of fish spoilage organisms and related effects on shelf-life prolongation of fresh gilthead sea bream fillets.

    Science.gov (United States)

    Giarratana, Filippo; Muscolino, Daniele; Beninati, Chiara; Ziino, Graziella; Giuffrida, Alessandro; Panebianco, Antonio

    2016-11-21

    R(+)limonene (LMN) is the major aromatic compound in essential oils obtained from oranges, grapefruits, and lemons. The improvement of preservation techniques to reduce the growth and activity of spoilage microorganisms in foods is crucial to increase their shelf life and to reduce the losses due to spoilage. The aim of this work is to evaluate the effect of LMN on the shelf life of fish fillets. Its effectiveness was preliminarily investigated in vitro against 60 strains of Specific Spoilage Organisms (SSOs) and then on gilt-head sea bream fillets stored at 2±0.5°C for 15days under vacuum. LMN showed a good inhibitory effect against tested SSOs strains. On gilt-head sea bream fillets, LMN inhibited the growth SSOs effectively, and its use resulted in a shelf-life extension of ca. 6-9days of treated fillets, compared to the control samples. The LMN addition in Sparus aurata fillets giving a distinctive smell and like-lemon taste to fish fillets that resulted pleasant to panellists. Its use contributed to a considerable reduction of fish spoilage given that the fillets treated with LMN were still sensory acceptable after 15days of storage. LMN may be used as an effective antimicrobial system to reduce the microbial growth and to improve the shelf life of fresh gilt-head sea bream fillets. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. ``Out To Sea: Life as a Crew Member Aboard a Geologic Research Ship'' - Production of a Video and Teachers Guide.

    Science.gov (United States)

    Rack, F. R.; Tauxe, K.

    2004-12-01

    In May 2002, Joint Oceanographic Institutions (JOI) received a proposal entitled "Motivating Middle School Students with the JOIDES Resolution", from a middle school teacher in New Mexico named Katie Tauxe. Katie was a former Marine Technician who has worked aboard the R/V JOIDES Resolution in the early years of the Ocean Drilling Program (ODP). She proposed to engage the interest of middle school students using the ODP drillship as the centerpiece of a presentation focused on the lives of the people who work aboard the ship and the excitement of science communicated through an active shipboard experience. The proposal asked for travel funds to and from the ship, the loan of video camera equipment from JOI, and a small amount of funding to cover expendable supplies, video editing, and production at the local Public Broadcasting Station in Los Alamos, NM. Katie sailed on the transit of the JOIDES Resolution through the Panama Canal, following the completion of ODP Leg 206 in late 2002. This presentation will focus on the outcome of this video production effort, which is a 19 minute-long video entitled "Out to Sea: Life as a Crew Member Aboard a Geologic Research Ship", and a teacher's guide that can be found online.

  4. Natural products from microbes associated with insects

    DEFF Research Database (Denmark)

    Beemelmanns, Christine; Guo, Huijuan; Rischer, Maja

    2016-01-01

    Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We...

  5. MVP: a microbe-phage interaction database.

    Science.gov (United States)

    Gao, Na L; Zhang, Chengwei; Zhang, Zhanbing; Hu, Songnian; Lercher, Martin J; Zhao, Xing-Ming; Bork, Peer; Liu, Zhi; Chen, Wei-Hua

    2018-01-04

    Phages invade microbes, accomplish host lysis and are of vital importance in shaping the community structure of environmental microbiota. More importantly, most phages have very specific hosts; they are thus ideal tools to manipulate environmental microbiota at species-resolution. The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific microbes of interest. We first collected 50 782 viral sequences from various sources and clustered them into 33 097 unique viral clusters based on sequence similarity. We then identified 26 572 interactions between 18 608 viral clusters and 9245 prokaryotes (i.e. bacteria and archaea); we established these interactions based on 30 321 evidence entries that we collected from published datasets, public databases and re-analysis of genomic and metagenomic sequences. Based on these interactions, we calculated the host range for each of the phage clusters and accordingly grouped them into subgroups such as 'species-', 'genus-' and 'family-' specific phage clusters. MVP is equipped with a modern, responsive and intuitive interface, and is freely available at: http://mvp.medgenius.info. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. The mucosal firewalls against commensal intestinal microbes.

    Science.gov (United States)

    Macpherson, Andrew J; Slack, Emma; Geuking, Markus B; McCoy, Kathy D

    2009-07-01

    Mammals coexist with an extremely dense microbiota in the lower intestine. Despite the constant challenge of small numbers of microbes penetrating the intestinal surface epithelium, it is very unusual for these organisms to cause disease. In this review article, we present the different mucosal firewalls that contain and allow mutualism with the intestinal microbiota.

  7. Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation.

    Science.gov (United States)

    Weber, Kristina; Zuschin, Martin

    2013-01-15

    Life-death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats and in practice this has to be distinguished using taphonomic preservation pattern and estimates of time-averaging. It remains to be rigorously evaluated, however, how to distinguish between sources of LD disagreement. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). The northern Adriatic Sea is an ecosystem under anthropogenic pressure, and we studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) associated with the delta of the Isonzo River (Gulf of Trieste). Specifically we evaluated the fidelity of richness, evenness, abundance, habitat discrimination and beta diversity. A total of 10,740 molluscs from fifteen tidal flat and fourteen sublittoral sites were analyzed for species composition and distribution of living and dead molluscs. Of 78 recorded species, only eleven were numerically abundant. There were many more dead than living individuals and rarefied species richness in the DA was higher at all spatial scales, but the differences are lower in habitats and in the region than at individual stations. Evenness was always higher in death assemblages, and probably due to temporally more variable LAs the differences are stronger in the sublittoral habitats. Distinct assemblages characterized intertidal and sublittoral habitats, and the distribution and abundance of empty shells generally corresponded to that of the living species. Death assemblages have lower beta diversity than life assemblages, but empty shells capture compositional differences between habitats to a higher degree than living shells

  8. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development

    Directory of Open Access Journals (Sweden)

    XiaoLi Bing

    2018-03-01

    Full Text Available Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR and germ-free (GF flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions.

  9. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development

    Science.gov (United States)

    Bing, XiaoLi; Gerlach, Joseph; Loeb, Gregory

    2018-01-01

    ABSTRACT Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions. PMID:29559576

  10. Diversity and adaptations of deep-sea microorganisms

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, C.

    -tolerant enzymes, natural products of potential use in human health management and environmental bioremediation using solvent-tolerant microorganisms are some of the potential biotechnological applications of these deep-sea microbes....

  11. Detection of emamectin benzoate tolerance emergence in different life stages of sea lice, Lepeophtheirus salmonis, on farmed Atlantic salmon, Salmo salar L.

    Science.gov (United States)

    Jones, P G; Hammell, K L; Gettinby, G; Revie, C W

    2013-03-01

    Emamectin benzoate has been used to treat sea lice, Lepeophtheirus salmonis, infestations on farmed Atlantic salmon, Salmo salar. Recent evidence suggests a reduction in effectiveness in some locations. A major challenge in the detection of tolerance emergence can be the typically low proportion of resistant individuals in a population during the early phases. The objectives of this study were to develop a method for determining differences in temporal development of tolerance between sea lice life stages and to explore how these differences might be used to improve the monitoring of treatment effectiveness in a clinical setting. This study examined two data sets based on records of sea lice abundance following emamectin benzoate treatments from the west coast of Scotland (2002-2006) and from New Brunswick, Canada (2004-2008). Life stages were categorized into two groups (adult females and the remaining mobile stages) to examine the trends in mean abundance and treatment effectiveness. Differences in emamectin benzoate effectiveness were found between the two groups by year and location, suggesting that an important part of monitoring drug resistance development in aquatic ectoparasites may be the need to focus on key life stages. © 2013 Blackwell Publishing Ltd.

  12. Environmental bacteriophages : viruses of microbes in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    Télesphore eSIME - NGANDO

    2014-07-01

    Full Text Available Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/, was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea, as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

  13. The role of microbes in snowmelt and radiative forcing on an Alaskan icefield

    Science.gov (United States)

    Ganey, Gerard Q.; Loso, Michael G.; Burgess, Annie Bryant; Dial, Roman J.

    2017-10-01

    A lack of liquid water limits life on glaciers worldwide but specialized microbes still colonize these environments. These microbes reduce surface albedo, which, in turn, could lead to warming and enhanced glacier melt. Here we present results from a replicated, controlled field experiment to quantify the impact of microbes on snowmelt in red-snow communities. Addition of nitrogen-phosphorous-potassium fertilizer increased alga cell counts nearly fourfold, to levels similar to nitrogen-phosphorus-enriched lakes; water alone increased counts by half. The manipulated alga abundance explained a third of the observed variability in snowmelt. Using a normalized-difference spectral index we estimated alga abundance from satellite imagery and calculated microbial contribution to snowmelt on an icefield of 1,900 km2. The red-snow area extended over about 700 km2, and in this area we determined that microbial communities were responsible for 17% of the total snowmelt there. Our results support hypotheses that snow-dwelling microbes increase glacier melt directly in a bio-geophysical feedback by lowering albedo and indirectly by exposing low-albedo glacier ice. Radiative forcing due to perennial populations of microbes may match that of non-living particulates at high latitudes. Their contribution to climate warming is likely to grow with increased melt and nutrient input.

  14. The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia under ambient and elevated ocean temperatures

    Directory of Open Access Journals (Sweden)

    Rael Horwitz

    2017-02-01

    Full Text Available Ocean warming represents a major threat to marine biota worldwide, and forecasting ecological ramifications is a high priority as atmospheric carbon dioxide (CO2 emissions continue to rise. Fitness of marine species relies critically on early developmental and reproductive stages, but their sensitivity to environmental stressors may be a bottleneck in future warming oceans. The present study focuses on the tropical sea hare, Stylocheilus striatus (Gastropoda: Opisthobranchia, a common species found throughout the Indo-West Pacific and Atlantic Oceans. Its ecological importance is well-established, particularly as a specialist grazer of the toxic cyanobacterium, Lyngbya majuscula. Although many aspects of its biology and ecology are well-known, description of its early developmental stages is lacking. First, a detailed account of this species’ life history is described, including reproductive behavior, egg mass characteristics and embryonic development phases. Key developmental features are then compared between embryos developed in present-day (ambient and predicted end-of-century elevated ocean temperatures (+3 °C. Results showed developmental stages of embryos reared at ambient temperature were typical of other opisthobranch species, with hatching of planktotrophic veligers occurring 4.5 days post-oviposition. However, development times significantly decreased under elevated temperature, with key embryonic features such as the velum, statocysts, operculum, eyespots and protoconch developing approximately 24 h earlier when compared to ambient temperature. Although veligers hatched one day earlier under elevated temperature, their shell size decreased by approximately 20%. Our findings highlight how an elevated thermal environment accelerates planktotrophic development of this important benthic invertebrate, possibly at the cost of reducing fitness and increasing mortality.

  15. Honey Bee Health: The Potential Role of Microbes

    Science.gov (United States)

    Microbes, are a diverse group of unicellular organisms that include bacteria, fungi, archaea, protists, and sometimes viruses. Bees carry a diverse assemblage of microbes (mostly bacteria and fungi). Very few are pathogenic; most microbes are likely commensal or even beneficial to the colony. Mic...

  16. Survey of Hawksbill Turtle (Eretmochelys imbricate Health Condition in Terms of Parasites and Microbes in Alas Purwo National Park, Indonesia

    Directory of Open Access Journals (Sweden)

    Qurrota A'yunin

    2017-07-01

    Full Text Available Indonesian waters have six types of turtles that can live, spawn and breed. Sea turtle conservation becomes an important and urgent program to be done in order to protect and save sea turtle population in Indonesia. One of the factors that most affect the turtle population is the cause of degradation of pathogenic factors. Alas Purwo National Park, East Java, there is some communities that have activities turtle conservation. Conservation is done by securing and protecting turtle eggs. Turtle eggs that have hatched are released into the sea once it is ready. This study aims was to determine the type of bacteria and fungi that infect hatchlings and environmental factors that influence. This research is descriptive method to Hawksbill turtle (Eretmochelys imbricate is by way of random sampling. Sampling of microbes in sea turtle was conducted using cotton swab method and then microbes was cultured and indentified in laboratory. The results showed The kind of parasites and microbes which were indentified in hatching and adult Hawksbill sea turtles were fungus with genus Aspergillus sp., Geotrichum sp., Fusarium sp., and Gliocladium sp. ; bacteria are Pseudomonas aeruginosa and Enterobacter cloaceae; and parasite is Chelonibia testudinaria barnacles.  The parameter average value of water in pond indicated 28.1 – 29.2°C for temperature, 32 - 34 ‰ for salinity, 7.78 – 8.2 for pH, and 3.86 – 4.21 mg/L for DO.

  17. Long-range transport of airborne microbes over the global tropical and subtropical ocean

    KAUST Repository

    Mayol, Eva; Arrieta, J M; Jimé nez, Maria A.; Martí nez-Asensio, Adriá n; Garcias Bonet, Neus; Dachs, Jordi; Gonzá lez-Gaya, Belé n; Royer, Sarah-J.; Bení tez-Barrios, Veró nica M.; Fraile-Nuez, Eugenio; Duarte, Carlos M.

    2017-01-01

    The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth's surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33-68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

  18. Long-range transport of airborne microbes over the global tropical and subtropical ocean

    KAUST Repository

    Mayol, Eva

    2017-07-28

    The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth\\'s surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33-68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

  19. Microbiological changes, shelf life and identification of initial and spoilage microbiota of sea bream fillets stored under various conditions using 16S rRNA gene analysis.

    Science.gov (United States)

    Parlapani, Foteini F; Kormas, Konstantinos Ar; Boziaris, Ioannis S

    2015-09-01

    Sea bream fillets are one of the most important value-added products of the seafood market. Fresh seafood spoils mainly owing to bacterial action. In this study an exploration of initial and spoilage microbiota of sea bream fillets stored under air and commercial modified atmosphere packaging (MAP) at 0 and 5 °C was conducted by 16S rRNA gene sequence analysis of isolates grown on plates. Sensory evaluation and enumeration of total viable counts and spoilage microorganisms were also conducted to determine shelf life and bacterial growth respectively. Different temperatures and atmospheres affected growth and synthesis of spoilage microbiota as well as shelf life. Shelf life under air at 0 and 5 °C was 14 and 5 days respectively, while under MAP it was 20 and 8 days respectively. Initial microbiota were dominated by Pseudomonas fluorescens, Psychrobacter and Macrococcus caseolyticus. Different temperatures and atmospheres affected the synthesis of spoilage microbiota. At the end of shelf life, different phylotypes of Pseudomonas closely related to Pseudomonas fragi were found to dominate in most cases, while Pseudomonas veronii dominated in fillets under MAP at 0 °C. Furthermore, in fillets under MAP at 5 °C, new dominant species such as Carnobacterium maltaromaticum, Carnobacterium divergens and Vagococcus fluvialis were revealed. Different temperature and atmospheric conditions affected bacterial growth, shelf life and the synthesis of spoilage microbiota. Molecular identification revealed species and strains of microorganisms that have not been reported before for sea bream fillets stored under various conditions, thus providing valuable information regarding microbiological spoilage. © 2014 Society of Chemical Industry.

  20. The Study of the Microbes Degraded Polystyrene

    Directory of Open Access Journals (Sweden)

    Zhi-Long Tang

    2017-01-01

    Full Text Available Under the observation that Tenebrio molitor and Zophobas morio could eat polystyrene (PS, we setup the platform to screen the gut microbes of these two worms. To take advantage of that Tenebrio molitor and Zophobas morio can eat and digest polystyrene as its diet, we analyzed these special microbes with PS plate and PS turbidity system with time courses. There were two strains TM1 and ZM1 which isolated from Tenebrio molitor and Zophobas morio, and were identified by 16S rDNA sequencing. The results showed that TM1 and ZM1 were cocci-like and short rod shape Gram-negative bacteria under microscope. The PS plate and turbidity assay showed that TM1 and ZM1 could utilize polystyrene as their carbon sources. The further study of PS degraded enzyme and cloning warrants our attention that this platform will be an excellent tools to explore and solve this problem.

  1. Engineering tailored nanoparticles with microbes: quo vadis?

    Science.gov (United States)

    Prasad, Ram; Pandey, Rishikesh; Barman, Ishan

    2016-01-01

    In the quest for less toxic and cleaner methods of nanomaterials production, recent developments in the biosynthesis of nanoparticles have underscored the important role of microorganisms. Their intrinsic ability to withstand variable extremes of temperature, pressure, and pH coupled with the minimal downstream processing requirements provide an attractive route for diverse applications. Yet, controlling the dispersity and facile tuning of the morphology of the nanoparticles of desired chemical compositions remains an ongoing challenge. In this Focus Review, we critically review the advances in nanoparticle synthesis using microbes, ranging from bacteria and fungi to viruses, and discuss new insights into the cellular mechanisms of such formation that may, in the near future, allow complete control over particle morphology and functionalization. In addition to serving as paradigms for cost-effective, biocompatible, and eco-friendly synthesis, microbes hold the promise for a unique template for synthesis of tailored nanoparticles targeted at therapeutic and diagnostic platform technologies. © 2015 Wiley Periodicals, Inc.

  2. Electrifying microbes for the production of chemicals

    Directory of Open Access Journals (Sweden)

    Pier-Luc eTremblay

    2015-03-01

    Full Text Available Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES is one of the bioelectrochemical approaches developed in the last decade that could have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind turbine or wastewater treatment processes. The net outcome is that renewable energy is stored in the covalent bonds of organic compounds synthesized from greenhouse gas. This review will discuss the future of MES and the challenges that lie ahead for its development into a mature technology.

  3. Electrifying microbes for the production of chemicals

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Zhang, Tian

    2015-01-01

    have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind......Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES) is one of the bioelectrochemical approaches developed in the last decade that could...... turbine, or wastewater treatment processes. The net outcome is that renewable energy is stored in the covalent bonds of organic compounds synthesized from greenhouse gas. This review will discuss the future of MES and the challenges that lie ahead for its development into a mature technology....

  4. Visualizing conserved gene location across microbe genomes

    Science.gov (United States)

    Shaw, Chris D.

    2009-01-01

    This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

  5. An Astrobiology Microbes Exhibit and Education Module

    Science.gov (United States)

    Lindstrom, Marilyn M.; Allen, Jaclyn S.; Stocco, Karen; Tobola, Kay; Olendzenski, Lorraine

    2001-01-01

    Telling the story of NASA-sponsored scientific research to the public in exhibits is best done by partnerships of scientists and museum professionals. Likewise, preparing classroom activities and training teachers to use them should be done by teams of teachers and scientists. Here we describe how we used such partnerships to develop a new astrobiology augmentation to the Microbes! traveling exhibit and a companion education module. "Additional information is contained in the original extended abstract."

  6. Dilution-to-extinction culturing of SAR11 members and other marine bacteria from the Red Sea

    KAUST Repository

    Mohamed, Roslinda B.

    2013-12-01

    Life in oceans originated about 3.5 billion years ago where microbes were the only life form for two thirds of the planet’s existence. Apart from being abundant and diverse, marine microbes are involved in nearly all biogeochemical processes and are vital to sustain all life forms. With the overgrowing number of data arising from culture-independent studies, it became necessary to improve culturing techniques in order to obtain pure cultures of the environmentally significant bacteria to back up the findings and test hypotheses. Particularly in the ultra-oligotrophic Red Sea, the ubiquitous SAR11 bacteria has been reported to account for more than half of the surface bacterioplankton community. It is therefore highly likely that SAR11, and other microbial life that exists have developed special adaptations that enabled them to thrive successfully. Advances in conventional culturing have made it possible for abundant, unculturable marine bacteria to be grown in the lab. In this study, we analyzed the effectiveness of the media LNHM and AMS1 in isolating marine bacteria from the Red Sea, particularly members of the SAR11 clade. SAR11 strains obtained from this study AMS1, and belonged to subgroup 1a and phylotype 1a.3. We also obtained other interesting strains which should be followed up with in the future. In the long run, results from this study will enhance our knowledge of the pelagic ecosystem and allow the impacts of rising temperatures on marine life to be understood.

  7. Engineered microbes and methods for microbial oil production

    Energy Technology Data Exchange (ETDEWEB)

    Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

    2018-01-09

    Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

  8. Engineered microbes and methods for microbial oil production

    Science.gov (United States)

    Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

    2015-02-10

    Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

  9. Planetary protection protecting earth and planets against alien microbes

    International Nuclear Information System (INIS)

    Leys, N.

    2006-01-01

    Protecting Earth and planets against the invasion of 'alien life forms' is not military science fiction, but it is the peaceful daily job of engineers and scientists of space agencies. 'Planetary Protection' is preventing microbial contamination of both the target planet and the Earth when sending robots on interplanetary space mission. It is important to preserve the 'natural' conditions of other planets and to not bring with robots 'earthly microbes' (forward contamination) when looking for 'spores of extra terrestrial life'. The Earth and its biosphere must be protected from potential extraterrestrial biological contamination when returning samples of other planets to the Earth (backward contamination). The NASA-Caltech Laboratory for Planetary Protection of Dr. Kasthuri Venkateswaran at the Jet Propulsion Laboratory (JPL) (California, USA) routinely monitors and characterizes the microbes of NASA spacecraft assembly rooms and space robots prior to flight. They have repeatedly isolated Cupriavidus and Ralstonia strains pre-flight from spacecraft assembly rooms (floor and air) and surfaces of space robots such as the Mars Odyssey Orbiter (La Duc et al., 2003). Cupriavidus and Ralstonia strains have also been found in-flight, in ISS cooling water and Shuttle drinking water (Venkateswaran et al., Pyle et al., Ott et al., all unpublished). The main objective of this study is to characterise the Cupriavidus and Ralstonia strains isolated at JPL and compare them to the Cupriavidus metallidurans CH34T model strain, isolated from a Belgian contaminated soil and studied since 25 years at SCK-CEN and to enhance our knowledge by performing additional tests at JPL and gathering information regarding the environmental conditions and the cleaning and isolation methods used in such spacecraft assembling facilities

  10. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

    KAUST Repository

    Bang, Corinna

    2018-02-15

    From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.

  11. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

    KAUST Repository

    Bang, Corinna; Dagan, Tal; Deines, Peter; Dubilier, Nicole; Duschl, Wolfgang J.; Fraune, Sebastian; Hentschel, Ute; Hirt, Heribert; Hü lter, Nils; Lachnit, Tim; Picazo, Devani; Pita, Lucia; Pogoreutz, Claudia; Radecker, Nils; Saad, Maged; Schmitz, Ruth A.; Schulenburg, Hinrich; Voolstra, Christian R.; Weiland-Brä uer, Nancy; Ziegler, Maren; Bosch, Thomas C.G.

    2018-01-01

    From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.

  12. Potential Evaporite Biomarkers from the Dead Sea

    Science.gov (United States)

    Morris, Penny A.; Wentworth, Susan J.; Thomas-Keprta, Kathie; Allen, Carlton C.; McKay, David S.

    2001-01-01

    The Dead Sea is located on the northern branch of the African-Levant Rift systems. The rift system, according to one model, was formed by a series of strike slip faults, initially forming approximately two million years ago. The Dead Sea is an evaporite basin that receives freshwater from springs and from the Jordan River. The Dead Sea is different from other evaporite basins, such as the Great Salt Lake, in that it possesses high concentrations of magnesium and has an average pH of 6.1. The dominant cation in the Great Salt Lake is sodium, and the pH is 7.7. Calcium concentrations are also higher in the Dead Sea than in the Great Salt Lake. Both basins are similar in that the dominant anion is chlorine and the salinity levels are approximately 20 %. Other common cations that have been identified from the waters of the Dead Sea and the Great Salt Lake include sodium and potassium. A variety of Archea, Bacteria, and a single genus of a green algal, Dunaliella, has been described from the Dead Sea. Earlier studies concentrated on microbial identification and analysis of their unique physiology that allows them to survive in this type of extreme environment. Potential microbial fossilization processes, microbial fossils, and the metallic ions associated with fossilization have not been studied thoroughly. The present study is restricted to identifying probable microbial morphologies and associated metallic ions. XRD (X Ray Diffraction) analysis indicates the presence of halite, quartz, and orthoclase feldspar. In addition to these minerals, other workers have reported potassium chloride, magnesium bromide, magnesium chloride, calcium chloride, and calcium sulfate. Halite, calcium sulfate, and orthoclase were examined in this report for the presence of microbes, microbially induced deposits or microbial alteration. Neither the gypsum nor the orthoclase surfaces possesses any obvious indications of microbial life or fossilization. The sand-sized orthoclase particles are

  13. Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea.

    Science.gov (United States)

    Johannesson, Kerstin; André, Carl

    2006-07-01

    Marginal populations are often isolated and under extreme selection pressures resulting in anomalous genetics. Consequently, ecosystems that are geographically and ecologically marginal might have a large share of genetically atypical populations, in need of particular concern in management of these ecosystems. To test this prediction, we analysed genetic data from 29 species inhabiting the low saline Baltic Sea, a geographically and ecologically marginal ecosystem. On average Baltic populations had lost genetic diversity compared to Atlantic populations: a pattern unrelated to dispersal capacity, generation time of species and taxonomic group of organism, but strongly related to type of genetic marker (mitochondrial DNA loci had lost c. 50% diversity, and nuclear loci 10%). Analyses of genetic isolation by geographic distance revealed clinal patterns of differentiation between Baltic and Atlantic regions. For a majority of species, clines were sigmoid with a sharp slope around the Baltic Sea entrance, indicating impeded gene flows between Baltic and Atlantic populations. Some species showed signs of allele frequencies being perturbed at the edge of their distribution inside the Baltic Sea. Despite the short geological history of the Baltic Sea (8000 years), populations inhabiting the Baltic have evolved substantially different from Atlantic populations, probably as a consequence of isolation and bottlenecks, as well as selection on adaptive traits. In addition, the Baltic Sea also acts a refuge for unique evolutionary lineages. This marginal ecosystem is thus vulnerable but also exceedingly valuable, housing unique genes, genotypes and populations that constitute an important genetic resource for management and conservation.

  14. Roles and Importance of Microbes in the Radioactive Waste Disposal

    International Nuclear Information System (INIS)

    Baik, Min Hoon; Lee, Seung Yeop; Roh, Yeol

    2009-01-01

    Recently the importance and interest for the microbes has been increased because several important results for the effects of microbes on the radioactive waste disposal have been published continuously. In this study, research status and major results on the various roles and effects of microbes in the radioactive waste disposal have been investigated. We investigated and summarized the roles and major results of microbes in a multi-barrier system consisting of an engineered barrier and a natural barrier which is considered in radioactive waste disposal systems. For the engineered barrier, we discussed about the effects of microbes on the corrosion of a waste container and investigated the survival possibility and roles of microbes in a compacted bentonite buffer. For the natural barrier, the roles of microbes present in groundwaters and rocks were discussed and summarized with major results from natural analogue studies. Furthermore, we investigated and summarized the roles and various interactions processes of microbes and their effects on the radionuclide migration and retardation including recent research status. Therefore, it is expected that the effects and roles of microbes on the radioactive waste disposal can be rigorously evaluated if further researches are carried out for a long-term behavior of the disposal system in the deep geological environments and for the effects of microbes on the radionuclide migration through geological media.

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

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry

    2007-12-31

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

  16. Modelling the beginning and end of a planktonic life stage — the distribution of cod eggs and settled juveniles in the North Sea

    DEFF Research Database (Denmark)

    Höffle, Hannes; Munk, Peter

    2012-01-01

    distribution of haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), and plaice (Pleuronectes platessa). Findings indicated that in the egg stage, the environment is more important for the probability of occurrence, while abundance is more under the control of spatial dependency. Modelling......The North Sea cod stock is close to the southern limit of the species’ range. Therefore, it might be vulnerable to future climate change. Direct as well as indirect effects of climate forcing may have the greatest effects on early life stages. Here we present a study on the distribution of cod...

  17. Investigating Microbe-Mineral Interactions: Recent Advances in X-Ray and Electron Microscopy and Redox-Sensitive Methods

    Science.gov (United States)

    Miot, Jennyfer; Benzerara, Karim; Kappler, Andreas

    2014-05-01

    Microbe-mineral interactions occur in diverse modern environments, from the deep sea and subsurface rocks to soils and surface aquatic environments. They may have played a central role in the geochemical cycling of major (e.g., C, Fe, Ca, Mn, S, P) and trace (e.g., Ni, Mo, As, Cr) elements over Earth's history. Such interactions include electron transfer at the microbe-mineral interface that left traces in the rock record. Geomicrobiology consists in studying interactions at these organic-mineral interfaces in modern samples and looking for traces of past microbe-mineral interactions recorded in ancient rocks. Specific tools are required to probe these interfaces and to understand the mechanisms of interaction between microbes and minerals from the scale of the biofilm to the nanometer scale. In this review, we focus on recent advances in electron microscopy, in particular in cryoelectron microscopy, and on a panel of electrochemical and synchrotron-based methods that have recently provided new understanding and imaging of the microbe-mineral interface, ultimately opening new fields to be explored.

  18. Endogenous System Microbes as Treatment Process ...

    Science.gov (United States)

    Monitoring the efficacy of treatment strategies to remove pathogens in decentralized systems remains a challenge. Evaluating log reduction targets by measuring pathogen levels is hampered by their sporadic and low occurrence rates. Fecal indicator bacteria are used in centralized systems to indicate the presence of fecal pathogens, but are ineffective decentralized treatment process indicators as they generally occur at levels too low to assess log reduction targets. System challenge testing by spiking with high loads of fecal indicator organisms, like MS2 coliphage, has limitations, especially for large systems. Microbes that are endogenous to the decentralized system, occur in high abundances and mimic removal rates of bacterial, viral and/or parasitic protozoan pathogens during treatment could serve as alternative treatment process indicators to verify log reduction targets. To identify abundant microbes in wastewater, the bacterial and viral communities were examined using deep sequencing. Building infrastructure-associated bacteria, like Zoogloea, were observed as dominant members of the bacterial community in graywater. In blackwater, bacteriophage of the order Caudovirales constituted the majority of contiguous sequences from the viral community. This study identifies candidate treatment process indicators in decentralized systems that could be used to verify log removal during treatment. The association of the presence of treatment process indic

  19. Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that 'everything is not everywhere'.

    Science.gov (United States)

    Rout, Marnie E; Callaway, Ragan M

    2012-07-01

    The study of soil biota in the context of exotic plant invasions has led to an explosion in our understanding of the ecological roles of many different groups of microbes that function in roots or at the root-soil interface. Part of this progress has been the emergence of two biogeographic patterns involving invasive plants and soil microbes. First, in their non-native ranges invasive plants commonly interact differently with the same soil microbes than native plants. Second, in their native ranges, plants that are invasive elsewhere commonly interact functionally with soil microbes differently in their home ranges than they do in their non-native ranges. These studies pose a challenge to a long-held paradigm about microbial biogeography - the idea that microbes are not limited by dispersal and are thus free from the basic taxonomic, biogeographical and evolutionary framework that characterizes all other life on Earth. As an analogy, the global distribution of animals that function as carnivores does not negate the fascinating evolutionary biogeographic patterns of carnivores. Other challenges to this notion come from new measurements of genetic differences among microbes across geographic boundaries, which also suggest that meaningful biogeographic patterns exist for microorganisms. We expand this discussion of whether or not 'everything is everywhere' by using the inherently biogeographic context of plant invasions by reviewing the literature on interactions among invasive plants and the microorganisms in the rhizosphere. We find that these interactions can be delineated at multiple scales: from individual plants to continents. Thus the microbes that regulate major aspects of plant biology do not appear to be exempt from the fundamental evolutionary processes of geographical isolation and natural selection. At the important scales of taxonomy, ecotype and ecosystem functions, the fundamental ecology of invaders and soil microbes indicates that everything might

  20. New CRISPR-Cas systems from uncultivated microbes

    Science.gov (United States)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2017-02-01

    CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  1. Seasonal and life-phase related differences in growth in Scarus ferrugineus on a southern Red Sea fringing reef

    NARCIS (Netherlands)

    Afeworki, Y.; Videler, J. J.; Berhane, Y. H.; Bruggemann, J. H.

    Temporal trends in growth of the rusty parrotfish Scarus ferrugineus were studied on a southern Red Sea fringing reef that experiences seasonal changes in environmental conditions and benthic algal resources. Length increment data from tagging and recapture were compared among periods and sexes and

  2. Husbandry streaa during early life stages affects the stress response and health status of juvenile sea bass, Dicentrarchus labrax.

    NARCIS (Netherlands)

    Varsamos, S.; Flik, G.; Pepin, S.E.; Wendelaar Bonga, S.E.; Breuil, G.

    2006-01-01

    Abstract In aquaculture management it is important to establish objective criteria to assess health and welfare of the fish. Here we show that European sea bass (Dicentrarchus labrax) confronted with husbandry-associated stress (tank cleaning, i.e. scrubbing, and water temperature variation) during

  3. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin

    DEFF Research Database (Denmark)

    Inagaki, F.; Nunoura, T.; Nakagawa, S.

    2006-01-01

    The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes and their ......The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes...... of the uncultivated Deep-Sea Archaeal Group were consistently the dominant phylotype in sediments associated with methane hydrate. Sediment cores lacking methane hydrates displayed few or no Deep-Sea Archaeal Group phylotypes. Bacterial communities in the methane hydrate-bearing sediments were dominated by members...

  4. Comparative metagenomics of the Red Sea

    KAUST Repository

    Mineta, Katsuhiko

    2016-01-26

    Metagenome produces a tremendous amount of data that comes from the organisms living in the environments. This big data enables us to examine not only microbial genes but also the community structure, interaction and adaptation mechanisms at the specific location and condition. The Red Sea has several unique characteristics such as high salinity, high temperature and low nutrition. These features must contribute to form the unique microbial community during the evolutionary process. Since 2014, we started monthly samplings of the metagenomes in the Red Sea under KAUST-CCF project. In collaboration with Kitasato University, we also collected the metagenome data from the ocean in Japan, which shows contrasting features to the Red Sea. Therefore, the comparative metagenomics of those data provides a comprehensive view of the Red Sea microbes, leading to identify key microbes, genes and networks related to those environmental differences.

  5. Indoor Air '93. Particles, microbes, radon

    International Nuclear Information System (INIS)

    Kalliokoski, P.; Jantunen, M.; Seppaenen, O.

    1993-01-01

    The conference was held in Helsinki, Finland, July 4-8, 1993. The proceedings of the conference were published in 6 volumes. The main topics of the volume 5 are: (1) particles, fibers and dust - their concentrations and sources in buildings, (2) Health effects of particles, (3) Need of asbestos replacement and encapsulation, (4) Seasonal and temporal variation of fungal and bacterial concentration, (5) The evaluation of microbial contamination of buildings, (6) New methods and comparison of different methods for microbial sampling and evaluation, (7) Microbes in building materials and HVAC-systems, (8) Prevention of microbial contamination in buildings, (9) Dealing with house dust mites, (10) Radon measurements and surveys in different countries, (11) The identification of homes with high radon levels, (12) The measurement methods and prediction of radon levels in buildings, and (13) Prevention of radon penetration from the soil

  6. The elemental composition of purple sea urchin (Strongylocentrotus purpuratus) calcite and potential effects of pCO2 during early life stages

    Science.gov (United States)

    LaVigne, M.; Hill, T. M.; Sanford, E.; Gaylord, B.; Russell, A. D.; Lenz, E. A.; Hosfelt, J. D.; Young, M. K.

    2013-06-01

    Ocean acidification will likely have negative impacts on invertebrates producing skeletons composed of calcium carbonate. Skeletal solubility is partly controlled by the incorporation of "foreign" ions (e.g. magnesium) into the crystal lattice of these skeletal structures, a process that is sensitive to a variety of biological and environmental factors. Here we explore effects of life stage, oceanographic region of origin, and changes in the partial pressure of carbon dioxide in seawater (pCO2) on trace elemental composition in the purple sea urchin (Strongylocentrotus purpuratus). We show that, similar to other urchin taxa, adult purple sea urchins have the ability to precipitate skeleton composed of a range of biominerals spanning low- to high-Mg calcites. Mg / Ca and Sr / Ca ratios were substantially lower in adult spines compared to adult tests. On the other hand, trace elemental composition was invariant among adults collected from four oceanographically distinct regions spanning a range of carbonate chemistry conditions (Oregon, Northern California, Central California, and Southern California). Skeletons of newly settled juvenile urchins that originated from adults from the four regions exhibited intermediate Mg / Ca and Sr / Ca between adult spine and test endmembers, indicating that skeleton precipitated during early life stages is more soluble than adult spines and less soluble than adult tests. Mean skeletal Mg / Ca or Sr / Ca of juvenile skeleton did not vary with source region when larvae were reared under present-day, global-average seawater carbonate conditions (400 μatm; pHT = 8.02 ± 0.03 1 SD; Ωcalcite = 3.3 ± 0.2 1 SD). However, when reared under elevated pCO2 (900 μatm; pHT = 7.73 ± 0.03; Ωcalcite = 1.8 ± 0.1), skeletal Sr / Ca in juveniles exhibited increased variance across the four regions. Although larvae from the northern populations (Oregon, Northern California, Central California) did not exhibit differences in Mg or Sr

  7. The elemental composition of purple sea urchin (Strongylocentrotus purpuratus calcite and potential effects of pCO2 during early life stages

    Directory of Open Access Journals (Sweden)

    M. LaVigne

    2013-06-01

    Full Text Available Ocean acidification will likely have negative impacts on invertebrates producing skeletons composed of calcium carbonate. Skeletal solubility is partly controlled by the incorporation of "foreign" ions (e.g. magnesium into the crystal lattice of these skeletal structures, a process that is sensitive to a variety of biological and environmental factors. Here we explore effects of life stage, oceanographic region of origin, and changes in the partial pressure of carbon dioxide in seawater (pCO2 on trace elemental composition in the purple sea urchin (Strongylocentrotus purpuratus. We show that, similar to other urchin taxa, adult purple sea urchins have the ability to precipitate skeleton composed of a range of biominerals spanning low- to high-Mg calcites. Mg / Ca and Sr / Ca ratios were substantially lower in adult spines compared to adult tests. On the other hand, trace elemental composition was invariant among adults collected from four oceanographically distinct regions spanning a range of carbonate chemistry conditions (Oregon, Northern California, Central California, and Southern California. Skeletons of newly settled juvenile urchins that originated from adults from the four regions exhibited intermediate Mg / Ca and Sr / Ca between adult spine and test endmembers, indicating that skeleton precipitated during early life stages is more soluble than adult spines and less soluble than adult tests. Mean skeletal Mg / Ca or Sr / Ca of juvenile skeleton did not vary with source region when larvae were reared under present-day, global-average seawater carbonate conditions (400 μatm; pHT = 8.02 ± 0.03 1 SD; Ωcalcite = 3.3 ± 0.2 1 SD. However, when reared under elevated pCO2 (900 μatm; pHT = 7.73 ± 0.03; Ωcalcite = 1.8 ± 0.1, skeletal Sr / Ca in juveniles exhibited increased variance across the four regions. Although larvae from the northern populations (Oregon, Northern California, Central California did not exhibit differences in Mg or Sr

  8. Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

    International Nuclear Information System (INIS)

    Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J.; Brey, R.F.; Wright, R.N.; Windes, W.F.

    1999-01-01

    Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10 3 and 6 x 10 4 rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10 4 rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10 5 rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance

  9. Why microbes will rule the world – and our industries

    DEFF Research Database (Denmark)

    Lykke, Anne Wärme; Palsson, Bernhard; Nielsen, Jens

    2017-01-01

    Microbes have ruled the world for approximately 4 billion years. But the future actually depends on their dominance, some would argue. Why? Because microbes, as well as mammalian cells, can be engineered into producing high-value chemicals and medicine. Therefore, scientists at The Novo Nordisk...... Foundation Center for Biosustainability are hard at work developing cell factories to benefit us all....

