A microbial ecosystem beneath the West Antarctic ice sheet.

PubMed

Christner, Brent C; Priscu, John C; Achberger, Amanda M; Barbante, Carlo; Carter, Sasha P; Christianson, Knut; Michaud, Alexander B; Mikucki, Jill A; Mitchell, Andrew C; Skidmore, Mark L; Vick-Majors, Trista J

2014-08-21

Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.

Unique honey bee (Apis mellifera) hive component-based communities as detected by a hybrid of phospholipid fatty-acid and fatty-acid methyl ester analyses.

PubMed

Grubbs, Kirk J; Scott, Jarrod J; Budsberg, Kevin J; Read, Harry; Balser, Teri C; Currie, Cameron R

2015-01-01

Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components.

Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses

PubMed Central

2015-01-01

Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components. PMID:25849080

Quorum-Sensing Signal-Response Systems in Gram-Negative Bacteria

PubMed Central

Papenfort, Kai; Bassler, Bonnie

2016-01-01

Abstract / Preface Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy. PMID:27510864

Regulation of dendritic cell function through toll-like receptors.

PubMed

Kaisho, Tsuneyasu; Akira, Shizuo

2003-12-01

Higher animals establish host defense by orchestrating innate and adaptive immunity. This is mediated by professional antigen presenting cells, i.e. dendritic cells (DCs). DCs can incorporate pathogens, produce a variety of cytokines, maturate, and present pathogen-derived peptides to T cells, thereby inducing T cell activation and differentiation. These responses are triggered by microbial recognition through type I transmembrane proteins, Toll-like receptors (TLRs) on DCs. TLRs consist of ten members and each TLR is involved in recognizing a variety of microorganism-derived molecular structures. TLR ligands include cell wall components, proteins, nucleic acids, and synthetic chemical compounds, all of which can activate DCs as immune adjuvants.

Plant immunity triggered by microbial molecular signatures.

PubMed

Zhang, Jie; Zhou, Jian-Min

2010-09-01

Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are recognized by host cell surface-localized pattern-recognition receptors (PRRs) to activate plant immunity. PAMP-triggered immunity (PTI) constitutes the first layer of plant immunity that restricts pathogen proliferation. PTI signaling components often are targeted by various Pseudomonas syringae virulence effector proteins, resulting in diminished plant defenses and increased bacterial virulence. Some of the proteins targeted by pathogen effectors have evolved to sense the effector activity by associating with cytoplasmic immune receptors classically known as resistance proteins. This allows plants to activate a second layer of immunity termed effector-triggered immunity (ETI). Recent studies on PTI regulation and P. syringae effector targets have uncovered new components in PTI signaling. Although MAP kinase (MAPK) cascades have been considered crucial for PTI, emerging evidence indicates that a MAPK-independent pathway also plays an important role in PTI signaling.

The Earth Microbiome Project and modeling the planets microbial potential (Invited)

NASA Astrophysics Data System (ADS)

Gilbert, J. A.

2013-12-01

The understanding of Earth's climate and ecology requires multiscale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP captures the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >17,000 samples from 40 different biomes. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important functional processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires recognition and accommodation of sources of uncertainty.

Immunological Tolerance, Pregnancy, and Preeclampsia: The Roles of Semen Microbes and the Father†

PubMed Central

Kenny, Louise C.; Kell, Douglas B.

2018-01-01

Although it is widely considered, in many cases, to involve two separable stages (poor placentation followed by oxidative stress/inflammation), the precise originating causes of preeclampsia (PE) remain elusive. We have previously brought together some of the considerable evidence that a (dormant) microbial component is commonly a significant part of its etiology. However, apart from recognizing, consistent with this view, that the many inflammatory markers of PE are also increased in infection, we had little to say about immunity, whether innate or adaptive. In addition, we focused on the gut, oral and female urinary tract microbiomes as the main sources of the infection. We here marshall further evidence for an infectious component in PE, focusing on the immunological tolerance characteristic of pregnancy, and the well-established fact that increased exposure to the father’s semen assists this immunological tolerance. As well as these benefits, however, semen is not sterile, microbial tolerance mechanisms may exist, and we also review the evidence that semen may be responsible for inoculating the developing conceptus (and maybe the placenta) with microbes, not all of which are benign. It is suggested that when they are not, this may be a significant cause of PE. A variety of epidemiological and other evidence is entirely consistent with this, not least correlations between semen infection, infertility and PE. Our view also leads to a series of other, testable predictions. Overall, we argue for a significant paternal role in the development of PE through microbial infection of the mother via insemination. PMID:29354635

Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

PubMed Central

Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru; Kaneko, Kunihiko; Futamata, Hiroyuki

2013-01-01

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature. PMID:23995424

Post-translational modification of host proteins in pathogen-triggered defence signalling in plants.

PubMed

Stulemeijer, Iris J E; Joosten, Matthieu H A J

2008-07-01

Microbial plant pathogens impose a continuous threat to global food production. Similar to animals, an innate immune system allows plants to recognize pathogens and swiftly activate defence. To activate a rapid response, receptor-mediated pathogen perception and subsequent downstream signalling depends on post-translational modification (PTM) of components essential for defence signalling. We discuss different types of PTMs that play a role in mounting plant immunity, which include phosphorylation, glycosylation, ubiquitination, sumoylation, nitrosylation, myristoylation, palmitoylation and glycosylphosphatidylinositol (GPI)-anchoring. PTMs are rapid, reversible, controlled and highly specific, and provide a tool to regulate protein stability, activity and localization. Here, we give an overview of PTMs that modify components essential for defence signalling at the site of signal perception, during secondary messenger production and during signalling in the cytoplasm. In addition, we discuss effectors from pathogens that suppress plant defence responses by interfering with host PTMs.

21 CFR 172.325 - Bakers yeast protein.

Code of Federal Regulations, 2014 CFR

2014-04-01

... ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION Special Dietary and Nutritional... botulinum, or any other recognized microbial pathogen or any harmful microbial toxin. (d) The ingredient is used in food as a nutrient supplement as defined in § 170.3(o)(20) of this chapter. ...

Response of microbial communities to experimental warming and precipitation decrease in Rzecin peatland (Poland)

NASA Astrophysics Data System (ADS)

Basińska, Anna M.; Gąbka, Maciej; Reczuga, Monika; Łuców, Dominika; Stróżecki, Marcin; Samson, Mateusz; Józefczyk, Damian; Chojnicki, Bogdan; Urbaniak, Marek; Leśny, Jacek; Olejnik, Janusz; Gilbert, Daniel; Silvennoinen, Hanna; Juszczak, Radosław; Lamentowicz, Mariusz