  10. Microbes as interesting source of novel insecticides: A review ...

    African Journals Online (AJOL)

    ... strains with good insecticidal properties can be identified, evaluated and utilized for pest control. This paper reviews the insecticidal properties of microbes and their potential utility in pest management. Keywords: Microbes, insecticides, metabolites, pest management. African Journal of Biotechnology, Vol 13(26) 2582- ...

  11. Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

    Energy Technology Data Exchange (ETDEWEB)

    Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J. [INEEL (US); Brey, R.F. [ISU (US); Wright, R.N.; Windes, W.F.

    1999-09-03

    Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.

  12. Microbes, Minerals and Electrodes at the Sanford Underground Research Facility (SURF): Electrochemistry 4100 ft below the surface.

    Science.gov (United States)

    Rowe, A. R.; Abuyen, K.; Casar, C. P.; Osburn, M. R.; Kruger, B.; El-Naggar, M.; Amend, J.

    2017-12-01

    Little is known about the importance of mineral oxidation processes in subsurface environments. This stems, in part from our limited insight into the biochemistry of many of these metabolisms, especially where redox interactions with solid surfaces is concerned. To this aim, we have been developing electrochemical cultivation techniques, to target enrichment and isolation of microbes capable of oxidative extracellular electron transfer (oxEET)—transfer of electrons from the exterior of the cell to the interior. Our previous worked focused on marine sediments; using an electrode poised at a given redox potential to isolate mineral-oxidizing microbes. Electrode oxidizing microbes isolated from these enrichments belong to the genera Thioclava, Marinobacter, Halomonas, Idiomarina, Thalassospira, and Pseudamonas; organisms commonly detected in marine and deep sea sediments but not generally associated with mineral, sulfur and/or iron oxidation. At the Sanford Underground Research Facility (SURF) in Leed, South Dakota, we have been utilizing similar electrocultivation techniques to understand: 1) the potential for mineral oxidation by subsurface microbes, 2) their selective colonization on mineral vs. electrode surfaces, as well as 3) the community composition of microbes capable of these metabolic interactions. An electrochemical and mineral enrichment scheme was designed and installed into a sulfidic groundwater flow, located at the 4100 ft level of the former gold mine. The communities enriched on electrodes (graphite and indium tin oxide coated glass) and minerals (sulfur, pyrite, and schists from the location) were compared to the long-term ground water microbial community observed. Ultimately, these observations will help inform the potential activity of a lithotrophic microbes in situ and will in turn guide our culturing efforts.

  13. Colonial life under the Humboldt Current System: deep-sea corals from O'Higgins I seamount

    OpenAIRE

    Cañete,Juan I; Haussermann,Verena

    2012-01-01

    A benthic community constituted by an assemblage of at least four species of deep-sea corals collected in only one trawl carried-out on the summit of the O'Higgins I seamount, central Chile. The corals were collected in only one trawl carried-out during a Chilean-Japanese cruise onboard the R/V" Koyo Maru" in December 29, 2004. Presence of oxygenated and cold Antarctic Intermediate Water (>400 m depth) on the plateau was recorded under of the Equatorial Subsurface Water associated to the o...

  14. Colonial life under the Humboldt Current System: deep-sea corals from O'Higgins I seamount

    OpenAIRE

    Cañete, Juan I; Haussermann, Verena

    2012-01-01

    A benthic community constituted by an assemblage of at least four species of deep-sea corals collected in only one trawl carried-out on the summit of the O'Higgins I seamount, central Chile. The corals were collected in only one trawl carried-out during a Chilean-Japanese cruise onboard the R/V" Koyo Maru" in December 29, 2004. Presence of oxygenated and cold Antarctic Intermediate Water (>400 m depth) on the plateau was recorded under of the Equatorial Subsurface Water associated to the oxyg...

  15. Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea

    KAUST Repository

    Pascual, Marta; Rives, Borja; Schunter, Celia Marei; Macpherson, Enrique

    2017-01-01

    . We assessed the relevance of seven major oceanographic fronts on species connectivity while considering their dispersal capacity and life strategy.We systematically reviewed the scientific articles reporting population genetic differentiation along

  16. Taxonomy of the early life stages of arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni) in the eastern Bering Sea, with notes on distribution and condition

    Science.gov (United States)

    De Forest, Lisa; Duffy-Anderson, J. T.; Heintz, R. A.; Matarese, A. C.; Siddon, E. C.; Smart, T. I.; Spies, I. B.

    2014-11-01

    Arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni) are closely related flatfish species that co-occur in the eastern Bering Sea. As adults, arrowtooth flounder can be distinguished from Kamchatka flounder; however, larvae and early juveniles can only be indentified to the genus level due to morphological similarities. This has precluded studies of ecology for the early life stages of both species in the eastern Bering Sea. In this study, we developed a genetic technique to identify the larvae and early juveniles of the two species using mtDNA cytochrome oxidase subunit I (COI). Genetically identified specimens were then examined to determine a visual identification method based on pigment patterns and morphology. Specimens 6.0-12.0 mm SL and≥18.0 mm SL can be identified to the species level, but species identification of individuals 12.1-17.9 mm SL by visual means alone remains elusive. The distribution of larvae (<25.0 mm SL) of both arrowtooth flounder and Kamchatka flounder is similar in the eastern Bering Sea; however, juvenile (≥25.0 mm SL) Kamchatka flounder occur closer to the shelf break and in deeper water than juvenile arrowtooth flounder. Condition was determined for larvae and juveniles of each species by analyzing lipid content (%) and energy density (kJ/g dry mass). Kamchatka flounder larvae on average had higher lipid content than arrowtooth flounder larvae, but were also larger on average than arrowtooth flounder larvae in the summer. When corrected for length, both species had similar lipid content in the larval and juvenile stages.

  17. Life history inhomogeneity in Baltic Sea whitefish populations revealed by otolith strontium signatures – identification of stocked fish

    Directory of Open Access Journals (Sweden)

    Henry Hägerstrand

    2015-11-01

    The strontium concentrations in the otolith cores of whitefish from River Tornionjoki were higher than that of the four otoliths with low core strontium from fishes caught at sea (Table 1. Supposing that this latter group represent stocked fish raised in freshwater ponds, the vast majority of River Tornionjoki whitefish is naturally reproduced fish. This is plausible because in River Tornionjoki, the major whitefish spawning river in Finland, no larger stocking have been made since 1990s (Jokikokko and Huhmarniemi 2014. In conclusion, the concentration of otolith core strontium differs in whitefish hatched in fresh-water and in whitefish hatched in river water or in brackish Baltic Sea water. This difference can be used to reveal stocked whitefish. Barium concentration may be an even better indicator in this respect than strontium, as previous results indicate (Hägerstrand et al., 2015. Stocked river spawning whitefish appear in large amount at the southern feeding grounds around the Åland Islands, as already indicated by e.g. Leskelä et al. (2009.

  18. Impacts of ocean acidification on sea urchin growth across the juvenile to mature adult life-stage transition is mitigated by warming.

    Science.gov (United States)

    Dworjanyn, Symon A; Byrne, Maria

    2018-04-11

    Understanding how growth trajectories of calcifying invertebrates are affected by changing climate requires acclimation experiments that follow development across life-history transitions. In a long-term acclimation study, the effects of increased acidification and temperature on survival and growth of the tropical sea urchin Tripneustes gratilla from the early juvenile (5 mm test diameter-TD) through the developmental transition to the mature adult (60 mm TD) were investigated. Juveniles were reared in a combination of three temperature and three pH/ p CO 2 treatments, including treatments commensurate with global change projections. Elevated temperature and p CO 2 /pH both affected growth, but there was no interaction between these factors. The urchins grew more slowly at pH 7.6, but not at pH 7.8. Slow growth may be influenced by the inability to compensate coelomic fluid acid-base balance at pH 7.6. Growth was faster at +3 and +6°C compared to that in ambient temperature. Acidification and warming had strong and interactive effects on reproductive potential. Warming increased the gonad index, but acidification decreased it. At pH 7.6 there were virtually no gonads in any urchins regardless of temperature. The T. gratilla were larger at maturity under combined near-future warming and acidification scenarios (+3°C/pH 7.8). Although the juveniles grew and survived in near-future warming and acidification conditions, chronic exposure to these stressors from an early stage altered allocation to somatic and gonad growth. In the absence of phenotypic adjustment, the interactive effects of warming and acidification on the benthic life phases of sea urchins may compromise reproductive fitness and population maintenance as global climatic change unfolds. © 2018 The Author(s).

  19. Gut-associated microbes of Drosophila melanogaster

    Science.gov (United States)

    Broderick, Nichole; Lemaitre, Bruno

    2012-01-01

    There is growing interest in using Drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. In addition to the many genetic resources and tools Drosophila provides, its associated microbiota is relatively simple (1–30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). These attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur between a host and its microbiota. In this review, we summarize what is known regarding the composition of gut-associated microbes of Drosophila and their impact on host physiology. We also discuss these interactions in the context of their natural history and ecology and describe some recent insights into mechanisms by which Drosophila and its gut microbiota interact. “Workers with Drosophila have been considered fortunate in that they deal with the first multicellular invertebrate to be cultured monoxenically (Delcourt and Guyenot, 1910); the first to be handled axenically on a semisynthetic diet (Guyenot, 1917); and the first to be grown on a defined diet (Schultz et al., 1946). This list of advantages is somewhat embarrassing, since it implies an interest in nutrition that, in reality, was only secondary. The very first studies were concerned with the reduction of variability in genetic experiments (Delcourt and Guyenot, 1910) and standardization of the nutritional environment.” -James Sang, 1959 Ann NY Acad 1 PMID:22572876

  20. Acetaldehyde production by major oral microbes.

    Science.gov (United States)

    Moritani, K; Takeshita, T; Shibata, Y; Ninomiya, T; Kiyohara, Y; Yamashita, Y

    2015-09-01

    To assess acetaldehyde (ACH) production by bacteria constituting the oral microbiota and the inhibitory effects of sugar alcohols on ACH production. The predominant bacterial components of the salivary microbiota of 166 orally healthy subjects were determined by barcoded pyrosequencing analysis of the 16S rRNA gene. Bacterial ACH production from ethanol or glucose was measured using gas chromatography. In addition, inhibition by four sugars and five sugar alcohols of ACH production was assayed. Forty-one species from 16 genera were selected as predominant and prevalent bacteria based on the following criteria: identification in ≥95% of the subjects, ≥1% of mean relative abundance or ≥5% of maximum relative abundance. All Neisseria species tested produced conspicuous amounts of ACH from ethanol, as did Rothia mucilaginosa, Streptococcus mitis and Prevotella histicola exhibited the ability to produce ACH. In addition, xylitol and sorbitol inhibited ACH production by Neisseria mucosa by more than 90%. The oral microbiota of orally healthy subjects comprises considerable amounts of bacteria possessing the ability to produce ACH, an oral carcinogen. Consumption of sugar alcohols may regulate ACH production by oral microbes. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Flowers and Wild Megachilid Bees Share Microbes.

    Science.gov (United States)

    McFrederick, Quinn S; Thomas, Jason M; Neff, John L; Vuong, Hoang Q; Russell, Kaleigh A; Hale, Amanda R; Mueller, Ulrich G

    2017-01-01

    Transmission pathways have fundamental influence on microbial symbiont persistence and evolution. For example, the core gut microbiome of honey bees is transmitted socially and via hive surfaces, but some non-core bacteria associated with honey bees are also found on flowers, and these bacteria may therefore be transmitted indirectly between bees via flowers. Here, we test whether multiple flower and wild megachilid bee species share microbes, which would suggest that flowers may act as hubs of microbial transmission. We sampled the microbiomes of flowers (either bagged to exclude bees or open to allow bee visitation), adults, and larvae of seven megachilid bee species and their pollen provisions. We found a Lactobacillus operational taxonomic unit (OTU) in all samples but in the highest relative and absolute abundances in adult and larval bee guts and pollen provisions. The presence of the same bacterial types in open and bagged flowers, pollen provisions, and bees supports the hypothesis that flowers act as hubs of transmission of these bacteria between bees. The presence of bee-associated bacteria in flowers that have not been visited by bees suggests that these bacteria may also be transmitted to flowers via plant surfaces, the air, or minute insect vectors such as thrips. Phylogenetic analyses of nearly full-length 16S rRNA gene sequences indicated that the Lactobacillus OTU dominating in flower- and megachilid-associated microbiomes is monophyletic, and we propose the name Lactobacillus micheneri sp. nov. for this bacterium.

  2. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Science.gov (United States)

    Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

  3. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

    Science.gov (United States)

    Osborn, A. Mark

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the

  4. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Directory of Open Access Journals (Sweden)

    Sonja Oberbeckmann

    Full Text Available Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate (PET drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates and diatoms (e.g. Coscinodiscophytina, Bacillariophytina. The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact

  5. Chemical signaling involved in plant-microbe interactions.

    Science.gov (United States)

    Chagas, Fernanda Oliveira; Pessotti, Rita de Cassia; Caraballo-Rodríguez, Andrés Mauricio; Pupo, Mônica Tallarico

    2018-03-05

    Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

  6. The smallest form of life yet?

    Indian Academy of Sciences (India)

    ously unsuspected form of life (Uwins et al 1998). Because it is so much ... Curiously, though, most living creatures appear to be microbes; and among microbes, prokaryotes (in- cluding both the ... Haldane J B S 1927 On being the right size; in Possible Worlds and Other Essays (London: Chatto and. Windus). Raup D M ...

  7. Environmental restoration using plant-microbe bioaugmentation

    International Nuclear Information System (INIS)

    Kingsley, M.T.; Fredrickson, J.K.; Metting, F.B.; Seidler, R.J.

    1993-04-01

    Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10 8 or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10 9 /g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PPO301/pRO101 and PPO301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation

  8. Remembering the Sea: Personal and Communal Recollections of Maritime Life in Jizan and the Farasan Islands, Saudi Arabia

    Science.gov (United States)

    Agius, Dionisius A.; Cooper, John P.; Semaan, Lucy; Zazzaro, Chiara; Carter, Robert

    2016-08-01

    People create narratives of their maritime past through the remembering and forgetting of seafaring experiences, and through the retention and disposal of maritime artefacts that function mnemonically to evoke or suppress those experiences. The sustenance and reproduction of the resulting narratives depends further on effective media of intergenerational transmission; otherwise, they are lost. Rapid socio-economic transformation across Saudi Arabia in the age of oil has disrupted longstanding seafaring economies in the Red Sea archipelago of the Farasan Islands, and the nearby mainland port of Jizan. Vestiges of wooden boatbuilding activity are few; long-distance dhow trade with South Asia, the Arabian-Persian Gulf and East Africa has ceased; and a once substantial pearling and nacre (mother of pearl) collection industry has dwindled to a tiny group of hobbyists: no youth dive today. This widespread withdrawal from seafaring activity among many people in these formerly maritime-oriented communities has diminished the salience of such activity in cultural memory, and has set in motion narrative creation processes, through which memories are filtered and selected, and objects preserved, discarded, or lost. This paper is a product of the encounter of the authors with keepers of maritime memories and objects in the Farasan Islands and Jizan. An older generation of men recall memories of their experiences as boat builders, captains, seafarers, pearl divers and fishermen. Their recounted memories are inscribed, and Arabic seafaring terms recorded. The extent of the retention of maritime material cultural items as memorials is also assessed, and the rôle of individual, communal and state actors in that retention is considered. Through this reflection, it becomes clear that the extra-biological memory and archive of the region's maritime past is sparse; that intergenerational transmission is failing; that the participation of state agencies in maritime heritage creation

  9. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution.

    Science.gov (United States)

    Gatheru Waigi, Michael; Sun, Kai; Gao, Yanzheng

    2017-09-01

    Soil pollution has become a major concern in various terrestrial ecosystems worldwide. One in situ soil bioremediation strategy that has gained popularity recently is microbe-assisted phytoremediation, which is promising for remediating pollutants. Sphingomonads, a versatile bacteria group comprising four well-known genera, are ubiquitous in vegetation grown in contaminated soils. These Gram-negative microbes have been investigated for their ability to induce innate plant growth-promoting (PGP) traits, including the formation of phytohormones, siderophores, and chelators, in addition to their evolutionary adaptations enabling biodegradation and microbe-assisted removal of contaminants. However, their capacity for bacterial-assisted phytoremediation has to date been undervalued. Here, we highlight the specific features, roles, advantages, and challenges associated with using sphingomonads in plant-microbe interactions, from the perspective of future phytotechnologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Scientists discover how deadly fungal microbes enter host cells

    OpenAIRE

    Whyte, Barry James

    2010-01-01

    A research team led by scientists at the Virginia Bioinformatics Institute at Virginia Tech has discovered a fundamental entry mechanism that allows dangerous fungal microbes to infect plants and cause disease.

  11. Volume 10 No. 11 November 2010 4340 SOIL MICROBE ...

    African Journals Online (AJOL)

    user

    2010-11-11

    Nov 11, 2010 ... SOIL MICROBE MEDIATED ZINC UPTAKE IN SOY BEAN: A REVIEW. Jefwa JM. 1* .... Porg, lipid Plp, high-energetic~P, sugar. Psuc and .... encouragement to prepare this presentation. ... Enviroquest Ltd Ontario, Canada.

  12. Anti-radiation microbe separated from traditional Chinese medicine

    International Nuclear Information System (INIS)

    Zou Zhaohui; Zhao Junqi; Deng Gangqiao; Wang Qian; Li Wenge; Peng Ling; Luo Zhiping

    2007-01-01

    One batch of Jinsuo pills, a kind of Chinese herbal medicine, treated by standardized irradiation process but failed to meet the sanitation requirement. Radiation resistant microbe was separated from the pills sample and the Gram stain showed positive, the colony of the microbe is milky white and concentric circle shape. It is observed as one of bacillus by microscope, its D 10 values in physiological saline and filter paper are 6.75 and 7.18 kGy, respectively. (authors)

  13. A Molecular Study of Microbe Transfer between Distant Environments

    OpenAIRE

    Hooper, Sean D.; Raes, Jeroen; Foerstner, Konrad U.; Harrington, Eoghan D.; Dalevi, Daniel; Bork, Peer

    2008-01-01

    BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecu...

  14. The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

    Science.gov (United States)

    Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E.

    2018-01-01

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe. PMID:29630066

  15. [Development of a microenvironment test chamber for airborne microbe research].

    Science.gov (United States)

    Zhan, Ningbo; Chen, Feng; Du, Yaohua; Cheng, Zhi; Li, Chenyu; Wu, Jinlong; Wu, Taihu

    2017-10-01

    One of the most important environmental cleanliness indicators is airborne microbe. However, the particularity of clean operating environment and controlled experimental environment often leads to the limitation of the airborne microbe research. This paper designed and implemented a microenvironment test chamber for airborne microbe research in normal test conditions. Numerical simulation by Fluent showed that airborne microbes were evenly dispersed in the upper part of test chamber, and had a bottom-up concentration growth distribution. According to the simulation results, the verification experiment was carried out by selecting 5 sampling points in different space positions in the test chamber. Experimental results showed that average particle concentrations of all sampling points reached 10 7 counts/m 3 after 5 minutes' distributing of Staphylococcus aureus , and all sampling points showed the accordant mapping of concentration distribution. The concentration of airborne microbe in the upper chamber was slightly higher than that in the middle chamber, and that was also slightly higher than that in the bottom chamber. It is consistent with the results of numerical simulation, and it proves that the system can be well used for airborne microbe research.

  16. Deep sea minerals prolong life span of streptozotocin-induced diabetic rats by compensatory augmentation of the IGF-I-survival signaling and inhibition of apoptosis.

    Science.gov (United States)

    Liao, Hung-En; Shibu, Marthandam Asokan; Kuo, Wei-Wen; Pai, Pei-Ying; Ho, Tsung-Jung; Kuo, Chia-Hua; Lin, Jing-Ying; Wen, Su-Ying; Viswanadha, Vijaya Padma; Huang, Chih-Yang

    2016-07-01

    Consumption of deep sea minerals (DSM), such as magnesium, calcium, and potassium, is known to reduce hypercholesterolemia-induced myocardial hypertrophy and cardiac-apoptosis and provide protection against cardiovascular diseases. Heart diseases develop as a lethal complication among diabetic patients usually due to hyperglycemia-induced cardiac-apoptosis that causes severe cardiac-damages, heart failure, and reduced life expectancy. In this study, we investigated the potential of DSM and its related cardio-protection to increase the life expectancy in diabetic rats. In this study, a heart failure rat model was developed by using streptozotocin (65 mg kg(-1) ) IP injection. Different doses of DSM-1× (37 mg kg(-1) day(-1) ), 2× (74 mg kg(-1) day(-1) ) and 3× (111 mg kg(-1) day(-1) ), were administered to the rats through gavages for 4 weeks. The positive effects of DSM on the survival rate of diabetes rats were determined with respect to the corresponding effects of MgSO4 . Further, to understand the mechanism by which DSM enhances the survival of diabetic rats, their potential to regulate cardiac-apoptosis and control cardiac-dysfunction were examined. Echocardiogram, tissue staining, TUNEL assay, and Western blotting assay were used to investigate modulations in the myocardial contractile function and related signaling protein expression. The results showed that DSM regulate apoptosis and complement the cardiomyocyte proliferation by enhancing survival mechanisms. Moreover DSM significantly reduced the mortality rate and enhanced the survival rate of diabetic rats. Experimental results show that DSM administration can be an effective strategy to improve the life expectancy of diabetic subjects by improving cardiac-cell proliferation and by controlling cardiac-apoptosis and associated cardiac-dysfunction. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 769-781, 2016. © 2015 Wiley Periodicals, Inc.

  17. Recent Research Status on the Microbes in the Radioactive Waste Disposal and Identification of Aerobic Microbes in a Groundwater Sampled from the KAERI Underground Research Tunnel(KURT)

    International Nuclear Information System (INIS)

    Baik, Min Hoon; Lee, Seung Yeop; Cho, Won Jin

    2006-11-01

    In this report, a comprehensive review on the research results and status for the various effects of microbes in the radioactive waste disposal including definition and classification of microbes, and researches related with the waste containers, engineered barriers, natural barriers, natural analogue studies, and radionuclide migration and retardation. Cultivation, isolation, and classification of aerobic microbes found in a groundwater sampled from the KAERI Underground Research Tunnel (KURT) located in the KAERI site have carried out and over 20 microbes were found to be present in the groundwater. Microbial identification by a 16S rDNA genetic analysis of the selected major 10 aerobic microbes was performed and the identified microbes were characterized

  18. The street children of Manila are affected by early-in-life periodontal infection: description of a treatment modality: sea salt.

    Science.gov (United States)

    Michel, J F; Michel, M G; Nadan, J; Nowzari, H

    2013-01-01

    Thousands of street children of Manila are affected by early-in-life oral infection. The aim of the present investigation was to evaluate the effectiveness of a sea-salt mouthrinse solution in street children of Manila affected by mild to severe forms of periodontal disease. These children were all in need of special protection: abandoned, abused, exploited, neglected, orphaned, poor. During 3 oral-health missions in 2003, 2004 and 2005, 617 abandoned children (5 to 13 year-old), received oral examination at a non-sectarian child-caring institution in Metro Manila (Virlanie Foundation) by calibrated examiners. A treatment based on what could be done was proposed: 1. Teaching of a precise tooth brushing technique with sea-salt, controlled and reinforced every two days for one week by calibrated health educators, 2. The application of sea-salt water mouthrinse (2.5 gram in 20 ml). Periodontal measurements were repeated at the end of each mission. All children returned to child-caring institution for the followup examinations. In 2003, 10 male and 11 female (n=21) were diagnosed with aggressive periodontitis. In 2009 and 2010, none was affected by aggressive periodontitis. For all patients, the gingival index decreased from 1.08 at the first mission to 1.04 at the end of the second mission and 0.98 at the end of the third mission. The periodontal index decreased from 1.33 at the first mission to 0.98 at the second mission and 0.92 at the last mission. The present investigation confirms that prevention and early diagnosis can result in success with minimum cost. The provided oral health program empowered street children in the most desperate circumstances to be educated and become self-reliant, independent, and responsible. We propose here an antimicrobial approach which has a high degree of efficacy and tolerability, and can be implemented in virtually all parts of the world using low-cost resources.

  19. Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites.

    Science.gov (United States)

    Mustafa, Ghada A; Abd-Elgawad, Amr; Abdel-Haleem, Alyaa M; Siam, Rania

    2014-01-01

    The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.-suggesting a "marine Vibrio phenomenon"; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites.

  20. Parameter Estimations of Dynamic Energy Budget (DEB Model over the Life History of a Key Antarctic Species: The Antarctic Sea Star Odontaster validus Koehler, 1906.

    Directory of Open Access Journals (Sweden)

    Antonio Agüera

    Full Text Available Marine organisms in Antarctica are adapted to an extreme ecosystem including extremely stable temperatures and strong seasonality due to changes in day length. It is now largely accepted that Southern Ocean organisms are particularly vulnerable to global warming with some regions already being challenged by a rapid increase of temperature. Climate change affects both the physical and biotic components of marine ecosystems and will have an impact on the distribution and population dynamics of Antarctic marine organisms. To predict and assess the effect of climate change on marine ecosystems a more comprehensive knowledge of the life history and physiology of key species is urgently needed. In this study we estimate the Dynamic Energy Budget (DEB model parameters for key benthic Antarctic species the sea star Odontaster validus using available information from literature and experiments. The DEB theory is unique in capturing the metabolic processes of an organism through its entire life cycle as a function of temperature and food availability. The DEB model allows for the inclusion of the different life history stages, and thus, becomes a tool that can be used to model lifetime feeding, growth, reproduction, and their responses to changes in biotic and abiotic conditions. The DEB model presented here includes the estimation of reproduction handling rules for the development of simultaneous oocyte cohorts within the gonad. Additionally it links the DEB model reserves to the pyloric caeca an organ whose function has long been ascribed to energy storage. Model parameters described a slowed down metabolism of long living animals that mature slowly. O. validus has a large reserve that-matching low maintenance costs- allow withstanding long periods of starvation. Gonad development is continuous and individual cohorts developed within the gonads grow in biomass following a power function of the age of the cohort. The DEB model developed here for O

  1. Explorative analysis of microbes, colloids and gases

    Energy Technology Data Exchange (ETDEWEB)

    Hallbeck, Lotta; Pedersen, Karsten (Microbial Analytics Sweden AB, Goeteborg (Sweden))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. In this report, part of the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on 2.2 data and complementary 2.3 data, was carried out during September 2006 to December 2007. This report focuses on microbiology, colloids and gases: - Microbes (Chapter 1): Several methods must be used to characterize active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of microorganisms. Different microbial groups influence the environment in different ways, depending on what metabolic group is dominant. Typically, the following redox couples are utilized by bacteria in granitic groundwater: H{sub 2}O/O{sub 2}, NO{sub 3}-/N{sub 2}, Mn2+/Mn(IV), Fe2+/Fe(III), S2-/SO{sub 4}2-, CH{sub 4}/CO{sub 2}, CH{sub 3}COOH/CO{sub 2}, and H{sub 2}/H+. The data will indicate the activity of specific microbial populations at particular sites and how they may affect the geochemistry. - Colloids (Chapter 2): Particles in the size range from 1 to 1x10-3 mum are regarded as colloids. Their small size prohibits them from settling, which gives them the

  2. Explorative analysis of microbes, colloids and gases

    International Nuclear Information System (INIS)

    Hallbeck, Lotta; Pedersen, Karsten

    2008-08-01

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. In this report, part of the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on 2.2 data and complementary 2.3 data, was carried out during September 2006 to December 2007. This report focuses on microbiology, colloids and gases: - Microbes (Chapter 1): Several methods must be used to characterize active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of microorganisms. Different microbial groups influence the environment in different ways, depending on what metabolic group is dominant. Typically, the following redox couples are utilized by bacteria in granitic groundwater: H 2 O/O 2 , NO 3 - /N 2 , Mn 2+ /Mn(IV), Fe 2+ /Fe(III), S 2- /SO 4 2- , CH 4 /CO 2 , CH 3 COOH/CO 2 , and H 2 /H + . The data will indicate the activity of specific microbial populations at particular sites and how they may affect the geochemistry. - Colloids (Chapter 2): Particles in the size range from 1 to 1x10 -3 μm are regarded as colloids. Their small size prohibits them from settling, which gives them the potential to transport

  3. Evolutionary adaptation in three-way interactions between plants, microbes and arthropods

    OpenAIRE

    Biere, A.; Tack, A.J.M.

    2013-01-01

    Evolutionary adaptations in interactions between plants, microbes and arthropods are generally studied in interactions that involve only two of these groups, that is, plants and microbes, plants and arthropods or arthropods and microbes. We review the accumulating evidence from a wide variety of systems, including plant- and arthropod-associated microbes, and symbionts as well as antagonists, that selection and adaptation in seemingly two-way interactions between plants and microbes, plants a...

  4. Divergent trends in life-history traits between Atlantic salmon Salmo salar of wild and hatchery origin in the Baltic Sea.

    Science.gov (United States)

    Vainikka, A; Kallio-Nyberg, I; Heino, M; Koljonen, M-L

    2010-02-01

    Four Atlantic salmon Salmo salar stocks in the Baltic Sea, varying in their breeding history, were studied for changes in life-history traits over the years 1972-1995. Total length (L(T)) at age of captured (L(TC)) fish had increased throughout the study period, partly due to increased temperature and increased L(T) at release, (L(TR)) but also due to remaining cohort effects that could represent unaccounted environmental or genetic change. Simultaneously, maturation probabilities controlled for water temperature, L(TC) and L(TR) had increased in all stocks. The least change was observed in the River Tornionjoki S. salar that was subject only to supportive stockings originating from wild parents. These results suggest a long-term divergence between semi-natural and broodstock-based S. salar stocks. Increased L(T) at age explained advanced maturation only marginally, and it remains an open question to what extent the generally increased probabilities to mature at early age reflected underlying genetic changes.

  5. Impacts of ocean acidification on early life-history stages and settlement of the coral-eating sea star Acanthaster planci.

    Science.gov (United States)

    Uthicke, Sven; Pecorino, Danilo; Albright, Rebecca; Negri, Andrew Peter; Cantin, Neal; Liddy, Michelle; Dworjanyn, Symon; Kamya, Pamela; Byrne, Maria; Lamare, Miles

    2013-01-01

    Coral reefs are marine biodiversity hotspots, but their existence is threatened by global change and local pressures such as land-runoff and overfishing. Population explosions of coral-eating crown of thorns sea stars (COTS) are a major contributor to recent decline in coral cover on the Great Barrier Reef. Here, we investigate how projected near-future ocean acidification (OA) conditions can affect early life history stages of COTS, by investigating important milestones including sperm motility, fertilisation rates, and larval development and settlement. OA (increased pCO2 to 900-1200 µatm pCO2) significantly reduced sperm motility and, to a lesser extent, velocity, which strongly reduced fertilization rates at environmentally relevant sperm concentrations. Normal development of 10 d old larvae was significantly lower under elevated pCO2 but larval size was not significantly different between treatments. Settlement of COTS larvae was significantly reduced on crustose coralline algae (known settlement inducers of COTS) that had been exposed to OA conditions for 85 d prior to settlement assays. Effect size analyses illustrated that reduced settlement may be the largest bottleneck for overall juvenile production. Results indicate that reductions in fertilisation and settlement success alone would reduce COTS population replenishment by over 50%. However, it is unlikely that this effect is sufficient to provide respite for corals from other negative anthropogenic impacts and direct stress from OA and warming on corals.

  6. Microfabricated microbial fuel cell arrays reveal electrochemically active microbes.

    Directory of Open Access Journals (Sweden)

    Huijie Hou

    Full Text Available Microbial fuel cells (MFCs are remarkable "green energy" devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.

  7. Natural antifouling compound production by microbes associated with marine macroorganisms — A review

    Directory of Open Access Journals (Sweden)

    Sathianeson Satheesh

    2016-05-01

    Full Text Available In the marine environment, all hard surfaces including marine macroorganims are colonized by microorganisms mainly from the surrounding environment. The microorganisms associated with marine macroorganisms offer tremendous potential for exploitation of bioactive metabolites. Biofouling is a continuous problem in marine sectors which needs huge economy for control and cleaning processes. Biotechnological way for searching natural product antifouling compounds gained momentum in recent years because of the environmental pollution associated with the use of toxic chemicals to control biofouling. While, natural product based antifoulants from marine organisms particularly sponges and corals attained significance due to their activities in field assays, collection of larger amount of organisms from the sea is not a viable one. The microorganisms associated with sponges, corals, ascidians, seaweeds and seagrasses showed strong antimicrobial and also antifouling activities. This review highlights the advances in natural product antifoulants research from microbes associated with marine organisms.

  8. Collaborative web-based annotation of video footage of deep-sea life, ecosystems and geological processes

    Science.gov (United States)

    Kottmann, R.; Ratmeyer, V.; Pop Ristov, A.; Boetius, A.

    2012-04-01

    More and more seagoing scientific expeditions use video-controlled research platforms such as Remote Operating Vehicles (ROV), Autonomous Underwater Vehicles (AUV), and towed camera systems. These produce many hours of video material which contains detailed and scientifically highly valuable footage of the biological, chemical, geological, and physical aspects of the oceans. Many of the videos contain unique observations of unknown life-forms which are rare, and which cannot be sampled and studied otherwise. To make such video material online accessible and to create a collaborative annotation environment the "Video Annotation and processing platform" (V-App) was developed. A first solely web-based installation for ROV videos is setup at the German Center for Marine Environmental Sciences (available at http://videolib.marum.de). It allows users to search and watch videos with a standard web browser based on the HTML5 standard. Moreover, V-App implements social web technologies allowing a distributed world-wide scientific community to collaboratively annotate videos anywhere at any time. It has several features fully implemented among which are: • User login system for fine grained permission and access control • Video watching • Video search using keywords, geographic position, depth and time range and any combination thereof • Video annotation organised in themes (tracks) such as biology and geology among others in standard or full screen mode • Annotation keyword management: Administrative users can add, delete, and update single keywords for annotation or upload sets of keywords from Excel-sheets • Download of products for scientific use This unique web application system helps making costly ROV videos online available (estimated cost range between 5.000 - 10.000 Euros per hour depending on the combination of ship and ROV). Moreover, with this system each expert annotation adds instantaneous available and valuable knowledge to otherwise uncharted

  9. Bioactive secondary metabolites from marine microbes for drug discovery.

    Science.gov (United States)

    Nikapitiya, Chamilani

    2012-01-01

    The isolation and extraction of novel bioactive secondary metabolites from marine microorganisms have a biomedical potential for future drug discovery as the oceans cover 70% of the planet's surface and life on earth originates from sea. Wide range of novel bioactive secondary metabolites exhibiting pharmacodynamic properties has been isolated from marine microorganisms and many to be discovered. The compounds isolated from marine organisms (macro and micro) are important in their natural form and also as templates for synthetic modifications for the treatments for variety of deadly to minor diseases. Many technical issues are yet to overcome before wide-scale bioprospecting of marine microorganisms becomes a reality. This chapter focuses on some novel secondary metabolites having antitumor, antivirus, enzyme inhibitor, and other bioactive properties identified and isolated from marine microorganisms including bacteria, actinomycetes, fungi, and cyanobacteria, which could serve as potentials for drug discovery after their clinical trials. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.

    Science.gov (United States)

    Lang, Jenna M; Eisen, Jonathan A; Zivkovic, Angela M

    2014-01-01

    Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories

  11. Microbial electrosynthesis: understanding and strengthening microbe-electrode interactions

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Höglund, Daniel; Ammam, Fariza

    2014-01-01

    in the last decade that could significantly change the current ways of synthesizing chemicals. MES is a process in which electroautotrophic microbes reduce CO2 to multicarbon organics using electrical current as a source of electron. Electricity necessary for MES can be harvested from renewable resources...... relying on co-cultures and investigating extracellular electron transfer from the cathode to the microbes are some of the strategies that we are implementing to transform MES into a commercially viable technology....... such as solar energy, wind turbine or wastewater treatment processes. The net outcome is that renewable energy get store in the covalent bonds of valuable chemicals synthesized from greenhouse gas. However, low electron transferrates from the electrode to microbes, poor adherence of cells on the electrode...

  12. Towards a systems understanding of plant-microbe interactions

    Directory of Open Access Journals (Sweden)

    Akira eMine

    2014-08-01

    Full Text Available Plants are closely associated with microorganisms including pathogens and mutualists that influence plant fitness. Molecular genetic approaches have uncovered a number of signaling components from both plants and microbes and their mode of actions. However, signaling pathways are highly interconnected and influenced by diverse sets of environmental factors. Therefore, it is important to have systems views in order to understand the true nature of plant-microbe interactions. Indeed, systems biology approaches have revealed previously overlooked or misinterpreted properties of the plant immune signaling network. Experimental reconstruction of biological networks using exhaustive combinatorial mutants is particularly powerful to elucidate network structure and properties and relationships among network components. Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. In this review, we highlight the importance of a systems understanding of plant-microbe interactions, with a special emphasis on reconstruction strategies.

  13. The microbe-free plant: fact or artefact?

    Directory of Open Access Journals (Sweden)

    Laila P. Pamela Partida-Martinez

    2011-12-01

    Full Text Available Plant-microbe interactions are ubiquitous. Plants are often colonized by pathogens but even more commonly engaged in neutral or mutualistic interactions with microbes: below-ground microbial plant associates are mycorrhizal fungi, Rhizobia and rhizosphere bacteria, above-ground plant parts are colonized by bacterial and fungal endophytes and by microbes in the phyllosphere. We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host plant affects plant nutrition, growth rate, resistance to biotic and abiotic stress, and plant survival and distribution. The mechanisms involved reach from nutrient acquisition, the production of plant hormones or direct antibiosis to effects on host resistance genes or interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the environment. Thus, the outcome of the interaction is highly context-dependent. Considering the microbe-free plant as the ‘normal’ or control stage significantly impairs research into important phenomena such as (1 phenotypic and epigenetic plasticity, (2 the ‘normal’ ecological outcome of a given interaction and (3 the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host-endophyte combinations under various environmental conditions and study at the genetic, transcriptional and physiological level the parameters that shift the interaction along the mutualism

  14. Musing over Microbes in Microgravity: Microbial Physiology Flight Experiment

    Science.gov (United States)

    Schweickart, Randolph; McGinnis, Michael; Bloomberg, Jacob; Lee, Angie (Technical Monitor)

    2002-01-01

    New York City, the most populated city in the United States, is home to over 8 million humans. This means over 26,000 people per square mile! Imagine, though, what the view would be if you peeked into the world of microscopic organisms. Scientists estimate that a gram of soil may contain up to 1 billion of these microbes, which is as much as the entire human population of China! Scientists also know that the world of microbes is incredibly diverse-possibly 10,000 different species in one gram of soil - more than all the different types of mammals in the world. Microbes fill every niche in the world - from 20 miles below the Earth's surface to 20 miles above, and at temperatures from less than -20 C to hotter than water's boiling point. These organisms are ubiquitous because they can adapt quickly to changing environments, an effective strategy for survival. Although we may not realize it, microbes impact every aspect of our lives. Bacteria and fungi help us break down the food in our bodies, and they help clean the air and water around us. They can also cause the dark, filmy buildup on the shower curtain as well as, more seriously, illness and disease. Since humans and microbes share space on Earth, we can benefit tremendously from a better understanding of the workings and physiology of the microbes. This insight can help prevent any harmful effects on humans, on Earth and in space, as well as reap the benefits they provide. Space flight is a unique environment to study how microbes adapt to changing environmental conditions. To advance ground-based research in the field of microbiology, this STS-107 experiment will investigate how microgravity affects bacteria and fungi. Of particular interest are the growth rates and how they respond to certain antimicrobial substances that will be tested; the same tests will be conducted on Earth at the same times. Comparing the results obtained in flight to those on Earth, we will be able to examine how microgravity induces

  15. Host-microbe interactions in the gut of Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Takayuki eKuraishi

    2013-12-01

    Full Text Available Many insect species subsist on decaying and contaminated matter and are thus exposed to large quantities of microorganisms. To control beneficial commensals and combat infectious pathogens, insects must be armed with efficient systems for microbial recognition, signaling pathways, and effector molecules. The molecular mechanisms regulating these host-microbe interactions in insects have been largely clarified in Drosophila melanogaster with its powerful genetic and genomic tools. Here we review recent advances in this field, focusing mainly on the relationships between microbes and epithelial cells in the intestinal tract where the host exposure to the external environment is most frequent.

  16. Radionuclides in the sea

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1971-07-01

    Water covers a little more than two-thirds of the earth's surface. What is thrown into the sea from a ship may be washed up on a shore thousands of miles away; wastes discharged into the seas or into rivers flowing into them can affect marine life and possibly also the health of man. The study, prevention and control of pollution of the seas and oceans by radionuclides introduced as by-products of man's use of nuclear energy is thus of global interest. (author)

  17. Terrestrial microbes in martian and chondritic meteorites

    Science.gov (United States)

    Airieau, S.; Picenco, Y.; Andersen, G.

    2007-08-01

    Bank sequences using the BLAST program. The closest matches were in the genus Microbacterium. Soil and plant isolates were close relatives by sequence comparison. Los Angeles. After 11 months of incubation in a fridge, a yellow colony grew at the center of a culture plate of Los Angeles dust grains (1:1000 R2A). There was no cell activity in the other agars. A DNA extraction yielded no usable results [7]. Sequencing was not performed because the culture plate became contaminated with outside organisms that overtook the colony of interest. Conclusions: The sequences for EET 87770 and Leoville were of a good quality and the sequence reads were long, so the data are clear that these are typical soil and/or plant-related bacteria commonly found in Earth habitats. Microbial species present in a dozen chondritic samples from isolates are not yet identified, and the contaminant in Los Angeles needs to be recovered. In addition, isotopic analyses of samples with various amounts of microbial contamination could help quantified isotopic impact of microbes on protoplanetary chemistry in these rocks. References : [1] Gounelle, M. and Zolensky M. LPS, (2001) LPS XXXII, Abstract #999. [2] Fries, M. et al. (2005) Meteoritical Society Meeting 68, Abstract # 5201. [3] Burckle, L. H. and Delaney, J. S (1999) Meteoritics & Planet. Sci., 32, 475-478. [4] Whitby, C. et al. (2000) ) LPS XXXI, Abstract #1732. [5] Airieau, S. A. et al (2005) Geochim. Cosmochim. Acta, 69, 4166-4171. [6] Unpublished data, with H. J. Cleaves, A. Aubrey, J. Bada (Scripps Institution of Oceanography), M. Thiemens (UC San Diego) and M. Fogel (Carnegie Institution of Washington). [7] Unpublished data, with A. Steele (CIW), and N. Wainwright (Marine Biological Laboratory). Acknowledgements: Lisa Welleberger for access to SNC samples at USNM; Ralph Harvey for organizing ANSMET; Denise C. Thiry and Andrew Steele for long term storage of samples, NormWainwright for LAL measurements. A small portion of this work was funded with a

  18. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... Population dynamics of soil microbes and diversity of ... 25.78, 25.78, 86.26, 24.73, 68.0, 26.8 and 26.8 kDa proteins and equivalent to Cyt, Cry5 and Cry2 toxins ..... Molecular weight (kDa) of protein fractions of the BT isolates.

  19. Comparative gut physiology symposium: The microbe-gut-brain axis

    Science.gov (United States)

    The Comparative Gut Physiology Symposium titled “The Microbe-Gut-Brain Axis” was held at the Joint Annual Meeting of the American Society of Animal Science and the American Dairy Science Association on Thursday, July 21, 2016, in Salt Lake City Utah. The goal of the symposium was to present basic r...

  20. Microbes, molecules, maladies and man | Duse | South African ...

    African Journals Online (AJOL)

    South African Medical Journal. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 92, No 3 (2002) >. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register. Microbes, molecules, maladies and man. AG Duse. Abstract.

  1. Preliminary biological screening of microbes isolated from cow dung ...

    African Journals Online (AJOL)

    Preliminary biological screening of microbes isolated from cow dung in Kampar. KC Teo, SM Teoh. Abstract. Five distinct morphologically and physiologically isolates were isolated from cow dung at Kampar, Perak, Malaysia and cultured on nutrient agar (NA) plates. Morphological studies including microscopic examination ...

  2. Microbes from raw milk for fermented dairy products

    NARCIS (Netherlands)

    Wouters, J.T.M.; Ayad, E.H.E.; Hugenholtz, J.; Smit, G.

    2002-01-01

    Milk has a high nutritive value, not only For the new-born mammal and for the human consumer, but also for microbes. Raw milk kept at roam temperature will be liable to microbial spoilage. After some days, the milk will spontaneously become sour. This is generally due to the activity of lactic acid

  3. A microbent fiber optic pH sensor

    NARCIS (Netherlands)

    Thomas Lee, S.; Aneeshkumar, B.N.; Radhakrishnan, P.; Vallabhan, C.P.G.; Nampoori, V.P.N.

    2002-01-01

    Optical fiber sensors developed for measuring pH values usually employ an unclad and unstrained section of the fiber. In this paper, we describe the design and fabrication of a microbent fiber optic sensor that can be used for pH sensing. In order to obtain the desired performance, a permanently

  4. Mathematics make microbes beautiful, beneficial, and bountiful.

    Science.gov (United States)

    Jungck, John R

    2012-01-01

    biodiversity by using game theory, of epidemics with algebraic models, bacterial motion by using motion picture analysis and fluid mechanics of motility in multiple dimensions through the physics of "Life at Low Reynolds Numbers," and pattern formation of quorum sensing bacterial populations. Through a developmental model for preprofessional education that emphasizes the beauty, utility, and diversity of microbiological systems, we hope to foster creativity as well as mathematically rigorous reasoning. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Spatial heterogeneity in soil microbes alters outcomes of plant competition.

    Directory of Open Access Journals (Sweden)

    Karen C Abbott

    Full Text Available Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the microbe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established microbe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dispersal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particularly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical

  6. Spatial heterogeneity in soil microbes alters outcomes of plant competition.

    Science.gov (United States)

    Abbott, Karen C; Karst, Justine; Biederman, Lori A; Borrett, Stuart R; Hastings, Alan; Walsh, Vonda; Bever, James D

    2015-01-01

    Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the microbe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established microbe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dispersal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particularly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical results constitute an

  7. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions.

    Science.gov (United States)

    Thompson, Janelle R; Rivera, Hanny E; Closek, Collin J; Medina, Mónica

    2014-01-01

    In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health-not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.

  8. Microbes in the upper atmosphere and unique opportunities for astrobiology research.

    Science.gov (United States)

    Smith, David J

    2013-10-01

    Microbial taxa from every major biological lineage have been detected in Earth's upper atmosphere. The goal of this review is to communicate (1) relevant astrobiology questions that can be addressed with upper atmosphere microbiology studies and (2) available sampling methods for collecting microbes at extreme altitudes. Precipitation, mountain stations, airplanes, balloons, rockets, and satellites are all feasible routes for conducting aerobiology research. However, more efficient air samplers are needed, and contamination is also a pervasive problem in the field. Measuring microbial signatures without false positives in the upper atmosphere might contribute to sterilization and bioburden reduction methods for proposed astrobiology missions. Intriguingly, environmental conditions in the upper atmosphere resemble the surface conditions of Mars (extreme cold, hypobaria, desiccation, and irradiation). Whether terrestrial microbes are active in the upper atmosphere is an area of intense research interest. If, in fact, microbial metabolism, growth, or replication is achievable independent of Earth's surface, then the search for habitable zones on other worlds should be broadened to include atmospheres (e.g., the high-altitude clouds of Venus). Furthermore, viable cells in the heavily irradiated upper atmosphere of Earth could help identify microbial genes or enzymes that bestow radiation resistance. Compelling astrobiology questions on the origin of life (if the atmosphere synthesized organic aerosols), evolution (if airborne transport influenced microbial mutation rates and speciation), and panspermia (outbound or inbound) are also testable in Earth's upper atmosphere.

  9. Evolutionary adaptation in three-way interactions between plants, microbes and arthropods

    NARCIS (Netherlands)

    Biere, A.; Tack, A.J.M.

    2013-01-01

    Evolutionary adaptations in interactions between plants, microbes and arthropods are generally studied in interactions that involve only two of these groups, that is, plants and microbes, plants and arthropods or arthropods and microbes. We review the accumulating evidence from a wide variety of

  10. Dual oxidase in mucosal immunity and host-microbe homeostasis.

    Science.gov (United States)

    Bae, Yun Soo; Choi, Myoung Kwon; Lee, Won-Jae

    2010-07-01

    Mucosal epithelia are in direct contact with microbes, which range from beneficial symbionts to pathogens. Accordingly, hosts must have a conflicting strategy to combat pathogens efficiently while tolerating symbionts. Recent progress has revealed that dual oxidase (DUOX) plays a key role in mucosal immunity in organisms that range from flies to humans. Information from the genetic model of Drosophila has advanced our understanding of the regulatory mechanism of DUOX and its role in mucosal immunity. Further investigations of DUOX regulation in response to symbiotic or non-symbiotic bacteria and the in vivo consequences in host physiology will give a novel insight into the microbe-controlling system of the mucosa. Copyright 2010 Elsevier Ltd. All rights reserved.

  11. Macrophage–Microbe Interactions: Lessons from the Zebrafish Model

    Directory of Open Access Journals (Sweden)

    Nagisa Yoshida

    2017-12-01

    Full Text Available Macrophages provide front line defense against infections. The study of macrophage–microbe interplay is thus crucial for understanding pathogenesis and infection control. Zebrafish (Danio rerio larvae provide a unique platform to study macrophage–microbe interactions in vivo, from the level of the single cell to the whole organism. Studies using zebrafish allow non-invasive, real-time visualization of macrophage recruitment and phagocytosis. Furthermore, the chemical and genetic tractability of zebrafish has been central to decipher the complex role of macrophages during infection. Here, we discuss the latest developments using zebrafish models of bacterial and fungal infection. We also review novel aspects of macrophage biology revealed by zebrafish, which can potentiate development of new therapeutic strategies for humans.

  12. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly......, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations....... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...

  13. Characteristics of the repair - deficient mutants 1435 plague microbe strain

    International Nuclear Information System (INIS)

    Temiralieva, G.A.

    1977-01-01

    Repair-deficient mutants 1435 A uvr - hcr - , 1435-17 uvr - hcr + and 1435-35 lon have been obtained from 1435 plague microbe strain, isolated from a large gerbil living in the Central Asian desert region. The mutants have the same cultural-morphological and enzymatic characteristics, the same need in growth factors and similar virulence determinants as the original strain, but they do not cause death of the experimental animals

  14. Do airborne microbes matter for atmospheric chemistry and cloud formation?

    Science.gov (United States)

    Konstantinidis, Konstantinos T

    2014-06-01

    The role of airborne microbial cells in the chemistry of the atmosphere and cloud formation remains essentially speculative. Recent studies have indicated that microbes might be more important than previously anticipated for atmospheric processes. However, more work and direct communication between microbiologists and atmospheric scientists and modellers are necessary to better understand and model bioaerosol-cloud-precipitation-climate interactions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

    OpenAIRE

    Krajmalnik-Brown, Rosa; Ilhan, Zehra-Esra; Kang, Dae-Wook; DiBaise, John K.

    2012-01-01

    Malnutrition may manifest as either obesity or undernutrition. Accumulating evidence suggests that the gut microbiota plays an important role in the harvest, storage, and expenditure of energy obtained from the diet. The composition of the gut microbiota has been shown to differ between lean and obese humans and mice; however, the specific roles that individual gut microbes play in energy harvest remain uncertain. The gut microbiota may also influence the development of conditions characteriz...

  16. Soil Microbes and soil microbial proteins: interactions with clay minerals

    International Nuclear Information System (INIS)

    Spence, A.; Kelleher, B. P.

    2009-01-01

    Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

  17. Three-dimensional optofluidic device for isolating microbes

    Science.gov (United States)

    Keloth, A.; Paterson, L.; Markx, G. H.; Kar, A. K.

    2015-03-01

    Development of efficient methods for isolation and manipulation of microorganisms is essential to study unidentified and yet-to-be cultured microbes originating from a variety of environments. The discovery of novel microbes and their products have the potential to contribute to the development of new medicines and other industrially important bioactive compounds. In this paper we describe the design, fabrication and validation of an optofluidic device capable of redirecting microbes within a flow using optical forces. The device holds promise to enable the high throughput isolation of single microbes for downstream culture and analysis. Optofluidic devices are widely used in clinical research, cell biology and biomedical engineering as they are capable of performing analytical functions such as controlled transportation, compact and rapid processing of nanolitres to millilitres of clinical or biological samples. We have designed and fabricated a three dimensional optofluidic device to control and manipulate microorganisms within a microfluidic channel. The device was fabricated in fused silica by ultrafast laser inscription (ULI) followed by selective chemical etching. The unique three-dimensional capability of ULI is utilized to integrate microfluidic channels and waveguides within the same substrate. The main microfluidic channel in the device constitutes the path of the sample. Optical waveguides are fabricated at right angles to the main microfluidic channel. The potential of the optical scattering force to control and manipulate microorganisms is discussed in this paper. A 980 nm continuous wave (CW) laser source, coupled to the waveguide, is used to exert radiation pressure on the particle and particle migrations at different flow velocities are recorded. As a first demonstration, device functionality is validated using fluorescent microbeads and initial trials with microalgae are presented.

  18. Sterilization of microbes by using various plasma jets

    Energy Technology Data Exchange (ETDEWEB)

    Uhm, Han S.; Choi, Eun H.; Cho, Guang S. [Kwangwoon University, Seoul (Korea, Republic of); Hong, Yong C. [National Fusion Research Institute, Daejeon (Korea, Republic of)

    2012-03-15

    Sterilization of various microbes was carried out by using several plasma jets. Argon plasma jets penetrate deep into ambient air and create a path for oxygen radicals to sterilize microbes including spores. A sterilization experiment with bacterial endospores indicates that an argon-oxygen plasma jet very effectively kills endospores of Bacillus atrophaeus (ATCC 9372), thereby demonstrating its capability to clean surfaces and its usefulness for reinstating contaminated equipment as free from toxic biological agents. The key element of the sterilization is oxygen radicals. The penciltype configuration produces a long, cold plasma jet capable of reaching 3.5 cm and having various excited plasma species shown through the optical emission spectrum. Operation of an air plasma jet at 2 W in a pencil-type electrode provides an excellent opportunity for sterilization of microbes. An electron microscope was used to observe the effects of the plasma on bacterial cell morphology. Transmission electron micrographs showed morphological changes in E. coli cells treated with an atmospheric plasma at 75 W for 2 min. The treated cells had severe cytoplasmic deformations and leakage of bacterial chromosome. The chromosomal DNA was either attached to the bacterial cells or released freely into the surrounding medium. The results clearly explain the loss of viability of bacterial cells after plasma treatment.

  19. Rarity in aquatic microbes: placing protists on the map.

    Science.gov (United States)

    Logares, Ramiro; Mangot, Jean-François; Massana, Ramon

    2015-12-01

    Most microbial richness at any given time tends to be represented by low-abundance (rare) taxa, which are collectively referred to as the "rare biosphere". Here we review works on the rare biosphere using high-throughput sequencing (HTS), with a particular focus on unicellular eukaryotes or protists. Evidence thus far indicates that the rare biosphere encompasses dormant as well as metabolically active microbes that could potentially play key roles in ecosystem functioning. Rare microbes appear to have biogeography, and sometimes the observed patterns can be similar to what is observed among abundant taxa, suggesting similar community-structuring mechanisms. There is limited evidence indicating that the rare biosphere contains taxa that are phylogenetically distantly related to abundant counterparts; therefore, the rare biosphere may act as a reservoir of deep-branching phylogenetic diversity. The potential role of the rare biosphere as a bank of redundant functions that can help to maintain continuous ecosystem function following oscillations in taxonomic abundances is hypothesized as its main ecological role. Future studies focusing on rare microbes are crucial for advancing our knowledge of microbial ecology and evolution and unveiling their links with ecosystem function. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  20. Food microbe tracker: a web-based tool for storage and comparison of food-associated microbes.

    Science.gov (United States)

    Vangay, Pajau; Fugett, Eric B; Sun, Qi; Wiedmann, Martin

    2013-02-01

    Large amounts of molecular subtyping information are generated by the private sector, academia, and government agencies. However, use of subtype data is limited by a lack of effective data storage and sharing mechanisms that allow comparison of subtype data from multiple sources. Currently available subtype databases are generally limited in scope to a few data types (e.g., MLST. net) or are not publicly available (e.g., PulseNet). We describe the development and initial implementation of Food Microbe Tracker, a public Web-based database that allows archiving and exchange of a variety of molecular subtype data that can be cross-referenced with isolate source data, genetic data, and phenotypic characteristics. Data can be queried with a variety of search criteria, including DNA sequences and banding pattern data (e.g., ribotype or pulsed-field gel electrophoresis type). Food Microbe Tracker allows the deposition of data on any bacterial genus and species, bacteriophages, and other viruses. The bacterial genera and species that currently have the most entries in this database are Listeria monocytogenes, Salmonella, Streptococcus spp., Pseudomonas spp., Bacillus spp., and Paenibacillus spp., with over 40,000 isolates. The combination of pathogen and spoilage microorganism data in the database will facilitate source tracking and outbreak detection, improve discovery of emerging subtypes, and increase our understanding of transmission and ecology of these microbes. Continued addition of subtyping, genetic or phenotypic data for a variety of microbial species will broaden the database and facilitate large-scale studies on the diversity of food-associated microbes.

  1. Microbes on a bottle: substrate, season and geography influence community composition of microbes colonizing marine plastic debris

    OpenAIRE

    Carter, Dee A.; Oberbeckmann, Sonja; Osborn, A. Mark; Duhaime, Melissa B.

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial com...

  2. A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

    Science.gov (United States)

    Gopalan, Suresh; Ausubel, Frederick M

    2008-01-01

    An unintended consequence of global industrialization and associated societal rearrangements is new interactions of microbes and potential hosts (especially mammals and plants), providing an opportunity for the rapid emergence of host-microbe adaptation and eventual establishment of new microbe-related diseases. We describe a new model system comprising the model plant Arabidopsis thaliana and several microbes, each representing different modes of interaction, to study such "maladaptations". The model microbes include human and agricultural pathogens and microbes that are commonly considered innocuous. The system has a large knowledge base corresponding to each component organism and is amenable to high-throughput automation assisted perturbation screens for identifying components that modulate host-pathogen interactions. This would aid in the study of emergence and progression of host-microbe maladaptations in a controlled environment.

  3. Lunar and Planetary Science XXXV: Astrobiology Stew: Pinch of Microbes, Smidgen of UV, Touch of Organics, and Dash of Meteorites

    Science.gov (United States)

    2004-01-01

    The session Astrobiology Stew: Pinch of Microbes, Smidgen of UV, Touch of Organics, and Dash of Meteorites includes the following topics: 1) Investigating the Impact of UV Radiation on High-Altitude Shallow Lake Habitats, Life Diversity, and Life Survival Strategies: Clues for Mars' Past Habitability Potential? 2) An Analysis of Potential Photosynthetic Life on Mars; 3) Radiation Inactivation of Bacterial spores on Mars; 4) Hydrophobic Surfaces of Spacecraft Components Enhance the Aggregation of Microorganisms and May Lead to Higher Survival Rates of Bacteria on Mars Landers; 5) Optical Detection of Organic Chemical Biosignatures at Hydrothermal Vents; 6) Signs of Life in Meridiani Planum-What Might Opportunity See (or Miss)? 7) Isolation of PUrines and Pyrimidines from the Murchison Meteorite Using Sublimation; and 8) Relative Amino Acid Composition of CM1 Carbonaceous Chondrites.

  4. Seasonal dynamics of early life stages of invasive and native ctenophores give clues to invasion and bloom potential in the Baltic Sea

    DEFF Research Database (Denmark)

    Jaspers, Cornelia; Haraldsson, Matilda; Lombard, Fabien

    2013-01-01

    and distribution of larvae and eggs of these two species. We show that their occurrence is significantly but inversely related to salinity. Mertensia ovum was present year round throughout the brackish Baltic Sea but also occurred in high-saline areas during cold seasons. Larvae of M. leidyi occurred throughout......Recently, both the invasive ctenophore Mnemiopsis leidyi and the arctic Mertensia ovum were discovered in the Baltic Sea but their range expansion remains unclear due to misidentification of their larval stages. Supported by molecular species verification we describe seasonal abundance...

  5. Screening assays of termite gut microbes that potentially as probiotic for human to digest cellulose as new food source

    Science.gov (United States)

    Abdullah, R.; Ananda, K. R. T.; Wijanarka

    2018-05-01

    According to UN, earth population will increase approximately 7.3 billion people up to 11.2 billion from 2015 until 2100. On the other side, food needs are not balance with the availability of food on earth. People of the world need solution for a new food source. By cellulose digesting ability, people analyzed can consume cellulose as the new food source to get glucose. The aims of research is obtaining termite gut cellulase bacteria selected which is potential as probiotic to split cellulose. Method used was as follows; isolation of termite gut microbes, microbial cellulase purification by screening method and probiotic test includes microbial pathogenicity test and human stomach acid and salt osmotic concentration resistance test. The result shows, 3 pure isolates of termite gut microbes can break down cellulose in the medium 1% CMC and 0.1% congo red (indicator of cellulose degradation activity) and life at pH 2- 2.5 and osmotic salt condition. Two isolates show the activity of gamma hemolysis (non-pathogenic in terms of pathogenicity on human blood). In conclusion, there are isolated termite gut microbes can be used as probiotic candidate for human to digest cellulose of the new food source for global food scarcity era.

  6. Extraction of gold (Au) particles from sea water by Delftia Acidovorans microbes

    Science.gov (United States)

    Yusoff, A. H. M.; Nading, M. E.; Salimi, M. N.

    2017-10-01

    Gold-mining activities have been an issue, especially when it involves in contamination of chemicals, for example arsenic and mercury. However, despite of these hazards, gold-mining activities are still being conducted. This is because the gold is worth, regardless of the problems. Gold-mining, as known needs a very large area of land, or site plant. Vast amount of labor force, mechanical force and fund are a must in order for the mining process to be continued. High demand of gold, made gold-mining industries as ones of the most profitable industries in the world. Thus, this has encouraged another alternative way to extract gold. At the mining site, researchers found that biomineralization of gold by Delftia acidovorans can be conducted. How it is done still cannot be understood. It is said that the bacteria secretes secondary metabolites, Delftibactin as a defensive mechanism against the toxicity of the soluble gold. Researchers try to find another source of elemental gold besides of the earth’s core. The options are either lava of a volcano or ocean. Here, the focus is seawater. The problem of seawater is that its composition still not yet to be proved. Dissolve gold existed as gold chloride in seawater, but in a very small amount. So, the gold separation should be focused, in order to make this process to be a successful one. Factors such as depth, climate, region, temperature need to be considered. If this difference affecting the separating process, standardized seawater composition have to be proposed.

  7. Shelf-life extension of refrigerated sea bass slices wrapped with fish protein isolate/fish skin gelatin-ZnO nanocomposite film incorporated with basil leaf essential oil.

    Science.gov (United States)

    Arfat, Yasir Ali; Benjakul, Soottawat; Vongkamjan, Kitiya; Sumpavapol, Punnanee; Yarnpakdee, Suthasinee

    2015-10-01

    Microbiological, chemical and sensory changes of sea bass slices wrapped with fish protein isolate (FPI)/fish skin gelatin (FSG) films incorporated with 3 % ZnO nanoparticles (ZnONP) (w/w, based on protein content) and 100 % basil leaf essential oil (BEO) (w/w, based on protein content) during storage of 12 days at 4 °C were investigated. Sea bass slices wrapped with FPI/FSG-ZnONP-BEO film had the lowest growth of psychrophilic bacteria, lactic acid bacteria and spoilage microorganisms including Pseudomonas , H2S-producing bacteria and Enterobacteriaceae throughout storage of 12 days in comparison with those wrapped with FPI/FSG-BEO, FPI/FSG-ZnONP, FPI/FSG film, polypropylene film (PP film) and the control (without wrapping), respectively (P < 0.05). Lowered increases in pH, total volatile base, peroxide value and TBARS value were found in FPI/FSG-ZnO-BEO film wrapped samples, compared with others (P < 0.05). Sensory evaluation revealed that shelf-life of sea bass slices was longest for samples wrapped with FPI/FSG-ZnONP-BEO film (12 days), as compared to the control (6 days) (P < 0.05).

  8. Control of bleaching in mushroom coral populations (Scleractinia: Fungiidae) in the Java Sea: stress tolerance and interference by life history strategy

    NARCIS (Netherlands)

    Hoeksema, B.W.

    1991-01-01

    Bleaching was studied in populations of phylogenetically closely related species (n = 21) of mushroom corals (Scleractinia: Fungiidae) around Pari Island (Java Sea) during a period of excessive seawater warming in 1983. The interspecific variation in the proportions of affected individuals was

  9. Application of RNA-seq and Bioimaging Methods to Study Microbe-Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression

    DEFF Research Database (Denmark)

    Amador Hierro, Cristina Isabel; Sternberg, Claus; Jelsbak, Lars

    2017-01-01

    Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. We describe two different experimental approaches to study microbe-microbe interactions in in vitro systems containing surface-associated microbial populations. One method i...

  10. Sea Dragon

    National Research Council Canada - National Science Library

    1997-01-01

    .... In preparation for these changes, the Navy is exploring new command and control relationships, and the Marine Corps established Sea Dragon to experiment with emerging technologies, operational...

  11. Microbe participation in aroma production during soy sauce fermentation.

    Science.gov (United States)

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2018-06-01

    Soy sauce is a traditional Japanese fermented seasoning that contains various constituents such as amino acids, organic acids, and volatiles that are produced during the long fermentation process. Although studies regarding the correlation between microbes and aroma constituents have been performed, there are no reports about the influences of the microbial products, such as lactic acid, acetic acid, and ethanol, during fermentation. Because it is known that these compounds contribute to microbial growth and to changes in the constituent profile by altering the moromi environment, understanding the influence of these compounds is important. Metabolomics, the comprehensive study of low molecular weight metabolites, is a promising strategy for the deep understanding of constituent contributions to food characteristics. Therefore, the influences of microbes and their products such as lactic acid, acetic acid, and ethanol on aroma profiles were investigated using gas chromatography/mass spectrometry (GC/MS)-based metabolic profiling. The presence of aroma constituents influenced by microbes and chemically influenced by lactic acid, acetic acid, and ethanol were proposed. Most of the aroma constituents were not produced by adding ethanol alone, confirming the participation of yeast in aroma production. It was suggested that lactic acid bacterium relates to a key aromatic compound, 2,5-dimethyl-4-hydroxy-3(2H)-furanone. However, most of the measured aroma constituents changed similarly in both samples with lactic acid bacterium and acids. Thus, it was clear that the effect of lactic acid and acetic acid on the aroma profile was significant. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  12. Big Data Approaches To Coral-Microbe Symbiosis

    Science.gov (United States)

    Zaneveld, J.; Pollock, F. J.; McMinds, R.; Smith, S.; Payet, J.; Hanna, B.; Welsh, R.; Foster, A.; Ohdera, A.; Shantz, A. A.; Burkepile, D. E.; Maynard, J. A.; Medina, M.; Vega Thurber, R.

    2016-02-01

    Coral reefs face increasing challenges worldwide, threatened by overfishing and nutrient pollution, which drive growth of algal competitors of corals, and periods of extreme temperature, which drive mass coral bleaching. I will discuss two projects that examine how coral's complex relationships with microorganisms affect the response of coral colonies and coral species to environmental challenge. Microbiological studies have documented key roles for coral's microbial symbionts in energy harvest and defense against pathogens. However, the evolutionary history of corals and their microbes is little studied. As part of the Global Coral Microbiome Project, we are characterizing bacterial, archaeal, fungal, and Symbiodinium diversity across >1400 DNA samples from all major groups of corals, collected from 15 locations worldwide. This collection will allow us to ask how coral- microbe associations evolved over evolutionary time, and to determine whether microbial symbiosis helps predict the relative vulnerability of certain coral species to environmental stress. In the second project, we experimentally characterized how the long-term effects of human impacts such as overfishing and nutrient pollution influence coral-microbe symbiosis. We conducted a three-year field experiment in the Florida Keys applying nutrient pollution or simulated overfishing to reef plots, and traced the effects on reef communities, coral microbiomes, and coral health. The results show that extremes of temperature and algal competition destabilize coral microbiomes, increasing pathogen blooms, coral disease, and coral death. Surprisingly, these local stressors interacted strongly with thermal stress: the greatest microbiome disruption, and >80% of coral mortality happened in the hottest periods. Thus, overfishing and nutrient pollution may interact with increased climate-driven episodes of sub-bleaching thermal stress to increase coral mortality by disrupt reef communities down to microbial scales.

  13. Gut microbes may facilitate insect herbivory of chemically defended plants.

    Science.gov (United States)

    Hammer, Tobin J; Bowers, M Deane

    2015-09-01

    The majority of insect species consume plants, many of which produce chemical toxins that defend their tissues from attack. How then are herbivorous insects able to develop on a potentially poisonous diet? While numerous studies have focused on the biochemical counter-adaptations to plant toxins rooted in the insect genome, a separate body of research has recently emphasized the role of microbial symbionts, particularly those inhabiting the gut, in plant-insect interactions. Here we outline the "gut microbial facilitation hypothesis," which proposes that variation among herbivores in their ability to consume chemically defended plants can be due, in part, to variation in their associated microbial communities. More specifically, different microbes may be differentially able to detoxify compounds toxic to the insect, or be differentially resistant to the potential antimicrobial effects of some compounds. Studies directly addressing this hypothesis are relatively few, but microbe-plant allelochemical interactions have been frequently documented from non-insect systems-such as soil and the human gut-and thus illustrate their potential importance for insect herbivory. We discuss the implications of this hypothesis for insect diversification and coevolution with plants; for example, evolutionary transitions to host plant groups with novel allelochemicals could be initiated by heritable changes to the insect microbiome. Furthermore, the ecological implications extend beyond the plant and insect herbivore to higher trophic levels. Although the hidden nature of microbes and plant allelochemicals make their interactions difficult to detect, recent molecular and experimental techniques should enable research on this neglected, but likely important, aspect of insect-plant biology.

  14. The ``Adopt A Microbe'' project: Web-based interactive education connected with scientific ocean drilling

    Science.gov (United States)

    Orcutt, B. N.; Bowman, D.; Turner, A.; Inderbitzen, K. E.; Fisher, A. T.; Peart, L. W.; Iodp Expedition 327 Shipboard Party

    2010-12-01

    We launched the "Adopt a Microbe" project as part of Integrated Ocean Drilling Program (IODP) Expedition 327 in Summer 2010. This eight-week-long education and outreach effort was run by shipboard scientists and educators from the research vessel JOIDES Resolution, using a web site (https://sites.google.com/site/adoptamicrobe) to engage students of all ages in an exploration of the deep biosphere inhabiting the upper ocean crust. Participants were initially introduced to a cast of microbes (residing within an ‘Adoption Center’ on the project website) that live in the dark ocean and asked to select and virtually ‘adopt’ a microbe. A new educational activity was offered each week to encourage learning about microbiology, using the adopted microbe as a focal point. Activities included reading information and asking questions about the adopted microbes (with subsequent responses from shipboard scientists), writing haiku about the adopted microbes, making balloon and fabric models of the adopted microbes, answering math questions related to the study of microbes in the ocean, growing cultures of microbes, and examining the gases produced by microbes. In addition, the website featured regular text, photo and video updates about the science of the expedition using a toy microbe as narrator, as well as stories written by shipboard scientists from the perspective of deep ocean microbes accompanied by watercolor illustrations prepared by a shipboard artist. Assessment methods for evaluating the effectiveness of the Adopt a Microbe project included participant feedback via email and online surveys, website traffic monitoring, and online video viewing rates. Quantitative metrics suggest that the “Adope A Microbe” project was successful in reaching target audiences and helping to encourage and maintain interest in topics related to IODP Expedition 327. The “Adopt A Microbe” project mdel can be adapted for future oceanographic expeditions to help connect the

  15. Turbidity and microbes removal from water using an electrochemical filter

    International Nuclear Information System (INIS)

    Venkateswaran, G.; Gokhale, B.K.; Belapurkar, A.D.; Kumbhar, A.G.; Balaji, V.

    2004-01-01

    An in-house designed and fabricated Electrochemical fibrous graphite filter (ECF) was used to remove turbidity and microbes. The filter was found to be effective in removing sub micron size indium turbidity from RAPS-1 moderator water, iron turbidity from Active Process Cooling Water (APCW) of Kaiga Generating Station and microbial reduction from process cooling water RAPS-2. Unlike conventional turbidity removal by addition of coagulants and biocide chemical additions for purification, ECF is a clean way to remove the turbidity without contaminating the system and is best suited for close loop systems

  16. Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

    Science.gov (United States)

    Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

    2016-10-01

    Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  17. Characterization of Methane Degradation and Methane-Degrading Microbes in Alaska Coastal Water

    Energy Technology Data Exchange (ETDEWEB)

    Kirchman, David L. [Univ. of Delaware, Lewes, DE (United States)

    2012-03-29

    The net flux of methane from methane hydrates and other sources to the atmosphere depends on methane degradation as well as methane production and release from geological sources. The goal of this project was to examine methane-degrading archaea and organic carbon oxidizing bacteria in methane-rich and methane-poor sediments of the Beaufort Sea, Alaska. The Beaufort Sea system was sampled as part of a multi-disciplinary expedition (Methane in the Arctic Shelf or MIDAS) in September 2009. Microbial communities were examined by quantitative PCR analyses of 16S rRNA genes and key methane degradation genes (pmoA and mcrA involved in aerobic and anaerobic methane degradation, respectively), tag pyrosequencing of 16S rRNA genes to determine the taxonomic make up of microbes in these sediments, and sequencing of all microbial genes (metagenomes ). The taxonomic and functional make-up of the microbial communities varied with methane concentrations, with some data suggesting higher abundances of potential methane-oxidizing archaea in methane-rich sediments. Sequence analysis of PCR amplicons revealed that most of the mcrA genes were from the ANME-2 group of methane oxidizers. According to metagenomic data, genes involved in methane degradation and other degradation pathways changed with sediment depth along with sulfate and methane concentrations. Most importantly, sulfate reduction genes decreased with depth while the anaerobic methane degradation gene (mcrA) increased along with methane concentrations. The number of potential methane degradation genes (mcrA) was low and inconsistent with other data indicating the large impact of methane on these sediments. The data can be reconciled if a small number of potential methane-oxidizing archaea mediates a large flux of carbon in these sediments. Our study is the first to report metagenomic data from sediments dominated by ANME-2 archaea and is one of the few to examine the entire microbial assemblage potentially involved in

  18. African dust carries microbes across the ocean: are they affecting human and ecosystem health?

    Science.gov (United States)

    Kellogg, Christina A.; Griffin, Dale W.

    2003-01-01

    Atmospheric transport of dust from northwest Africa to the western Atlantic Ocean region may be responsible for a number of environmental hazards, including the demise of Caribbean corals; red tides; amphibian diseases; increased occurrence of asthma in humans; and oxygen depletion (eutrophication) in estuaries. Studies of satellite images suggest that hundreds of millions of tons of dust are trans-ported annually at relatively low altitudes across the Atlantic Ocean to the Caribbean Sea and southeastern United States. The dust emanates from the expanding Sahara/Sahel desert region in Africa and carries a wide variety of bacteria and fungi. The U.S. Geological Survey, in collaboration with the NASA/Goddard Spaceflight Center, is conducting a study to identify microbes--bacteria, fungi, viruses--transported across the Atlantic in African soil dust. Each year, millions of tons of desert dust blow off the west African coast and ride the trade winds across the ocean, affecting the entire Caribbean basin, as well as the southeastern United States. Of the dust reaching the U.S., Florida receives about 50 percent, while the rest may range as far north as Maine or as far west as Colorado. The dust storms can be tracked by satellite and take about one week to cross the Atlantic.

  19. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  20. Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds.

    Science.gov (United States)

    Indraningrat, Anak Agung Gede; Smidt, Hauke; Sipkema, Detmer

    2016-05-02

    Sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. However, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. This review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. We discuss the current state-of-the-art by grouping the bioactive compounds produced by sponge-associated microorganisms in four categories: antiviral, antibacterial, antifungal and antiprotozoal compounds. Based on in vitro activity tests, identified targets of potent antimicrobial substances derived from sponge-associated microbes include: human immunodeficiency virus 1 (HIV-1) (2-undecyl-4-quinolone, sorbicillactone A and chartarutine B); influenza A (H1N1) virus (truncateol M); nosocomial Gram positive bacteria (thiopeptide YM-266183, YM-266184, mayamycin and kocurin); Escherichia coli (sydonic acid), Chlamydia trachomatis (naphthacene glycoside SF2446A2); Plasmodium spp. (manzamine A and quinolone 1); Leishmania donovani (manzamine A and valinomycin); Trypanosoma brucei (valinomycin and staurosporine); Candida albicans and dermatophytic fungi (saadamycin, 5,7-dimethoxy-4-p-methoxylphenylcoumarin and YM-202204). Thirty-five bacterial and 12 fungal genera associated with sponges that produce antimicrobials were identified, with Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the prominent producers of antimicrobial compounds. Furthemore culture-independent approaches to more comprehensively exploit the genetic richness of antimicrobial compound-producing pathways from sponge-associated bacteria are addressed.

  1. Nitrilase enzymes and their role in plant–microbe interactions

    Science.gov (United States)

    Howden, Andrew J. M.; Preston, Gail M.

    2009-01-01

    Summary Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant–microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth‐promoting microorganisms, and their activities may have a significant impact on the outcome of plant–microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant‐associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. PMID:21255276

  2. Induction of abiotic stress tolerance in plants by endophytic microbes.

    Science.gov (United States)

    Lata, R; Chowdhury, S; Gond, S K; White, J F

    2018-04-01

    Endophytes are micro-organisms including bacteria and fungi that survive within healthy plant tissues and promote plant growth under stress. This review focuses on the potential of endophytic microbes that induce abiotic stress tolerance in plants. How endophytes promote plant growth under stressful conditions, like drought and heat, high salinity and poor nutrient availability will be discussed. The molecular mechanisms for increasing stress tolerance in plants by endophytes include induction of plant stress genes as well as biomolecules like reactive oxygen species scavengers. This review may help in the development of biotechnological applications of endophytic microbes in plant growth promotion and crop improvement under abiotic stress conditions. Increasing human populations demand more crop yield for food security while crop production is adversely affected by abiotic stresses like drought, salinity and high temperature. Development of stress tolerance in plants is a strategy to cope with the negative effects of adverse environmental conditions. Endophytes are well recognized for plant growth promotion and production of natural compounds. The property of endophytes to induce stress tolerance in plants can be applied to increase crop yields. With this review, we intend to promote application of endophytes in biotechnology and genetic engineering for the development of stress-tolerant plants. © 2018 The Society for Applied Microbiology.