2017-04-01

In the last decade researchers are intensively testing the consequences of different climate change scenarios. Due to high biodiversity, huge amount of stored carbon and their sensitivity to environmental changes, peatlands became important for the temperature increase and drought experiments. Analyses showed that mosses, vascular plants and microbial communities were affected by warming or drought, but still not all effects are clear. Studying the response of microbial groups and indicators (e.g. mixotrophic species of testate amoeba) to warming in combination with decrease of precipitation will allow to better understand the future environmental changes. To recognize the inflow of organic matter and the carbon fixing processes in disturbed environment, we need to analyse the structure and biomass of main groups living in peatlands and the response of those groups to disturbances. The Polish - Norway "WETMAN" project was designed to recognize biotic and abiotic components of ecosystem response to active warming and decrease of precipitation. In this study we present the response of microbial communities and chosen testate amoeba species (TA) to different treatments: warming, warming and decreased precipitation and only decreased precipitation, in relation to control plots. The microbial biomass of upper and lower Sphagnum segments were analysed separately. Particular microbial groups were positively correlated with manipulations e. g. microalgae and rotifers, and other were negatively affected by combination of drought and warming e.g. cyanobacteria and testate amoeba. The structure of community was modified by manipulations, and differed in the case of upper and lower segment of Sphagnum. RDA analyses showed that different factors were crucial for the biomass of microbial groups in upper (conductivity, temperature and phosphorus) and lower (nitrates and sodium) segment. Considering higher taxonomic resolution we found that at the beginning of the experiment TA community was characterised by higher abundance of mixotrophic species (Hyalosphenia papilio, Archerella flavum, Heleopera sphagni) in all plots, after half year of warming and decreased precipitation we found significant decrease of mixotrophic species biomass. Redundancy analysis showed that TA species distribution (in first year of manipulation) was significantly affected by the treatment type and upper and lower Sphagnum segment. The combination of warming and decreased precipitation led to significant testate amoeba biomass decrease (especially of mixotrophic dominant Hyalosphenia papilio). For less abundant species like Nebela tincta we found an increase of biomass in all treatments, compared to control plots. Changes in microbial communities structure, caused by the combination of drought and warming can influence peatland functioning. For instance, reduction of microbial primary production and intensified consumption may modify physicochemical water parameters as well as carbon dynamics. Project financed by the Polish-Norwegian Research Programme operated by the National Centre for Research and Development under the Norwegian Financial Mechanism (No. Pol-Nor/203258/31/2013, WETMAN). Anna M. Basinska acknowledges support from Franche-Comté regional council and Université Bourgogne Franche-Comté.

Pathogen recognition in the innate immune response.

PubMed

Kumar, Himanshu; Kawai, Taro; Akira, Shizuo

2009-04-28

Immunity against microbial pathogens primarily depends on the recognition of pathogen components by innate receptors expressed on immune and non-immune cells. Innate receptors are evolutionarily conserved germ-line-encoded proteins and include TLRs (Toll-like receptors), RLRs [RIG-I (retinoic acid-inducible gene-I)-like receptors] and NLRs (Nod-like receptors). These receptors recognize pathogens or pathogen-derived products in different cellular compartments, such as the plasma membrane, the endosomes or the cytoplasm, and induce the expression of cytokines, chemokines and co-stimulatory molecules to eliminate pathogens and instruct pathogen-specific adaptive immune responses. In the present review, we will discuss the recent progress in the study of pathogen recognition by TLRs, RLRs and NLRs and their signalling pathways.

Formation of higher plant component microbial community in closed ecological system

NASA Astrophysics Data System (ADS)

Tirranen, L. S.

2001-07-01

Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

Sensing of dangerous DNA.

PubMed

Gasser, Stephan; Zhang, Wendy Y L; Tan, Nikki Yi Jie; Tripathi, Shubhita; Suter, Manuel A; Chew, Zhi Huan; Khatoo, Muznah; Ngeow, Joanne; Cheung, Florence S G

2017-07-01

The presence of damaged and microbial DNA can pose a threat to the survival of organisms. Cells express various sensors that recognize specific aspects of such potentially dangerous DNA. Recognition of damaged or microbial DNA by sensors induces cellular processes that are important for DNA repair and inflammation. Here, we review recent evidence that the cellular response to DNA damage and microbial DNA are tightly intertwined. We also discuss insights into the parameters that enable DNA sensors to distinguish damaged and microbial DNA from DNA present in healthy cells. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Reactivity of TNT & TNT - Microbial Reduction Products with Soil Components

DTIC Science & Technology

1983-07-01

TECHNICAL REPORT REACTIVITY OF N TNT & TNT - MICROBIAL REDUCTION PRODUCTS WITH SOIL COMPONENTS BY D. L.KAPLAN ANDDTI C A. M. KAPLAN APPPoVrD FOPJUY1S...3. RECIPIENT’S CATALOG NUMBER NATICK TR-83/041 / 5c ’_______________ 4. TITLE (and Subtitle) S. TYPE OF REPORT & PERIOD -COVERED REACTIVITY OF TNT... REACTIVITY OF TNT AND TNT-MICROBIAL REDUCTION PRODUCTS WITH SOIL COMPONENTS INTRODUCTION Contamination of soils by hazardous wastes (toxic

Sub-Optimal Treatment of Bacterial Biofilms

PubMed Central

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

2016-01-01

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

Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus

PubMed Central

Foster, Timothy J.; Geoghegan, Joan A.; Ganesh, Vannakambadi K.; Höök, Magnus

2014-01-01

Staphylococcus aureus is an important opportunistic pathogen and persistently colonizes about 20% of the human population. Its surface is ‘decorated’ with proteins that are covalently anchored to the cell wall peptidoglycan. Structural and functional analysis has identified four distinct classes of surface proteins, of which microbial surface component recognizing adhesive matrix molecules (MSCRAMMs) are the largest class. These surface proteins have numerous functions, including adhesion to and invasion of host cells and tissues, evasion of immune responses and biofilm formation. Thus, cell wall-anchored proteins are essential virulence factors for the survival of S. aureus in the commensal state and during invasive infections, and targeting them with vaccines could combat S. aureus infections. PMID:24336184

Microbial ingrowth around single- and multi-component adhesives studied in vitro.

PubMed

Preussker, S; Klimm, W; Pöschmann, M; Koch, R

2003-01-01

The aim of this study was to compare the in vitro microbial leakage in 4 micro-hybrid composites in combination with 4 single-component dental adhesives (Scotchbond 1/Z100 MP = group 1; Syntac Single-Component/Tetric Flow = group 3; OptiBond Solo/XRV Herculite = group 5; Solobond M/Arabesk Top = group 7) and 4 multi-component dental adhesives (Scotchbond Multi-Purpose/Z100 MP = group 2; Syntac/Tetric Flow = group 4; OptiBond FL/XRV Herculite = group 6; Solobond Plus/Arabesk Top = group 8). Ninety-four mixed standardized Class V cavities of human caries-free extracted premolars were filled with eight different composite adhesive systems using a one-layer (groups 1-4) or a two-layer technique (groups 5-8). After thermocycling and incubation in a broth culture of Streptococcus mutans and Lactobacillus acidophilus, followed by decalcification and staining, the extent and the type of microbial leakage were measured histologically. The extent of microbial leakage in the composite restorations was very low in all groups and there were no significant differences between adhesives. Z100 MP in combination with single- and multi-component adhesives showed a significantly higher microbial leakage than Tetric Flow systems (U test: p=0.037). XRV Herculite adhesive systems showed significantly less extensive microbial leakage than Arabesk Top adhesive systems (U test: p<0.001). The single-component dental adhesives achieved a marginal adaptation of composites comparable to that of multi-component adhesives in vitro. Copyright 2003 S. Karger AG, Basel

Global abundance of planktonic heterotrophic protists in the deep ocean

PubMed Central

Pernice, Massimo C; Forn, Irene; Gomes, Ana; Lara, Elena; Alonso-Sáez, Laura; Arrieta, Jesus M; del Carmen Garcia, Francisca; Hernando-Morales, Victor; MacKenzie, Roy; Mestre, Mireia; Sintes, Eva; Teira, Eva; Valencia, Joaquin; Varela, Marta M; Vaqué, Dolors; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2015-01-01

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml−1 in mesopelagic waters down to 11±1 cells ml−1 in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml−1. The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web. PMID:25290506

Global abundance of planktonic heterotrophic protists in the deep ocean.

PubMed

Pernice, Massimo C; Forn, Irene; Gomes, Ana; Lara, Elena; Alonso-Sáez, Laura; Arrieta, Jesus M; del Carmen Garcia, Francisca; Hernando-Morales, Victor; MacKenzie, Roy; Mestre, Mireia; Sintes, Eva; Teira, Eva; Valencia, Joaquin; Varela, Marta M; Vaqué, Dolors; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2015-03-01

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml(-1) in mesopelagic waters down to 11±1 cells ml(-1) in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml(-1). The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation.