  3. Utilizing thermophilic microbe in lignocelluloses based bioethanol production: Review

    Science.gov (United States)

    Sriharti, Agustina, Wawan; Ratnawati, Lia; Rahman, Taufik; Salim, Takiyah

    2017-01-01

    The utilization of thermophilic microbe has attracted many parties, particularly in producing an alternative fuel like ethanol. Bioethanol is one of the alternative energy sources substituting for earth oil in the future. The advantage of using bioethanol is that it can reduce pollution levels and global warming because the result of bioethanol burning doesn't bring in a net addition of CO2 into environment. Moreover, decrease in the reserves of earth oil globally has also contributed to the notion on searching renewable energy resources such as bioethanol. Indonesia has a high biomass potential and can be used as raw material for bioethanol. The utilization of these raw materials will reduce fears of competition foodstuffs for energy production. The enzymes that play a role in degrading lignocelluloses are cellulolytic, hemicellulolytic, and lignolytic in nature. The main enzyme with an important role in bioethanol production is a complex enzyme capable of degrading lignocelluloses. The enzyme can be produced by the thermophilik microbes of the groups of bacteria and fungi such as Trichoderma viride, Clostridium thermocellum, Bacillus sp. Bioethanol production is heavily affected by raw material composition, microorganism type, and the condition of fermentation used.

  4. Fluorogenic Cell-Based Biosensors for Monitoring Microbes

    Science.gov (United States)

    Curtis, Theresa; Salazar, Noe; Tabb, Joel; Chase, Chris

    2010-01-01

    Fluorogenic cell-based sensor systems for detecting microbes (especially pathogenic ones) and some toxins and allergens are undergoing development. These systems harness the natural signaltransduction and amplification cascades that occur in mast cells upon activation with antigens. These systems include (1) fluidic biochips for automated containment of samples, reagents, and wastes and (2) sensitive, compact fluorometers for monitoring the fluorescent responses of mast cells engineered to contain fluorescent dyes. It should be possible to observe responses within minutes of adding immune complexes. The systems have been shown to work when utilizing either immunoglobulin E (IgE) antibodies or traditionally generated rat antibodies - a promising result in that it indicates that the systems could be developed to detect many target microbes. Chimeric IgE antibodies and rat immunoglobulin G (IgG) antibodies could be genetically engineered for recognizing biological and chemical warfare agents and airborne and food-borne allergens. Genetic engineering efforts thus far have yielded (1) CD14 chimeric antibodies that recognize both Grampositive and Gram-negative bacteria and bind to the surfaces of mast cells, eliciting a degranulation response and (2) rat IgG2a antibodies that act similarly in response to low levels of canine parvovirus.

  5. Nitrilase enzymes and their role in plant-microbe interactions.

    Science.gov (United States)

    Howden, Andrew J M; Preston, Gail M

    2009-07-01

    Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

  6. Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases.

    Science.gov (United States)

    Dolan, Kyle T; Chang, Eugene B

    2017-01-01

    The rising incidence of inflammatory bowel diseases in recent decades has notably paralleled changing lifestyle habits in Western nations, which are now making their way into more traditional societies. Diet plays a key role in IBD pathogenesis, and there is a growing appreciation that the interaction between diet and microbes in a susceptible person contributes significantly to the onset of disease. In this review, we examine what is known about dietary and microbial factors that promote IBD. We summarize recent findings regarding the effects of diet in IBD epidemiology from prospective population cohort studies, as well as new insights into IBD-associated dysbiosis. Microbial metabolism of dietary components can influence the epithelial barrier and the mucosal immune system, and understanding how these interactions generate or suppress inflammation will be a significant focus of IBD research. Our knowledge of dietary and microbial risk factors for IBD provides important considerations for developing therapeutic approaches through dietary modification or re-shaping the microbiota. We conclude by calling for increased sophistication in designing studies on the role of diet and microbes in IBD pathogenesis and disease resolution in order to accelerate progress in response to the growing challenge posed by these complex disorders. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

    Directory of Open Access Journals (Sweden)

    Patrice D. Cani

    2017-09-01

    Full Text Available Metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. Among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. Among the next-generation beneficial microbes that have been identified, Akkermansia muciniphila is a promising candidate. Indeed, A. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation. Besides the numerous correlations observed, a large body of evidence has demonstrated the causal beneficial impact of this bacterium in a variety of preclinical models. Translating these exciting observations to human would be the next logic step and it now appears that several obstacles that would prevent the use of A. muciniphila administration in humans have been overcome. Moreover, several lines of evidence indicate that pasteurization of A. muciniphila not only increases its stability but more importantly increases its efficacy. This strongly positions A. muciniphila in the forefront of next-generation candidates for developing novel food or pharma supplements with beneficial effects. Finally, a specific protein present on the outer membrane of A. muciniphila, termed Amuc_1100, could be strong candidate for future drug development. In conclusion, as plants and its related knowledge, known as pharmacognosy, have been the source for designing drugs over the last century, we propose that microbes and microbiomegnosy, or knowledge of our gut microbiome, can become a novel source of future therapies.

  8. Understanding Plant-Microbe Interactions for Phytoremediation of Petroleum-Polluted Soil

    Science.gov (United States)

    Nie, Ming; Wang, Yijing; Yu, Jiayi; Xiao, Ming; Jiang, Lifen; Yang, Ji; Fang, Changming; Chen, Jiakuan; Li, Bo

    2011-01-01

    Plant-microbe interactions are considered to be important processes determining the efficiency of phytoremediation of petroleum pollution, however relatively little is known about how these interactions are influenced by petroleum pollution. In this experimental study using a microcosm approach, we examined how plant ecophysiological traits, soil nutrients and microbial activities were influenced by petroleum pollution in Phragmites australis, a phytoremediating species. Generally, petroleum pollution reduced plant performance, especially at early stages of plant growth. Petroleum had negative effects on the net accumulation of inorganic nitrogen from its organic forms (net nitrogen mineralization (NNM)) most likely by decreasing the inorganic nitrogen available to the plants in petroleum-polluted soils. However, abundant dissolved organic nitrogen (DON) was found in petroleum-polluted soil. In order to overcome initial deficiency of inorganic nitrogen, plants by dint of high colonization of arbuscular mycorrhizal fungi might absorb some DON for their growth in petroleum-polluted soils. In addition, through using a real-time polymerase chain reaction method, we quantified hydrocarbon-degrading bacterial traits based on their catabolic genes (i.e. alkB (alkane monooxygenase), nah (naphthalene dioxygenase) and tol (xylene monooxygenase) genes). This enumeration of target genes suggests that different hydrocarbon-degrading bacteria experienced different dynamic changes during phytoremediation and a greater abundance of alkB was detected during vegetative growth stages. Because phytoremediation of different components of petroleum is performed by different hydrocarbon-degrading bacteria, plants’ ability of phytoremediating different components might therefore vary during the plant life cycle. Phytoremediation might be most effective during the vegetative growth stages as greater abundances of hydrocarbon-degrading bacteria containing alkB and tol genes were observed

  9. Clinical laboratory evaluation of the Auto-Microbic system for rapid identification of Enterobacteriaceae.

    OpenAIRE

    Hasyn, J J; Cundy, K R; Dietz, C C; Wong, W

    1981-01-01

    The capability of the Auto-Microbic system (Vitek Systems, Inc., Hazelwood, Mo.) has been expanded to identify members of the family Enterobacteriaceae with the use of a sealed, disposable accessory card (the Enterobacteriaceae Biochemical Card) containing 26 biochemical tests. To judge the accuracy of the AutoMicrobic system's identification in a hospital laboratory, 933 Enterobacteriaceae isolates were studied. The AutoMicrobic system provided the correct identification for 905 of the isola...

  10. Synchrotron X-ray Investigations of Mineral-Microbe-Metal Interactions

    International Nuclear Information System (INIS)

    Kemner, Kenneth M.; O'Loughlin, Edward J.; Kelly, Shelly D.; Boyanov, Maxim I.

    2005-01-01

    Interactions between microbes and minerals can play an important role in metal transformations (i.e. changes to an element's valence state, coordination chemistry, or both), which can ultimately affect that element's mobility. Mineralogy affects microbial metabolism and ecology in a system; microbes, in turn, can affect the system's mineralogy. Increasingly, synchrotron-based X-ray experiments are in routine use for determining an element's valence state and coordination chemistry, as well as for examining the role of microbes in metal transformations.

  11. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.

    Science.gov (United States)

    Cerqueira, Teresa; Barroso, Cristina; Froufe, Hugo; Egas, Conceição; Bettencourt, Raul

    2018-01-21

    The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.

  12. An ultrasonic method for separation of epiphytic microbes from freshwater submerged macrophytes.

    Science.gov (United States)

    Cai, Xianlei; Gao, Guang; Yang, Jing; Tang, Xiangming; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

    2014-07-01

    Epiphytic microbes are common inhabitants of freshwater submerged macrophytes, which play an important role in aquatic ecosystems. An important precondition for studying the epiphytic microbes is having an effective method of separating the attached microbes from the host macrophytes. We developed an ultrasound-based method for separating epiphytic microbes from freshwater submerged macrophytes, optimized the conditions of ultrasonic separation with an orthogonal experimental design, and compared the optimized ultrasonic method with manual separation. This method can be particularly useful for freshwater submerged macrophytes having a complex morphology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. The RNA World: Life Before DNA and Protein

    Science.gov (United States)

    Joyce, Gerald F.

    1993-01-01

    All of the life that is known, all organisms that exist on Earth today or are known to have existed on Earth in the past, are of the same life form: a life form based on DNA and protein. It does not necessarily have to be that way. Why not have two competing life forms on this planet? Why not have biology as we know it and some other biology that occupies its own distinct niche? Yet that is not how evolution has played out. From microbes living on the surface of antarctic ice to tube worms lying near the deep-sea hydrothermal vents, all known organisms on this planet are of the same biology. Looking at the single known biology on Earth, it is clear that this biology could not have simply sprung forth from the primordial soup. The biological system that is the basis for all known. life is far too complicated to have arisen spontaneously. This brings us to the notion that something else something simpler, must have preceded life based on DNA and protein. One suggestion that has gained considerable acceptance over the past decade is that DNA and protein-based life was preceded by RNA-based life in a period referred to as the 'RNA world'. Even an RNA-based life form would have been fairly complicated - not as complicated as our own DNA- and protein-based life form - but far too complicated, according to prevailing scientific thinking, to have arisen spontaneously from the primordial soup. Thus, it has been argued that something else must have preceded RNA-based life, or even that there was a succession of life forms leading from the primordial soup to RNA-based life. The experimental evidence to support this conjecture is not strong because, after all, the origin of life was a historical event that left no direct physical record. However, based on indirect evidence in both the geological record and the phylogenetic record of evolutionary history on earth, it is possible to reconstruct a rough picture of what life was like before DNA and protein.

  14. Hydrothermal Fluid Permeability, Temperature, and Nutrient Fluxes: Three Controls on the Structure and the Dynamics of Subsurface Extremophilic Microbe Communities

    Science.gov (United States)

    Ryan, M. P.; Yang, J.

    2002-05-01

    We continue to develop a set of models whose aim is to provide broad constraints on the range of possible community structures for subsurface thermally-tolerant microbes. We combine studies of the three-dimensional internal structure of the dike and sill complexes of active volcanoes, studies of the scale- and direction-dependent 3-D in-situ permeability of intrusive and extrusive rocks from in-situ and laboratory data, numerical modelling of hydrothermal convection in volcanic interiors, data on the optimal metabolic and life-limiting thermal requirements of extremophilic microbes, with the set of nutrients and nutrient pathways required for the survival of given species of thermophiles and hyperthermophiles. With this mix of data bases and analysis tools, we can begin to divine a set of broad theoretical guidelines for constraining the structure and dynamics of extremophilic communities in the subsurface environments of volcanoes. We are searching for the first-order controls on transport. The effects of mineral attachment, detachment, and microbial reproduction may be incorporated in refinements of this basic model. Critical thermal intervals and/or isotherms that correlate with (1) optimal metabolic and (2) life-limiting temperatures for thermophilic microbes are, e.g., in degrees Celcius: Thermus thermophilius [70, 85]; Thermomicrobium roseum [70-75, 85]; Thermus aquaticus [70, 79]; and Sulfolobus acidocaldarius [70-75, 90]. Numerical models of the convective migration of thermophilic (50-80 C), and hyperthermophilic (80-113 C) microbes and their macromolecular amino acid building blocks (113- ~200 C) have been developed that explicitly incorporate the roles of fractures and fluid properties. Fluid transport properties are evaluated through the optimal metabolic and life-limiting temperate ranges and beyond. These models quantify our intuition with respect to controls on community structure and dynamics. Important relationships appear to be: (1) Great

  15. Diverse deep-sea fungi from the South China Sea and their antimicrobial activity.

    Science.gov (United States)

    Zhang, Xiao-Yong; Zhang, Yun; Xu, Xin-Ya; Qi, Shu-Hua

    2013-11-01

    We investigated the diversity of fungal communities in nine different deep-sea sediment samples of the South China Sea by culture-dependent methods followed by analysis of fungal internal transcribed spacer (ITS) sequences. Although 14 out of 27 identified species were reported in a previous study, 13 species were isolated from sediments of deep-sea environments for the first report. Moreover, these ITS sequences of six isolates shared 84-92 % similarity with their closest matches in GenBank, which suggested that they might be novel phylotypes of genera Ajellomyces, Podosordaria, Torula, and Xylaria. The antimicrobial activities of these fungal isolates were explored using a double-layer technique. A relatively high proportion (56 %) of fungal isolates exhibited antimicrobial activity against at least one pathogenic bacterium or fungus among four marine pathogenic microbes (Micrococcus luteus, Pseudoaltermonas piscida, Aspergerillus versicolor, and A. sydowii). Out of these antimicrobial fungi, the genera Arthrinium, Aspergillus, and Penicillium exhibited antibacterial and antifungal activities, while genus Aureobasidium displayed only antibacterial activity, and genera Acremonium, Cladosporium, Geomyces, and Phaeosphaeriopsis displayed only antifungal activity. To our knowledge, this is the first report to investigate the diversity and antimicrobial activity of culturable deep-sea-derived fungi in the South China Sea. These results suggest that diverse deep-sea fungi from the South China Sea are a potential source for antibiotics' discovery and further increase the pool of fungi available for natural bioactive product screening.

  16. Toward design-based engineering of industrial microbes.

    Science.gov (United States)

    Tyo, Keith E J; Kocharin, Kanokarn; Nielsen, Jens

    2010-06-01

    Engineering industrial microbes has been hampered by incomplete knowledge of cell biology. Thus an iterative engineering cycle of modeling, implementation, and analysis has been used to increase knowledge of the underlying biology while achieving engineering goals. Recent advances in Systems Biology technologies have drastically improved the amount of information that can be collected in each iteration. As well, Synthetic Biology tools are melding modeling and molecular implementation. These advances promise to move microbial engineering from the iterative approach to a design-oriented paradigm, similar to electrical circuits and architectural design. Genome-scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward Design-based Engineering. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. Lung Homeostasis: Influence of Age, Microbes, and the Immune System.

    Science.gov (United States)

    Lloyd, Clare M; Marsland, Benjamin J

    2017-04-18

    Pulmonary immune homeostasis is maintained by a network of tissue-resident cells that continually monitor the external environment, and in health, instruct tolerance to innocuous inhaled particles while ensuring that efficient and rapid immune responses can be mounted against invading pathogens. Here we review the multiple pathways that underlie effective lung immunity in health, and discuss how these may be affected by external environmental factors and contribute to chronic inflammation during disease. In this context, we examine the current understanding of the impact of the microbiota in immune development and function and in the setting of the threshold for immune responses that maintains the balance between tolerance and chronic inflammation in the lung. We propose that host interactions with microbes are critical for establishing the immune landscape of the lungs. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

    DEFF Research Database (Denmark)

    Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca

    2018-01-01

    , we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical......Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational...... engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined...

  19. Arsenic-Microbe-Mineral Interactions in Mining-Affected Environments

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson-Edwards

    2013-10-01

    Full Text Available The toxic element arsenic (As occurs widely in solid and liquid mine wastes. Aqueous forms of arsenic are taken up in As-bearing sulfides, arsenides, sulfosalts, oxides, oxyhydroxides, Fe-oxides, -hydroxides, -oxyhydroxides and -sulfates, and Fe-, Ca-Fe- and other arsenates. Although a considerable body of research has demonstrated that microbes play a significant role in the precipitation and dissolution of these As-bearing minerals, and in the alteration of the redox state of As, in natural and simulated mining environments, the molecular-scale mechanisms of these interactions are still not well understood. Further research is required using traditional and novel mineralogical, spectroscopic and microbiological techniques to further advance this field, and to help design remediation schemes.

  20. Busting dust: from cosmic grains to terrestrial microbes

    International Nuclear Information System (INIS)

    Mendis, D.A.

    2001-01-01

    Electrostatic charging can have important consequences for both the growth and disruption of microparticulates immersed in a plasma. In this topical review, my emphasis is on the latter process, while I extend the term microparticulates not only to include ordinary inanimate cosmic or terrestrial dust but also to include terrestrial microbes whose sizes range from tens of nanometers (viruses) to tens of micrometers (bacteria). Following a description of the basic mechanism of electrostatic disruption of a solid body, I will discuss the role of size, shape and surface irregularity on the process. I will also consider the mitigating role of electric field emission of electrons on the disruption process of a negatively charged grain as its size falls below a critical size. I will conclude by reviewing some early evidence for the electrostatic disruption of cosmic grains, and the very recent evidence for the electrostatic disruption of the bacterial cell membranes in terrestrial sterilization experiments. (orig.)

  1. Aminoacid composition of wheat grain gluten under microbe impact

    Directory of Open Access Journals (Sweden)

    Sokolova М. G.

    2012-11-01

    Full Text Available The study was focused on characteristics of gluten, protein and aminoacids content in wheat grain under the impact of microbe preparations including bacteria of Azotobacter and Bacillus geni, which inhabit plant rhizosphere. The increase of aminoacids leveland particularly the level of essential aminoacids in wheat grain under bacterization was demonstrated, this fact accounting for the quality of grain as an important protein source. Increase of aminoacids content with the use of biopreparations on low-fertile soil ensures acquisition of biologically valuable grain with the decrease of mineral fertilizers dosage and emphasizes the role of biopreparations in the production of ecologically pure high quality products. The latter is due to introdcution of environmentally safe agricultural methods.

  2. An overview of the ecological half-life of the 137Cs radioisotope and a determination of radioactivity levels in sediment samples after Chernobyl in the Eastern Black Sea, Turkey

    Science.gov (United States)

    Baltas, Hasan; Sirin, Murat; Dalgic, Goktug; Cevik, Ugur

    2018-01-01

    A study which determined the activity concentration of 137Cs in sediments contaminated by effluents from the Chernobyl accident which had collected along the coast of the Eastern Black Sea region in Turkey was carried out in 1993. Marine sediment samples were collected in 2015 from the same fifteen sampling points, and the activity concentrations of 226Ra, 232Th, 40K and 137Cs were determined for the sediment samples. The activity concentrations ranged from 10.94-25.95, 12.14-33.05, 265.74-459.89 and 2.08-37.45 Bq kg- 1 for 226Ra, 232Th, 40K and 137Cs respectively. The results showed that there was a steep decline in 137Cs within the sediment at most of the sampling sites from the Eastern Black Sea region during the 22-year period, except for two sites at which the measured levels were much higher. This may be the result of the combined effects of radioactive contaminant entry into this area from rivers, environmental changes and nuclear testing between 1993 and 2015. Furthermore, the ecological half-life (EHL) of the 137Cs radionuclide was estimated for the sediment samples, and radiological hazard parameters such as the absorbed dose rate in air (D), the annual effective dose equivalent (AEDE) and the excess lifetime cancer risk (ELCR) were calculated and compared with the international recommended values. It was shown that these sediments do not present any significant health risk for humans in this area.

  3. Functional metagenomics to decipher food-microbe-host crosstalk.

    Science.gov (United States)

    Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

    2015-02-01

    The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

  4. Exploring the Optimal Strategy to Predict Essential Genes in Microbes

    Directory of Open Access Journals (Sweden)

    Yao Lu

    2011-12-01

    Full Text Available Accurately predicting essential genes is important in many aspects of biology, medicine and bioengineering. In previous research, we have developed a machine learning based integrative algorithm to predict essential genes in bacterial species. This algorithm lends itself to two approaches for predicting essential genes: learning the traits from known essential genes in the target organism, or transferring essential gene annotations from a closely related model organism. However, for an understudied microbe, each approach has its potential limitations. The first is constricted by the often small number of known essential genes. The second is limited by the availability of model organisms and by evolutionary distance. In this study, we aim to determine the optimal strategy for predicting essential genes by examining four microbes with well-characterized essential genes. Our results suggest that, unless the known essential genes are few, learning from the known essential genes in the target organism usually outperforms transferring essential gene annotations from a related model organism. In fact, the required number of known essential genes is surprisingly small to make accurate predictions. In prokaryotes, when the number of known essential genes is greater than 2% of total genes, this approach already comes close to its optimal performance. In eukaryotes, achieving the same best performance requires over 4% of total genes, reflecting the increased complexity of eukaryotic organisms. Combining the two approaches resulted in an increased performance when the known essential genes are few. Our investigation thus provides key information on accurately predicting essential genes and will greatly facilitate annotations of microbial genomes.

  5. Climate change driven plant-metal-microbe interactions.

    Science.gov (United States)

    Rajkumar, Mani; Prasad, Majeti Narasimha Vara; Swaminathan, Sandhya; Freitas, Helena

    2013-03-01

    Various biotic and abiotic stress factors affect the growth and productivity of crop plants. Particularly, the climatic and/or heavy metal stress influence various processes including growth, physiology, biochemistry, and yield of crops. Climatic changes particularly the elevated atmospheric CO₂ enhance the biomass production and metal accumulation in plants and help plants to support greater microbial populations and/or protect the microorganisms against the impacts of heavy metals. Besides, the indirect effects of climatic change (e.g., changes in the function and structure of plant roots and diversity and activity of rhizosphere microbes) would lead to altered metal bioavailability in soils and concomitantly affect plant growth. However, the effects of warming, drought or combined climatic stress on plant growth and metal accumulation vary substantially across physico-chemico-biological properties of the environment (e.g., soil pH, heavy metal type and its bio-available concentrations, microbial diversity, and interactive effects of climatic factors) and plant used. Overall, direct and/or indirect effects of climate change on heavy metal mobility in soils may further hinder the ability of plants to adapt and make them more susceptible to stress. Here, we review and discuss how the climatic parameters including atmospheric CO₂, temperature and drought influence the plant-metal interaction in polluted soils. Other aspects including the effects of climate change and heavy metals on plant-microbe interaction, heavy metal phytoremediation and safety of food and feed are also discussed. This review shows that predicting how plant-metal interaction responds to altering climatic change is critical to select suitable crop plants that would be able to produce more yields and tolerate multi-stress conditions without accumulating toxic heavy metals for future food security. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

    Science.gov (United States)

    Chen, M.; Kocar, B. D.

    2016-12-01

    Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

  7. The origin of life: The growing evidence for panspermia

    International Nuclear Information System (INIS)

    Wickramasinghe, C.

    2008-01-01

    Evidence from astronomy, biology, and geology are converging to point to life being a cosmic phenomenon. Microbial life was already evolved and widely dispersed in the galaxy at the time of the formation of the solar nebula. Life on Earth originates with the warm liquid interiors of comets amplifying an incipient galactic microbiology, and introducing viable microbes onto the planet

  8. Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge

    DEFF Research Database (Denmark)

    Aslam, Shazia N.; Erbs, Gitte; Morrissey, Kate L.

    2009-01-01

    Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidops...

  9. Plant-microbe and plant-insect interactions meet common grounds

    NARCIS (Netherlands)

    Schenk, P.; McGrath, K.C.; Lorito, M.; Pieterse, C.M.J.

    2008-01-01

    Plant–microbe and plant–insect interactions are of global importance for agriculture and of high interest to many plant scientists, microbiologists and entomologists. Traditionally, plant–microbe and plant–insect interactions have been looked at as two separate issues, but in recent years it has

  10. Biogeographical diversity of plant associated microbes in arcto-alpine plants

    NARCIS (Netherlands)

    Kumar, Manoj Gopala Krishnan

    2016-01-01

    Terrestrial plants and microbes have co-evolved since the emergence of the former on Earth. Associations with microorganisms can be either beneficial or detrimental for plants. Microbes can be found in the soil surrounding the plant roots, but also in all plant tissues, including seeds. In

  11. Coercion in the Evolution of Plant-Microbe Communication: A Perspective.

    Science.gov (United States)

    Rowe, S L; Norman, J S; Friesen, M L

    2018-06-06

    Plants and microbes are dependent on chemical signals as a means of interkingdom communication. There are two predicted paths for the evolution of these signals. Ritualization is the oft-assumed pathway for the evolution of plant-microbe communication systems. In this process, chemical signals, which benefit both receiver and sender, evolve from chemical cues, which benefit only the receiver. However, plant-microbe signaling may evolve from coercive interactions as well, a process known as sensory manipulation. Here, we aim to highlight the prevalence of coercive interactions and discuss sensory manipulation in the context of plant-microbe interactions. We present two examples of stabilized coercion: microbial coercion of plants via the release of phytohormones and plant coercion of microbes via manipulation of quorum-sensing compounds. Furthermore, we provide an evolutionary framework for the emergence of signaling from coercive plant-microbe interactions through the process of sensory manipulation. We hope that researchers will recognize the relevance of coercive interactions in plant-microbe systems and consider sensory manipulation as a plausible evolutionary trajectory for the emergence of plant-microbe signaling.

  12. Earthworms, Microbes and the Release of C and N in Biochar Amended Soil

    Science.gov (United States)

    Land application of biochar has the potential to increase soil fertility and sequester carbon. It is unclear how soil microbes and earthworms interact with biochar and affect release or retention of nutrients. In order to determine the effects and interactions among soil microbes, earthworms, and bi...

  13. Influence of body size, metabolic rate and life history stage on the uptake and excretion of the lampricide 3-trifluoromethyl-4-nitrophenol (TFM) by invasive sea lampreys (Petromyzon marinus).

    Science.gov (United States)

    Tessier, Laura R; Long, Tristan A F; Wilkie, Michael P

    2018-01-01

    Invasive sea lamprey (Petromyzon marinus) are controlled in the Great Lakes using the lampricide 3-trifluoromethyl-4-nitrophenol (TFM), which is applied to streams infested with larval lamprey. However, lamprey that survive treatments (residuals) remain a challenge because they may subsequently undergo metamorphosis into parasitic juvenile animals that migrate downstream to the Great Lakes, where they feed on important sport and commercial fishes. The goal of this study was to determine if body size and life stage could potentially influence sea lamprey tolerance to TFM by influencing patterns of TFM uptake and elimination. Because mass specific rates of oxygen consumption (M˙O 2 ) are lower in larger compared to smaller lamprey, we predicted that TFM uptake would be negatively correlated to body size, suggesting that large larvae would be more tolerant to TFM exposure. Accordingly, TFM uptake and M˙O 2 were measured in larvae ranging in size from 0.2-4.2g using radio-labelled TFM ( 14 C-TFM) and static respirometry. Both were inversely proportional to wet mass (M), and could be described usingthe allometric power relationship: Y=aM b , in which M˙O 2 =1.86M 0.53 and TFM Uptake=7.24M 0.34 . We also predicted that body size would extend to rates of TFM elimination, which was measured following the administration of 14 C-TFM (via intraperitoneal injection). However, there were no differences in the half-lives of elimination of TFM (T 1/2 -TFM). There were also no differences in M˙O 2 or TFM uptake amongst size-matched larval, metamorphosing (stages 6-7), or post-metamorphic (juvenile) sea lamprey. However, the T 1/2 -TFM was significantly lower in larval than post-metamorphic lamprey (juvenile), indicating the larval lamprey cleared TFM more efficiently than juvenile lamprey. We conclude that larger larval sea lamprey are more likely to survive TFM treatments suggesting that body size might be an important variable to consider when treating streams with TFM to

  14. Reference life cycle assessment scenarios for manure management in the Baltic Sea Regions - An assessment covering six animal production, five BSR countries, and four manure types

    DEFF Research Database (Denmark)

    Hamelin, Lorie; Baky, A; Cano-Bernal, J

    the manure is applied, specific legislations governing the manure management practices, etc.). Further, it presents a reference manure composition for each of these reference systems, including key parameters such as dry matter, nitrogen (inorganic and total), phosphorus, carbon and volatile solids content......One major pre-condition for assessing a manure management technique in a whole system or LCA-approach is to define a reference system against which this technique can be assessed. This report thus presents and details the establishment of such reference systems, comprising eight different manure...... types (fattening pig slurry, dairy cow slurry, hens manure, bulls deep litter, fattening pig solid manure, dairy cow solid manure, horse manure & broilers manure) and five Baltic Sea Regions (Denmark, Sweden, Finland, Estonia, Poland), for a total of 15 reference systems. It presents, for each...

  15. Life in the fluvial hinterland of the late Sarmatian Sea (middle Miocene): a rare terrestrial fossil site in the Styrian Basin (Austria)

    Science.gov (United States)

    Doubrawa, Monika; Gross, Martin; Harzhauser, Mathias

    2018-02-01

    This paper describes the section and fossil content of a former gravel pit in the Eastern Styrian Basin (SE Austria), which exposes sediments of a fluvial system, ranging from within channel to overbank environments. A predominately terrestrial gastropod fauna of 15 species so far, was recovered from a palaeosol formed in a moist and vegetated, floodplain or abandoned channel. Up-section, a shallow freshwater pond/lake developed within the floodplain, settled by fishes, molluscs and ostracods. By integrating regional geological and biostratigraphical data derived from the terrestrial gastropod fauna as well as from the other recovered biota, these strata are of late middle Miocene (late Sarmatian s.str.) age. Hence, this fossil site provides a rare insight into the terrestrial habitats in the hinterland of the Sarmatian Sea and their biota, which are otherwise barely known in Central Europe.

  16. Sea level trends in South East Asian Seas (SEAS)

    Science.gov (United States)

    Strassburg, M. W.; Hamlington, B. D.; Leben, R. R.; Manurung, P.; Lumban Gaol, J.; Nababan, B.; Vignudelli, S.; Kim, K.-Y.

    2014-10-01

    Southeast Asian Seas (SEAS) span the largest archipelago in the global ocean and provide a complex oceanic pathway connecting the Pacific and Indian Oceans. The SEAS regional sea level trends are some of the highest observed in the modern satellite altimeter record that now spans almost two decades. Initial comparisons of global sea level reconstructions find that 17 year sea level trends over the past 60 years exhibit good agreement in areas and at times of strong signal to noise associated decadal variability forced by low frequency variations in Pacific trade winds. The SEAS region exhibits sea level trends that vary dramatically over the studied time period. This historical variation suggests that the strong regional sea level trends observed during the modern satellite altimeter record will abate as trade winds fluctuate on decadal and longer time scales. Furthermore, after removing the contribution of the Pacific Decadal Oscillation (PDO) to sea level trends in the past twenty years, the rate of sea level rise is greatly reduced in the SEAS region. As a result of the influence of the PDO, the SEAS regional sea level trends during 2010s and 2020s are likely to be less than the global mean sea level (GMSL) trend if the observed oscillations in wind forcing and sea level persist. Nevertheless, long-term sea level trends in the SEAS will continue to be affected by GMSL rise occurring now and in the future.

  17. Viral lysis of marine microbes in relation to vertical stratification

    NARCIS (Netherlands)

    Mojica, K.D.A.

    2015-01-01

    Marine microorganisms represent the largest reservoir of living organic carbon in the ocean and collectively manage the pools and fluxes of nutrients and energy. Climate-induced increases in sea surface temperature and associated modifications to vertical stratification are affecting the structure

  18. Microbes versus microbes

    DEFF Research Database (Denmark)

    Jordan, Kieran; Dalmasso, Marion; Zentek, Juergen

    2014-01-01

    been used in food processing to improve food safety. An understanding of the mode of action of this microbial antagonism has been gained in recent years and potential applications in food and feed safety are now being explored. This review focuses on the potential opportunities presented......Foodborne illness continues as a considerable threat to public health. Despite improved hygiene management systems and increased regulation, pathogenic bacteria still contaminate food, causing sporadic cases of illness and disease outbreaks worldwide. For many centuries, microbial antagonism has......, and the limitations, of using microbial antagonism as a biocontrol mechanism to reduce contamination along the food chain; including animal feed as its first link. © 2014 Society of Chemical Industry....

  19. Copepods in ice-covered seas—Distribution, adaptations to seasonally limited food, metabolism, growth patterns and life cycle strategies in polar seas

    Science.gov (United States)

    Conover, R. J.; Huntley, M.

    1991-07-01

    While a seasonal ice cover limits light penetration into both polar seas for up to ten months a year, its presence is not entirely negative. The mixed layer under sea ice will generally be shallower than in open water at the same latitude and season. Ice forms a substrate on which primary production can be concentrated, a condition which contrasts with the generally dilute nutritional conditions which prevail in the remaining ocean. The combination of a shallow, generally stable mixed layer with a close proximity to abundant food make the under-ice zone a suitable nursery for both pelagic and benthic species, an upside-down benthos for opportunistic substrate browsers, and a rich feeding environment for species often considered to be neritic in temperate environments. Where the ice cover is not continuous there may be a retreating ice edge that facilitates the seasonal production of phytoplankton primarily through increased stability from the melt water. Ice edge blooms similarly encourage secondary production by pelagic animals. Pseudocalanus acuspes, which may be the most abundant and productive copepod in north polar latitudes, initiates growth at the start of the "spring bloom" of epontic algae, reaching sexual maturity at breakup or slightly before. In the Southern Hemisphere, the small neritic copepod Paralabidocera antarctica and adult krill have been observed to utilize ice algae. Calanus hyperboreus breeds in the dark season at depth and its buoyant eggs, slowly developing on the ascent, reach the under-ice layer in April as nauplii ready to benefit from the primary production there. On the other hand, C. glacialis may initiate ontogenetic migrations and reproduction in response to increased erosion of ice algae due to solar warming and melting at the ice-water interface. While the same species in a phytoplankton bloom near the ice edge reproduces actively, those under still-consolidated ice nearby can have immature gonads. Diel migration and diel feeding

  20. Saharan dust - a carrier of persistent organic pollutants, metals and microbes to the Caribbean?

    Directory of Open Access Journals (Sweden)

    V.H Garrison

    2006-12-01

    Full Text Available An international team of scientists from government agencies and universities in the United States, U.S. Virgin Islands (USVI, Trinidad & Tobago, the Republic of Cape Verde, and the Republic of Mali (West Africa is working together to elucidate the role Saharan dust may play in the degradation of Caribbean ecosystems. The first step has been to identify and quantify the persistent organic pollutants (POPs, trace metals, and viable microorganisms in the atmosphere in dust source areas of West Africa, and in dust episodes at downwind sites in the eastern Atlantic (Cape Verde and the Caribbean (USVI and Trinidad & Tobago. Preliminary findings show that air samples from Mali contain a greater number of pesticides, polychlorinated biphenyls (PCBs and polycyclic aromatic hydrocarbons (PAHs and in higher concentrations than the Caribbean sites. Overall, POP concentrations were similar in USVI and Trinidad samples. Trace metal concentrations were found to be similar to crustal composition with slight enrichment of lead in Mali. To date, hundreds of cultureable micro-organisms have been identified from Mali, Cape Verde, USVI, and Trinidad air samples. The sea fan pathogen, Aspergillus sydowii, has been identified in soil from Mali and in air samples from dust events in the Caribbean. We have shown that air samples from a dust-source region contain orders of magnitude more cultureable micro-organisms per volume than air samples from dust events in the Caribbean, which in turn contain 3-to 4-fold more cultureable microbes than during non-dust conditions. Rev. Biol. Trop. 54 (Suppl. 3: 9-21. Epub 2007 Jan. 15.

  1. Microbes Characteristics in Groundwater Flow System in Mountainous Area

    Science.gov (United States)

    Yamamoto, Chisato; Tsujimura, Maki; Kato, Kenji; Sakakibara, Koichi; Ogawa, Mahiro; Sugiyama, Ayumi; Nagaosa, Kazuyo

    2017-04-01

    We focus on a possibility of microbes as a tracer for groundwater flow investigation. Some previous papers showed that the total number of prokaryotes in groundwater has correlation with depth and geology (Parkes et al., 1994; Griebler et al., 2009; Kato et al., 2012). However, there are few studies investigating both microbe characteristics and groundwater flow system. Therefore, we investigated a relationship between the total number of prokaryotes and age of spring water and groundwater. Intensive field survey was conducted at four mountainous areas, namely Mt. Fuji (volcano), a headwater at Mt. Setohachi, a headwater at River Oi and a headwater at River Nagano underlain by volcanic lava at Mt. Fuji, granite at Mt. Setohachi and sedimentary rock at River Oi and River Nagano. We collected totally 40 spring water/ groundwater samples in these mountainous areas in October 2015, August, October and November 2016 and analyzed concentration of inorganic ions, the stable isotopes of oxygen - 18, deuterium, CFCs and SF6. Also, we counted prokaryotic cells under the epifluorescence microscopy after fixation and filteration. The total number of prokaryotes in the spring water/ groundwater ranged from 1.0×102 to 7.0×103cells mL-1 at the Mt. Fuji, 1.3×104 to 2.7×105cells mL-1 at Mt. Setohachi, 3.1×104cells mL-1 at River Oi and 1.8×105 to 3.2×106cells mL-1 at River Nagano. The SF6 age of the spring water/ groundwater ranged from 8 to 64 years at Mt. Fuji, 2 to 32.5 years at Mt. Setohachi, 2.5 years at River Oi and 15 to 16 years at River Nagano. The total number of prokaryotes showed a clear negative correlation with residence time of spring water/ groundwater in all regions. Especially the prokaryotes number increased in the order of 102 cells mL-1 with decreasing of residence time in approximately 10 years in the groundwater and spring water with the age less than 15 years.

  2. Sea Ice

    Science.gov (United States)

    Perovich, D.; Gerland, S.; Hendricks, S.; Meier, Walter N.; Nicolaus, M.; Richter-Menge, J.; Tschudi, M.

    2013-01-01

    During 2013, Arctic sea ice extent remained well below normal, but the September 2013 minimum extent was substantially higher than the record-breaking minimum in 2012. Nonetheless, the minimum was still much lower than normal and the long-term trend Arctic September extent is -13.7 per decade relative to the 1981-2010 average. The less extreme conditions this year compared to 2012 were due to cooler temperatures and wind patterns that favored retention of ice through the summer. Sea ice thickness and volume remained near record-low levels, though indications are of slightly thicker ice compared to the record low of 2012.

  3. Potential Physiologies of Deep Branches on the Tree of Life with Deep Subsurface Samples from IODP Leg 347: Baltic Sea Paleoenvironment

    Science.gov (United States)

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

    2014-12-01

    Very little is known about how evolutionary branches that are distantly related to cultured microorganisms make a living in the deep subsurface marine environment. Here, sediments are cut-off from surface inputs of organic substrates for tens of thousands of years; yet somehow support a diverse population of microorganisms. We examined the potential metabolic and ecological roles of uncultured archaea and bacteria in IODP Leg 347: Baltic Sea Paleoenvironment samples, using quantitative PCR holes 60B, 63E, 65C, and 59C and single cell genomic analysis for hole 60B. We quantified changes in total archaea and bacteria, as well as deeply-branching archaeal taxa with depth. These sediment cores alternate between high and low salinities, following a glacial cycle. This allows changes in the quantities of these groups to be placed in the context of potentially vastly different organic matter sources. In addition, single cells were isolated, and their genomes were amplified and sequenced to allow a deeper look into potential physiologies of uncultured deeply-branching organisms found up to 86 meters deep in marine sediments. Together, these data provide deeper insight into the relationship between microorganisms and their organic matter substrates in this extreme environments.