PubMed

Faustin, Benjamin; Lartigue, Lydia; Bruey, Jean-Marie; Luciano, Frederic; Sergienko, Eduard; Bailly-Maitre, Beatrice; Volkmann, Niels; Hanein, Dorit; Rouiller, Isabelle; Reed, John C

2007-03-09

Interleukin (IL)-1beta maturation is accomplished by caspase-1-mediated proteolysis, an essential element of innate immunity. NLRs constitute a recently recognized family of caspase-1-activating proteins, which contain a nucleotide-binding oligomerization domain and leucine-rich repeat (LRR) domains and which assemble into multiprotein complexes to create caspase-1-activating platforms called "inflammasomes." Using purified recombinant proteins, we have reconstituted the NALP1 inflammasome and have characterized the requirements for inflammasome assembly and caspase-1 activation. Oligomerization of NALP1 and activation of caspase-1 occur via a two-step mechanism, requiring microbial product, muramyl-dipeptide, a component of peptidoglycan, followed by ribonucleoside triphosphates. Caspase-1 activation by NALP1 does not require but is enhanced by adaptor protein ASC. The findings provide the biochemical basis for understanding how inflammasome assembly and function are regulated, and shed light on NALP1 as a direct sensor of bacterial components in host defense against pathogens.

A Test of the Biogenicity Criteria Established for Microfossils and Stromatolites on Quaternary Tufa and Speleothem Materials Formed in the "Twilight Zone" at Caerwys, UK.

PubMed

Brasier, A T; Rogerson, M R; Mercedes-Martin, R; Vonhof, H B; Reijmer, J J G

2015-10-01

The ability to distinguish the features of a chemical sedimentary rock that can only be attributed to biology is a challenge relevant to both geobiology and astrobiology. This study aimed to test criteria for recognizing petrographically the biogenicity of microbially influenced fabrics and fossil microbes in complex Quaternary stalactitic carbonate rocks from Caerwys, UK. We found that the presence of carbonaceous microfossils, fabrics produced by the calcification of microbial filaments, and the asymmetrical development of tufa fabrics due to the more rapid growth of microbially influenced laminations could be recognized as biogenic features. Petrographic evidence also indicates that the development of "speleothem-like" laminae was related to episodes of growth interrupted by intervals of nondeposition and erosion. The lack of any biogenic characteristics in these laminae is consistent with their development as a result of variation in the physicochemical parameters that drive calcite precipitation from meteoric waters in such environmental settings.

Microbial and human heat shock proteins as 'danger signals' in sarcoidosis.

PubMed

Dubaniewicz, Anna

2013-12-01

In the light of the Matzinger's model of immune response, human heat shock proteins (HSPs) as main 'danger signals' (tissue damage-associated molecular patterns-DAMPs) or/and microbial HSPs as pathogen-associated molecular patterns (PAMPs) recognized by pattern recognition receptors (PRR), may induce sarcoid granuloma by both infectious and non-infectious factors in genetically different predisposed host. Regarding infectious causes of sarcoid models, low-virulence strains of, e.g. mycobacteria and propionibacteria recognized through changed PRR and persisting in altered host phagocytes, generate increased release of both human and microbial HSPs with their molecular and functional homology. High chronic spread of human and microbial HSPs altering cytokines, co-stimulatory molecules, and Tregs expression, apoptosis, oxidative stress, induces the autoimmunity, considered in sarcoidosis. Regarding non-infectious causes of sarcoidosis, human HSPs may be released at high levels during chronic low-grade exposure to misfolding amyloid precursor protein in stressed cells, phagocyted metal fumes, pigments with/without aluminum in tattoos, and due to heat shock in firefighters. Therefore, human HSPs as DAMPs and/or microbial HSPs as PAMPs produced as a result of non-infectious and infectious factors may induce different models of sarcoidosis, depending on the genetic background of the host. The number/expression of PRRs/ligands may influence the occurrence of sarcoidosis in particular organs. Copyright © 2013 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

DOE PAGES

Feng, Wenting; Liang, Junyi; Hale, Lauren E.; ...

2017-06-09

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

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

Feng, Wenting; Liang, Junyi; Hale, Lauren E.

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming.

PubMed

Feng, Wenting; Liang, Junyi; Hale, Lauren E; Jung, Chang Gyo; Chen, Ji; Zhou, Jizhong; Xu, Minggang; Yuan, Mengting; Wu, Liyou; Bracho, Rosvel; Pegoraro, Elaine; Schuur, Edward A G; Luo, Yiqi

2017-11-01

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon-climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming. Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change. © 2017 John Wiley & Sons Ltd.

Association of TLR1, TLR2, TLR4, TLR6, and TIRAP polymorphisms with disease susceptibility.

PubMed

Noreen, Mamoona; Arshad, Muhammad

2015-06-01

Toll like receptors (TLRs) play a crucial role in regulation of innate as well as adaptive immunity. TLRs recognize a distinct but limited repertoire of conserved microbial products. Ligand binding to TLRs activates the signaling cascade and results in activation of multiple inflammatory genes. Variation in this immune response is under genetic control. Polymorphisms in genes associated with inflammatory pathway especially influence the outcome of diseases. TLR2 makes heterodimer with TLR1 or TLR6 and recognizes a wide variety of microbial ligands. In this review, we summarize studies of polymorphisms in genes encoding TLR1, TLR2, TLR4, TLR6, and most polymorphic adaptor protein, Mal/TIRAP, revealing their effect on susceptibility to diseases.

Sorptive fractionation of organic matter and formation of organo-hydroxy-aluminum complexes during litter biodegradation in the presence of gibbsite

Treesearch

K. Heckman; A.S. Grandy; X. Gao; M. Keiluweit; K. Wickings; K. Carpenter; J. Chorover; C. Rasmussen

2013-01-01

Solid and aqueous phase Al species are recognized to affect organic matter (OM) stabilization in forest soils. However, little is known about the dynamics of formation, composition and dissolution of organo-Al hydroxide complexes in microbially-active soil systems, where plant litter is subject to microbial decomposition in close proximity to mineral weathering...

Effects of combination of ultraviolet light and hydrogen peroxide on inactivation of Escherichia coli O157:H7, native microbial loads, and quality of button mushrooms

USDA-ARS?s Scientific Manuscript database

Mushrooms are prone to microbial spoilage and browning during growing and processing. Ultraviolet light (UV-C) has been used as an alternative technology to chemical sanitizers for food products. Hydrogen peroxide is classified as generally recognized as safe for use in foods as a bleaching and ant...

Free-Living Nematodes in the Freshwater Food Web: A Review

PubMed Central

Majdi, Nabil; Traunspurger, Walter

2015-01-01

Free-living nematodes are well-recognized as an abundant and ubiquitous component of benthic communities in inland waters. Compelling evidence from soil and marine ecosystems has highlighted the importance of nematodes as trophic intermediaries between microbial production and higher trophic levels. However, the paucity of empirical evidence of their role in freshwater ecosystems has hampered their inclusion in our understanding of freshwater food web functioning. This literature survey provides an overview of research efforts in the field of freshwater nematode ecology and of the complex trophic interactions between free-living nematodes and microbes, other meiofauna, macro-invertebrates, and fishes. Based on an analysis of the relevant literature and an appreciation of the potential of emerging approaches for the evaluation of nematode trophic ecology, we point out research gaps and recommend relevant directions for further research. The latter include (i) interactions of nematodes with protozoans and fungi; (ii) nonconsumptive effects of nematodes on microbial activity and the effects of nematodes on associated key ecosystem processes (decomposition, primary production); and (iii) the feeding selectivity and intraspecific feeding variability of nematodes and their potential impacts on the structure of benthic communities. PMID:25861114

[Soil microbial community structure in Picea asperata plantations with different ages in subalpine of western Sichuan, Southwest China.

PubMed

Luo, Da; Liu, Shun; Shi, Zuo Min; Feng, Qiu Hong; Liu, Qian Li; Zhang, Li; Huang, Quan; He, Jian She

2017-02-01

The effects of four Picea asperata plantations with different ages (50-, 38-, 27- and 20-year-old), in subalpine of western Sichuan, on the characteristics of soil microbial diversity and microbial community structure were studied by the method of phospholipid fatty acid (PLFA) profiles. The results showed that, with the increase of age, the contents of soil organic carbon and total nitrogen gradually improved, while Shannon's diversity index and Pielou's evenness index of soil microorganisms increased at first and then decreased. The amounts of microbial total PLFAs, bacterial PLFAs, fungal PLFAs, actinobacterial PLFAs, and arbuscular mycorrhizal fungal (AMF) PLFAs in soils consistently increased with increasing age. The principal component analysis (PCA) indicated that the soil microbial communities in different plantations were structurally distinct from each other. The first principal component (PC1) and the second principal component (PC2) together accounted for 66.8% of total variation of the soil microbial community structure. The redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil organic carbon, total nitrogen, total potassium, and fine root mass were the key determinants influencing the microbial community structure. Our study suggested that, with the extension of artificialafforestation time, the soil fertility and microbial biomass were enhanced, and the restoration processes of forest ecosystem were stable.

Application of Sequence-based Methods in Human MicrobialEcology

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

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

2005-08-29

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

Toxicity of essential oil of Satureja khuzistanica: in vitro cytotoxicity and anti-microbial activity.

PubMed

Yousefzadi, Morteza; Riahi-Madvar, Ali; Hadian, Javad; Rezaee, Fatemeh; Rafiee, Roya; Biniaz, Mehdi

2014-01-01

In nature, essential oils play an important role in the protection of the plants by exerting anti-bacterial, -viral, -fungal, -oxidative, -genotoxic, and free radical scavenging properties, as well as in some cases acting as insecticides. Several Satureja species are used in traditional medicine due to recognized therapeutic properties, namely anti-microbial and cytotoxic activities. The purpose of the present work was to determine the biologic activity of the essential oil of S. khuzistanica Jamzad (Lamiaceae) against four human cancer cell lines, as well as its inhibitory effects against a wide array (i.e. n = 11) of pathogenic bacteria and fungi. The essential oil was isolated by hydro-distillation and analyzed by GC-FID and GC-MS. Carvacrol (92.87%) and limonene (1.2%) were found to be the main components of the isolated oil. Anti-microbial activity of the essential oil was assessed using a disc diffusion method; an MTT cytotoxicity assay was employed to test effects of the oil on each cancer cell line. The oil exhibited considerable anti-microbial activity against the majority of the tested bacteria and fungi. The test oil also significantly reduced cell viability of Vero, SW480, MCF7, and JET 3 cells in a dose-dependent manner, with the IC50 values calculated for each cell type being, respectively, 31.2, 62.5, 125, and 125 μg/ml. Based on the findings, it is concluded that the essential oil of S. khuzistanica and its major constituents have a potential for further use in anti-bacterial and anti-cancer applications, pending far more extensive testing of toxicities in normal (i.e. primary) cells.

Lipid biomarker and microbial community of 49.6°E hydrothermal field at Southwest Indian Ocean Ridge

NASA Astrophysics Data System (ADS)

Lei, J.; Chu, F.; Yu, X.; Li, X.; Tao, C.

2012-12-01

In 2007, Chinese Research Cruises Discovered the First Active Hydrothermal Vent Field at the Ultraslow Spreading Southwest Indian Ridge. This study intent to get composition, evolution and origin information of lipid compounds in SWIR, and recognize the style of lipid biomarkers which have obviously indicative significance for community structure.Soluble organic matter were extracted from geological samples (including chimney sulfide, oxide, around hydrothermal vents) in Southwest Indian Ridge (SWIR), and divided into hydrocarbon, fatty acid component by column chromatography. GC, GC-MS, HPLC-MS were applied for composition and abundance analysis. Lipid in hydrothermal sulfide contains obvious isoprenoidal hydrocarbon biomarkers (Sq, IS40) and GDGTs (m/z=653) that associated with methanogenic archaea which belongs to Euryarchaeota, and iso /anti-iso fatty acid (iC15:0, aiC15:0, iC17:0, aiC17:0)which may originated from sulfate reducing bacteria (SRB).Lipids extracted from hydrothermal oxide lack isoprenoidal hydrocarbon, and Ph/C18 (0.57) is much lower than sulfide (1.22). Fatty acid compound of oxide include abundant saturated fatty (C16:0, C18:0) acid and mono-unsaturated fatty acids (C16:1n7, C18:1n7), but much less iso/anti-iso was detected. Lipid composition of hydrothermal oxide showed that archaea activity was seldom in hydrothermal oxide, and sulfur-oxidizing bacteria was the main microbial community.Study of Jaeschke (2010) showed that high temperature hydrothermal venting encompassed different microbial community from low temperature hydrothermal venting. Our study showed that in different stage of hydrothermal, microbial community structure may be distinct.

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

PubMed

Villageliu, Daniel N; Lyte, Mark

2017-08-01

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

Tracing Biosignature Preservation of Geothermally Silicified Microbial Textures into the Geological Record.

PubMed

Campbell, Kathleen A; Lynne, Bridget Y; Handley, Kim M; Jordan, Sacha; Farmer, Jack D; Guido, Diego M; Foucher, Frédéric; Turner, Susan; Perry, Randall S

2015-10-01

New Zealand and Argentine (Late Jurassic-Recent) siliceous hot-spring deposits (sinter) reveal preservation pathways of environmentally controlled, microbe-dominated sedimentary facies over geological time scales. Texturally distinctive, laminated to thinly layered, dense and vertically oriented, microtubular "palisade" fabric is common in low-temperature (<40°C) sinter-apron terraces. In modern hot springs, the dark green to brown, sheathed, photosynthetic cyanobacterium Calothrix spp. (family Rivulariaceae) constructs felted palisade mats in shallow terrace(tte) pools actively accreting opaline silica. The resulting stacked layers of silicified coarse filaments-a stromatolite-are highly porous and readily modified by postdepositional environmental perturbations, secondary silica infill, and diagenetic silica phase mineral transformations (opal-A to quartz). Fossil preservation quality is affected by relative timing of silicification, and later environmental and geological events. A systematic approach was used to characterize palisade fabric in sinters of different ages to refine tools for recognizing biosignatures in extreme environments and to track their long-term preservation pathways into the geological record. Molecular techniques, scanning electron microscopy, Raman spectrometry, X-ray powder diffraction, petrography, and lipid biomarker analyses were applied. Results indicate that microbial communities vary at the micron scale and that early and rapid silicification is paramount to long-term preservation, especially where minimal postdepositional disturbance follows fossilization. Overall, it appears that the most robust biomarkers of fossil microbial activity in hot-spring deposits are their characteristic macro- and microtextures and laser micro-Raman identified carbon. Studies of Phanerozoic geothermal deposits with mineralized microbial components are relevant analogs for Precambrian geobiology because early life is commonly preserved as microbial microfossils and biofilms in silica, some of it hydrothermal in origin. Yet the diagenetic "movie" has already been run. Hence, studying younger sinters of a range of ages provides an opportunity to "play it again" and follow the varied influences on biosignatures into the deep-time geological record.

Clumping factor B, a fibrinogen-binding MSCRAMM (microbial surface components recognizing adhesive matrix molecules) adhesin of Staphylococcus aureus, also binds to the tail region of type I cytokeratin 10.