  4. Sea level change

    Digital Repository Service at National Institute of Oceanography (India)

    Church, J.A.; Clark, P.U.; Cazenave, A.; Gregory, J.M.; Jevrejeva, S.; Levermann, A.; Merrifield, M.A.; Milne, G.A.; Nerem, R.S.; Nunn, P.D.; Payne, A.J.; Pfeffer, W.T.; Stammer, D.; Unnikrishnan, A.S.

    This chapter considers changes in global mean sea level, regional sea level, sea level extremes, and waves. Confidence in projections of global mean sea level rise has increased since the Fourth Assessment Report (AR4) because of the improved...

  5. Reduction of nutrients, microbes, and personal care products in domestic wastewater by a benchtop electrocoagulation unit

    Science.gov (United States)

    Symonds, E. M.; Cook, M. M.; McQuaig, S. M.; Ulrich, R. M.; Schenck, R. O.; Lukasik, J. O.; van Vleet, E. S.; Breitbart, M.

    2015-03-01

    To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic wastewater. EC treatment resulted in significant reductions (p < 0.05, α = 0.05) in phosphate, all microbial surrogates, and several personal care products from raw and tertiary-treated domestic wastewater. When wastewater was augmented with microbial surrogates representing bacterial, viral, and protozoan pathogens to measure the extent of reduction, EC treatment resulted in up to 7-log10 reduction of microbial surrogates. Future pilot and full-scale investigations are needed to optimize EC treatment for the following: reducing nitrogen species, personal care products, and energy consumption; elucidating the mechanisms behind microbial reductions; and performing life cycle analyses to determine the appropriateness of implementation.

  6. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

    Directory of Open Access Journals (Sweden)

    Jenna M. Lang

    2014-12-01

    Full Text Available Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1 the Average American (AMERICAN: focused on convenience foods, (2 USDA recommended (USDA: emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3 Vegan (VEGAN: excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG

  7. Linking plant nutritional status to plant-microbe interactions.

    Science.gov (United States)

    Carvalhais, Lilia C; Dennis, Paul G; Fan, Ben; Fedoseyenko, Dmitri; Kierul, Kinga; Becker, Anke; von Wiren, Nicolaus; Borriss, Rainer

    2013-01-01

    Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N), phosphate (P), iron (Fe) and potassium (K) deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR) Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress.

  8. Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

    Science.gov (United States)

    Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

    2018-05-11

    Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

  9. Metabolic engineering of volatile isoprenoids in plants and microbes.

    Science.gov (United States)

    Vickers, Claudia E; Bongers, Mareike; Liu, Qing; Delatte, Thierry; Bouwmeester, Harro

    2014-08-01

    The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids. © 2014 John Wiley & Sons Ltd.

  10. Anaerobic Probiotics: The Key Microbes for Human Health.

    Science.gov (United States)

    El Enshasy, Hesham; Malik, Khairuddin; Malek, Roslinda Abd; Othman, Nor Zalina; Elsayed, Elsayed Ahmed; Wadaan, Mohammad

    Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.

  11. Diet, genes, and microbes: complexities of colon cancer prevention.

    Science.gov (United States)

    Birt, Diane F; Phillips, Gregory J

    2014-01-01

    Colorectal cancer is one of the leading causes of cancer-related deaths in the United States, and generally, as countries climb the economic ladder, their rates of colon cancer increase. Colon cancer was an early disease where key genetic mutations were identified as important in disease progression, and there is considerable interest in determining whether specific mutations sensitize the colon to cancer prevention strategies. Epidemiological studies have revealed that fiber- and vegetable-rich diets and physical activity are associated with reduced rates of colon cancer, while consumption of red and processed meat, or alcoholic beverages, and overconsumption as reflected in obesity are associated with increased rates. Animal studies have probed these effects and suggested directions for further refinement of diet in colon cancer prevention. Recently a central role for the microorganisms in the gastrointestinal tract in colon cancer development is being probed, and it is hypothesized that the microbes may integrate diet and host genetics in the etiology of the disease. This review provides background on dietary, genetic, and microbial impacts on colon cancer and describes an ongoing project using rodent models to assess the ability of digestion-resistant starch in the integration of these factors with the goal of furthering colon cancer prevention.

  12. The role of lipids in host microbe interactions.

    Science.gov (United States)

    Lang, Roland; Mattner, Jochen

    2017-06-01

    Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

  13. Utilization of waste as biogas substrateby dominan microbes identified

    Science.gov (United States)

    Nurlina, E.; Sambasri, S.; Hartati, E.; Safitri, R.; Hodijat, A.

    2018-05-01

    Indonesia as the tropics have a source of biomass feedstock which is very large, so the waste biomass can be used optimally as an energy source in the form of biogas. This study was conducted to obtain alternative energy from domestic waste materials, given the limited availability of petroleum and natural gas sourced from fossil fuels. This methodology is an experimental method, the process conditions at room temperature 25-27 °C, pH adjusted to the growth of microbes to produce biogas, retention time 20-60 days, the bioreactor is operated with a batch system, the volume of waste in the bioreactor is made permanent, so that the production of biogas in large scale will increase the pressure inside the bioreactor. Biogas is formed accommodated then distributed to the stove. Factors that determine the formation of biogas is a microbial species capable methanogens convert acetate into biogas. From the results of microbial identification of the isolates in the bioreactor, has identified three types of bacteria methanogens namely Methanospirillum hungatei, Methanobacterium polustre and Methanolacinapoynteri. The results of this study, domestic waste can be utilized as a substrate in biogas production, with the highest methane composition reaches 50.79%. This result is expected to increase public knowledge to utilize the waste into biogas as a renewable energy to sufficient the energy needs of household, so it does not depend on the energy derived from fossil fuels.

  14. Detoxification of Fusaric Acid by the Soil Microbe Mucor rouxii.

    Science.gov (United States)

    Crutcher, Frankie K; Puckhaber, Lorraine S; Bell, Alois A; Liu, Jinggao; Duke, Sara E; Stipanovic, Robert D; Nichols, Robert L

    2017-06-21

    Fusarium oxysporum f. sp. vasinfectum race 4 (VCG0114), which causes root rot and wilt of cotton (Gossypium hirsutum and G. barbadense), has been identified recently for the first time in the western hemisphere in certain fields in the San Joaquin Valley of California. This pathotype produces copious quantities of the plant toxin fusaric acid (5-butyl-2-pyridinecarboxylic acid) compared to other isolates of F. oxysporum f. sp. vasinfectum (Fov) that are indigenous to the United States. Fusaric acid is toxic to cotton plants and may help the pathogen compete with other microbes in the soil. We found that a laboratory strain of the fungus Mucor rouxii converts fusaric acid into a newly identified compound, 8-hydroxyfusaric acid. The latter compound is significantly less phytotoxic to cotton than the parent compound. On the basis of bioassays of hydroxylated analogues of fusaric acid, hydroxylation of the butyl side chain of fusaric acid may affect a general detoxification of fusaric acid. Genes that control this hydroxylation may be useful in developing biocontrol agents to manage Fov.

  15. Microbe-surface interactions in biofouling and biocorrosion processes.

    Science.gov (United States)

    Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

    2005-09-01

    The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

  16. Of genes and microbes: solving the intricacies in host genomes.

    Science.gov (United States)

    Wang, Jun; Chen, Liang; Zhao, Na; Xu, Xizhan; Xu, Yakun; Zhu, Baoli

    2018-05-01

    Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.

  17. Designer cells programming quorum-sensing interference with microbes.

    Science.gov (United States)

    Sedlmayer, Ferdinand; Hell, Dennis; Müller, Marius; Ausländer, David; Fussenegger, Martin

    2018-05-08

    Quorum sensing is a promising target for next-generation anti-infectives designed to address evolving bacterial drug resistance. The autoinducer-2 (AI-2) is a key quorum-sensing signal molecule which regulates bacterial group behaviors and is recognized by many Gram-negative and Gram-positive bacteria. Here we report a synthetic mammalian cell-based microbial-control device that detects microbial chemotactic formyl peptides through a formyl peptide sensor (FPS) and responds by releasing AI-2. The microbial-control device was designed by rewiring an artificial receptor-based signaling cascade to a modular biosynthetic AI-2 production platform. Mammalian cells equipped with the microbial-control gene circuit detect formyl peptides secreted from various microbes with high sensitivity and respond with robust AI-2 production, resulting in control of quorum sensing-related behavior of pathogenic Vibrio harveyi and attenuation of biofilm formation by the human pathogen Candida albicans. The ability to manipulate mixed microbial populations through fine-tuning of AI-2 levels may provide opportunities for future anti-infective strategies.

  18. Oil and the Caspian Sea

    International Nuclear Information System (INIS)

    Mohammad Poure Daryaei, N.

    2000-01-01

    Caspian Sea is the biggest lake in the world. It is almost F-shape and located between five Countries of Iran, Turkmenistan, Russia, Azarbayjohn, Ghazaghestan. Un fortunately, in the different region of the sea there are highly contaminated oil, in addition with other source of pollutants such as: agricultural, industrial and domestic pollution, which causes to eliminate the natural habitats of aquatic life and thus, the Caspian sea with all of the valuable natural sources of foods and energy is close to be destroyed. This paper studies the pollution by oil industry which causes the elimination of aquatic life and natural ecosystem, as well as, necessary plan to over come the present situation

  19. Trans-life cycle acclimation to experimental ocean acidification affects gastric pH homeostasis and larval recruitment in the sea star Asterias rubens.

    Science.gov (United States)

    Hu, Marian Y; Lein, Etienne; Bleich, Markus; Melzner, Frank; Stumpp, Meike

    2018-04-16

    Experimental simulation of near-future ocean acidification (OA) has been demonstrated to affect growth and development of echinoderm larval stages through energy allocation towards ion and pH compensatory processes. To date, it remains largely unknown how major pH regulatory systems and their energetics are affected by trans-generational exposure to near-future acidification levels. Here we used the common sea star Asterias rubens in a reciprocal transplant experiment comprising different combinations of OA scenarios, in order to study trans-generational plasticity using morphological and physiological endpoints. Acclimation of adults to pH T 7.2 (pCO 2 3500μatm) led to reductions in feeding rates, gonad weight, and fecundity. No effects were evident at moderate acidification levels (pH T 7.4; pCO 2 2000μatm). Parental pre-acclimation to pH T 7.2 for 85 days reduced developmental rates even when larvae were raised under moderate and high pH conditions, whereas pre-acclimation to pH T 7.4 did not alter offspring performance. Microelectrode measurements and pharmacological inhibitor studies carried out on larval stages demonstrated that maintenance of alkaline gastric pH represents a substantial energy sink under acidified conditions that may contribute up to 30% to the total energy budget. Parental pre-acclimation to acidification levels that are beyond the pH that is encountered by this population in its natural habitat (e.g. pH T 7.2) negatively affected larval size and development, potentially through reduced energy transfer. Maintenance of alkaline gastric pH and reductions in maternal energy reserves probably constitute the main factors for a reduced juvenile recruitment of this marine keystone species under simulated OA. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  20. Population Trend and Elasticities of Vital Rates for Steller Sea Lions (Eumetopias jubatus in the Eastern Gulf of Alaska: A New Life-History Table Analysis.

    Directory of Open Access Journals (Sweden)

    John M Maniscalco

    Full Text Available Steller sea lion (Eumetopias jubatus numbers are beginning to recover across most of the western distinct population segment following catastrophic declines that began in the 1970s and ended around the turn of the century. This study makes use of contemporary vital rate estimates from a trend-site rookery in the eastern Gulf of Alaska (a sub-region of the western population in a matrix population model to estimate the trend and strength of the recovery across this region between 2003 and 2013. The modeled population trend was projected into the future based on observed variation in vital rates and a prospective elasticity analysis was conducted to determine future trends and which vital rates pose the greatest threats to recovery. The modeled population grew at a mean rate of 3.5% per yr between 2003 and 2013 and was correlated with census count data from the local rookery and throughout the eastern Gulf of Alaska. If recent vital rate estimates continue with little change, the eastern Gulf of Alaska population could be fully recovered to pre-decline levels within 23 years. With density dependent growth, the population would need another 45 years to fully recover. Elasticity analysis showed that, as expected, population growth rate (λ was most sensitive to changes in adult survival, less sensitive to changes in juvenile survival, and least sensitive to changes in fecundity. A population decline could be expected with only a 6% decrease in adult survival, whereas a 32% decrease in fecundity would be necessary to bring about a population decline. These results have important implications for population management and suggest current research priorities should be shifted to a greater emphasis on survival rates and causes of mortality.

  1. Population Trend and Elasticities of Vital Rates for Steller Sea Lions (Eumetopias jubatus) in the Eastern Gulf of Alaska: A New Life-History Table Analysis.

    Science.gov (United States)

    Maniscalco, John M; Springer, Alan M; Adkison, Milo D; Parker, Pamela

    2015-01-01

    Steller sea lion (Eumetopias jubatus) numbers are beginning to recover across most of the western distinct population segment following catastrophic declines that began in the 1970s and ended around the turn of the century. This study makes use of contemporary vital rate estimates from a trend-site rookery in the eastern Gulf of Alaska (a sub-region of the western population) in a matrix population model to estimate the trend and strength of the recovery across this region between 2003 and 2013. The modeled population trend was projected into the future based on observed variation in vital rates and a prospective elasticity analysis was conducted to determine future trends and which vital rates pose the greatest threats to recovery. The modeled population grew at a mean rate of 3.5% per yr between 2003 and 2013 and was correlated with census count data from the local rookery and throughout the eastern Gulf of Alaska. If recent vital rate estimates continue with little change, the eastern Gulf of Alaska population could be fully recovered to pre-decline levels within 23 years. With density dependent growth, the population would need another 45 years to fully recover. Elasticity analysis showed that, as expected, population growth rate (λ) was most sensitive to changes in adult survival, less sensitive to changes in juvenile survival, and least sensitive to changes in fecundity. A population decline could be expected with only a 6% decrease in adult survival, whereas a 32% decrease in fecundity would be necessary to bring about a population decline. These results have important implications for population management and suggest current research priorities should be shifted to a greater emphasis on survival rates and causes of mortality.

  2. How Do Small Things Make a Big Difference? Activities to Teach about Human-Microbe Interactions.

    Science.gov (United States)

    Jasti, Chandana; Hug, Barbara; Waters, Jillian L; Whitaker, Rachel J

    2014-11-01

    Recent scientific studies are providing increasing evidence for how microbes living in and on us are essential to our good health. However, many students still think of microbes only as germs that harm us. The classroom activities presented here are designed to shift student thinking on this topic. In these guided inquiry activities, students investigate human-microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models. Through the activities, students learn and apply ecological concepts as they come to see the human body as a fascinatingly complex ecosystem.

  3. How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions

    Science.gov (United States)

    JASTI, CHANDANA; HUG, BARBARA; WATERS, JILLIAN L.; WHITAKER, RACHEL J.

    2014-01-01

    Recent scientific studies are providing increasing evidence for how microbes living in and on us are essential to our good health. However, many students still think of microbes only as germs that harm us. The classroom activities presented here are designed to shift student thinking on this topic. In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models. Through the activities, students learn and apply ecological concepts as they come to see the human body as a fascinatingly complex ecosystem. PMID:25520526

  4. Biosurfactant Producing Microbes from Oil Contaminated Soil - Isolation, Screening and Characterization

    OpenAIRE

    , A Pandey; , D Nandi; , N Prasad; , S Arora

    2016-01-01

    Th1s paper bas1cally deals W1th 1solat10n, productıon and characterızatıon of biosurfactant producing microbes from oil contaminated soil sample. In this paper, we are comparing and discussing different methods to screen & characterize microbes from soil which can degrade oil due to their biosurfactant producing activity which helps in reduction of surface tension of oil. Oils used to check the biosurfactant activity of microbes, were engine oil and vegetable oil. Further isolation of...

  5. The effects of packaging materials on microbe population in irradiated traditional herbal medicines

    International Nuclear Information System (INIS)

    Bagiawati, Sri; Hilmy, Nazly

    1983-01-01

    Microbial population and moisture content of traditional herbal medicines contaminated with 3 kinds of aerobic microbes, packed in 5 kinds of plastic packaging materials, followed by irradiation at minimum dose of 5 kGy and stored for 6 months were investigated. The highest reduction of microbial counts during storage was observed on samples packed in polyethylene bags. All of packaging materials used were found to be impermeable to microbes and water vapour. Radiation and packaging materials used acted synergistically to inactivate microbes durind storage. The microbial counts decreased as much as 2 to 4 log cycles during storage. (author)

  6. GOLD - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available search(/contents-en/) != -1 || url.search(/index-e.html/) != -1 ) { document.getElementById(lang).innerHTML=.../) != -1 ) { url = url.replace(-e.html,.html); document.getElementById(lang).innerHTML=[ Japanese |...en/,/jp/); document.getElementById(lang).innerHTML=[ Japanese | English ]; } else if ( url.search(//contents...//) != -1 ) { url = url.replace(/contents/,/contents-en/); document.getElementById(lang).innerHTML=[ Japanes...e(/contents-en/,/contents/); document.getElementById(lang).innerHTML=[ Japanese | English ]; } else if( url.

  7. Download - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available search(/contents-en/) != -1 || url.search(/index-e.html/) != -1 ) { document.getElementById(lang).innerHTML=.../) != -1 ) { url = url.replace(-e.html,.html); document.getElementById(lang).innerHTML=[ Japanese |...en/,/jp/); document.getElementById(lang).innerHTML=[ Japanese | English ]; } else if ( url.search(//contents...//) != -1 ) { url = url.replace(/contents/,/contents-en/); document.getElementById(lang).innerHTML=[ Japanes...e(/contents-en/,/contents/); document.getElementById(lang).innerHTML=[ Japanese | English ]; } else if( url.

  8. Bion M1. Peculiarities of life activities of microbes in 30-day spaceflight

    Science.gov (United States)

    Viacheslav, Ilyin; Korshunov, Denis; Morozova, Julia; Voeikova, Tatiana; Tyaglov, Boris; Novikova, Liudmila; Krestyanova, Irina; Emelyanova, Lydia

    The aim of this work was to analyze the influence of space flight factors ( SFF) to microorganism strains , exposed inside unmanned spacecraft Bion M-1 during the 30- day space flight. Objectives of the work - the study of the influence of the SFF exchange chromosomal DNA in crosses microorganisms of the genus Streptomyces; the level of spontaneous phage induction of lysogenic strains fS31 from Streptomyces lividans 66 and Streptomyces coelicolor A3 ( 2 ) on the biosynthesis of the antibiotic tylosin strain of Streptomyces fradiae; survival electrogenic bacteria Shewanella oneidensis MR- 1 is used in the microbial fuel cell As a result of this work it was found that the SFF affect the exchange of chromosomal DNA by crossing strains of Streptomyces. Was detected polarity crossing , expressed in an advantageous contribution chromosome fragment of one of the parent strains in recombinant offspring. This fact may indicate a more prolonged exposure of cells in microgravity and , as a consequence, the transfer of longer fragments of chromosomal DNA This feature is the transfer of genetic material in microgravity could lead to wider dissemination and horizontal transfer of chromosomal and plasmid DNA of symbiotic microflora astronauts and other strains present in the spacecraft. It was shown no effect on the frequency of recombination PCF and the level of mutation model reversion of auxotrophic markers to prototrophy It was demonstrated that PCF increase the level of induction of cell actinophage fS31 lysogenic strain of S. lividans 66, but did not affect the level of induction of this phage cells S. coelicolor A3 ( 2). It is shown that the lower the level of synthesis PCF antibiotic aktinorodina (actinorhodin) in lysogenic strain S. coelicolor A3 ( 2). 66 Strains of S. lividans and S. coelicolor A3 ( 2 ) can be used as a biosensor for studying the effect on microorganisms PCF It is shown that the effect of the PCF reduces synthesis of tylosin and desmicosyn S. fradiae at about 30 % as compared with the synchronous control, but the ratio of desmycosine to tylosin does not change. It was estimated that the strain S. oneidensis MR- 1 under the conditions of flight remains viable in all types of culture media Reducing the level of activity of the cells is similar in flight samples and the laboratory strain Strain S. oneidensis MR- 1 can be used in the microbial fuel cell while conducting experiments on board the spacecraft

  9. Database Description - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tor Name: Yasukazu Nakamura Creator Affiliation: Center for Information Biology, National Institute of Genet...ics Journal Search: Creator Name: Ikuo Uchiyama Creator Affiliation: National Institute for Basic Biology Jo...urnal Search: Creator Name: Hiroshi Mori Creator Affiliation: Center for Information Biology...ion: Center for Information Biology, National Institute of Genetics Journal Search: Creator Name: Hirokazu C...hiba Creator Affiliation: National Institute for Basic Biology Journal Search: Cr

  10. Sea level trends in Southeast Asian seas

    Science.gov (United States)

    Strassburg, M. W.; Hamlington, B. D.; Leben, R. R.; Manurung, P.; Lumban Gaol, J.; Nababan, B.; Vignudelli, S.; Kim, K.-Y.

    2015-05-01

    Southeast Asian seas span the largest archipelago in the global ocean and provide a complex oceanic pathway connecting the Pacific and Indian oceans. The Southeast Asian sea regional sea level trends are some of the highest observed in the modern satellite altimeter record that now spans almost 2 decades. Initial comparisons of global sea level reconstructions find that 17-year sea level trends over the past 60 years exhibit good agreement with decadal variability associated with the Pacific Decadal Oscillation and related fluctuations of trade winds in the region. The Southeast Asian sea region exhibits sea level trends that vary dramatically over the studied time period. This historical variation suggests that the strong regional sea level trends observed during the modern satellite altimeter record will abate as trade winds fluctuate on decadal and longer timescales. Furthermore, after removing the contribution of the Pacific Decadal Oscillation (PDO) to sea level trends in the past 20 years, the rate of sea level rise is greatly reduced in the Southeast Asian sea region. As a result of the influence of the PDO, the Southeast Asian sea regional sea level trends during the 2010s and 2020s are likely to be less than the global mean sea level (GMSL) trend if the observed oscillations in wind forcing and sea level persist. Nevertheless, long-term sea level trends in the Southeast Asian seas will continue to be affected by GMSL rise occurring now and in the future.

  11. Evolution of microbes and viruses: A paradigm shift in evolutionary biology?

    Directory of Open Access Journals (Sweden)

    Eugene V. Koonin

    2012-09-01

    Full Text Available When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain ‘ribosomal Tree of Life’ that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: i pervasive horizontal gene transfer (HGT, in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment of the Tree of Life concept, ii Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and iii evolution of evolvability, i.e. dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary

  12. Emergence, development, and maturity of the gonad of two species of chitons "sea cockroach" (Mollusca: Polyplacophora) through the early life stages.

    Science.gov (United States)

    Avila-Poveda, Omar Hernando; Abadia-Chanona, Quetzalli Yasú

    2013-01-01

    This study describes and recognises, using histological and microscopical examinations on a morphometrical basis, several gonad traits through the early life stages of Chiton articulatus and C. albolineatus. Gonadal ontogenesis, gonad development stages, sexual differentiation, onset of the first sexual maturity, and growth sequences or "early life stages" were determined. In addition, allometry between lengths and body weight pooled for both sexes per each chiton were calculated using equation Y = aX(b) . A total of 125 chitons (4≤TL≤40 mm, in total length "TL") were used. All allometric relations showed a strong positive correlation (r), close to 1, with b-values above three, indicating an isometric growth. Gonadal ontogenesis and gonad development stages were categorised into three periods ("Pw" without gonad, "Pe" gonad emergence, and "Pf" gonadal sac formed) and four stages ("S0" gametocytogenesis, "S1" gametogenesis, "S2" mature, and "S3" spawning), respectively. Compound digital images were attained for each process. Periods and stages are overlapped among them and between species, with the following overall confidence intervals in TL: Pw 6.13-14.32 mm, Pe 10.32-16.93 mm, Pf 12.99-25.01 mm, S0 16.08-24.34 mm (females) and 19.51-26.60 mm (males), S1 27.15-35.63 mm (females) and 23.45-32.27 mm (males), S2 24.48-40.24 mm (females) and 25.45-32.87 mm (males). Sexual differentiation (in S0) of both chitons occurs first as a female then as a male; although, males reach the onset of the first sexual maturity earlier than females, thus for C. articulatus males at 17 mm and females at 32 mm, and for C. albolineatus males at 23.5 mm and females at 28 mm, all in TL. Four early life stages (i.e., subjuvenile, juvenile, subadult, and adult) are described and proposed to distinguish growth sequences. Our results may be useful to diverse disciplines, from developmental biology to fisheries management.

  13. Emergence, development, and maturity of the gonad of two species of chitons "sea cockroach" (Mollusca: Polyplacophora through the early life stages.

    Directory of Open Access Journals (Sweden)

    Omar Hernando Avila-Poveda

    Full Text Available This study describes and recognises, using histological and microscopical examinations on a morphometrical basis, several gonad traits through the early life stages of Chiton articulatus and C. albolineatus. Gonadal ontogenesis, gonad development stages, sexual differentiation, onset of the first sexual maturity, and growth sequences or "early life stages" were determined. In addition, allometry between lengths and body weight pooled for both sexes per each chiton were calculated using equation Y = aX(b . A total of 125 chitons (4≤TL≤40 mm, in total length "TL" were used. All allometric relations showed a strong positive correlation (r, close to 1, with b-values above three, indicating an isometric growth. Gonadal ontogenesis and gonad development stages were categorised into three periods ("Pw" without gonad, "Pe" gonad emergence, and "Pf" gonadal sac formed and four stages ("S0" gametocytogenesis, "S1" gametogenesis, "S2" mature, and "S3" spawning, respectively. Compound digital images were attained for each process. Periods and stages are overlapped among them and between species, with the following overall confidence intervals in TL: Pw 6.13-14.32 mm, Pe 10.32-16.93 mm, Pf 12.99-25.01 mm, S0 16.08-24.34 mm (females and 19.51-26.60 mm (males, S1 27.15-35.63 mm (females and 23.45-32.27 mm (males, S2 24.48-40.24 mm (females and 25.45-32.87 mm (males. Sexual differentiation (in S0 of both chitons occurs first as a female then as a male; although, males reach the onset of the first sexual maturity earlier than females, thus for C. articulatus males at 17 mm and females at 32 mm, and for C. albolineatus males at 23.5 mm and females at 28 mm, all in TL. Four early life stages (i.e., subjuvenile, juvenile, subadult, and adult are described and proposed to distinguish growth sequences. Our results may be useful to diverse disciplines, from developmental biology to fisheries management.

  14. Small bugs, big business: the economic power of the microbe.

    Science.gov (United States)

    Demain, A L

    2000-10-01

    The versatility of microbial biosynthesis is enormous. The most industrially important primary metabolites are the amino acids, nucleotides, vitamins, solvents, and organic acids. Millions of tons of amino acids are produced each year with a total multibillion dollar market. Many synthetic vitamin production processes are being replaced by microbial fermentations. In addition to the multiple reaction sequences of fermentations, microorganisms are extremely useful in carrying out biotransformation processes. These are becoming essential to the fine chemical industry in the production of single-isomer intermediates. Microbially produced secondary metabolites are extremely important to our health and nutrition. As a group, they have tremendous economic importance. The antibiotic market amounts to almost 30 billion dollars and includes about 160 antibiotics and derivatives such as the beta-lactam peptide antibiotics, the macrolide polyketide erythromycin, tetracyclines, aminoglycosides and others. Other important pharmaceutical products produced by microrganisms are hypocholesterolemic agents, enzyme inhibitors, immunosuppressants and antitumor compounds, some having markets of over 1 billion dollars per year. Agriculturally important secondary metabolites include coccidiostats, animal growth promotants, antihelmintics and biopesticides. The modern biotechnology industry has made a major impact in the business world, biopharmaceuticals (recombinant protein drugs, vaccines and monoclonal antibodies) having a market of 15 billion dollars. Recombinant DNA technology has also produced a revolution in agriculture and has markedly increased markets for microbial enzymes. Molecular manipulations have been added to mutational techniques as means of increasing titers and yields of microbial procresses and in discovery of new drugs. Today, microbiology is a major participant in global industry. The best is yet to come as microbes move into the environmental and energy sectors.

  15. Insight and analysis problem solving in microbes to machines.

    Science.gov (United States)

    Clark, Kevin B

    2015-11-01

    A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright

  16. Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.

    2014-12-01

    The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.

  17. Universal ligation-detection-reaction microarray applied for compost microbes

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

    Full Text Available Abstract Background Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones. Results Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array. Conclusion This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

  18. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    DEFF Research Database (Denmark)

    Lloyd, Karen; Bird, Jordan; Schreiber, Lars

    Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as pr......Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes...... such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We ...

  19. Biological invasions: economic and environmental costs of alien plant, animal, and microbe species

    National Research Council Canada - National Science Library

    Pimentel, David

    2011-01-01

    ...: Economic and Environmental Costs of Alien Plant, Animal, and Microbe Species, this reference discusses how non-native species invade new ecosystems and the subsequent economic and environmental effects of these species...

  20. Grow Plants the Organic Way: Give Them the Soil Microbes They Crave

    Directory of Open Access Journals (Sweden)

    Phil Mixter

    2013-03-01

    Full Text Available Review of: Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web, revised ed.; Jeff Lowenfels and Wayne Lewis; (2010. Timber Press Inc., Portland, OR. 220 pages.

  1. Sea salt

    OpenAIRE

    Galvis-Sánchez, Andrea C.; Lopes, João Almeida; Delgadillo, Ivone; Rangel, António O. S. S.

    2013-01-01

    The geographical indication (GI) status links a product with the territory and with the biodiversity involved. Besides, the specific knowledge and cultural practices of a human group that permit transforming a resource into a useful good is protected under a GI designation. Traditional sea salt is a hand-harvested product originating exclusively from salt marshes from specific geographical regions. Once salt is harvested, no washing, artificial drying or addition of anti-caking agents are all...

  2. Revealing Holobiont Structure and Function of Three Red Sea Deep-Sea Corals

    KAUST Repository

    Yum, Lauren

    2014-12-01

    Deep-sea corals have long been regarded as cold-water coral; however a reevaluation of their habitat limitations has been suggested after the discovery of deep-sea coral in the Red Sea where temperatures exceed 20˚C. To gain further insight into the biology of deep-sea corals at these temperatures, the work in this PhD employed a holotranscriptomic approach, looking at coral animal host and bacterial symbiont gene expression in Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus sp. sampled from the deep Red Sea. Bacterial community composition was analyzed via amplicon-based 16S surveys and cultured bacterial strains were subjected to bioprospecting in order to gauge the pharmaceutical potential of coralassociated microbes. Coral host transcriptome data suggest that coral can employ mitochondrial hypometabolism, anaerobic glycolysis, and surface cilia to enhance mass transport rates to manage the low oxygen and highly oligotrophic Red Sea waters. In the microbial community associated with these corals, ribokinases and retron-type reverse transcriptases are abundantly expressed. In its first application to deep-sea coral associated microbial communities, 16S-based next-generation sequencing found that a single operational taxonomic unit can comprise the majority of sequence reads and that a large number of low abundance populations are present, which cannot be visualized with first generation sequencing. Bioactivity testing of selected bacterial isolates was surveyed over 100 cytological parameters with high content screening, covering several major organelles and key proteins involved in a variety of signaling cascades. Some of these cytological profiles were similar to those of several reference pharmacologically active compounds, which suggest that the bacteria isolates produce compounds with similar mechanisms of action as the reference compounds. The sum of this work offers several mechanisms by which Red Sea deep-sea corals cope with environmental

  3. Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

    Science.gov (United States)

    Wang, Guojun; Barrett, Nolan H; McCarthy, Peter J

    2017-02-02

    The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. Copyright © 2017 Wang et al.

  4. The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

    International Nuclear Information System (INIS)

    Xie, Yankai; Dong, Haoran; Zeng, Guangming; Tang, Lin; Jiang, Zhao; Zhang, Cong; Deng, Junmin; Zhang, Lihua; Zhang, Yi

    2017-01-01

    Highlights: • The interactions between various microbes and NZVI were summarized. • The adverse and positive effects of NZVI on the growth of microbes were reviewed. • The synergistic effects of NZVI and bacteria on pollutant removal were reviewed. • The effects of iron-reducing bacteria on the aged NZVI were reviewed. • Future challenges to study the interactions between NZVI and microbes are suggested. - Abstract: Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H_2) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.

  5. The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Yankai [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China); Dong, Haoran, E-mail: dongh@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China); Zeng, Guangming; Tang, Lin; Jiang, Zhao; Zhang, Cong; Deng, Junmin; Zhang, Lihua; Zhang, Yi [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China)

    2017-01-05

    Highlights: • The interactions between various microbes and NZVI were summarized. • The adverse and positive effects of NZVI on the growth of microbes were reviewed. • The synergistic effects of NZVI and bacteria on pollutant removal were reviewed. • The effects of iron-reducing bacteria on the aged NZVI were reviewed. • Future challenges to study the interactions between NZVI and microbes are suggested. - Abstract: Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H{sub 2}) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.

  6. Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?

    Science.gov (United States)

    King, Gary M

    2014-09-01

    Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems.

  7. Low salinity and high-level UV-B radiation reduce single-cell activity in antarctic sea ice bacteria.

    Science.gov (United States)

    Martin, Andrew; Hall, Julie; Ryan, Ken

    2009-12-01

    Experiments simulating the sea ice cycle were conducted by exposing microbes from Antarctic fast ice to saline and irradiance regimens associated with the freeze-thaw process. In contrast to hypersaline conditions (ice formation), the simulated release of bacteria into hyposaline seawater combined with rapid exposure to increased UV-B radiation significantly reduced metabolic activity.

  8. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir; Joachimiak, Marcin; Price, Morgan; Bates, John; Baumohl, Jason; Chivian, Dylan; Friedland, Greg; Huang, Kathleen; Keller, Keith; Novichkov, Pavel; Dubchak, Inna; Alm, Eric; Arkin, Adam

    2011-07-14

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  9. Turning the table: plants consume microbes as a source of nutrients.

    Directory of Open Access Journals (Sweden)

    Chanyarat Paungfoo-Lonhienne

    Full Text Available Interactions between plants and microbes in soil, the final frontier of ecology, determine the availability of nutrients to plants and thereby primary production of terrestrial ecosystems. Nutrient cycling in soils is considered a battle between autotrophs and heterotrophs in which the latter usually outcompete the former, although recent studies have questioned the unconditional reign of microbes on nutrient cycles and the plants' dependence on microbes for breakdown of organic matter. Here we present evidence indicative of a more active role of plants in nutrient cycling than currently considered. Using fluorescent-labeled non-pathogenic and non-symbiotic strains of a bacterium and a fungus (Escherichia coli and Saccharomyces cerevisiae, respectively, we demonstrate that microbes enter root cells and are subsequently digested to release nitrogen that is used in shoots. Extensive modifications of root cell walls, as substantiated by cell wall outgrowth and induction of genes encoding cell wall synthesizing, loosening and degrading enzymes, may facilitate the uptake of microbes into root cells. Our study provides further evidence that the autotrophy of plants has a heterotrophic constituent which could explain the presence of root-inhabiting microbes of unknown ecological function. Our discovery has implications for soil ecology and applications including future sustainable agriculture with efficient nutrient cycles.

  10. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan; Friedland, Greg D.; Huang, Katherine H.; Keller, Keith; Novichkov, Pavel S.; Dubchak, Inna L.; Alm, Eric J.; Arkin, Adam P.

    2009-09-17

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  11. Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

    Science.gov (United States)

    Beck, John J; Vannette, Rachel L

    2017-01-11

    Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

  12. Understanding the life of a sandy beach polychaete of functional importance - Scolelepis squamata (Polychaeta: Spionidae) on Belgian sandy beaches (northeastern Atlantic, North Sea)

    Science.gov (United States)

    Speybroeck, Jeroen; Alsteens, Lotte; Vincx, Magda; Degraer, Steven

    2007-08-01

    The cosmopolitan sandy beach polychaete Scolelepis squamata constitutes an important food resource for juvenile flatfish and wading birds in the northeastern Atlantic, thus playing an important role in sandy beach ecosystem functioning. However, its population dynamics and life history in this part of the world have gone widely uninvestigated. Eight beach transects on Belgian sandy beaches were sampled monthly from October 2003 until October 2004, in order to investigate seasonal trends in the species' abundance, biomass, secondary production, and patterns in reproduction and zonation. Average density, modal density and modal biomass (ash-free dry weight) (mean average density = 169 ± 9 SE ind/m 2; mean modal density = 505 ± 38 SE ind/m 2; mean modal biomass = 0.25 ± 0.02 SE g/m 2) did not exhibit major seasonal changes, whereas average biomass (0.081 ± 0.005 SE g/m 2) and individuals and biomass per strip transect (IST = 16286 ± 1330 SE ind/m; BMST = 7.8 + 0.7 SE g/m) did, peaking in May 2004. Production was calculated at 1.9 g/(m 2*year) (size-frequency method, SFM) and 0.88 g/(m 2*year) (mass specific growth rate method, MSGR) and mean annual biomass was 0.797 g/m 2; resulting in a P/B ratio of 2.40/year (SFM) and 1.11/year (MSGR), which is intermediate to moderately low compared to other polychaete species. Gravid individuals were found from February until August and a single recruitment period was observed from July until September. An average sex ratio of 1.41 ± 0.08 SE was calculated, with a female predominance. Highest densities (>200 ind/m 2) were mostly found above 3 m above MLLWS and at a median grain size from 190 to 320 μm. Average modal or peak density along each transect was situated from 3.95 m up to 4.40 m above MLLWS, in contrast to some other studies where the species was restricted to mid-tidal levels. Significant differences in elevation of peak density were found between non-gravid (411 ± 4 SE cm) and gravid (402 ± 5 SE cm) animals

  13. The watch on the sea

    International Nuclear Information System (INIS)

    1967-01-01

    The film introduces the International Atomic Energy Agency's Laboratory of Marine Radioactivity in Monaco. Established to conduct a special programme of research, the Monaco Laboratory is maintained through the cooperation of the Monaco and the French authorities and with the participation of the United Nations Educational, Scientific and Cultural Organization (UNESCO). The work of the Laboratory in surveying the radioactivity in seawater as well as the rate of absorption of radioactivity in the sea bed is described. Also shown is the laboratory's ship 'Winaretta Singer' as it trawls for specimens of sea life from the seabed and the method by which it obtains samples of seawater at various depths

  14. The watch on the sea

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1968-12-31

    The film introduces the International Atomic Energy Agency`s Laboratory of Marine Radioactivity in Monaco. Established to conduct a special programme of research, the Monaco Laboratory is maintained through the cooperation of the Monaco and the French authorities and with the participation of the United Nations Educational, Scientific and Cultural Organization (UNESCO). The work of the Laboratory in surveying the radioactivity in seawater as well as the rate of absorption of radioactivity in the sea bed is described. Also shown is the laboratory`s ship `Winaretta Singer` as it trawls for specimens of sea life from the seabed and the method by which it obtains samples of seawater at various depths

  15. Study on the interaction mechanism between the special geological environment and their extreme geo-microbes in Dagang Oilfield by combined methods

    Science.gov (United States)

    Yao, Jun

    2010-05-01

    Geo-microbes and their function were widespread ever since life appeared on the earth. Geo-microbiological process has left a rich and colorful material record in the geological body of earth, the most critical record of which is all sorts of organic hieroglyph and various forms of organic matter derived from bio-organisms, and oil field is the most ideal geological location to preserve these organic matters. It have already produced or might produce petroleum and natural gas sedimentary rocks under natural conditions, also known as olefiant (gas) rock or the parent rock, which is the product of the interaction between the life-system and earth environmental system in the specific geological conditions and integrate the whole microbial ecosystem in the geological time. The microbial community under extreme geological environment of Dagang Oilfield is relatively simple, therefore it is quite easy to investigate the special relationship between geo-microbes and biogeochemistry. We have mastered a large number of information related with the geological condition and biological species of Dagang Oilfield; what's more we also have isolated a number of archimycetes strains with different extremophiles capacity from the core samples collected in the Dagang oil field. At present, we are to proceed with the cooperative research at Environment School of Yale University and Institute of the Earth's biosphere using these strains. In the future, we will work together to carry out geological surveys in the field using international first-class equipment and methods and study the geological environment of Dagang Oilfield utilizing isotope techniques and mineral phase analysis method. Meanwhile we are going to undertake the on-line monitoring of the overall microbial activity of these collected geological samples, the specific metabolic activity of these extreme strains of microorganisms and the biomarkers produced during their metabolic processes under laboratory conditions

  16. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    Directory of Open Access Journals (Sweden)

    Nurmi ePangesti

    2013-10-01

    Full Text Available Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the host plant that influence interactions between plants and aboveground insects at several trophic levels. Aboveground, plants are under continuous attack by insect herbivores and mount multiple responses that also have systemic effects on belowground microbes. Until recently, both ecological and mechanistic studies have mostly focused on exploring these below- and above-ground interactions using simplified systems involving both single microbe and herbivore species, which is far from the naturally occurring interactions. Increasing the complexity of the systems studied is required to increase our understanding of microbe - plant - insect interactions and to gain more benefit from the use of non-pathogenic microbes in agriculture. In this review, we explore how colonization by either single non-pathogenic microbe species or a community of such microbes belowground affects plant growth and defense and how this affects the interactions of plants with aboveground insects at different trophic levels. Moreover, we review how plant responses to foliar herbivory by insects belonging to different feeding guilds affect interactions of plants with non-pathogenic soil-borne microbes. The role of phytohormones in coordinating plant growth, plant defenses against foliar herbivores while simultaneously establishing associations with non-pathogenic soil microbes is discussed.