PubMed

Walsh, Evelyn J; O'Brien, Louise M; Liang, Xiaowen; Hook, Magnus; Foster, Timothy J

2004-12-03

The primary habitat of Staphylococcus aureus in humans is the moist squamous epithelium of the anterior nares. We showed previously that S. aureus adheres to desquamated epithelial cells and that clumping factor B (ClfB), a surface-located MSCRAMM (microbial surface components recognizing adhesive matrix molecules) known for its ability to bind to the alpha-chain of fibrinogen, is partly responsible (O'Brien, L. M., Walsh, E. J., Massey, R. C., Peacock, S. J., and Foster, T. J. (2002) Cell. Microbiol. 4, 759-770). We identified cytokeratin 10 (K10) as the ligand recognized by ClfB. Here we have shown that purified recombinant human and murine K10 immobilized on a plastic surface supports adherence of S. aureus in a ClfB-dependent manner. Furthermore, the recombinant A domain of ClfB (rClfB 45-542) bound to immobilized K10 dose-dependently and saturably. Subdomains of human and murine K10 were expressed and purified. The N-terminal head domain (residues 1-145) did not support the binding of rClfB or adherence of S. aureus ClfB+. In contrast, the C-terminal tail domains (human rHK10 452-593, mouse rMK10 454-570) promoted avid binding and adherence. Isothermal titration microcalorimetry and intrinsic tryptophan fluorescence experiments gave dissociation constants for rClfB 45-542 binding to rMK10 454-570 of 1.4 and 1.7 microM, respectively. The tail region of K10 is composed largely of quasi-repeats of Tyr-(Gly/Ser)n. A synthetic peptide corresponding to a typical glycine loop (YGGGSSGGGSSGGY; Y-Y loop peptide) inhibited the adherence of S. aureus ClfB+ to immobilized MK10 to a level of 80%, whereas control peptides had no effect. The KD of rClfB 45-542 for the Y-Y loop peptide was 5.3 microm by intrinsic tryptophan fluorescence. Thus ClfB binds to the glycine loop region of the tail domain of keratin 10 where there are probably multiple binding sites. Binding is discussed in the context of the dock-lock-latch model for MSCRAMM-ligand interactions. We provide an explanation for the molecular basis for S. aureus adherence to the squamous epithelium and suggest that nasal colonization might be prevented by reagents that inhibit this interaction.

Exposure to grain dust and microbial components in the Norwegian grain and compound feed industry.

PubMed

Halstensen, Anne Straumfors; Heldal, Kari Kulvik; Wouters, Inge M; Skogstad, Marit; Ellingsen, Dag G; Eduard, Wijnand

2013-11-01

The aim of this study was to extensively characterize grain workers' personal exposure during work in Norwegian grain elevators and compound feed mills, to identify differences in exposures between the workplaces and seasons, and to study the correlations between different microbial components. Samples of airborne dust (n = 166) were collected by full-shift personal sampling during work in 20 grain elevators and compound feed mills during one autumn season and two winter seasons. The personal exposure to grain dust, endotoxins, β-1→3-glucans, bacteria, and fungal spores was quantified. Correlations between dust and microbial components and differences between workplaces and seasons were investigated. Determinants of endotoxin and β-1→3-glucan exposure were evaluated by linear mixed-effect regression modeling. The workers were exposed to an overall geometric mean of 1.0mg m(-3) inhalable grain dust [geometric standard deviation (GSD) = 3.7], 628 endotoxin units m(-3) (GSD = 5.9), 7.4 µg m(-3) of β-1→3-glucan (GSD = 5.6), 21 × 10(4) bacteria m(-3) (GSD = 7.9) and 3.6 × 10(4) fungal spores m(-3) (GSD = 3.4). The grain dust exposure levels were similar across workplaces and seasons, but the microbial content of the grain dust varied substantially between workplaces. Exposure levels of all microbial components were significantly higher in grain elevators compared with all other workplaces. The grain dust exposure was significantly correlated (Pearson's r) with endotoxin (rp = 0.65), β-1→3-glucan (rp = 0.72), bacteria (rp = 0.44) and fungal spore (rp = 0.48) exposure, whereas the explained variances were strongly dependent on the workplace. Bacteria, grain dust, and workplace were important determinants for endotoxin exposure, whereas fungal spores, grain dust, and workplace were important determinants for β-1→3-glucan exposure. Although the workers were exposed to a relatively low mean dust level, the microbial exposure was high. Furthermore, the exposure levels of microbial components varied between workplaces although the dust levels were similar. We therefore recommend that exposure levels at different workplaces should be assessed separately and a task-based assessment should be done for detailed evaluation of efficient dust-reducing measures. The microbial content and knowledge of health effects of the microbial components should be considered in health risk evaluations of these workplaces.

Sorptive fractionation of organic matter and formation of organo-hydroxy-aluminum complexes during litter biodegradation in the presence of gibbsite

NASA Astrophysics Data System (ADS)

Heckman, K.; Grandy, A. S.; Gao, X.; Keiluweit, M.; Wickings, K.; Carpenter, K.; Chorover, J.; Rasmussen, C.

2013-11-01

Solid and aqueous phase Al species are recognized to affect organic matter (OM) stabilization in forest soils. However, little is known about the dynamics of formation, composition and dissolution of organo-Al hydroxide complexes in microbially-active soil systems, where plant litter is subject to microbial decomposition in close proximity to mineral weathering reactions. We incubated gibbsite-quartz mineral mixtures in the presence of forest floor material inoculated with a native microbial consortium for periods of 5, 60 and 154 days. At each time step, samples were density separated into light (<1.6 g cm-3), intermediate (1.6-2.0 g cm-3), and heavy (>2.0 g cm-3) fractions. The light fraction was mainly comprised of particulate organic matter, while the intermediate and heavy density fractions contained moderate and large amounts of Al-minerals, respectively. Multi-method interrogation of the fractions indicated the intermediate and heavy fractions differed both in mineral structure and organic compound composition. X-ray diffraction analysis and SEM/EDS of the mineral component of the intermediate fractions indicated some alteration of the original gibbsite structure into less crystalline Al hydroxide and possibly proto-imogolite species, whereas alteration of the gibbsite structure was not evident in the heavy fraction. DRIFT, Py-GC/MS and STXM/NEXAFS results all showed that intermediate fractions were composed mostly of lignin-derived compounds, phenolics, and polysaccharides. Heavy fraction organics were dominated by polysaccharides, and were enriched in proteins, N-bearing compounds, and lipids. The source of organics appeared to differ between the intermediate and heavy fractions. Heavy fractions were enriched in 13C with lower C/N ratios relative to intermediate fractions, suggesting a microbial origin. The observed differential fractionation of organics among hydroxy-Al mineral types suggests that microbial activity superimposed with abiotic mineral-surface-mediated fractionation leads to strong density differentiation of organo-mineral complex composition even over the short time scales probed in these incubation experiments. The data highlight the strong interdependency of mineral transformation, microbial community activity, and organic matter stabilization during biodegradation.

Microbial contributions to the Precambrian Earth

NASA Technical Reports Server (NTRS)

Margulis, L.; Bermudes, D.; Obar, R.

1986-01-01

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Anaerobic microbial dehalogenation of organohalides-state of the art and remediation strategies.

PubMed

Nijenhuis, Ivonne; Kuntze, Kevin

2016-04-01

Contamination and remediation of groundwater with halogenated organics and understanding of involved microbial reactions still poses a challenge. Over the last years, research in anaerobic microbial dehalogenation has advanced in many aspects providing information about the reaction, physiology of microorganisms as well as approaches to investigate the activity of microorganisms in situ. Recently published crystal structures of reductive dehalogenases (Rdh), heterologous expression systems and advanced analytical, proteomic and stable isotope approaches allow addressing the overall reaction and specific enzymes as well as co-factors involved during anaerobic microbial dehalogenation. In addition to Dehalococcoides spp., Dehalobacter and Dehalogenimonas strains have been recognized as important and versatile organohalide respirers. Together, these provide perspectives for integrated concepts allowing to improve and monitor in situ biodegradation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial endocrinology and the microbiota-gut-brain axis.

PubMed

Lyte, Mark

2014-01-01

Microbial endocrinology is defined as the study of the ability of microorganisms to both produce and recognize neurochemicals that originate either within the microorganisms themselves or within the host they inhabit. As such, microbial endocrinology represents the intersection of the fields of microbiology and neurobiology. The acquisition of neurochemical-based cell-to-cell signaling mechanisms in eukaryotic organisms is believed to have been acquired due to late horizontal gene transfer from prokaryotic microorganisms. When considered in the context of the microbiota's ability to influence host behavior, microbial endocrinology with its theoretical basis rooted in shared neuroendocrine signaling mechanisms provides for testable experiments with which to understand the role of the microbiota in host behavior and as importantly the ability of the host to influence the microbiota through neuroendocrine-based mechanisms.

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

DOE PAGES

Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N.; Woyke, Tanja; ...

2016-02-01

Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here in this paper, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. In conclusion, thesemore » results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.« less

Saving seed microbiomes.

PubMed

Berg, Gabriele; Raaijmakers, Jos M

2018-05-01

Plant seeds are home to diverse microbial communities whose composition is determined by plant genotype, environment, and management practices. Plant domestication is now recognized as an important driver of plant-associated microbial diversity. To what extent and how domestication affects seed microbiomes is less well studied. Here we propose a 'back-to-the-future' approach to harness seed microbiomes of wild relatives of crop cultivars to save and re-instate missing beneficial seed microbes for improved plant tolerance to biotic and abiotic stress.

Abundance and biomass responses of microbial food web components to hydrology and environmental gradients within a floodplain of the River Danube.

PubMed

Palijan, Goran

2012-07-01

This study investigated the relationships of time-dependent hydrological variability and selected microbial food web components. Samples were collected monthly from the Kopački Rit floodplain in Croatia, over a period of 19 months, for analysis of bacterioplankton abundance, cell size and biomass; abundance of heterotrophic nanoflagellates and nanophytoplankton; and concentration of chlorophyll a. Similar hydrological variability at different times of the year enabled partition of seasonal effects from hydrological changes on microbial community properties. The results suggested that, unlike some other studies investigating sites with different connectivity, bacterioplankton abundance, and phytoplankton abundance and biomass increased during lentic conditions. At increasing water level, nanophytoplankton showed lower sensitivity to disturbance in comparison with total phytoplankton biomass: this could prolong autotrophic conditions within the floodplain. Bacterioplankton biomass, unlike phytoplankton, was not impacted by hydrology. The bacterial biomass less affected by hydrological changes can be an important additional food component for the floodplain food web. The results also suggested a mechanism controlling bacterial cell size independent of hydrology, as bacterial cell size was significantly decreased as nanoflagellate abundance increased. Hydrology, regardless of seasonal sucession, has the potential to structure microbial food webs, supporting microbial development during lentic conditions. Conversely, other components appear unaffected by hydrology or may be more strongly controlled by biotic interactions. This research, therefore, adds to understanding on microbial food web interactions in the context of flood and flow pulses in river-floodplain ecosystems.

Microbial Biosensors for Selective Detection of Disaccharides

USDA-ARS?s Scientific Manuscript database

Seven microbial strains were screened for their ability to detect disaccharides as components of Clark-type oxygen biosensors. Sensors responded to varying degrees to maltose, cellobiose, sucrose, and melibiose, but none responded strongly to lactose. Although microbial sensors are relatively nons...

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

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

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Becausemore » these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

Exploring the immune signalling pathway-related genes of the cattle tick Rhipicephalus microplus: From molecular characterization to transcriptional profile upon microbial challenge.

PubMed

Rosa, Rafael D; Capelli-Peixoto, Janaína; Mesquita, Rafael D; Kalil, Sandra P; Pohl, Paula C; Braz, Glória R; Fogaça, Andrea C; Daffre, Sirlei

2016-06-01

In dipteran insects, invading pathogens are selectively recognized by four major pathways, namely Toll, IMD, JNK, and JAK/STAT, and trigger the activation of several immune effectors. Although substantial advances have been made in understanding the immunity of model insects such as Drosophila melanogaster, knowledge on the activation of immune responses in other arthropods such as ticks remains limited. Herein, we have deepened our understanding of the intracellular signalling pathways likely to be involved in tick immunity by combining a large-scale in silico approach with high-throughput gene expression analysis. Data from in silico analysis revealed that although both the Toll and JAK/STAT signalling pathways are evolutionarily conserved across arthropods, ticks lack central components of the D. melanogaster IMD pathway. Moreover, we show that tick immune signalling-associated genes are constitutively transcribed in BME26 cells (a cell lineage derived from embryos of the cattle tick Rhipicephalus microplus) and exhibit different transcriptional patterns in response to microbial challenge. Interestingly, Anaplasma marginale, a pathogen that is naturally transmitted by R. microplus, causes downregulation of immune-related genes, suggesting that this pathogen may manipulate the tick immune system, favouring its survival and vector colonization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Importance of indoor dust biological ultrafine particles in the pathogenesis of chronic inflammatory lung diseases

PubMed Central

Kim, Yoon-Keun; Kang, Tae Soo; Kim, You-Young

2017-01-01

The role of infectious agents in the etiology of inflammatory diseases once believed to be non-infectious is increasingly being recognized. Many bacterial components in the indoor dust can evoke inflammatory lung diseases. Bacteria secrete nanometer-sized vesicles into the extracellular milieu, so-called extracellular vesicles (EV). which are pathophysiologically related to inflammatory diseases. Microbiota compositions in the indoor dust revealed the presence of both Gram-negative and Gram-positive bacteria. Escherichia coli is a model organism of Gram-negative Enterobacteriaceae. The repeated inhalation of E. coli-derived EVs caused neutrophilic inflammation and emphysema in a dose-dependent manner. The emphysema induced by E. coli-derived EVs was partially eliminated by the absence of Interferon-gamma or interleukin-17, suggesting that Th1 and/or Th17 cell responses are important in the emphysema development. Meanwhile, the repeated inhalation of Staphylococcus aureus-derived EVs did not induce emphysema, although they induced neutrophilic inflammation in the lung. In terms of microbial EV compositions in the indoor dust, genera Pseudomonas, Acinetobacter, Enterobacter, and Staphylococcus were dominant. As for the clinical significance of sensitization to EVs in the indoor dust, EV sensitization was closely associated with asthma, chronic obstructive pulmonary disorder (COPD), and lung cancer. These data indicate that biological ultrafine particles in the indoor dust, which are mainly composed of microbial EVs, are important in the pathogenesis of chronic lung diseases associated with neutrophilic inflammation. Taken together, microbial EVs in the indoor dust are an important diagnostic and therapeutic target for the control of chronic lung diseases, such as asthma, COPD, and lung cancer. PMID:29161804

Importance of indoor dust biological ultrafine particles in the pathogenesis of chronic inflammatory lung diseases.