  17. Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primary producers and microbes.

    Science.gov (United States)

    Lin, Ronghua; Buijse, Laura; Dimitrov, Mauricio R; Dohmen, Peter; Kosol, Sujitra; Maltby, Lorraine; Roessink, Ivo; Sinkeldam, Jos A; Smidt, Hauke; Van Wijngaarden, René P A; Brock, Theo C M

    2012-07-01

    The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints were investigated. Dissipation half-life (DT₅₀) of metiram was approximately 1-6 h in the water column of the microcosm test system and the metabolites formed were not persistent. Multivariate analysis indicated treatment-related effects on the zooplankton (NOEC(community) = 36 μg a.i./L). Consistent treatment-related effects on the phytoplankton and macroinvertebrate communities and on the sediment microbial community could not be demonstrated or were minor. There was no evidence that metiram affected the biomass, abundance or functioning of aquatic hyphomycetes on decomposing alder leaves. The most sensitive populations in the microcosms comprised representatives of Rotifera with a NOEC of 12 μg a.i./L on isolated sampling days and a NOEC of 36 μg a.i./L on consecutive samplings. At the highest treatment-level populations of Copepoda (zooplankton) and the blue-green alga Anabaena (phytoplankton) also showed a short-term decline on consecutive sampling days (NOEC = 108 μg a.i./L). Indirect effects in the form of short-term increases in the abundance of a few macroinvertebrate and several phytoplankton taxa were also observed. The overall community and population level no-observed-effect concentration (NOEC(microcosm)) was 12-36 μg a.i./L. At higher treatment levels, including the test systems that received the highest dose, ecological recovery of affected measurement endpoints was fast (effect period < 8 weeks).

  18. Soil-Plant-Microbe Interactions in Stressed Agriculture Management: A Review

    Institute of Scientific and Technical Information of China (English)

    Shobhit Raj VIMAL; Jay Shankar SINGH; Naveen Kumar ARORA; Surendra SINGH

    2017-01-01

    The expected rise in temperature and decreased precipitation owing to climate change and unabated anthropogenic activities add complexity and uncertainty to agro-industry.The impact of soil nutrient imbalance,mismanaged use of chemicals,high temperature,flood or drought,soil salinity,and heavy metal pollutions,with regard to food security,is increasingly being explored worldwide.This review describes the role of soil-plant-microbe interactions along with organic manure in solving stressed agriculture problems.Beneficial microbes associated with plants are known to stimulate plant growth and enhance plant resistance to biotic (diseases) and abiotic (salinity,drought,pollutions,etc.) stresses.The plant growth-promoting rhizobacteria (PGPR) and mycorrhizae,a key component of soil microbiota,could play vital roles in the maintenance of plant fitness and soil health under stressed environments.The application of organic manure as a soil conditioner to stressed soils along with suitable microbial strains could further enhance the plant-microbe associations and increase the crop yield.A combination of plant,stress-tolerant microbe,and organic amendment represents the tripartite association to offer a favourable environment to the proliferation of beneficial rhizosphere microbes that in turn enhance the plant growth performance in disturbed agro-ecosystem.Agriculture land use patterns with the proper exploitation of plant-microbe associations,with compatible beneficial microbial agents,could be one of the most effective strategies in the management of the concerned agriculture lands owing to climate change resilience.However,the association of such microbes with plants for stressed agriculture management still needs to be explored in greater depth.

  19. Polythene and Plastics-degrading microbes from the mangrove soil

    Directory of Open Access Journals (Sweden)

    K Kathiresan

    2003-09-01

    Full Text Available Biodegradation of polythene bags and plastic cups was analyzed after 2, 4, 6, and 9 months of incubation in the mangrove soil. The biodegradation of polythene bags was significantly higher (up to 4.21% in 9 months than that of plastic cups (up to 0.25% in 9 months. Microbial counts in the degrading materials were recorded up to 79.67 x 10 4 per gram for total heterotrophic bacteria, and up to 55.33 x 10 2 per gram for fungi. The microbial species found associated with the degrading materials were identified as five Gram positive and two Gram negative bacteria, and eight fungal species of Aspergillus. The species that were predominant were Streptococcus, Staphylococcus, Micrococcus (Gram +ve, Moraxella, and Pseudomonas (Gram -ve and two species of fungi (Aspergillus glaucus and A. niger. Efficacy of the microbial species in degradation of plastics and polythene was analyzed in shaker cultures. Among the bacteria, Pseudomonas species degraded 20.54% of polythene and 8.16% of plastics in one-month period. Among the fungal species, Aspergillus glaucus degraded 28.80% of polythene and 7.26% of plastics in one-month period. This work reveals that the mangrove soil is a good source of microbes capable of degrading polythene and plasticsLa biodegradación de las bolsas de polietileno y vasos de plástico fue analizada después de 2, 4, 6 y 9 meses de incubación en suelo de manglar. La biodegradación de las bolsas fue significativamente más alta (hasta 4.21% en 9 meses que los vasos plásticos (hasta 0.25% en 9 meses. Los conteos microbianos en los materiales degradados mostraron hasta 79.67 x 10(4 por gramo para las bacterias heterotroficas totales, y hasta 55.33 x 10² por gramo para los hongos. Se identificó 5 especies microbianas Gram positivas, 2 Gram negativas, y 8 especies de hongos del género Aspergillus en asociación con materiales degradados. Las especies predominantes fueron Streptococcus, Staphylococcus, Micrococcus (Gram +, Moraxella

  20. Dipteran larvae and microbes facilitate nutrient sequestration in the Nepenthes gracilis pitcher plant host.

    Science.gov (United States)

    Lam, Weng Ngai; Chong, Kwek Yan; Anand, Ganesh S; Tan, Hugh Tiang Wah

    2017-03-01

    The fluid-containing traps of Nepenthes carnivorous pitcher plants (Nepenthaceae) are often inhabited by organisms known as inquilines. Dipteran larvae are key components of such communities and are thought to facilitate pitcher nitrogen sequestration by converting prey protein into inorganic nitrogen, although this has never been demonstrated in Nepenthes Pitcher fluids are also inhabited by microbes, although the relationship(s) between these and the plant is still unclear. In this study, we examined the hypothesis of digestive mutualism between N. gracilis pitchers and both dipteran larvae and fluid microbes. Using dipteran larvae, prey and fluid volumes mimicking in situ pitcher conditions, we conducted in vitro experiments and measured changes in available fluid nitrogen in response to dipteran larvae and microbe presence. We showed that the presence of dipteran larvae resulted in significantly higher and faster releases of ammonium and soluble protein into fluids in artificial pitchers, and that the presence of fluid microbes did likewise for ammonium. We showed also that niche segregation occurs between phorid and culicid larvae, with the former fragmenting prey carcasses and the latter suppressing fluid microbe levels. These results clarify the relationships between several key pitcher-dwelling organisms, and show that pitcher communities facilitate nutrient sequestration in their host. © 2017 The Author(s).

  1. Thermo-tolerant phosphate-solubilizing microbes for multi-functional biofertilizer preparation.

    Science.gov (United States)

    Chang, Cheng-Hsiung; Yang, Shang-Shyng

    2009-02-01

    In order to prepare the multi-functional biofertilizer, thermo-tolerant phosphate-solubilizing microbes including bacteria, actinomycetes, and fungi were isolated from different compost plants and biofertilizers. Except Streptomycesthermophilus J57 which lacked pectinase, all isolates possessed amylase, CMCase, chitinase, pectinase, protease, lipase, and nitrogenase activities. All isolates could solubilize calcium phosphate and Israel rock phosphate; various isolates could solubilize aluminum phosphate, iron phosphate, and hydroxyapatite. During composting, biofertilizers inoculated with the tested microbes had a significantly higher temperature, ash content, pH, total nitrogen, soluble phosphorus content, and germination rate than non-inoculated biofertilizer; total organic carbon and carbon-to-nitrogen ratio showed the opposite pattern. Adding these microbes can shorten the period of maturity, improve the quality, increase the soluble phosphorus content, and enhance the populations of phosphate-solubilizing and proteolytic microbes in biofertilizers. Therefore, inoculating thermo-tolerant phosphate-solubilizing microbes into agricultural and animal wastes represents a practical strategy for preparing multi-functional biofertilizer.

  2. Red Sea as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-12-12

    King-Abdullah University of Science and Technology (KAUST) is located on the shores of the Red Sea in Saudi Arabia. The Red Sea is well known for its unique environment, harboring various microbes capable of surviving in salty brines. We collected sediment samples from brine pool adjacent to the Thuwal cold seeps in the Red Sea. The taxonomic analysis showed the diversity and abundance of bacterial and archaeal operational taxonomic units (OUT). Recently we established in the laboratory a microdroplet technology to encapsulate single cells. This technology enables us to analyze single-cell genomes and perform the high-throughput screening. The genomes of both cultivable and uncultivable organisms can be analyzed. We envision the collection of complimentary data, obtained by various techniques, such as single-cell genomics, metagenomics, and transcriptomics. That will enable us not only to understand the environment and microorganism communities but also will allow to discover the previously unknown genes, pathways, and whole genomes. These data will facilitate the enhancement of biological and chemical producers, and pave the way for bioprospecting.

  3. Quantitative Analysis of Microbes in Water Tank of G.A. Siwabessy Reactor

    International Nuclear Information System (INIS)

    Itjeu Karliana; Diah Dwiana Lestiani

    2003-01-01

    The quality of water in reactor system has an important role because it could effect the function as a coolant and the operation of reactor indirectly. The study of microbe analyzes has been carried out to detect the existence of microbes in water tank and quantitative analyzes of microbes also has been applied as a continuation of the previous study. The samples is taken out from the end side of reactor GA Siwabessy's tank, inoculated in TSA (Tripcase Soy Agar) medium, put in incubator at 30 - 35 o C for 4 days. The results of experiment show the reconfirmation for the existence of bacteria and the un-existence of yield. The quantitative analysis with TPC method show the growth rate of bacteria is twice in 24 hours. (author)

  4. Induction of Systemic Resistance against Insect Herbivores in Plants by Beneficial Soil Microbes

    Directory of Open Access Journals (Sweden)

    Md. Harun-Or Rashid

    2017-10-01

    Full Text Available Soil microorganisms with growth-promoting activities in plants, including rhizobacteria and rhizofungi, can improve plant health in a variety of different ways. These beneficial microbes may confer broad-spectrum resistance to insect herbivores. Here, we provide evidence that beneficial microbes modulate plant defenses against insect herbivores. Beneficial soil microorganisms can regulate hormone signaling including the jasmonic acid, ethylene and salicylic acid pathways, thereby leading to gene expression, biosynthesis of secondary metabolites, plant defensive proteins and different enzymes and volatile compounds, that may induce defenses against leaf-chewing as well as phloem-feeding insects. In this review, we discuss how beneficial microbes trigger induced systemic resistance against insects by promoting plant growth and highlight changes in plant molecular mechanisms and biochemical profiles.

  5. [Origin of the plague microbe Yersinia pestis: structure of the process of speciation].

    Science.gov (United States)

    Suntsov, V V

    2012-01-01

    The origin and evolution of the plague microbe Yersinia pestis are considered in the context of propositions of modern Darwinism. It was shown that the plague pathogen diverged from the pseudotuberculous microbe Yersinia pseudotuberculosis O:1b in the mountain steppe landscapes of Central Asia in the Sartan: 22000-15000 years ago. Speciation occurred in the tarbagan (Marmota sibirica)--flea (Oropsylla silantiewi) parasitic system. The structure of the speciation process included six stages: isolation, genetic drift, enhancement of intrapopulational polymorphism, the beginning of pesticin synthesis (genetic conflict and emergence of hiatus), specialization (stabilization of characteristics), and adaptive irradiation (transformation of the monotypic species Y. pestis tarbagani into a polytypic species). The scenario opens up wide prospects for construction of the molecular phylogeny of the plague microbe Y. pestis and for investigation of the biochemical and molecular-genetic aspects of "Darwinian" evolution of pathogens from many other nature-focal infections.

  6. Wars between microbes on roots and fruits [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Ben Lugtenberg

    2017-03-01

    Full Text Available Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.

  7. Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

    Directory of Open Access Journals (Sweden)

    Shivankar Agrawal

    2017-11-01

    Full Text Available Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs. Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.

  8. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City.

    Directory of Open Access Journals (Sweden)

    Julia M Maritz

    Full Text Available Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with-and potential exchange of-microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter and June (Summer 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills.Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency.We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.

  9. Companion animals symposium: role of microbes in canine and feline health.

    Science.gov (United States)

    Kil, D Y; Swanson, K S

    2011-05-01

    Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

  10. Soil microbes and successful invasions of an exotic weed Eupatorium adenophorum

    International Nuclear Information System (INIS)

    Zhou, P.; Tang, T.; Zhao, P.; Chen, J.

    2016-01-01

    The effects of soil microbes collected from the two invasive species Eupatorium adenophorum and E. odoratum and the two native species E. japonicum and E. chinense on the growth and biomass of E. adenophorum was examined to explore a possible link between soil microbes and successful invasions of the weed species E. adenophorum. In most cases, plant height, stem diameter, root number and root length were significantly enhanced when E. adenophorum was grown in sterilized soils compared with those when one was grown in non-sterilized soils collected from the rhizosphere of E. adenophorum, E. japonicum and E. chinense. In contrast, the growth and biomass of E. adenophorum were apparently inhibited when grown in soils collected from the rhizosphere of E. odoratum. Plant height, stem diameter, leaf area per plant and root length of E. adenophorum was greater when it was grown in soils collected from the rhizosphere of E. adenophorum compared with those when it was grown in soils collected from the rhizosphere of E. odoratum, but the enhancement considerably greater when it was grown in soils collected from the rhizosphere of E. japonicum and E. chinense compared with those when it was grown in soils collected from the rhizosphere of E. adenophorum. In addition, the biomass allocation of E. adenophorum was not significantly affected by soil microbes and soil sources. These Results suggest that although the competitive advantage of the invasive weed E. adenophorum is not achieved solely by soil microbes, successful invasions of E. adenophorum may result partly from its release from the harmful soil microbes in its native range and the positive feedbacks of soil microbes from itself and the native species in its invading range. (author)

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

    Science.gov (United States)

    Röthig, Till; Yum, Lauren K; Kremb, Stephan G; Roik, Anna; Voolstra, Christian R

    2017-03-17

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

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

    KAUST Repository

    Röthig, Till

    2017-03-17

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

  13. Sponge-microbe associations survive high nutrients and temperatures.

    Directory of Open Access Journals (Sweden)

    Rachel Simister

    Full Text Available Coral reefs are under considerable pressure from global stressors such as elevated sea surface temperature and ocean acidification, as well as local factors including eutrophication and poor water quality. Marine sponges are diverse, abundant and ecologically important components of coral reefs in both coastal and offshore environments. Due to their exceptionally high filtration rates, sponges also form a crucial coupling point between benthic and pelagic habitats. Sponges harbor extensive microbial communities, with many microbial phylotypes found exclusively in sponges and thought to contribute to the health and survival of their hosts. Manipulative experiments were undertaken to ascertain the impact of elevated nutrients and seawater temperature on health and microbial community dynamics in the Great Barrier Reef sponge Rhopaloeides odorabile. R. odorabile exposed to elevated nutrient levels including 10 µmol/L total nitrogen at 31°C appeared visually similar to those maintained under ambient seawater conditions after 7 days. The symbiotic microbial community, analyzed by 16S rRNA gene pyrotag sequencing, was highly conserved for the duration of the experiment at both phylum and operational taxonomic unit (OTU (97% sequence similarity levels with 19 bacterial phyla and 1743 OTUs identified across all samples. Additionally, elevated nutrients and temperatures did not alter the archaeal associations in R. odorabile, with sequencing of 16S rRNA gene libraries revealing similar Thaumarchaeota diversity and denaturing gradient gel electrophoresis (DGGE revealing consistent amoA gene patterns, across all experimental treatments. A conserved eukaryotic community was also identified across all nutrient and temperature treatments by DGGE. The highly stable microbial associations indicate that R. odorabile symbionts are capable of withstanding short-term exposure to elevated nutrient concentrations and sub-lethal temperatures.

  14. European Life-Modes at Sea

    DEFF Research Database (Denmark)

    Højrup, Thomas; Schriewer, Klaus

    2012-01-01

    Analyse og syntese af de biologiske livsformers betydning som mulighedsbetingelse for de anvendte teknologier og fangstmåders betydning som mulighedsbetingelse for de to produktionsmåders sameksistens i euroæisk fiskeri i 500 år og deres betydning som mulighedsbetingelser for de sameksisterende k...

  15. Adhesive Bioactive Coatings Inspired by Sea Life.

    Science.gov (United States)

    Rego, Sónia J; Vale, Ana C; Luz, Gisela M; Mano, João F; Alves, Natália M

    2016-01-19

    Inspired by nature, in particular by the marine mussels adhesive proteins (MAPs) and by the tough brick-and-mortar nacre-like structure, novel multilayered films are prepared in the present work. Organic-inorganic multilayered films, with an architecture similar to nacre based on bioactive glass nanoparticles (BG), chitosan, and hyaluronic acid modified with catechol groups, which are the main components responsible for the outstanding adhesion in MAPs, are developed for the first time. The biomimetic conjugate is prepared by carbodiimide chemistry and analyzed by ultraviolet-visible spectrophotometry. The buildup of the multilayered films is monitored with a quartz crystal microbalance with dissipation monitoring, and their topography is characterized by atomic force microscopy. The mechanical properties reveal that the films containing catechol groups and BG present an enhanced adhesion. Moreover, the bioactivity of the films upon immersion in a simulated body fluid solution is evaluated by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. It was found that the constructed films promote the formation of bonelike apatite in vitro. Such multifunctional mussel inspired LbL films, which combine enhanced adhesion and bioactivity, could be potentially used as coatings of a variety of implants for orthopedic applications.

  16. Microbes in biological processes for municipal landfill leachate treatment: Community, function and interaction

    DEFF Research Database (Denmark)

    Zhang, Duoying; Vahala, Riku; Wang, Yu

    2016-01-01

    Landfill leachate (LFL) contains high strength of ammonium and complex organic substances including biodegradable volatile fatty acids (VFAs), refractory aquatic humic substances (AHS) and micro-scale xenobiotic organic chemicals (XOCs), which promotes the diverse microbial community in LFL...... treatment bioreactors. These microbes cooperate to remove nitrogen, biodegrade organic matters, eliminate the toxicity of XOCs and produce energy. In these diverse microbes, some show dominant in the bioreactor and are prevalent in many kinds of LFL treatment bio-processes, such as Brocadia from the phylum...

  17. The Physical Microbe; An introduction to noise, control, and communication in the prokaryotic cell

    Science.gov (United States)

    Hagen, Stephen J.

    2017-10-01

    Physical biology is a fusion of biology and physics. This book narrows down the scope of physical biology by focusing on the microbial cell; exploring the physical phenomena of noise, feedback, and variability that arise in the cellular information-processing circuits used by bacteria. It looks at the microbe from a physics perspective, asking how the cell optimizes its function to live within the constraints of physics. It introduces a physical and information-based (as opposed to microbiological) perspective on communication and signalling between microbes.

  18. The Use of Stuffed Microbes in an Undergraduate Microbiology Course Increases Engagement and Student Learning

    Directory of Open Access Journals (Sweden)

    Ginny Webb

    2015-08-01

    Full Text Available Student engagement, attention, and attendance during a microbiology lecture are crucial for student learning.  In addition, it is challenging to cover a large number of infectious diseases during a one-semester introductory microbiology course.  The use of visual aids helps students retain the information presented during a lecture.  Here, I discuss the use of stuffed, plush microbes as visual aids during an introductory microbiology course.  The incorporation of these stuffed microbes during a microbiology lecture results in an increase in engagement, interest, attendance, and retention of material.

  19. Performance of duckweed and effective microbes in reducing arsenic in paddy and paddy soil

    Science.gov (United States)

    Ng, C. A.; Wong, L. Y.; Lo, P. K.; Bashir, M. J. K.; Chin, S. J.; Tan, S. P.; Chong, C. Y.; Yong, L. K.

    2017-04-01

    In this study phytoremediation plant (duckweed) and effective microbes were used to investigate their effectiveness in reducing arsenic concentration in paddy soil and paddy grain. The results show that using duckweed alone is a better choice as it could decrease the arsenic concentration in paddy by 27.697 % and 8.268 % in paddy grain and paddy husk respectively. The study also found out that the concentration of arsenic in soil would affect the performance of duckweed and also delayed the reproduction rate of duckweed. Using the mixture of effective microbes and duckweed together to decrease arsenic in paddy was noticed having the least potential in reducing the arsenic concentration in paddy.

  20. The geobiological nitrogen cycle: From microbes to the mantle.

    Science.gov (United States)

    Zerkle, A L; Mikhail, S

    2017-05-01

    Nitrogen forms an integral part of the main building blocks of life, including DNA, RNA, and proteins. N 2 is the dominant gas in Earth's atmosphere, and nitrogen is stored in all of Earth's geological reservoirs, including the crust, the mantle, and the core. As such, nitrogen geochemistry is fundamental to the evolution of planet Earth and the life it supports. Despite the importance of nitrogen in the Earth system, large gaps remain in our knowledge of how the surface and deep nitrogen cycles have evolved over geologic time. Here, we discuss the current understanding (or lack thereof) for how the unique interaction of biological innovation, geodynamics, and mantle petrology has acted to regulate Earth's nitrogen cycle over geologic timescales. In particular, we explore how temporal variations in the external (biosphere and atmosphere) and internal (crust and mantle) nitrogen cycles could have regulated atmospheric pN 2 . We consider three potential scenarios for the evolution of the geobiological nitrogen cycle over Earth's history: two in which atmospheric pN 2 has changed unidirectionally (increased or decreased) over geologic time and one in which pN 2 could have taken a dramatic deflection following the Great Oxidation Event. It is impossible to discriminate between these scenarios with the currently available models and datasets. However, we are optimistic that this problem can be solved, following a sustained, open-minded, and multidisciplinary effort between surface and deep Earth communities. © 2017 The Authors Geobiology Published by John Wiley & Sons Ltd.

  1. Antimicrobial and anticancer activity and DNA fingerprinting of extracts from Red Sea marine fungal symbiotes.

    OpenAIRE

    Asma Alsed; Marwa M. Azab; Amany K. Ibrahim

    2016-01-01

    Marine microorganisms have become an important source of pharmacologically active metabolites. More specifically, fungi from the marine environment have shown great potential as suggested by the diversity of secondary metabolites. The aim of this study was to look for bioactive natural products from Red Sea derived fungi. Numerous natural products with novel structures and distinct biological activities have been discovered as the secondary metabolites of marine- derived microbes....

  2. Coordinated motility of cyanobacteria favor mat formation, photosynthesis and carbon burial in low-oxygen, high-sulfur shallow sinkholes of Lake Huron; whereas deep-water aphotic sinkholes are analogs of deep-sea seep and vent ecosystems

    Science.gov (United States)

    Biddanda, B. A.; McMillan, A. C.; Long, S. A.; Snider, M. J.; Weinke, A. D.; Dick, G.; Ruberg, S. A.

    2016-02-01

    Microbial life in submerged sinkhole ecosystems of the Laurentian Great Lakes is relatively understudied in comparison to seeps and vents of the deep-sea. We studied the filamentous benthic mat-forming cyanobacteria consisting primarily of Oscillatoria-like cells growing under low-light, low-oxygen and high-sulfur conditions in Lake Huron's submerged sinkholes using in situ observations, in vitro measurements and time-lapse microscopy. Gliding movement of the cyanobacterial trichomes revealed individual as well as group-coordinated motility. When placed in a petri dish and dispersed in ground water from the sinkhole, filaments re-aggregated into defined colonies within minutes. Measured speed of individual filaments ranged from 50 µm minute-1 or 15 body lengths minute-1 to 215 µm minute-1 or 70 body lengths minute-1 - rates that are rapid relative to non-flagellated/ciliated microbes. Filaments exhibited precise and coordinated positive phototaxis towards pinpoints of light and congregated under the light of foil cutouts. Such light-responsive clusters showed an increase in photosynthetic yield - suggesting phototactic motility aids in light acquisition as well as photosynthesis. Pebbles and pieces of broken shells placed upon the mat in intact sediemnt cores were quickly covered by vertically motile filaments within hours and became fully buried in the anoxic sediments over 3-4 diurnal cycles - likely facilitating the preservation of falling plankton debris. Coordinated horizontal and vertical filament motility optimize mat cohesion and dynamics, photosynthetic efficiency and sedimentary carbon burial in modern-day sinkhole habitats where life operates across sharp redox gradients. Analogous cyanobacterial motility in the shallow seas during Earth's early history, may have played a key role in the oxygenation of the planet by optimizing photosynthesis while favoring carbon burial. We are now eagerly mapping and exploring life in deep-water aphotic sinkholes of

  3. Deep-Sea Trench Microbiology Down to 10.9 Kilometers Below the Surface

    Science.gov (United States)

    Bartlett, D. H.

    2012-12-01

    Deep-sea trenches, extending to more than 10.9 km below the sea surface, are among the most remote and infrequently sampled habitats. As a result a global perspective of microbial diversity and adaptation is lacking in these extreme settings. I will present the results of studies of deep-sea trench microbes collected in the Puerto Rico Trench (PRT), Tonga Trench, New Britain Trench and Mariana Trench. The samples collected include sediment, seawater and animals in baited traps. The analyses to be described include microbial community activity and viability measurements as a function of hydrostatic pressure, microbial culturing at high pressure under various physiological conditions, phylogenetics and metagenome and single-cell genome characterizations. Most of the results to date stem from samples recovered from the PRT. The deep-sea PRT Trench microbes have more in common at the species level with other deep-sea microbial communities previously characterized in the Pacific Ocean and the Mediterranean Sea than with the microbial populations above them in shallow waters. They also harbor larger genomes with more genes assigned to signal transduction, transcription, replication, recombination and repair and inorganic ion transport. The overrepresented transporters in the PRT metagenome include di- and tri-carboxylate transporters that correspond to the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. But, perhaps the most dramatic adaptational feature of the PRT microbes is heavy metal resistance, as reflected in the high numbers of metal efflux systems present. Single-cell genomics approaches have proven particularly useful for placing PRT metagenomic data into context.

  4. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    NARCIS (Netherlands)

    Pangesti, N.P.D.; Pineda Gomez, A.M.; Pieterse, C.M.J.; Dicke, M.; Loon, van J.J.A.

    2013-01-01

    Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the

  5. Formation of a symbiotic host-microbe interface: the role of SNARE-mediated regulation of exocytosis

    NARCIS (Netherlands)

    Huisman, Rik

    2018-01-01

    At the heart of endosymbiosis microbes are hosted inside living cells in specialized membrane compartments that from a host-microbe interface, where nutrients and signal are efficiently exchanged. Such symbiotic interfaces include arbuscules produced by arbuscular mycorrhiza (AM) and

  6. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir

    2011-10-12

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Eavesdropping on plant-insect-microbe chemical communications in agricultural ecology: a virtual issue on semiochemicals

    Science.gov (United States)

    Studies of plant-insect interactions, and more recently the interactions among plants, insects, and microbes, have revealed that volatiles often facilitate insect movement, aggregation, and host location by herbivores, predators and parasitoids, all of which could be used to help protect agriculture...

  8. The Hsp90 Complex in Microbes and Man | Center for Cancer Research

    Science.gov (United States)

    Why would cancer researchers be interested in how a bacteria named Escherichia coli (E. coli) rebuilds its cellular proteins after they have been inactivated by environmental stress such as heat?  The answer lies in a protein remodeling mechanism that is shared by microbes and man.

  9. Microstructured Block Copolymer Surfaces for Control of Microbe Adhesion and Aggregation

    Directory of Open Access Journals (Sweden)

    Ryan R. Hansen

    2014-03-01

    Full Text Available The attachment and arrangement of microbes onto a substrate is influenced by both the biochemical and physical surface properties. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe immobilization. Films of poly(glycidyl methacrylate-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA were patterned on silicon surfaces into line arrays or square grid patterns with 5 μm wide features and varied pitch. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates immobilized was dependent on the pattern dimensions. Films patterned as parallel lines or square grids with a pitch of 10 μm or less led to the immobilization of individual microbes with minimal formation of aggregates. Both geometries allowed for incremental increases in aggregate size distribution with each increase in pitch. These engineered surfaces combine spatial confinement with affinity-based capture to control the extent of microbe adhesion and aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.

  10. Experimental Activities in Primary School to Learn about Microbes in an Oral Health Education Context

    Science.gov (United States)

    Mafra, Paulo; Lima, Nelson; Carvalho, Graça S.

    2015-01-01

    Experimental science activities in primary school enable important cross-curricular learning. In this study, experimental activities on microbiology were carried out by 16 pupils in a Portuguese grade-4 classroom (9-10?years old) and were focused on two problem-questions related to microbiology and health: (1) do your teeth carry microbes? (2) why…

  11. Interactive effects of global climate change and pollution on marine microbes: the way ahead.

    Science.gov (United States)

    Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

    2013-06-01

    Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

  12. Progress of CRISPR-Cas based genome editing in Photosynthetic microbes

    NARCIS (Netherlands)

    Naduthodi, M.I.S.; Barbosa, M.J.; Oost, van der J.

    2018-01-01

    The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been

  13. Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes

    Science.gov (United States)

    Fructans are an important nonfiber carbohydrate in cool-season grasses. Their fermentation by ruminal microbes is not well described, though such information is needed to understand their nutritional value to ruminants. Our objective was to compare kinetics and product formation of orchardgrass fruc...

  14. Fungal innate immunity induced by bacterial microbe-associated molecular patterns (MAMPs)

    DEFF Research Database (Denmark)

    Ip Cho, Simon; Sundelin, Thomas; Erbs, Gitte

    2016-01-01

    Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal-bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposin...

  15. Uptake, Accumulation and Toxicity of Silver Nanoparticle in Autotrophic Plants, and Heterotrophic Microbes: A Concentric Review

    Science.gov (United States)

    Tripathi, Durgesh K.; Tripathi, Ashutosh; Shweta; Singh, Swati; Singh, Yashwant; Vishwakarma, Kanchan; Yadav, Gaurav; Sharma, Shivesh; Singh, Vivek K.; Mishra, Rohit K.; Upadhyay, R. G.; Dubey, Nawal K.; Lee, Yonghoon; Chauhan, Devendra K.

    2017-01-01

    Nanotechnology is a cutting-edge field of science with the potential to revolutionize today’s technological advances including industrial applications. It is being utilized for the welfare of mankind; but at the same time, the unprecedented use and uncontrolled release of nanomaterials into the environment poses enormous threat to living organisms. Silver nanoparticles (AgNPs) are used in several industries and its continuous release may hamper many physiological and biochemical processes in the living organisms including autotrophs and heterotrophs. The present review gives a concentric know-how of the effects of AgNPs on the lower and higher autotrophic plants as well as on heterotrophic microbes so as to have better understanding of the differences in effects among these two groups. It also focuses on the mechanism of uptake, translocation, accumulation in the plants and microbes, and resulting toxicity as well as tolerance mechanisms by which these microorganisms are able to survive and reduce the effects of AgNPs. This review differentiates the impact of silver nanoparticles at various levels between autotrophs and heterotrophs and signifies the prevailing tolerance mechanisms. With this background, a comprehensive idea can be made with respect to the influence of AgNPs on lower and higher autotrophic plants together with heterotrophic microbes and new insights can be generated for the researchers to understand the toxicity and tolerance mechanisms of AgNPs in plants and microbes. PMID:28184215

  16. Plant interactions with microbes and insects: from molecular mechanisms to ecology

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Dicke, M.

    2007-01-01

    Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, beneficial microbes and insects into the most appropriate adaptive response.

  17. Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology.

    Czech Academy of Sciences Publication Activity Database

    Salcher, Michaela M.; Šimek, Karel

    2016-01-01

    Roč. 77, č. 3 (2016), s. 183-196 ISSN 0948-3055 R&D Projects: GA ČR(CZ) GA13-00243S Institutional support: RVO:60077344 Keywords : autecology * axenic cultures * dilution to extinction * ecophysiology * genomics * isolation of freshwater microbes * targeted enrichment Subject RIV: EE - Microbiology, Virology Impact factor: 1.633, year: 2016

  18. Do volatiles produced by nectar-dwelling microbes affect honey bee preferences?

    Science.gov (United States)

    The microbiome of plants mediates many interactions in natural and managed systems. Among these, plant-pollinator interactions are important for ensuring high crop yields, pollinator health and successful plant reproduction. Despite initial work demonstrating effects of floral microbes on pollinatio...

  19. The MICROBE Project, A Report from the Interagency Working Group on Microbial Genomics

    Science.gov (United States)

    2001-01-01

    functional genomics tools (gene chips, technologies, etc.), comparative genomics, proteomics tools, novel culture techniques, in situ analyses, and...interested in supporting microarray/chip development for gene expression analysis for agricultural microbes, bioinformatics, and proteomics , and the...including one fungus ) in various stages of progress. The closely integrated Natural and Accelerated Bioremediation Research Program in the Office of

  20. Immobilization and mineralization of N and P by heterotrophic microbes during leaf decomposition

    Science.gov (United States)

    Beth Cheever; Erika Kratzer; Jackson Webster

    2012-01-01

    According to theory, the rate and stoichiometry of microbial mineralization depend, in part, on nutrient availability. For microbes associated with leaves in streams, nutrients are available from both the water column and the leaf. Therefore, microbial nutrient cycling may change with nutrient availability and during leaf decomposition. We explored spatial and temporal...

  1. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  2. Burstiness in Viral Bursts: How Stochasticity Affects Spatial Patterns in Virus-Microbe Dynamics

    Science.gov (United States)

    Lin, Yu-Hui; Taylor, Bradford P.; Weitz, Joshua S.

    Spatial patterns emerge in living systems at the scale of microbes to metazoans. These patterns can be driven, in part, by the stochasticity inherent to the birth and death of individuals. For microbe-virus systems, infection and lysis of hosts by viruses results in both mortality of hosts and production of viral progeny. Here, we study how variation in the number of viral progeny per lysis event affects the spatial clustering of both viruses and microbes. Each viral ''burst'' is initially localized at a near-cellular scale. The number of progeny in a single lysis event can vary in magnitude between tens and thousands. These perturbations are not accounted for in mean-field models. Here we developed individual-based models to investigate how stochasticity affects spatial patterns in virus-microbe systems. We measured the spatial clustering of individuals using pair correlation functions. We found that increasing the burst size of viruses while maintaining the same production rate led to enhanced clustering. In this poster we also report on preliminary analysis on the evolution of the burstiness of viral bursts given a spatially distributed host community.

  3. A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions.

    Science.gov (United States)

    Zhu, Qing; Riley, William J; Tang, Jinyun

    2017-04-01

    Terrestrial plants assimilate anthropogenic CO 2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in ESMs. We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15 N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15 N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition. © 2016 by the Ecological Society of America.

  4. Dietary inclusion of direct fed microbe on the growth performance of ...

    African Journals Online (AJOL)

    The birds were obtained from a reputable hatchery and randomly assigned to four dietary treatments, each with three replicate of ten birds. ... The results show that the growth performance of the broiler chicken fed diet containing different level of direct fed microbes did not differ significantly (P>0.05) in initial weight, final ...

  5. Prominent Human Health Impacts from Several Marine Microbes: History, Ecology, and Public Health Implications

    Directory of Open Access Journals (Sweden)

    P. K. Bienfang

    2011-01-01

    Full Text Available This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense, BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment.

  6. Bactericidal Permeability-Increasing Proteins Shape Host-Microbe Interactions

    Directory of Open Access Journals (Sweden)

    Fangmin Chen

    2017-04-01

    Full Text Available We characterized bactericidal permeability-increasing proteins (BPIs of the squid Euprymna scolopes, EsBPI2 and EsBPI4. They have molecular characteristics typical of other animal BPIs, are closely related to one another, and nest phylogenetically among invertebrate BPIs. Purified EsBPIs had antimicrobial activity against the squid’s symbiont, Vibrio fischeri, which colonizes light organ crypt epithelia. Activity of both proteins was abrogated by heat treatment and coincubation with specific antibodies. Pretreatment under acidic conditions similar to those during symbiosis initiation rendered V. fischeri more resistant to the antimicrobial activity of the proteins. Immunocytochemistry localized EsBPIs to the symbiotic organ and other epithelial surfaces interacting with ambient seawater. The proteins differed in intracellular distribution. Further, whereas EsBPI4 was restricted to epithelia, EsBPI2 also occurred in blood and in a transient juvenile organ that mediates hatching. The data provide evidence that these BPIs play different defensive roles early in the life of E. scolopes, modulating interactions with the symbiont.

  7. Wired to the roots: impact of root-beneficial microbe interactions on aboveground plant physiology and protection.

    Science.gov (United States)

    Kumar, Amutha Sampath; Bais, Harsh P

    2012-12-01

    Often, plant-pathogenic microbe interactions are discussed in a host-microbe two-component system, however very little is known about how the diversity of rhizospheric microbes that associate with plants affect host performance against pathogens. There are various studies, which specially direct the importance of induced systemic defense (ISR) response in plants interacting with beneficial rhizobacteria, yet we don't know how rhizobacterial associations modulate plant physiology. In here, we highlight the many dimensions within which plant roots associate with beneficial microbes by regulating aboveground physiology. We review approaches to study the causes and consequences of plant root association with beneficial microbes on aboveground plant-pathogen interactions. The review provides the foundations for future investigations into the impact of the root beneficial microbial associations on plant performance and innate defense responses.