PubMed

Yang, Jinho; Kim, Yoon-Keun; Kang, Tae Soo; Jee, Young-Koo; Kim, You-Young

2017-01-01

The role of infectious agents in the etiology of inflammatory diseases once believed to be non-infectious is increasingly being recognized. Many bacterial components in the indoor dust can evoke inflammatory lung diseases. Bacteria secrete nanometer-sized vesicles into the extracellular milieu, so-called extracellular vesicles (EV). which are pathophysiologically related to inflammatory diseases. Microbiota compositions in the indoor dust revealed the presence of both Gram-negative and Gram-positive bacteria. Escherichia coli is a model organism of Gram-negative Enterobacteriaceae. The repeated inhalation of E. coli-derived EVs caused neutrophilic inflammation and emphysema in a dose-dependent manner. The emphysema induced by E. coli-derived EVs was partially eliminated by the absence of Interferon-gamma or interleukin-17, suggesting that Th1 and/or Th17 cell responses are important in the emphysema development. Meanwhile, the repeated inhalation of Staphylococcus aureus-derived EVs did not induce emphysema, although they induced neutrophilic inflammation in the lung. In terms of microbial EV compositions in the indoor dust, genera Pseudomonas, Acinetobacter, Enterobacter, and Staphylococcus were dominant. As for the clinical significance of sensitization to EVs in the indoor dust, EV sensitization was closely associated with asthma, chronic obstructive pulmonary disorder (COPD), and lung cancer. These data indicate that biological ultrafine particles in the indoor dust, which are mainly composed of microbial EVs, are important in the pathogenesis of chronic lung diseases associated with neutrophilic inflammation. Taken together, microbial EVs in the indoor dust are an important diagnostic and therapeutic target for the control of chronic lung diseases, such as asthma, COPD, and lung cancer.

The intestinal complement system in inflammatory bowel disease: Shaping intestinal barrier function.

PubMed

Sina, Christian; Kemper, Claudia; Derer, Stefanie

2018-06-01

The complement system is part of innate sensor and effector systems such as the Toll-like receptors (TLRs). It recognizes and quickly systemically and/or locally respond to microbial-associated molecular patterns (MAMPs) with a tailored defense reaction. MAMP recognition by intestinal epithelial cells (IECs) and appropriate immune responses are of major importance for the maintenance of intestinal barrier function. Enterocytes highly express various complement components that are suggested to be pivotal for proper IEC function. Appropriate activation of the intestinal complement system seems to play an important role in the resolution of chronic intestinal inflammation, while over-activation and/or dysregulation may worsen intestinal inflammation. Mice deficient for single complement components suffer from enhanced intestinal inflammation mimicking the phenotype of patients with chronic inflammatory bowel disease (IBD) such as Crohn's disease (CD) or ulcerative colitis (UC). However, the mechanisms leading to complement expression in IECs seem to differ markedly between UC and CD patients. Hence, how IECs, intestinal bacteria and epithelial cell expressed complement components interact in the course of IBD still remains to be mostly elucidated to define potential unique patterns contributing to the distinct subtypes of intestinal inflammation observed in CD and UC. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

PubMed

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody.

PubMed

Ganesh, Vannakambadi K; Liang, Xiaowen; Geoghegan, Joan A; Cohen, Ana Luisa V; Venugopalan, Nagarajan; Foster, Timothy J; Hook, Magnus

2016-11-01

The Staphylococcus aureus fibrinogen binding MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules), ClfA (clumping factor A) is an important virulence factor in staphylococcal infections and a component of several vaccines currently under clinical evaluation. The mouse monoclonal antibody aurexis (also called 12-9), and the humanized version tefibazumab are therapeutic monoclonal antibodies targeting ClfA that in combination with conventional antibiotics were effective in animal models but showed less impressive efficacy in a limited Phase II clinical trial. We here report the crystal structure and a biochemical characterization of the ClfA/tefibazumab (Fab) complex. The epitope for tefibazumab is located to the "top" of the N3 subdomain of ClfA and partially overlaps with a previously unidentified second binding site for fibrinogen. A high-affinity binding of ClfA to fibrinogen involves both an interaction at the N3 site and the previously identified docking of the C-terminal segment of the fibrinogen γ-chain in the N2N3 trench. Although tefibazumab binds ClfA with high affinity we observe a modest IC 50 value for the inhibition of fibrinogen binding to the MSCRAMM. This observation, paired with a common natural occurring variant of ClfA that is not effectively recognized by the mAb, may partly explain the modest effect tefibazumab showed in the initial clinic trail. This information will provide guidance for the design of the next generation of therapeutic anti-staphylococcal mAbs targeting ClfA. Copyright © 2016. Published by Elsevier B.V.

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

PubMed Central

Bolnick, Daniel I; Snowberg, Lisa K; Hirsch, Philipp E; Lauber, Christian L; Knight, Rob; Caporaso, J Gregory; Svanbäck, Richard; Post, David

2014-01-01

Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity. PMID:24847735

Monoclonal antibodies for diagnosis and treatment.

PubMed

Dunn, D L

1993-11-01

One of the marvels of the host immune response is its response to antigenic foreign substances by manufacturing proteins that bind tenaciously to their targets. These proteins are antibodies or immunoglobulins produced in vast diversity during an individual's lifetime. By virtue of this process, the mammalian host possesses the innate ability to mount an initial response to antigens to which there has been no prior experience and to develop an even more effective response on reexposure to these same substances. This capacity to distinguish self from nonself is one of the most basic aspects of the cellular and humoral arms of the immune response and is one of the primary means by which the host combats infection caused by many different types of pathogens. In this context, antibodies have long been recognized as a critical component of host defenses and are capable of binding to invading microbes and microbial toxins.

Integrins and small GTPases as modulators of phagocytosis.

PubMed

Sayedyahossein, Samar; Dagnino, Lina

2013-01-01

Phagocytosis is the mechanism whereby cells engulf large particles. This process has long been recognized as a critical component of the innate immune response, which constitutes the organism's defense against microorganisms. In addition, phagocytic internalization of apoptotic cells or cell fragments plays important roles in tissue homeostasis and remodeling. Phagocytosis requires target interactions with receptors on the plasma membrane of the phagocytic cell. Integrins have been identified as important mediators of particle clearance, in addition to their well-established roles in cell adhesion, migration and mechanotransduction. Indeed, these ubiquitously expressed proteins impart phagocytic capacity to epithelial, endothelial and mesenchymal cell types. The importance of integrins in particle internalization is emphasized by the ability of microbial and viral pathogens to exploit their signaling pathways to invade host cells, and by the wide variety of disorders that arise from abnormalities in integrin-dependent phagocytic uptake. Copyright © 2013 Elsevier Inc. All rights reserved.

Interspecies chemical communication in bacterial development.

PubMed

Straight, Paul D; Kolter, Roberto

2009-01-01

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Microbial content of household dust associated with exhaled NO in asthmatic children.

EPA Science Inventory

Exhaled nitric oxide (eNO) is increasingly used as a non-invasive measure of airway inflammation. Despite this, little information exists regarding the potential effects of indoor microbial components on eNO. We determined the influence of microbial contaminants in house dust and...

Ecology, Microbial

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

Konopka, Allan

2009-05-15

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Designer cells programming quorum-sensing interference with microbes.

PubMed

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.

Maximizing efficiency of rumen microbial protein production

PubMed Central

Hackmann, Timothy J.; Firkins, Jeffrey L.

2015-01-01

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen. PMID:26029197

Ileal and cecal microbial populations in broilers given specific essential oil blends and probiotics in two consecutive grow-outs

USDA-ARS?s Scientific Manuscript database

Digestive microbial populations (MP) are key components for sustained healthy broiler production. Specific essential oil (EO) blends and probiotics used as feed additives have shown to promote healthy digestive microbials, resulting in improved poultry production. Two consecutive experiments were ...

Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems

PubMed Central

Decho, Alan W.; Gutierrez, Tony

2017-01-01

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured ‘biofilm’ communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called ‘marine snow.’ Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in ‘extreme’ environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans. PMID:28603518

Can environmental conditions trigger cyanobacterial surfaces and following carbonate formation: implication for biomineralization and biotechnology

NASA Astrophysics Data System (ADS)

Paulo, C.; Dittrich, M.; Zhu, T.