  8. Whole-Body Microbiota of Sea Cucumber (Apostichopus japonicus) from South Korea for Improved Seafood Management.

    Science.gov (United States)

    Kim, Tae-Yoon; Lee, Jin-Jae; Kim, Bong-Soo; Choi, Sang Ho

    2017-10-28

    Sea cucumber ( Apostichopus japonicus ) is a popular seafood source in Asia, including South Korea, and its consumption has recently increased with recognition of its medicinal properties. However, because raw sea cucumber contains various microbes, its ingestion can cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea cucumber can extend our understanding of foodborne illness caused by microorganisms and help to better manage products. We collected 40 sea cucumbers from four different sites in August and November, which are known as the maximum production areas in Korea. The microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August than in November. Alpha-, Beta-, and Gammaproteobacteria were common dominant classes in all samples. However, the microbiota composition differed according to sampling time and site. Staphylococcus warneri and Propionibacterium acnes were commonly detected potential pathogens in August and November samples, respectively. The effect of experimental Vibrio parahaemolyticus infection on the indigenous microbiota of sea cucumber was analyzed at different temperatures, revealing clear alterations of Psychrobacter and Moraxella ; thus, these shifts can be used as indicators for monitoring infection of sea cucumber. Although further studies are needed to clarify and understand the virulence and mechanisms of the identified pathogens of sea cucumber, our study provides a valuable reference for determining the potential of foodborne illness caused by sea cucumber ingestion and to develop monitoring strategies of products using microbiota information.

  9. A place for host-microbe symbiosis in the comparative physiologist's toolbox.

    Science.gov (United States)

    Kohl, Kevin D; Carey, Hannah V

    2016-11-15

    Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans. © 2016. Published by The Company of Biologists Ltd.

  10. Extracellular vesicles modulate host-microbe responses by altering TLR2 activity and phagocytosis.

    Directory of Open Access Journals (Sweden)

    Jeroen van Bergenhenegouwen

    Full Text Available Oral delivery of Gram positive bacteria, often derived from the genera Lactobacillus or Bifidobacterium, can modulate immune function. Although the exact mechanisms remain unclear, immunomodulatory effects may be elicited through the direct interaction of these bacteria with the intestinal epithelium or resident dendritic cell (DC populations. We analyzed the immune activation properties of Lactobacilli and Bifidobacterium species and made the surprising observation that cellular responses in vitro were differentially influenced by the presence of serum, specifically the extracellular vesicle (EV fraction. In contrast to the tested Lactobacilli species, tested Bifidobacterium species induce TLR2/6 activity which is inhibited by the presence of EVs. Using specific TLR ligands, EVs were found to enhance cellular TLR2/1 and TLR4 responses while TLR2/6 responses were suppressed. No effect could be observed on cellular TLR5 responses. We determined that EVs play a role in bacterial aggregation, suggesting that EVs interact with bacterial surfaces. EVs were found to slightly enhance DC phagocytosis of Bifidobacterium breve whereas phagocytosis of Lactobacillus rhamnosus was virtually absent upon serum EV depletion. DC uptake of a non-microbial substance (dextran was not affected by the different serum fractions suggesting that EVs do not interfere with DC phagocytic capacity but rather modify the DC-microbe interaction. Depending on the microbe, combined effects of EVs on TLR activity and phagocytosis result in a differential proinflammatory DC cytokine release. Overall, these data suggest that EVs play a yet unrecognized role in host-microbe responses, not by interfering in recipient cellular responses but via attachment to, or scavenging of, microbe-associated molecular patterns. EVs can be found in any tissue or bodily fluid, therefore insights into EV-microbe interactions are important in understanding the mechanism of action of potential

  11. Plant traits related to nitrogen uptake influence plant-microbe competition.

    Science.gov (United States)

    Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Philippot, Laurent; Mougel, Christophe

    2015-08-01

    Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more

  12. Saharan dust - a carrier of persistent organic pollutants, metals and microbes to the Caribbean?

    Directory of Open Access Journals (Sweden)

    V.H Garrison

    2006-12-01

    Full Text Available An international team of scientists from government agencies and universities in the United States, U.S. Virgin Islands (USVI, Trinidad & Tobago, the Republic of Cape Verde, and the Republic of Mali (West Africa is working together to elucidate the role Saharan dust may play in the degradation of Caribbean ecosystems. The first step has been to identify and quantify the persistent organic pollutants (POPs, trace metals, and viable microorganisms in the atmosphere in dust source areas of West Africa, and in dust episodes at downwind sites in the eastern Atlantic (Cape Verde and the Caribbean (USVI and Trinidad & Tobago. Preliminary findings show that air samples from Mali contain a greater number of pesticides, polychlorinated biphenyls (PCBs and polycyclic aromatic hydrocarbons (PAHs and in higher concentrations than the Caribbean sites. Overall, POP concentrations were similar in USVI and Trinidad samples. Trace metal concentrations were found to be similar to crustal composition with slight enrichment of lead in Mali. To date, hundreds of cultureable micro-organisms have been identified from Mali, Cape Verde, USVI, and Trinidad air samples. The sea fan pathogen, Aspergillus sydowii, has been identified in soil from Mali and in air samples from dust events in the Caribbean. We have shown that air samples from a dust-source region contain orders of magnitude more cultureable micro-organisms per volume than air samples from dust events in the Caribbean, which in turn contain 3-to 4-fold more cultureable microbes than during non-dust conditions. Rev. Biol. Trop. 54 (Suppl. 3: 9-21. Epub 2007 Jan. 15.Un grupo internacional de agencias gubernamentales y universidades de los Estados Unidos, las Islas Vírgenes (EUA, Trinidad y Tobago, la República de Cabo Verde y la República de Mali (África Oeste, está trabajando en conjunto para elucidar el papel que el polvo del Sahara puede estar jugando en el deterioro de los ecosistemas caribeños. El

  13. Reproductive performance of female goats fed life-enzyme ...

    African Journals Online (AJOL)

    Direct-fed-microbes (DFM) (life-enzyme) was prepared in a traditional setting using Zymomonas mobilis (bacteria from palm sap) to ferment sawdust. The result revealed an improvement in the nutrient content of the sawdust and its feed values (protein, fibre etc.), and the feed usage efficiency. The reproductive ...

  14. What Happens to Bio-degradables in the Ocean? Due to the increasing amount of plastic that ends up in the ocean there is much alarm about it killing sea life from ingestion and changing chemical properties of the ocean. But what really happens t these products in the ocean, and how do they affect the ocean.

    Science.gov (United States)

    Lavoie, A.

    2016-12-01

    What Happens to Bio-degradables in the Ocean? Due to the increasing amount of plastic that ends up in the ocean there is much alarm about it killing sea life from entanglement and ingestion and changing chemical properties of the ocean. Our society is trying to take action by purchasing and using materials that claim to be biodegradable. But how long do these materials take to degrade in ocean water and do they actually change the water composition? Answering these questions will determine if one should invest in these materials as an alternative to plastic.

  15. Sea Lion Diet Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — California sea lions pup and breed at four of the nine Channel Islands in southern California. Since 1981, SWFSC MMTD has been conducting a diet study of sea lions...

  16. Simulated microbe removal around finger rings using different hand sanitation methods.

    Science.gov (United States)

    Alur, Archana A; Rane, Madhavi J; Scheetz, James P; Lorenz, Douglas J; Gettleman, Lawrence

    2009-09-01

    It is our opinion that the CDC and the WHO have underestimated cross-contamination under examination gloves in dental clinics while wearing jewelry, such as finger rings. These agencies only "recommend" removing jewelry, and only washing hands for 15 seconds with soap and warm water before donning gloves. This study examined several washing procedures and finger rings using simulated microbes. A gloved rubber hand manikin was made and fitted with a fresh disposable vinyl glove. Four fingers were fitted with rings or no ring, dusted with simulated microbes, and washed with a scrub brush for 5, 15, and 25 seconds under 20 degrees C and 40 degrees C water alone, or with liquid hand soap. Light levels (in lux) of fluorescent powder before and after washing were measured and delta scores calculated for changes in light levels, equivalent to effectiveness of hand washing procedures. A full-factorial, 3-factor analysis of variance (ANOVA) was used to test for differences among levels of the three study factors-time, temperature, and soap use. Tukey's post hoc honestly significant difference (HSD) test was applied to significant factors to examine pair-wise differences between factor levels. It was found that the longer the hands with rings were washed with a scrub brush under flowing water, the more simulated microbes were removed. By 25 seconds, all methods were essentially the same. Simulated microbes were more difficult to remove from the palm compared to the back of the hand. The liquid hand soap used in this study was more effective with warm water than cold. When given a choice of washing with cold water up to 15 seconds, it would be preferable not to use soap to remove simulated microbes. Qualitatively, the outer surface of finger rings were more effectively cleaned than the crevice below the ring, and the ring with a stone setting appeared to accumulate and retain simulated microbes more than other rings. The most effective treatment was washing with warm water

  17. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

    Directory of Open Access Journals (Sweden)

    Feng Xueyang

    2012-08-01

    Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

  18. Diversity of life in ocean floor basalt

    Science.gov (United States)

    Thorseth, I. H.; Torsvik, T.; Torsvik, V.; Daae, F. L.; Pedersen, R. B.

    2001-12-01

    Electron microscopy and biomolecular methods have been used to describe and identify microbial communities inhabiting the glassy margins of ocean floor basalts. The investigated samples were collected from a neovolcanic ridge and from older, sediment-covered lava flows in the rift valley of the Knipovich Ridge at a water depth around 3500 m and an ambient seawater temperature of -0.7°C. Successive stages from incipient microbial colonisation, to well-developed biofilms occur on fracture surfaces in the glassy margins. Observed microbial morphologies are various filamentous, coccoidal, oval, rod-shaped and stalked forms. Etch marks in the fresh glass, with form and size resembling the attached microbes, are common. Precipitation of alteration products around microbes has developed hollow subspherical and filamentous structures. These precipitates are often enriched in Fe and Mn. The presence of branching and twisted stalks that resemble those of the iron-oxidising Gallionella, indicate that reduced iron may be utilised in an energy metabolic process. Analysis of 16S-rRNA gene sequences from microbes present in the rock samples, show that the bacterial population inhabiting these samples cluster within the γ- and ɛ-Proteobacteria and the Cytophaga/Flexibacter/Bacteroides subdivision of the Bacteria, while the Archaea all belong to the Crenarchaeota kingdom. This microbial population appears to be characteristic for the rock and their closest relatives have previously been reported from cold marine waters in the Arctic and Antarctic, deep-sea sediments and hydrothermal environments.

  19. Decreasing Fertilizer use by Optimizing Plant-microbe Interactions for Sustainable Supply of Nitrogen for Bioenergy Crops

    Science.gov (United States)

    Schicklberger, M. F.; Huang, J.; Felix, P.; Pettenato, A.; Chakraborty, R.

    2013-12-01

    Nitrogen (N) is an essential component of DNA and proteins and consequently a key element of life. N often is limited in plants, affecting plant growth and productivity. To alleviate this problem, tremendous amounts of N-fertilizer is used, which comes at a high economic price and heavy energy demand. In addition, N-fertilizer also significantly contributes to rising atmospheric greenhouse gas concentrations. Therefore, the addition of fertilizer to overcome N limitation is highly undesirable. To explore reduction in fertilizer use our research focuses on optimizing the interaction between plants and diazotrophic bacteria, which could provide adequate amounts of N to the host-plant. Therefore we investigated the diversity of microbes associated with Tobacco (Nicotiana tabacum) and Switchgrass (Panicum virgatum), considered as potential energy crop for bioenergy production. Several bacterial isolates with representatives from Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes and Bacilli were obtained from the roots, leaves, rhizoplane and rhizosphere of these plants. Majority of these isolates grew best with simple sugars and small organic acids. As shown by PCR amplification of nifH, several of these isolates are potential N2-fixing bacteria. We investigated diazotrophs for their response to elevated temperature and salinity (two common climate change induced stresses found on marginal lands), their N2-fixing ability, and their response to root exudates (which drive microbial colonization of the plant). Together this understanding is necessary for the development of eco-friendly, economically sustainable energy crops by decreasing their dependency on fertilizer.

  20. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan

    2011-01-01

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  1. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  2. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  3. 75 FR 81201 - 2011 Annual Determination for Sea Turtle Observer Requirement

    Science.gov (United States)

    2010-12-27

    ... implement programs to conserve marine life listed as endangered or threatened. All sea turtles found in U.S... endangered wherever they occur in U.S. waters. While some sea turtle populations have shown signs of recovery... attempting to engage in any such conduct), including incidental take, of endangered sea turtles. Pursuant to...

  4. 77 FR 75999 - 2013 Annual Determination for Sea Turtle Observer Requirement

    Science.gov (United States)

    2012-12-26

    ... to implement programs to conserve marine life listed as endangered or threatened. All sea turtles... (Dermochelys coriacea), and hawksbill (Eretmochelys imbricata) sea turtles are listed as endangered. Loggerhead... turtles endangered wherever they occur in U.S. waters. While some sea turtle populations have shown signs...

  5. Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.

    Science.gov (United States)

    Lamichhane, Santosh; Sen, Partho; Dickens, Alex M; Orešič, Matej; Bertram, Hanne Christine

    2018-04-30

    It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Heap bioleaching of uranium from low-grade granite-type ore by mixed acidophilic microbes

    International Nuclear Information System (INIS)

    Xuegang Wang; Zhongkui Zhou

    2017-01-01

    We evaluated uranium bioleaching from low-grade, granite-type uranium ore using mixed acidophilic microbes from uranium mine leachate. A 4854-ton plant-scale heap bioleaching process achieved sustained leaching with a uranium leaching efficiency of 88.3% using a pH of 1.0-2.0 and an Fe"3"+ dosage of 3.0-5.5 g/L. Acid consumption amounted to 25.8 g H_2SO_4 kg"-"1 ore. Uranium bioleaching follows a diffusion-controlled kinetic model with a correlation coefficient of 0.9136. Almost all uranium was dissolved in aqueous solution, except those encapsulated in quartz particles. Therefore, heap bioleaching by mixed acidophilic microbes enables efficient, economical, large-scale recovery of uranium from low-grade ores. (author)

  7. Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

    Energy Technology Data Exchange (ETDEWEB)

    Frank F. Roberto

    2008-08-01

    Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

  8. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry.

    Science.gov (United States)

    Stasulli, Nikolas M; Shank, Elizabeth A

    2016-11-01

    The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

  9. Towards a General Equation for the Survival of Microbes Transferred between Solar System Bodies

    Science.gov (United States)

    Fries, M.; Steele, A.

    2014-01-01

    It should be possible to construct a general equation describing the survival of microbes transferred between Solar System bodies. Such an equation will be useful for constraining the likelihood of transfer of viable organisms between bodies throughout the lifetime of the Solar System, and for refining Planetary Protection constraints placed on future missions. We will discuss the construction of such an equation, present a plan for definition of pertinent factors, and will describe what research will be necessary to quantify those factors. Description: We will examine the case of microbes transferred between Solar System bodies as residents in meteorite material ejected from one body (the "intial body") and deposited on another (the "target body"). Any microbes transferred in this fashion will experience four distinct phases between their initial state on the initial body, up to the point where they colonize the target body. Each of these phases features phenomena capable of reducing or exterminating the initial microbial population. They are: 1) Ejection: Material is ejected from the initial body, imparting shock followed by rapid desiccation and cooling. 2) Transport: Material travels through interplanetary space to the target body, exposing a hypothetical microbial population to extended desiccation, irradiation, and temperature extremes. 3) Infall: Material is deposited on the target body, diminishing the microbial population through shock, mass loss, and heating. 4) Adaptation: Any microbes which survive the previous three phases must then adapt to new chemophysical conditions of the target body. Differences in habitability between the initial and target bodies dominate this phase. A suitable general-form equation can be assembled from the above factors by defining the initial number of microbes in an ejected mass and applying multiplicitive factors based on the physical phenomena inherent to each phase. It should be possible to present the resulting equation

  10. Digestion of crude protein and organic matter of leaves by rumen microbes in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Ciszuk, A.; Murphy, M.

    1982-01-01

    22 leaf specimens, of which 6 were from an energy-woods project, were studied by incubation in vitro with rumen microbes or pepsin-hydrochloric acid. Several were also examined in situ using the nylon-bag technique. Many leaves, despite their low fiber and high crude protein content, gave low values for organic matter digestibility. The crude protein degradation by rumen microbes or pepsin-hydrochloric acid was low, on average, compared with hay. There was a wide variation among leaf specimens. Variation was also found as regards ammonia production in short-term (4 hours) incubation. No close correlation was found between crude protein content and crude protein degradation, or between the estimates of ruminal degradation and of pepsin-hydrochloric acid digestibility. This suggest that there are leaves that gives ruminants substantial amounts of digestible protein yet escape ruminal fermentation. (Refs. 12).

  11. Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions.

    Science.gov (United States)

    Dörmann, Peter; Kim, Hyeran; Ott, Thomas; Schulze-Lefert, Paul; Trujillo, Marco; Wewer, Vera; Hückelhoven, Ralph

    2014-12-01

    Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host cell reprogramming. Cell-autonomous defense reactions are typically polarized to the plant cell periphery underneath microbial contact sites, including de novo cell wall biosynthesis. Alternatively, host cell reprogramming converges in the biogenesis of membrane-enveloped compartments for accommodation of beneficial bacteria or invasive infection structures of filamentous microbes. Recent advances have revealed that, in response to microbial encounters, plasma membrane symmetry is broken, membrane tethering and SNARE complexes are recruited, lipid composition changes and plasma membrane-to-cytoskeleton signaling is activated, either for pre-invasive defense or for microbial entry. We provide a critical appraisal on recent studies with a focus on how plant cells re-structure membranes and the associated cytoskeleton in interactions with microbial pathogens, nitrogen-fixing rhizobia and mycorrhiza fungi. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  12. Glycine uptake in heath plants and soil microbes responds to elevated temperature, CO2 and drought

    DEFF Research Database (Denmark)

    Andresen, Luise C.; Michelsen, Anders; Jonasson, Sven

    2009-01-01

    the responses to single factors treatments. The soil microbes were superior to plants in the short-term competition for the added glycine, as indicated by an 18 times larger 15N recovery in the microbial biomass compared to the plant biomass. The soil microbes acquired glycine largely as an intact compound (87...... here present results from a field experiment in which the effects of these three climate change factors are investigated solely and in all combinations at a temperate heath dominated by heather (Calluna vulgaris) and wavy hair-grass (Deschampsia flexuosa). Climate induced increases in plant production...... may increase plant root exudation of dissolved organic compounds such as amino acids, and the release of amino acids during decomposition of organic matter. Such free amino acids in soil serve as substrates for soil microorganisms and are also acquired as nutrients directly by plants. We investigated...

  13. Microbe and Mineral Mediated Transformation of Heavy Metals, Radionuclides, and Organic Contaminants

    Science.gov (United States)

    Gerlach, R.

    2011-12-01

    Microorganisms influence their surroundings in many ways and humans have utilized microbially catalyzed reactions for benefit for centuries. Over the past few decades, microorganisms have been used for the control of contaminant transport in subsurface environments where many microbe mineral interactions occur. This presentation will discuss microbially influenced mineral formation and transformation as well as their influence on the fate of organic contaminants such as chlorinated aliphatics & 2,4,6-trinitrotoluene (TNT), heavy metals such as chromium, and radionuclides such as uranium & strontium. Both, batch and flow experiments have been performed, which monitor the net effect of microbe mineral interactions on the fate of these contaminants. This invited presentation will place an emphasis on the relative importance of direct microbial (i.e. biotic) transformations, mineral-mediated transformations as well as other abiotic reactions influencing the fate of environmental contaminants. Experiments will be summarized and placed in context of past and future engineered applications for the control of subsurface contaminants.

  14. How Much Are Floridians Willing to Pay for Protecting Sea Turtles from Sea Level Rise?

    Science.gov (United States)

    Hamed, Ahmed; Madani, Kaveh; Von Holle, Betsy; Wright, James; Milon, J Walter; Bossick, Matthew

    2016-01-01

    Sea level rise (SLR) is posing a great inundation risk to coastal areas. Some coastal nesting species, including sea turtle species, have experienced diminished habitat from SLR. Contingent valuation method (CVM) was used in an effort to assess the economic loss impacts of SLR on sea turtle nesting habitats for Florida coasts; and to elicit values of willingness to pay (WTP) of Central Florida residents to implement certain mitigation strategies, which would protect Florida's east coast sea turtle nesting areas. Using the open-ended and dichotomous choice CVM, we sampled residents of two Florida communities: Cocoa Beach and Oviedo. We estimated the WTP of households from these two cities to protect sea turtle habitat to be between $42 and $57 per year for 5 years. Additionally, we attempted to assess the impact of the both the respondents' demographics and their perception toward various situations on their WTP value. Findings include a negative correlation between the age of a respondent and the probability of an individual willing to pay the hypothetical WTP amount. We found that WTP of an individual was not dependent on prior knowledge of the effects of SLR on sea turtle habitat. The greatest indicators of whether or not an individual was willing to pay to protect sea turtle habitat were the respondents' perception regarding the trustworthiness and efficiency of the party which will implement the conservation measures and their confidence in the conservation methods used. Respondents who perceive sea turtles having an effect on their life were also more likely to pay.

  15. Antimicrobial photodynamic inactivation: a bright new technique to kill resistant microbes

    OpenAIRE

    Hamblin, Michael R

    2016-01-01

    Photodynamic therapy (PDT) uses photosensitizers (non-toxic dyes) that are activated by absorption of visible light to form reactive oxygen species (including singlet oxygen) that can oxidize biomolecules and destroy cells. Antimicrobial photodynamic inactivation (aPDI) can treat localized infections. aPDI neither causes any resistance to develop in microbes, nor is affected by existing drug resistance status. We discuss some recent developments in aPDI. New photosensitizers including polycat...

  16. Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union

    Directory of Open Access Journals (Sweden)

    Theodor Brodmann

    2017-09-01

    Full Text Available Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB, and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available, publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market.

  17. Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primany producers and microbes

    OpenAIRE

    Ronghua, Lin; Buijse-Bogdan, L.L.; Rocha Dimitrov, M.; Dohmen, P.; Kosol, Sujitra; Maltby, L.; Roessink, I.; Sinkeldam, J.A.; Smidt, H.; Wijngaarden, van, R.P.A.; Brock, T.C.M.

    2012-01-01

    The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints we...

  18. Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection, Quantification, and Characterization of Microbes

    Science.gov (United States)

    2015-11-16

    Approved for Public Release; Distribution Unlimited Final Report: 14.3 Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection...Fluroesence; Raman Spectroscopy; Microbiology REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR/MONITOR’S ACRONYM(S) ARO...14.3 Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection, Quantification, and Characterization of Microbes Report Title

  19. Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2

    Science.gov (United States)

    Benjamin N. Sulman; Richard P. Phillips; A. Christopher Oishi; Elena Shevliakova; Stephen W. Pacala

    2014-01-01

    The sensitivity of soil organic carbon (SOC) to changing environmental conditions represents a critical uncertainty in coupled carbon cycle–climate models1.Much of this uncertainty arises from our limited understanding of the extent to which root–microbe interactions induce SOC losses (through accelerated decomposition or ‘priming’2) or indirectly promote SOC gains (...

  20. Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

    Science.gov (United States)

    Tiwari, Shalini; Lata, Charu

    2018-01-01

    Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant–microbe–metal interaction. PMID:29681916

  1. Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

    Directory of Open Access Journals (Sweden)

    Shalini Tiwari

    2018-04-01

    Full Text Available Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant–microbe–metal interaction.

  2. A Hair & a Fungus: Showing Kids the Size of a Microbe

    Science.gov (United States)

    Richter, Dana L.

    2013-01-01

    A simple method is presented to show kids the size of a microbe--a fungus hypha--compared to a human hair. Common household items are used to make sterile medium on a stove or hotplate, which is dispensed in the cells of a weekly plastic pill box. Mold fungi can be easily and safely grown on the medium from the classroom environment. A microscope…

  3. Soil microbes shift C-degrading activity along an ambient and experimental nitrogen gradient

    Science.gov (United States)

    Moore, J.; Frey, S. D.

    2017-12-01

    The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of soil microbes, and yet their sensitivity to global changes remains unresolved. Atmospheric nitrogen (N) deposition has increased 22% (for NH4+) in the last two decades despite initiation of the Clean Air Act. Nitrogen deposition alters ecosystem processes by changing nutrient availability and soil pH, creating physiologically stressful environments that select for stress tolerant microbes. The functional fungal community may switch from domination by species with traits associated with decomposition via oxidative enzymes to traits associated with stress tolerance if global changes push fungal physiological limits. We examined changes in soil microbial activity across seven sites representing a gradient of ambient atmospheric N deposition, and five of these sites also had long-term N addition experiments. We measured changes in abundance of decomposition genes and C mineralization rates as indicators of microbial activity. We expected microbes to be less active with high N deposition, thus decreasing C mineralization rates. We found that C mineralization rates declined with total N deposition (ambient plus experimental additions), and this decline was more sensitive to N deposition where it occurred naturally compared to experimental treatments. Carbon mineralization declined by 3% in experimentally fertilized soils compared to 10% in control soils for every 1 kg/ha/y increase in ambient N deposition. Thus, microbes exposed to ambient levels of N deposition (2 - 12 kg/ha/y) had a stronger response than those exposed to fertilized soils (20 - 50 kg/ha/y). Long-term experimental N-addition seems to have selected for a microbial community that is tolerant of high N deposition. In sum, we provide evidence that soil microbial activity responded to N deposition, and may shift over time to a community capable of tolerating environmental change.

  4. Mechanisms of Heavy Metal Sequestration in Soils: Plant-Microbe Interactions and Organic Matter Aging

    Energy Technology Data Exchange (ETDEWEB)

    Teresa W.-M. Fan; Richard M. Higashi; David Crowley; Andrew N. Lane: Teresa A. Cassel; Peter G. Green

    2004-12-31

    For stabilization of heavy metals at contaminated sites, the three way interaction among soil organic matter (OM)-microbes-plants, and their effect on heavy metal binding is critically important for long-term sustainability, a factor that is poorly understood at the molecular level. Using a soil aging system, the humification of plant matter such as wheat straw was probed along with the effect on microbial community on soil from the former McClellan Air Force Base.

  5. Some Case Studies on Metal-Microbe Interactions to Remediate Heavy Metals- Contaminated Soils in Korea

    Science.gov (United States)

    Chon, Hyo-Taek

    2015-04-01

    Conventional physicochemical technologies to remediate heavy metals-contaminated soil have many problems such as low efficiency, high cost and occurrence of byproducts. Recently bioremediation technology is getting more and more attention. Bioremediation is defined as the use of biological methods to remediate and/or restore the contaminated land. The objectives of bioremediation are to degrade hazardous organic contaminants and to convert hazardous inorganic contaminants to less toxic compounds of safe levels. The use of bioremediation in the treatment of heavy metals in soils is a relatively new concept. Bioremediation using microbes has been developed to remove toxic heavy metals from contaminated soils in laboratory scale to the contaminated field sites. Recently the application of cost-effective and environment-friendly bioremediation technology to the heavy metals-contaminated sites has been gradually realized in Korea. The merits of bioremediation include low cost, natural process, minimal exposure to the contaminants, and minimum amount of equipment. The limitations of bioremediation are length of remediation, long monitoring time, and, sometimes, toxicity of byproducts for especially organic contaminants. From now on, it is necessary to prove applicability of the technologies to contaminated sites and to establish highly effective, low-cost and easy bioremediation technology. Four categories of metal-microbe interactions are generally biosorption, bioreduction, biomineralization and bioleaching. In this paper, some case studies of the above metal-microbe interactions in author's lab which were published recently in domestic and international journals will be introduced and summarized.

  6. Does plant-Microbe interaction confer stress tolerance in plants: A review?

    Science.gov (United States)

    Kumar, Akhilesh; Verma, Jay Prakash

    2018-03-01

    The biotic and abiotic stresses are major constraints for crop yield, food quality and global food security. A number of parameters such as physiological, biochemical, molecular of plants are affected under stress condition. Since the use of inorganic fertilizers and pesticides in agriculture practices cause degradation of soil fertility and environmental pollutions. Hence it is necessary to develop safer and sustainable means for agriculture production. The application of plant growth promoting microbes (PGPM) and mycorrhizal fungi enhance plant growth, under such conditions. It offers an economically fascinating and ecologically sound ways for protecting plants against stress condition. PGPM may promote plant growth by regulating plant hormones, improve nutrition acquisition, siderophore production and enhance the antioxidant system. While acquired systemic resistance (ASR) and induced systemic resistance (ISR) effectively deal with biotic stress. Arbuscular mycorrhiza (AM) enhance the supply of nutrients and water during stress condition and increase tolerance to stress. This plant-microbe interaction is vital for sustainable agriculture and industrial purpose, because it depends on biological processes and replaces conventional agriculture practices. Therefore, microbes may play a key role as an ecological engineer to solve environmental stress problems. So, it is a feasible and potential technology in future to feed global population at available resources with reduced impact on environmental quality. In this review, we have attempted to explore about abiotic and biotic stress tolerant beneficial microorganisms and their modes of action to enhance the sustainable agricultural production. Copyright © 2017 Elsevier GmbH. All rights reserved.

  7. Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells.

    Science.gov (United States)

    Atarashi, Koji; Tanoue, Takeshi; Ando, Minoru; Kamada, Nobuhiko; Nagano, Yuji; Narushima, Seiko; Suda, Wataru; Imaoka, Akemi; Setoyama, Hiromi; Nagamori, Takashi; Ishikawa, Eiji; Shima, Tatsuichiro; Hara, Taeko; Kado, Shoichi; Jinnohara, Toshi; Ohno, Hiroshi; Kondo, Takashi; Toyooka, Kiminori; Watanabe, Eiichiro; Yokoyama, Shin-Ichiro; Tokoro, Shunji; Mori, Hiroshi; Noguchi, Yurika; Morita, Hidetoshi; Ivanov, Ivaylo I; Sugiyama, Tsuyoshi; Nuñez, Gabriel; Camp, J Gray; Hattori, Masahira; Umesaki, Yoshinori; Honda, Kenya

    2015-10-08

    Intestinal Th17 cells are induced and accumulate in response to colonization with a subgroup of intestinal microbes such as segmented filamentous bacteria (SFB) and certain extracellular pathogens. Here, we show that adhesion of microbes to intestinal epithelial cells (ECs) is a critical cue for Th17 induction. Upon monocolonization of germ-free mice or rats with SFB indigenous to mice (M-SFB) or rats (R-SFB), M-SFB and R-SFB showed host-specific adhesion to small intestinal ECs, accompanied by host-specific induction of Th17 cells. Citrobacter rodentium and Escherichia coli O157 triggered similar Th17 responses, whereas adhesion-defective mutants of these microbes failed to do so. Moreover, a mixture of 20 bacterial strains, which were selected and isolated from fecal samples of a patient with ulcerative colitis on the basis of their ability to cause a robust induction of Th17 cells in the mouse colon, also exhibited EC-adhesive characteristics. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

    Science.gov (United States)

    Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

    2011-01-01

    Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement. PMID:21873232

  9. The Effect of Antibacterial Formula Hand Cleaners on the Elimination of Microbes on Hands

    Science.gov (United States)

    Coleman, J. R.

    2002-05-01

    : The purpose of this project is to find out which one of the antibacterial hand cleanser (antibacterial bar soap, antibacterial liquid hand soap, and liquid hand sanitizer) is more effective in eliminating microbes. If antibacterial- formula liquid hand soap is used on soiled hands, then it will be more effective in eliminating microbes. Germs are microorganisms that cause disease and can spread from person-to-person. Bacteria are a kind of microbe, an example of which is Transient Flora that is often found on hands. Hand washing prevents germs from spreading to others. During the procedure, swabs were used to take samples before and after the soiled hands had been washed with one of the antibacterial hand cleansers. Nutrient Easygel was poured into petri dishes to harden for 1 day, and then samples were swabbed on the gel. The Petri dishes were placed in an incubator for 24 hours, and then data was recorded accordingly. The antibacterial liquid hand soap was sufficient in eliminating the majority of bacteria. The hands had 65% of the bacteria on them, and after the liquid hand soap was used only 37% of the bacteria remained.

  10. Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators.

    Science.gov (United States)

    Vannette, Rachel L; Fukami, Tadashi

    2016-06-01

    Secondary metabolites that are present in floral nectar have been hypothesized to enhance specificity in plant-pollinator mutualism by reducing larceny by non-pollinators, including microorganisms that colonize nectar. However, few studies have tested this hypothesis. Using synthetic nectar, we conducted laboratory and field experiments to examine the effects of five chemical compounds found in nectar on the growth and metabolism of nectar-colonizing yeasts and bacteria, and the interactive effects of these compounds and nectar microbes on the consumption of nectar by pollinators. In most cases, focal compounds inhibited microbial growth, but the extent of these effects depended on compound identity, concentration, and microbial species. Moreover, most compounds did not substantially decrease sugar metabolism by microbes, and microbes reduced the concentration of some compounds in nectar. Using artificial flowers in the field, we also found that the common nectar yeast Metschnikowia reukaufii altered nectar consumption by small floral visitors, but only in nectar containing catalpol. This effect was likely mediated by a mechanism independent of catalpol metabolism. Despite strong compound-specific effects on microbial growth, our results suggest that the secondary metabolites tested here are unlikely to be an effective general defense mechanism for preserving nectar sugars for pollinators. Instead, our results indicate that microbial colonization of nectar could reduce the concentration of secondary compounds in nectar and, in some cases, reduce deterrence to pollinators.

  11. [Effects of different organic fertilizers on the microbes in rhizospheric soil of flue-cured tobacco].

    Science.gov (United States)

    Zhang, Yun-Wei; Xu, Zhi; Tang, Li; Li, Yan-Hong; Song, Jian-Qun; Xu, Jian-Qin

    2013-09-01

    A field experiment was conducted to study the effects of applying different organic fertilizers (refined organic fertilizer and bio-organic fertilizer) and their combination with 20% reduced chemical fertilizers on the microbes in rhizospheric soil of flue-cured tobacco, the resistance of the tobacco against bacterial wilt, and the tobacco yield and quality. As compared with conventional chemical fertilization (CK), applying refined organic fertilizer (ROF) or bio-organic fertilizer (BIO) in combining with 20% reduced chemical fertilization increased the bacterial number and the total microbial number in the rhizospheric soil significantly. Applying BIO in combining with 20% reduced chemical fertilization also increased the actinomyces number in the rhizospheric soil significantly, with an increment of 44.3% as compared with that under the application of ROF in combining with 20% reduced chemical fertilization, but decreased the fungal number. As compared with CK, the ROF and BIO increased the carbon use capacity of rhizospheric microbes significantly, and the BIO also increased the capacity of rhizospheric microbes in using phenols significantly. Under the application of ROF and BIO, the disease incidence and the disease index of bacterial wilt were decreased by 4% and 8%, and 23% and 15.9%, and the proportions of high grade tobacco leaves increased significantly by 10.5% and 9.7%, respectively, as compared with those in CK. BIO increased the tobacco yield and its output value by 17.1% and 18.9% , respectively, as compared with ROF.

  12. Enzymes from solvent-tolerant microbes: useful biocatalysts for non-aqueous enzymology.

    Science.gov (United States)

    Gupta, Anshu; Khare, S K

    2009-01-01

    Solvent-tolerant microbes are a newly emerging class that possesses the unique ability to thrive in the presence of organic solvents. Their enzymes adapted to mediate cellular and metabolic processes in a solvent-rich environment and are logically stable in the presence of organic solvents. Enzyme catalysis in non-aqueous/low-water media is finding increasing applications for the synthesis of industrially important products, namely peptides, esters, and other trans-esterification products. Solvent stability, however, remains a prerequisite for employing enzymes in non-aqueous systems. Enzymes, in general, get inactivated or give very low rates of reaction in non-aqueous media. Thus, early efforts, and even some recent ones, have aimed at stabilization of enzymes in organic media by immobilization, surface modifications, mutagenesis, and protein engineering. Enzymes from solvent-tolerant microbes appear to be the choicest source for studying solvent-stable enzymes because of their unique ability to survive in the presence of a range of organic solvents. These bacteria circumvent the solvent's toxic effects by virtue of various adaptations, e.g. at the level of the cytoplasmic membrane, by degradation and transformation of solvents, and by active excretion of solvents. The recent screening of these exotic microbes has generated some naturally solvent-stable proteases, lipases, cholesterol oxidase, cholesterol esterase, cyclodextrin glucanotransferase, and other important enzymes. The unique properties of these novel biocatalysts have great potential for applications in non-aqueous enzymology for a range of industrial processes.

  13. INTERACTIONS AMONG PHOSPHATE AMENDMENTS, MICROBES AND URANIUM MOBILITY IN CONTAMINATED SEDIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Knox, A

    2007-08-30

    The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for long-term environmental cleanup. This study evaluated the influence of four phosphate amendments and two microbial amendments on U availability. The synchrotron X-ray fluorescence mapping of the untreated U-contaminated sediment showed that U was closely associated with Mn. All tested phosphate amendments reduced aqueous U concentration more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31% respectively. Uranium sorption in phosphate treatments was significantly reduced in the presence of microbes. However, increased microbial activity in the treated sediment led to reduction of phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U amended sediment was 437 {micro}g/kg, but in the same sediment without microbes (autoclaved sediment), the extractable U concentration was only 103 {micro}g/kg. When the autoclaved amended sediment was treated with autoclaved biological apatite, U concentration in the 1 M MgCl{sub 2} extract was {approx}0 {micro}g/kg. Together these tests suggest that microbes may enhance U leaching and reduce phosphate amendment remedial effectiveness.

  14. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

    Directory of Open Access Journals (Sweden)

    Zixi Chen

    2017-09-01

    Full Text Available Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS, and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

  15. Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Shu-Hsien; Yang, Shang-Shyng [Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 10617, (Taiwan); Liu, Ching-Piao [Department of Biological Science and Technology, Meiho Institute of Technology, Pingtung 91201, (Taiwan)

    2007-05-15

    Food waste is approximately one quarter of the total garbage in Taiwan. To investigate the feasibility of microbial conversion of food waste to multiple functional biofertilizer, food waste was mixed with bulking materials, inoculated with thermophilic and lipolytic microbes and incubated at 50{sup o}C in a mechanical composter. Microbial inoculation enhanced the degradation of food wastes, increased the total nitrogen and the germination rate of alfalfa seed, shortened the maturity period and improved the quality of biofertilizer. In food waste inoculated with thermophilic and lipolytic Brevibacillus borstelensis SH168 for 28 days, total nitrogen increased from 2.01% to 2.10%, ash increased from 24.94% to 29.21%, crude fat decreased from 4.88% to 1.34% and the C/N ratio decreased from 18.02 to 17.65. Each gram of final product had a higher population of thermophilic microbes than mesophilic microbes. Microbial conversion of food waste to biofertilizer is a feasible and potential technology in the future to maintain the natural resources and to reduce the impact on environmental quality. (author)

  16. Sea level report

    International Nuclear Information System (INIS)

    Schwartz, M.L.

    1979-01-01

    Study of Cenozoic Era sea levels shows a continual lowering of sea level through the Tertiary Period. This overall drop in sea level accompanied the Pleistocene Epoch glacio-eustatic fluctuations. The considerable change of Pleistocene Epoch sea level is most directly attributable to the glacio-eustatic factor, with a time span of 10 5 years and an amplitude or range of approximately 200 m. The lowering of sea level since the end of the Cretaceous Period is attributed to subsidence and mid-ocean ridges. The maximum rate for sea level change is 4 cm/y. At present, mean sea level is rising at about 3 to 4 mm/y. Glacio-eustacy and tectono-eustacy are the parameters for predicting sea level changes in the next 1 my. Glacio-eustatic sea level changes may be projected on the basis of the Milankovitch Theory. Predictions about tectono-eustatic sea level changes, however, involve predictions about future tectonic activity and are therefore somewhat difficult to make. Coastal erosion and sedimentation are affected by changes in sea level. Erosion rates for soft sediments may be as much as 50 m/y. The maximum sedimentation accumulation rate is 20 m/100 y

  17. Life histories of potamodromous fishes [Chapter 4

    Science.gov (United States)

    Russell F. Thurow

    2016-01-01

    Potamodromous fishes move and complete their life cycle entirely within freshwater. Myers (1949) proposed the term potamodromous to distinguish freshwater migratory fishes from diadromous fishes, which migrate between the sea and freshwater and oceanodromous fishes that migrate wholly within the sea. Diadromous fishes include anadromous, catadromous and amphidromous...

  18. Enriching Metal-Oxidizing Microbes from Marine Sediment on Cathodic Currents

    Science.gov (United States)

    Rowe, A. R.; Nealson, K. H.

    2013-12-01

    The ability of organisms to transfer electrons to and from substrates outside the cell is reshaping the way we look at microbial respiration. While this process, termed extracellular electron transport (EET), has been described in a number of metal reducing organisms, current evidence suggests that this process is widespread in nature and across physiologies. Additionally, it has been speculated that these previously overlooked electrochemical interactions may play an important role in global biogeochemical cycles. Requirements for EET could play a role in why the ';uncultured majority' have so far been resistant to culturing. As such, we are currently developing culturing techniques to target microbes capable of utilizing insoluble electron acceptors utilizing electrochemical techniques. Microbe-electrode interactions are analogous to the reactions that occur between microbes and minerals and may provide an apt way to mimic the environmental conditions (i.e., insoluble electron donor/acceptor at specific redox potentials) required for culturing specialized or EET dependent metabolisms. It has been previously demonstrated that aquatic sediments are capable of utilizing anodes as electron acceptors, thereby generating a current. While, it is known that microbes utilize electrons from a cathode for the reduction of different metals and oxygen in microbial fuel cells, currently there are no reports of environmental enrichments of microbes using cathodes. Replicate microcosms from marine sediments (sampled from Catalina Harbor, California) were incubated with ITO plated glass electrodes. Negative current production at -400mV (vs. Ag/AgCl reference electrodes) potentials was sustained for four weeks. Secondary enrichments were then constructed using the cathode as the primary electron source and a variety of anaerobic terminal electron acceptors--Nitrate, Fe3+, and SO42-. Positive current was maintained in enrichment cultures (compared to abiotic control containing

  19. Spatial distribution of residence time, microbe and storage volume of groundwater in headwater catchments

    Science.gov (United States)

    Tsujimura, Maki; Ogawa, Mahiro; Yamamoto, Chisato; Sakakibara, Koichi; Sugiyama, Ayumi; Kato, Kenji; Nagaosa, Kazuyo; Yano, Shinjiro

    2017-04-01

    Headwater catchments in mountainous region are the most important recharge area for surface and subsurface waters, and time and stock information of the water is principal to understand hydrological processes in the catchments. Also, a variety of microbes are included in the groundwater and spring water, and those varies in time and space, suggesting that information of microbe could be used as tracer for groundwater flow system. However, there have been few researches to evaluate the relationship among the residence time, microbe and storage volume of the groundwater in headwater catchments. We performed an investigation on age dating using SF6 and CFCs, microbe counting in the spring water, and evaluation of groundwater storage volume based on water budget analysis in 8 regions underlain by different lithology, those are granite, dacite, sedimentary rocks, serpentinite, basalt and volcanic lava all over Japan. We conducted hydrometric measurements and sampling of spring water in base flow conditions during the rainless periods 2015 and 2016 in those regions, and SF6, CFCs, stable isotopic ratios of oxygen-18 and deuterium, inorganic solute concentrations and total number of prokaryotes were determined on all water samples. Residence time of spring water ranged from 0 to 16 years in all regions, and storage volume of the groundwater within topographical watershed was estimated to be 0.1 m to 222 m in water height. The spring with the longer residence time tends to have larger storage volume in the watershed, and the spring underlain by dacite tends to have larger storage volume as compared with that underlain by sand stone and chert. Also, total number of prokaryotes in the spring water ranged from 103 to 105 cells/mL, and the spring tends to show clear increasing of total number of prokaryotes with decreasing of residence time. Thus, we observed a certain relationship among residence time, storage volume and total number of prokaryotes in the spring water, and

  20. Preferences for different nitrogen forms by coexisting plant species and soil microbes.

    Science.gov (United States)

    Harrison, Kathryn A; Bol, Roland; Bardgett, Richard D

    2007-04-01

    The growing awareness that plants might use a variety of nitrogen (N) forms, both organic and inorganic, has raised questions about the role of resource partitioning in plant communities. It has been proposed that coexisting plant species might be able to partition a limited N pool, thereby avoiding competition for resources, through the uptake of different chemical forms of N. In this study, we used in situ stable isotope labeling techniques to assess whether coexisting plant species of a temperate grassland (England, UK) display preferences for different chemical forms of N, including inorganic N and a range of amino acids of varying complexity. We also tested whether plants and soil microbes differ in their preference for different N forms, thereby relaxing competition for this limiting resource. We examined preferential uptake of a range of 13C15N-labeled amino acids (glycine, serine, and phenylalanine) and 15N-labeled inorganic N by coexisting grass species and soil microbes in the field. Our data show that while coexisting plant species simultaneously take up a variety of N forms, including inorganic N and amino acids, they all showed a preference for inorganic N over organic N and for simple over the more complex amino acids. Soil microbes outcompeted plants for added N after 50 hours, but in the long-term (33 days) the proportion of added 15N contained in the plant pool increased for all N forms except for phenylalanine, while the proportion in the microbial biomass declined relative to the first harvest. These findings suggest that in the longer-term plants become more effective competitors for added 15N. This might be due to microbial turnover releasing 15N back into the plant-soil system or to the mineralization and subsequent plant uptake of 15N transferred initially to the organic matter pool. We found no evidence that soil microbes preferentially utilize any of the N forms added, despite previous studies showing that microbial preferences for N forms

  1. Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

    Science.gov (United States)

    Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

    2017-12-01

    Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

  2. Salish Sea Genetics - Salish Sea genetic inventory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Salish Sea comprises most of the Puget Sound water area. Marine species are generally assemblages of discrete populations occupying various ecological niches....

  3. A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling.

    Science.gov (United States)

    Nathoo, Naeem; Bernards, Mark A; MacDonald, Jacqueline; Yuan, Ze-Chun

    2017-07-22

    An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.

  4. Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

    OpenAIRE

    Saad Rama; Rizkallah Mariam R; Aziz Ramy K

    2012-01-01

    Abstract The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based ph...

  5. Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila-microbe interactions.

    Science.gov (United States)

    Broderick, Nichole A

    2016-05-26

    Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

  6. Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions

    Science.gov (United States)

    2016-01-01

    Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. PMID:27160597

  7. Contemporary Arctic Sea Level

    Science.gov (United States)

    Cazenave, A. A.

    2017-12-01

    During recent decades, the Arctic region has warmed at a rate about twice the rest of the globe. Sea ice melting is increasing and the Greenland ice sheet is losing mass at an accelerated rate. Arctic warming, decrease in the sea ice cover and fresh water input to the Arctic ocean may eventually impact the Arctic sea level. In this presentation, we review our current knowledge of contemporary Arctic sea level changes. Until the beginning of the 1990s, Arctic sea level variations were essentially deduced from tide gauges located along the Russian and Norwegian coastlines. Since then, high inclination satellite altimetry missions have allowed measuring sea level over a large portion of the Arctic Ocean (up to 80 degree north). Measuring sea level in the Arctic by satellite altimetry is challenging because the presence of sea ice cover limits the full capacity of this technique. However adapted processing of raw altimetric measurements significantly increases the number of valid data, hence the data coverage, from which regional sea level variations can be extracted. Over the altimetry era, positive trend patterns are observed over the Beaufort Gyre and along the east coast of Greenland, while negative trends are reported along the Siberian shelf. On average over the Arctic region covered by satellite altimetry, the rate of sea level rise since 1992 is slightly less than the global mea sea level rate (of about 3 mm per year). On the other hand, the interannual variability is quite significant. Space gravimetry data from the GRACE mission and ocean reanalyses provide information on the mass and steric contributions to sea level, hence on the sea level budget. Budget studies show that regional sea level trends over the Beaufort Gyre and along the eastern coast of Greenland, are essentially due to salinity changes. However, in terms of regional average, the net steric component contributes little to the observed sea level trend. The sea level budget in the Arctic

  8. The Search for Life in the Universe

    Science.gov (United States)

    Rothschild, Lynn

    2016-01-01

    Each recent report of liquid water existing elsewhere in the solar system has reverberated through the international press and excited the imagination of humankind. We have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. Dr. Lynn Rothschild, an evolutionary biologist known for her work on life in extreme environments and a founder of the field of astrobiology, tells us about intriguing new data. The prevalence of potential abodes for life in our solar system and beyond, the survival of microbes in the space environment, modeling of the potential for transfer of life between celestial bodies, and advances in synthetic biology suggest that life could be more common than previously thought. Are we truly "alone"?

  9. Arctic Sea Level Reconstruction

    DEFF Research Database (Denmark)

    Svendsen, Peter Limkilde

    Reconstruction of historical Arctic sea level is very difficult due to the limited coverage and quality of tide gauge and altimetry data in the area. This thesis addresses many of these issues, and discusses strategies to help achieve a stable and plausible reconstruction of Arctic sea level from...... 1950 to today.The primary record of historical sea level, on the order of several decades to a few centuries, is tide gauges. Tide gauge records from around the world are collected in the Permanent Service for Mean Sea Level (PSMSL) database, and includes data along the Arctic coasts. A reasonable...... amount of data is available along the Norwegian and Russian coasts since 1950, and most published research on Arctic sea level extends cautiously from these areas. Very little tide gauge data is available elsewhere in the Arctic, and records of a length of several decades,as generally recommended for sea...

  10. Life Beyond the Planet of Origin and Implications for the Search for Life on Mars

    Science.gov (United States)

    Mancinelli, Rocco L.

    2015-01-01

    Outer space is vast, cold, devoid of matter, radiation filled with essentially no gravity. These factors present an environmental challenge for any form of life. Earth's biosphere has evolved for more than 3 billion years shielded from the hostile environment of outer space by the protective blanket of the atmosphere and magnetosphere. Space is a nutritional wasteland with no liquid water and readily available organic carbon. Moving beyond a life's planet of origin requires a means for transport, the ability to withstand transport, and the ability to colonize, thrive and ultimately evolve in the new environment. Can life survive beyond its home planet? The key to answering this question is to identify organisms that first have the ability to withstand space radiation, space vacuum desiccation and time in transit, and second the ability to grow in an alien environment. Within the last 60 years space technology allowed us to transport life beyond Earth's protective shield so we may study, in situ, their responses to selected conditions of space. To date a variety of microbes ranging from viruses, to Bacteria, to Archaea, to Eukarya have been tested in the space environment. Most died instantly, but not all. These studies revealed that ultraviolet radiation is the near-term lethal agent, while hard radiation is the long-term lethal agent when the organism is shielded from ultraviolet radiation. In fact, bacterial spores, halophilic cyanobacteria and Archaea as well as some lichens survive very well if protected from ultraviolet radiation [1]. Some microbes, then, may be able to survive the trip in outer space to Mars on a spacecraft or in a meteorite. Once on Mars can a terrestrial microbe survive? Although the conditions on Mars are not as harsh as those in space, they are not hospitable for a terrestrial microbe. Studies, however, have shown that certain microbes that can survive in space for several years may also be able to survive on Mars if protected from

  11. SEA and planning

    DEFF Research Database (Denmark)

    Stoeglehner, G.; Brown, A.L.; Kørnøv, Lone

    2009-01-01

    , and the relationship of the SEA to the planning activity itself. This paper focuses on the influence that planners have in these implementation processes, postulating the hypothesis that these are key players in achieving effectiveness in SEA. Based upon implementation theory and empirical experience, the paper......As the field of strategic environmental assessment (SEA) has matured, the focus has moved from the development of legislation, guidelines and methodologies towards improving the effectiveness of SEA. Measuring and of course achieving effectiveness is both complex and challenging. This paper...

  12. Tropical forest soil microbes and climate warming: An Andean-Amazon gradient and `SWELTR'

    Science.gov (United States)

    Nottingham, A.; Turner, B. L.; Fierer, N.; Whitaker, J.; Ostle, N. J.; McNamara, N. P.; Bardgett, R.; Silman, M.; Bååth, E.; Salinas, N.; Meir, P.

    2017-12-01

    Climate warming predicted for the tropics in the coming century will result in average temperatures under which no closed canopy forest exists today. There is, therefore, great uncertainty associated with the direction and magnitude of feedbacks between tropical forests and our future climate - especially relating to the response of soil microbes and the third of global soil carbon contained in tropical forests. While warming experiments are yet to be performed in tropical forests, natural temperature gradients are powerful tools to investigate temperature effects on soil microbes. Here we draw on studies from a 3.5 km elevation gradient - and 20oC mean annual temperature gradient - in Peruvian tropical forest, to investigate how temperature affects the structure of microbial communities, microbial metabolism, enzymatic activity and soil organic matter cycling. With decreased elevation, soil microbial diversity increased and community composition shifted, from taxa associated with oligotrophic towards copiotrophic traits. A key role for temperature in shaping these patterns was demonstrated by a soil translocation experiment, where temperature-manipulation altered the relative abundance of specific taxa. Functional implications of these community composition shifts were indicated by changes in enzyme activities, the temperature sensitivity of bacterial and fungal growth rates, and the presence of temperature-adapted iso-enzymes at different elevations. Studies from a Peruvian elevation transect indicated that soil microbial communities are adapted to long-term (differences with elevation) and short-term (translocation responses) temperature changes. These findings indicate the potential for adaptation of soil microbes in tropical soils to future climate warming. However, in order to evaluate the sensitivity of these processes to climate warming in lowland forests, in situ experimentation is required. Finally, we describe SWELTR (Soil Warming Experiment in Lowland

  13. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  14. Flavor Profile of Chinese Liquor Is Altered by Interactions of Intrinsic and Extrinsic Microbes.

    Science.gov (United States)

    Wu, Qun; Kong, Yu; Xu, Yan

    2016-01-15

    The flavor profile of Chinese liquor is the result of the metabolic activity of its microbial community. Given the importance of the microbial interaction, a novel way to control the liquor's flavor is by regulating the composition of the community. In this study, we efficiently improved the liquor's flavor by perturbing the intrinsic microbial metabolism with extrinsic microbes. We first constructed a basic microbial group (intrinsic) containing Saccharomyces cerevisiae, Wickerhamomyces anomalus, and Issatchenkia orientalis and added special flavor producers (extrinsic), Saccharomyces uvarum and Saccharomyces servazzii, to this intrinsic group. Upon the addition of the extrinsic microbes, the maximum specific growth rates of S. cerevisiae and I. orientalis increased from 6.19 to 43.28/day and from 1.15 to 14.32/day, respectively, but that of W. anomalus changed from 1.00 to 0.96/day. In addition, most volatile compounds known to be produced by the extrinsic strains were not produced. However, more esters, alcohols, and acids were produced by S. cerevisiae and I. orientalis. Six compounds were significantly different by random forest analysis after perturbation. Among them, increases in ethyl hexanoate, isobutanol, and 3-methylbutyric acid were correlated with S. cerevisiae and I. orientalis, and a decrease in geranyl acetone was correlated with W. anomalus. Variations in ethyl acetate and 2-phenylethanol might be due to the varied activity of W. anomalus and S. cerevisiae. This work showed the effect of the interaction between the intrinsic and extrinsic microbes on liquor flavor, which would be beneficial for improving the quality of Chinese liquor. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  15. Effects of atrazine, metolachlor, carbaryl and chlorothalonil on benthic microbes and their nutrient dynamics.

    Directory of Open Access Journals (Sweden)

    Daniel Elias

    Full Text Available Atrazine, metolachlor, carbaryl, and chlorothalonil are detected in streams throughout the U.S. at concentrations that may have adverse effects on benthic microbes. Sediment samples were exposed to these pesticides to quantify responses of ammonium, nitrate, and phosphate uptake by the benthic microbial community. Control uptake rates of sediments had net remineralization of nitrate (-1.58 NO3 µg gdm⁻¹ h⁻¹, and net assimilation of phosphate (1.34 PO4 µg gdm⁻¹ h⁻¹ and ammonium (0.03 NH4 µg gdm⁻¹ h⁻¹. Metolachlor decreased ammonium and phosphate uptake. Chlorothalonil decreased nitrate remineralization and phosphate uptake. Nitrate, ammonium, and phosphate uptake rates are more pronounced in the presence of these pesticides due to microbial adaptations to toxicants. Our interpretation of pesticide availability based on their water/solid affinities supports no effects for atrazine and carbaryl, decreasing nitrate remineralization, and phosphate assimilation in response to chlorothalonil. Further, decreased ammonium and phosphate uptake in response to metolachlor is likely due to affinity. Because atrazine target autotrophs, and carbaryl synaptic activity, effects on benthic microbes were not hypothesized, consistent with results. Metolachlor and chlorothalonil (non-specific modes of action had significant effects on sediment microbial nutrient dynamics. Thus, pesticides with a higher affinity to sediments and/or broad modes of action are likely to affect sediment microbes' nutrient dynamics than pesticides dissolved in water or specific modes of action. Predicted nutrient uptake rates were calculated at mean and peak concentrations of metolachlor and chlorothalonil in freshwaters using polynomial equations generated in this experiment. We concluded that in natural ecosystems, peak chlorothalonil and metolachlor concentrations could affect phosphate and ammonium by decreasing net assimilation, and nitrate uptake rates by

  16. Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes.

    Science.gov (United States)

    Bircher, Lea; Geirnaert, Annelies; Hammes, Frederik; Lacroix, Christophe; Schwab, Clarissa

    2018-04-17

    Strict anaerobic gut microbes have been suggested as 'next-generation probiotics' for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (-80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant-free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03-2% in protectant-free cultures to 11-37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process- and species-specific. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  17. Bioprospecting of South African Plants as a Unique Resource for Bioactive Endophytic Microbes

    Directory of Open Access Journals (Sweden)

    Muna Ali Abdalla

    2018-05-01

    Full Text Available South Africa has a long history and strong belief in traditional herbal medicines. Using ethnobotanical knowledge as a lead, a large number of South African medicinal plants have been discovered to possess a wide spectrum of pharmacological properties. In this review, bioprospecting of endophytes is highlighted by following the advantages of the ethnomedicinal approach together with identifying unique medicinal plants where biological activity may be due to endophytes. This review focuses on the current status of South African medicinal plants to motivate the research community to harness the benefits of ethnobotanical knowledge to investigate the presence of endophytic microbes from the most potent South African medicinal plants. The potential chemical diversity and subsequent putative medicinal value of endophytes is deserving of further research. A timely and comprehensive review of literature on recently isolated endophytes and their metabolites was conducted. Worldwide literature from the last 2 years demonstrating the importance of ethnobotanical knowledge as a useful approach to discover endophytic microbes was documented. Information was obtained from scientific databases such as Pubmed, Scopus, Scirus, Google Scholar, Dictionary of Natural Products, Chemical Abstracts Services, official websites, and scientific databases on ethnomedicines. Primary sources such as books, reports, dissertations, and thesises were accessed where available. Recently published information on isolated endophytes with promising bioactivity and their bioactive natural products worldwide (2015-2017 was summarized. The potential value of South African medicinal plants as sources of endophytes is discussed. The insights provided through this study indicate that medicinal plants in South Africa are highly under-investigated sources of potentially useful endophytic microbes. New approaches may be used by medicinal plant scientists for further exploration of natural

  18. Is there a role for modified probiotics as beneficial microbes: a systematic review of the literature.

    Science.gov (United States)

    Zorzela, L; Ardestani, S K; McFarland, L V; Vohra, S

    2017-10-13

    Our objective was to conduct a systematic review and meta-analysis for the use of modified (heat-killed or sonicated) probiotics for the efficacy and safety to prevent and treat various diseases. Recent clinical research has focused on living strains of probiotics, but use in high-risk patients and potential adverse reactions including bacteremia has focused interest on alternatives to the use of live probiotics. We searched MEDLINE/PubMed, Embase, Cochrane Central Register of Controlled Trials, CINAHL, Alt Health Watch, Web of Science, Scopus, PubMed, from inception to February 14, 2017 for randomised controlled trials involving modified probiotic strains. The primary outcome was efficacy to prevent or treat disease and the secondary outcome was incidence of adverse events. A total of 40 trials were included (n=3,913): 14 trials (15 arms with modified probiotics and 20 control arms) for the prevention of diseases and 26 trials (29 arms with modified probiotics and 32 control arms) for treatment of various diseases. Modified microbes were compared to either placebo (44%), or the same living probiotic strain (39%) or to only standard therapies (17%). Modified microbes were not significantly more or less effective than the living probiotic in 86% of the preventive trials and 69% of the treatment trials. Modified probiotic strains were significantly more effective in 15% of the treatment trials. Incidence rates of adverse events were similar for modified and living probiotics and other control groups, but many trials did not collect adequate safety data. Although several types of modified probiotics showed significant efficacy over living strains of probiotics, firm conclusions could not be reached due to the limited number of trials using the same type of modified microbe (strain, daily dose and duration) for a specific disease indication. Further research may illuminate other strains of modified probiotics that may have potential as clinical biotherapeutics.

  19. Dispersal, density dependence, and population dynamics of a fungal microbe on leaf surfaces.

    Science.gov (United States)

    Woody, Scott T; Ives, Anthony R; Nordheim, Erik V; Andrews, John H

    2007-06-01

    Despite the ubiquity and importance of microbes in nature, little is known about their natural population dynamics, especially for those that occupy terrestrial habitats. Here we investigate the dynamics of the yeast-like fungus Aureobasidium pullulans (Ap) on apple leaves in an orchard. We asked three questions. (1) Is variation in fungal population density among leaves caused by variation in leaf carrying capacities and strong density-dependent population growth that maintains densities near carrying capacity? (2) Do resident populations have competitive advantages over immigrant cells? (3) Do Ap dynamics differ at different times during the growing season? To address these questions, we performed two experiments at different times in the growing season. Both experiments used a 2 x 2 factorial design: treatment 1 removed fungal cells from leaves to reveal density-dependent population growth, and treatment 2 inoculated leaves with an Ap strain engineered to express green fluorescent protein (GFP), which made it possible to track the fate of immigrant cells. The experiments showed that natural populations of Ap vary greatly in density due to sustained differences in carrying capacities among leaves. The maintenance of populations close to carrying capacities indicates strong density-dependent processes. Furthermore, resident populations are strongly competitive against immigrants, while immigrants have little impact on residents. Finally, statistical models showed high population growth rates of resident cells in one experiment but not in the other, suggesting that Ap experiences relatively "good" and "bad" periods for population growth. This picture of Ap dynamics conforms to commonly held, but rarely demonstrated, expectations of microbe dynamics in nature. It also highlights the importance of local processes, as opposed to immigration, in determining the abundance and dynamics of microbes on surfaces in terrestrial systems.

  20. The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life

    Science.gov (United States)

    Bains, William; Schulze-Makuch, Dirk

    2016-01-01

    Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe. PMID:27376334

  1. The Cosmic Zoo: The (Near Inevitability of the Evolution of Complex, Macroscopic Life

    Directory of Open Access Journals (Sweden)

    William Bains

    2016-06-01

    Full Text Available Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe.

  2. Metagenomic studies of the Red Sea.

    Science.gov (United States)

    Behzad, Hayedeh; Ibarra, Martin Augusto; Mineta, Katsuhiko; Gojobori, Takashi

    2016-02-01

    Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and

  3. Colonial life under the Humboldt Current System: deep-sea corals from O'Higgins I seamount La vida colonial bajo el sistema de la corriente de Humboldt: corales de aguas profundas en el monte submarino O'Higgins I

    OpenAIRE

    Juan I Cañete; Verena Haussermann

    2012-01-01

    A benthic community constituted by an assemblage of at least four species of deep-sea corals collected in only one trawl carried-out on the summit of the O'Higgins I seamount, central Chile. The corals were collected in only one trawl carried-out during a Chilean-Japanese cruise onboard the R/V" Koyo Maru" in December 29, 2004. Presence of oxygenated and cold Antarctic Intermediate Water (>400 m depth) on the plateau was recorded under of the Equatorial Subsurface Water associated to the oxyg...

  4. Research Advances and Detection Methodologies for Microbe-Derived Acetylcholinesterase Inhibitors: A Systemic Review

    Directory of Open Access Journals (Sweden)

    Jingqian Su

    2017-01-01

    Full Text Available Acetylcholinesterase inhibitors (AChEIs are an attractive research subject owing to their potential applications in the treatment of neurodegenerative diseases. Fungi and bacteria are major producers of AChEIs. Their active ingredients of fermentation products include alkaloids, terpenoids, phenylpropanoids, and steroids. A variety of in vitro acetylcholinesterase inhibitor assays have been developed and used to measure the activity of acetylcholinesterases, including modified Ellman’s method, thin layer chromatography bioautography, and the combined liquid chromatography-mass spectrometry/modified Ellman’s method. In this review, we provide an overview of the different detection methodologies, the microbe-derived AChEIs, and their producing strains.

  5. Pilot tests of microbe-soil combined treatment of waste drilling sludge

    OpenAIRE

    Lirong Chen; Min Huang; Xuebin Jiang; Hui Li; Qiang Chen; Min Zhang; Shenglin Li

    2015-01-01

    Microbe-soil combined treatment is a newly developed technology in view of the defects of the curing process and waste drilling mud slag properties. In particular, 0.3%–0.5% bioremediation reagents were fully mixed with the waste drilling sludge according to its wet and dry degree, and 1.5 folds to twice weight of more finely ground soil was added in the mix, which was covered by soil of 5–15 cm thick and thereby grasses or greeneries were planted on the soil. The process was successfully app...

  6. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces.

    Science.gov (United States)

    Adams, Rachel I; Lymperopoulou, Despoina S; Misztal, Pawel K; De Cassia Pessotti, Rita; Behie, Scott W; Tian, Yilin; Goldstein, Allen H; Lindow, Steven E; Nazaroff, William W; Taylor, John W; Traxler, Matt F; Bruns, Thomas D

    2017-09-26

    Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is known about how surface-borne microorganisms influence the chemistry of the indoor spaces. Here, we applied multidisciplinary approaches to investigate aspects of chemical microbiology in a house. We characterized the microbial and chemical composition of two common and frequently wet surfaces in a residential setting: kitchen sink and bathroom shower. Microbial communities were studied using culture-dependent and independent techniques, including targeting RNA for amplicon sequencing. Volatile and soluble chemicals from paired samples were analyzed using state-of-the-art techniques to explore the links between the observed microbiota and chemical exudates. Microbial analysis revealed a rich biological presence on the surfaces exposed in kitchen sinks and bathroom shower stalls. Microbial composition, matched for DNA and RNA targets, varied by surface type and sampling period. Bacteria were found to have an average of 25× more gene copies than fungi. Biomass estimates based on qPCR were well correlated with measured total volatile organic compound (VOC) emissions. Abundant VOCs included products associated with fatty acid production. Molecular networking revealed a diversity of surface-borne compounds that likely originate from microbes and from household products. Microbes played a role in structuring the chemical profiles on and emitted from kitchen sinks and shower stalls. Microbial VOCs (mVOCs) were predominately associated with the processing of fatty acids. The mVOC composition may be more stable than that of microbial communities, which can show temporal and spatial variation in their responses to changing environmental conditions. The mVOC output from microbial metabolism on kitchen sinks and bathroom showers should be apparent through careful

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

    Science.gov (United States)

    Dimkpa, Christian O

    2014-09-01

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

  8. Utilization of oil palm empty bunches waste as biochar-microbes for improving availibity of soil nutrients

    Directory of Open Access Journals (Sweden)

    G . I . Ichriani

    2016-01-01

    Full Text Available There are about 23% waste oil palm empty fruit bunches (OPEFB of total waste generated from the production of crude palm oil in oil palm plantations. Pyrolysis technology can be used to convert waste into biochar and further can be utilized for the improvement of soil. Biochar-microbes of OPEFB are biochar from OPEFB biomass that enriched with soil microbes. Biochar-microbes is expected to be used for the improvement of the soil and plants. Therefore the purpose of this research was to study the ability of biochar-microbes OPEFB to increase availability of the nutrients in sandy soils. The process of making biochar done by using slow pyrolysis technology by heating 300oC and 400oC for 2 and 3 hours, and with sizes 40 and 80 mesh, as well as indigenous microbial Bulkhorderia nodosa G.52.Rif1 and Trichoderma sp. added. The biochar production and research were conducted in the Department of Forestry Laboratory and in the Department of Agronomy Laboratory, Faculty of Agriculture, Palangka Raya University. In general, the study showed that biochar-microbes could maintain the soil pH value and tends to increase the soil pH, increasing the holding capacity of sandy soil to the elements of P and K as well as increasing the availability of nutrients N, P and K. Furthermore, this study showed that the biochar process by 400oC heating for 3 hours and 40 mesh with microbes or without microbes were the best effect on the improvement of the quality of holding capacity and the nutrients supply in sandy soils.

  9. From sea to sea: Canada's three oceans of biodiversity.

    Science.gov (United States)

    Archambault, Philippe; Snelgrove, Paul V R; Fisher, Jonathan A D; Gagnon, Jean-Marc; Garbary, David J; Harvey, Michel; Kenchington, Ellen L; Lesage, Véronique; Levesque, Mélanie; Lovejoy, Connie; Mackas, David L; McKindsey, Christopher W; Nelson, John R; Pepin, Pierre; Piché, Laurence; Poulin, Michel

    2010-08-31

    Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a

  10. Sea surface temperatures and salinities from platforms in the Barents Sea, Sea of Japan, North Atlantic Ocean, Philippine Sea, Red Sea, and the South China Sea (Nan Hai) from 1896-1950 (NODC Accession 0000506)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Surface temperatures and salinities were collected in the Barents Sea, Sea of Japan, North Atlantic Ocean, Philippine Sea, Red Sea, and South China Sea (Nan Hai)...

  11. Dilemmas in SEA application

    DEFF Research Database (Denmark)

    Lyhne, Ivar

    Dilemmas in SEA Application: The DK Energy SectorIvar Lyhne - lyhne@plan.aau.dk. Based on three years of collaborative research, this paper outlines dilemmas in the application of SEA in the strategic development of the Danish energy sector. The dilemmas are based on concrete examples from practice...

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

    Science.gov (United States)

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

    2002-01-01

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

  13. From the Earliest Evidence of Life to Complex Single-cell Organisms: The First 3 Gyr on Earth

    Science.gov (United States)

    Buick, Roger

    2006-12-01

    Life has probably been present on Earth since the time of the oldest sedimentary rock record 3.8 Gyr ago, as indicated by graphite with light carbon isotope ratios consistent with derivation from organic matter. But certain evidence for life appears only at 3.52 Gyr, in the form of kerogen (insoluble organic matter) in sedimentary carbonate showing a -25‰ carbon isotope fractionation identical to that imparted by biological carbon fixation. Soon after, at 3.48 Gyr, the first visible evidence for life appears as stromatolites (sediment mounds constructed by microbes), as well as the first evidence for a specific metabolism (large negative sulfur isotope fractionations indicating microbial sulfate reduction). By 2.7 Gyr ago, molecular biomarkers (hydrocarbons derived from biomolecules with distinctive carbon skeletons such as steroids) indicate that all 3 Domains of life: bacteria, eukaryotes (organisms with compartmentalized cells like us) and archaea (bacteria-like organisms with different biochemistry, often inhabiting extreme environments); had evolved. The first multicellular eukaryotes appeared by 1.84 Gyr in the form of fossilized filamentous algae, after the atmosphere changed from anoxic to moderately oxygenated at 2.4 Gyr and following a series of extreme “Snowball Earth” glaciations between 2.4-2.2 Gyr. Planktonic algae diversified thereafter and modern algal groups arose 1.2 Gyr ago, apparently at the end of a prolonged period of ocean anoxia when the deep sea was sulfidic and presumably toxic. Animal evolution was delayed until 0.65 Gyr ago when biomarkers for sponges first appear in the record, evidently after a further rise in atmospheric oxygen to modern levels but surprisingly pre-dating the last of another series of “Snowball Earth” glaciations. These sponges co-existed with an enigmatic extinct group of large flat marine organisms called “Ediacaran fossils” that may have been ancestral to modern animal groups but might also have been

  14. Indicators and SEA

    DEFF Research Database (Denmark)

    Gao, Jingjing; Kørnøv, Lone; Christensen, Per

    Abstract: Indicators are widely used in SEA to measure, communicate and monitor impacts from a proposed policy, plan or programme, and can improve the effectiveness for the SEA by simplifying the complexity of both assessment and presentation. Indicators can be seen as part of the implementation...... and if the information requirement for different target groups is not addressed. Indicators are widely used in SEA to measure, communicate and monitor impacts from a proposed policy, plan or programme, and can improve the effectiveness for the SEA by simplifying the complexity of both assessment and presentation...... process helping to understand, communicate and, integrate important environmental issues in planning and decision-making. On the other hand, use of indicators can also limit SEA effectiveness, if the ones chosen are biased or limited, if the aggregation gives incorrect interpretation...

  15. The secret life of microbes: soil bacteria and fungi undaunted by the harvesting of fire-killed trees

    Science.gov (United States)

    Paul Meznarich; Jane Smith; Tara Jennings

    2013-01-01

    Soil health is fundamental to ecosystem health. Disturbances such as fire and timber harvesting can affect the abundance, activity, and composition of soil microbial communities and thus affect soil productivity. In response to forest managers, scientists with the Pacific Northwest Research Station compared health and productivity indicators between soils disturbed by...

  16. An end-to-end microfluidic platform for engineering life supporting microbes in space exploration missions, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — HJ Science & Technology proposes a programmable, low-cost, and compact microfluidic platform capable of running automated end-to-end processes and optimization...

  17. Prediction of microbe-disease association from the integration of neighbor and graph with collaborative recommendation model.

    Science.gov (United States)

    Huang, Yu-An; You, Zhu-Hong; Chen, Xing; Huang, Zhi-An; Zhang, Shanwen; Yan, Gui-Ying

    2017-10-16

    Accumulating clinical researches have shown that specific microbes with abnormal levels are closely associated with the development of various human diseases. Knowledge of microbe-disease associations can provide valuable insights for complex disease mechanism understanding as well as the prevention, diagnosis and treatment of various diseases. However, little effort has been made to predict microbial candidates for human complex diseases on a large scale. In this work, we developed a new computational model for predicting microbe-disease associations by combining two single recommendation methods. Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graph-based scoring method to compute association possibility of microbe-disease pairs. The promising prediction performance could be attributed to the use of hybrid approach based on two single recommendation methods as well as the introduction of Gaussian kernel-based similarity and symptom-based disease similarity. To evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed microbe-disease associations. As a result, NGRHMDA achieved reliable results with AUCs of 0.9023 ± 0.0031 and 0.9111 in the validation frameworks of fivefold CV and LOOCV. In addition, 78.2% microbe samples and 66.7% disease samples are found to be consistent with the basic assumption of our work that microbes tend to get involved in the similar disease clusters, and vice versa. Compared with other methods, the prediction results yielded by NGRHMDA demonstrate its effective prediction performance for microbe-disease associations. It is anticipated that NGRHMDA can be used as a useful tool to search the most potential microbial candidates for various diseases, and therefore

  18. Environmental pollution of the Black Sea: A search for answers

    International Nuclear Information System (INIS)

    Fabry, V.; Osvath, I.; Froehlich, K.

    1993-01-01

    The Black Sea region governments have initiated a regional approach to the management and protection of the marine environment supported by research at national and international levels. Environmental problems in the Black Sea are serious. The Sea's shallow, mixed surface waters receive river discharges which are heavily loaded with nutrients containing nitrogen and phosphorus and contaminated with industrial and mining wastes. In addition, coastal industries appear to discharge wastes directly into the sea with little or no treatment. Thus the water quality of the life-supporting surface layer has seriously deteriorated. Eutrophication (an enrichment in nutrients) presently prevails in many parts of the Black Sea. It has dramatically changed the marine food chain, thus contributing to the demise of the Black Sea fishery and, especially in the northwestern region, to its diminished amenity value. Other factors also are at work, including changes in the hydrological balance, overfishing, and chemical pollution. Following the Chernobyl accident in 1986, riparian countries further identified radioactive pollution as having a high priority. This article looks at major aspects of the state of the Black Sea's environment, and outlines the potential of, and first results derived from, the use of isotope tracers in Black Sea studies. It further discusses IAEA initiatives to join concerted international actions directed towards rehabilitation of the Black Sea environment. 1 fig., 3 tabs, 2 maps

  19. Application of slightly acidic electrolyzed water for inactivating microbes in a layer breeding house.

    Science.gov (United States)

    Hao, X X; Li, B M; Wang, C Y; Zhang, Q; Cao, W

    2013-10-01

    Lots of microorganisms exist in layer houses can cause bird diseases and worker health concerns. Spraying chemical disinfectants is an effective way to decontaminate pathogenic microorganisms in the air and on surfaces in poultry houses. Slightly acidic electrolyzed water (SAEW, pH 5.0-6.5) is an ideal, environmentally friendly broad-spectrum disinfectant to prevent and control bacterial or viral infection in layer farms. The purpose of this work was to investigate the cleaning effectiveness of SAEW for inactivating the microbes in layer houses. The effect of SAEW was evaluated by solid materials and surface disinfection in a hen house. Results indicate that SAEW with an available chlorine concentration of 250 mg/L, pH value of 6.19, and oxygen reduction potential of 974 mV inactivated 100% of bacteria and fungi in solid materials (dusts, feces, feather, and feed), which is more efficient than common chemical disinfectant such as benzalkonium chloride solution (1:1,000 vol/vol) and povidone-iodine solution (1:1,000 vol/vol). Also, it significantly reduced the microbes on the equipment or facility surfaces (P < 0.05), including floor, wall, feed trough, and water pipe surfaces. Moreover, SAEW effectively decreased the survival rates of Salmonella and Escherichia coli by 21 and 16 percentage points. In addition, spraying the target with tap water before disinfection plays an important role in spray disinfection.

  20. Diversity of Cellulolytic Microbes and the Biodegradation of Municipal Solid Waste by a Potential Strain

    Science.gov (United States)

    Gautam, S. P.; Bundela, P. S.; Pandey, A. K.; Jamaluddin; Awasthi, M. K.; Sarsaiya, S.

    2012-01-01

    Municipal solid waste contains high amounts of cellulose, which is an ideal organic waste for the growth of most of microorganism as well as composting by potential microbes. In the present study, Congo red test was performed for screening of microorganism, and, after selecting a potential strains, it was further used for biodegradation of organic municipal solid waste. Forty nine out of the 250 different microbes tested (165 belong to fungi and 85 to bacteria) produced cellulase enzyme and among these Trichoderma viride was found to be a potential strain in the secondary screening. During the biodegradation of organic waste, after 60 days, the average weight losses were 20.10% in the plates and 33.35% in the piles. There was an increase in pH until 20 days. pH however, stabilized after 30 days in the piles. Temperature also stabilized as the composting process progressed in the piles. The high temperature continued until 30 days of decomposition, after which the temperature dropped to 40°C and below during the maturation. Good quality compost was obtained in 60 days. PMID:22518141