2015-12-01

In this presentation we will give an overview what kind of the factors may trigger carbonate formations at the cell surfaces under a variety of environmental conditions. As examples, we will present the results from our recent studies on formation of calcium carbonates, dolomites and bio-cements. The extracellular polymeric substances (EPS) in the Synechococcuscell envelope are recognized key players in the nucleation of carbonates in marine and freshwater environments. Yet, little is known about a nutrient contents control over the molecular composition of Synechococcus cell envelope, and consequently, biomineralization. In the first study, we investigated how a variation of the phosphorus (P) in the growth media can lead to changes in the surface reactivity of the cells and impact their ability to form carbonates. The objective of the second study is to gain insights into the spatial distribution of cyanobacterial EPS and dolomite from different sediment layers of Khor Al-Adaid sabkha (Qatar). Here, we characterized microbial mats on molecular level in respect of organic and inorganic components using in-situ 2D Raman spectroscopy and Atomic Force Microscopy (AFM) were used. Additionally, 2D chemical maps of sediment layers documented spectral characterizations of minerals and organic matter of microbial origins at high spatial resolution. Finally, we will show the results from the experiments with auto-phototrophic cyanobacteria Gloeocapsa PCC73106, which habitat on the monument surfaces, towards its application for bio-concrete, a product of microbial carbonate precipitation. We studied the biomineralization in biofilm forming Gloeocapsa PCC73106 on the concrete surface as a pre-requirement for microbial carbonate precipitation. Biomineralization on the concrete surface by live cells and killed cells were compared with that under the abiotic condition. Our experiments allow us to conclude that environmental conditions play a significant role in the control of the EPS dynamics and synthesis by cyanobacteria cells and, hence, these factors should be considered in biomineralization experiments.

Sulfate-dependent Anaerobic Oxidation of Methane as a Generation Mechanism for Calcite Cap Rock in Gulf Coast Salt Domes

NASA Astrophysics Data System (ADS)

Caesar, K. H.; Kyle, R.; Lyons, T. W.; Loyd, S. J.

2015-12-01

Gulf Coast salt domes, specifically their calcite cap rocks, have been widely recognized for their association with significant reserves of crude oil and natural gas. However, the specific microbial reactions that facilitate the precipitation of these cap rocks are still largely unknown. Insight into the mineralization mechanism(s) can be obtained from the specific geochemical signatures recorded in these structures. Gulf Coast cap rocks contain carbonate and sulfur minerals that exhibit variable carbon (d13C) and sulfur isotope (δ34S) signatures. Calcite d13C values are isotopically depleted and show a large range of values from -1 to -52‰, reflecting a mixture of various carbon sources including a substantial methane component. These depleted carbon isotope compositions combined with the presence of abundant sulfide minerals in cap rocks have led to interpretations that invoke microbial sulfate reduction as an important carbonate mineral-yielding process in salt dome environments. Sulfur isotope data from carbonate-associated sulfate (CAS: trace sulfate incorporated within the carbonate mineral crystal lattice) provide a more direct proxy for aqueous sulfate in salt dome systems and may provide a means to directly fingerprint ancient sulfate reduction. We find CAS sulfur isotope compositions (δ34SCAS) significantly greater than those of the precursor Jurassic sulfate-salt deposits (which exhibit δ34S values of ~ +15‰). This implies that cap rock carbonate generation occurred via microbial sulfate reduction under closed-system conditions. The co-occurrence of depleted carbonate d13C values (< ~30‰) and the enriched δ34SCAS values are evidence for sulfate-dependent anaerobic oxidation of methane (AOM). AOM, which has been shown to yield extensive seafloor carbonate authigenesis, is also potentially partly responsible for the carbonate minerals of the Gulf Coast calcite cap rocks through concomitant production of alkalinity. Collectively, these data shed new light on a potential hotspot of microbial activity in the deep biosphere.

Activation of iNKT cells by a distinct constituent of the endogenous glucosylceramide fraction

PubMed Central

Brennan, Patrick J.; Tatituri, Raju V. V.; Heiss, Christian; Watts, Gerald F. M.; Hsu, Fong-Fu; Veerapen, Natacha; Cox, Liam R.; Azadi, Parastoo; Besra, Gurdyal S.; Brenner, Michael B.

2014-01-01

Invariant natural killer T (iNKT) cells are a specialized T-cell subset that recognizes lipids as antigens, contributing to immune responses in diverse disease processes. Experimental data suggests that iNKT cells can recognize both microbial and endogenous lipid antigens. Several candidate endogenous lipid antigens have been proposed, although the contextual role of specific antigens during immune responses remains largely unknown. We have previously reported that mammalian glucosylceramides (GlcCers) activate iNKT cells. GlcCers are found in most mammalian tissues, and exist in variable molecular forms that differ mainly in N-acyl fatty acid chain use. In this report, we purified, characterized, and tested the GlcCer fractions from multiple animal species. Although activity was broadly identified in these GlcCer fractions from mammalian sources, we also found activity properties that could not be reconciled by differences in fatty acid chain use. Enzymatic digestion of β-GlcCer and a chromatographic separation method demonstrated that the activity in the GlcCer fraction was limited to a rare component of this fraction, and was not contained within the bulk of β-GlcCer molecular species. Our data suggest that a minor lipid species that copurifies with β-GlcCer in mammals functions as a lipid self antigen for iNKT cells. PMID:25197085

Exploring the diversity-stability paradigm using sponge microbial communities.

PubMed

Glasl, Bettina; Smith, Caitlin E; Bourne, David G; Webster, Nicole S

2018-05-30

A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.

The Fluorescent Properties of Dissolved Organic Matter and Assessment of Total Nitrogen in Overlying Water with Different Dissolved Oxygen Conditions.

PubMed

Zhang Hua; Kuan, Wang; Song, Jian; Zhang, Yong; Huang, Ming; Huang, Jian; Zhu, Jing; Huang, Shan; Wang, Meng

2016-03-01

This paper used excitation-emission matrix spectroscopy (EEMs) to probe the fluorescence properties of dissolved organic matter (DOM) in the overlying water with different dissolved oxygen (DO) conditions, investigating the relationship between protein-like fluorescence intensity and total nitrogen concentration. The resulting fluorescence spectra revealed three protein-like components (high-excitation wavelength tyrosine, low-excitation wavelength tyrosine, low-excitation wavelength tryptophan) and two fulvic-like components (ultraviolet fulvic-like components, visible fulvic-like components) in the overlying water. Moreover, the protein-like components were dominant in the overlying water's DOM. The fluorescence intensity of the protein-like components decreased significantly after aeration. Two of the protein-like components--the low-excitation wavelength tyrosine and the low-excitation wavelength tryptophan--were more susceptible to degradation by microorganisms within the degradable organic matter with respect to the high-excitation wavelength tyrosine. In contrast, the ultraviolet and visible fulvic-like fluorescence intensity increased along with increasing DO concentration, indicating that the fulvic-like components were part of the refractory organics. The fluorescence indices of the DOM in the overlying water were between 1.65-1.80, suggesting that the sources of the DOM were related to terrigenous sediments and microbial metabolic processes, with the primary source being the contribution from microbial metabolism. The fluorescence indices increased along with DO growth, which showed that microbial biomass and microbial activity gradually increased with increasing DO while microbial metabolism also improved, which also increased the biogenic components in the overlying water. The fluorescence intensity of the high-excitation wavelength tyrosine peak A showed a good linear relationship with the total nitrogen concentration at higher DO concentrations of 2.5, 3.5, and 5.5 mg x L(-1), with r2 being 0.956, 0.946, and 0.953, respectively. This study demonstrated that excitation-emission matrix spectroscopy can distinguish the transformation characteristics of the DOM and identify the linear relationship between the fluorescence intensity of the high-excitation wavelength tyrosine peak A and total nitrogen concentration, thus providing a quick and effective technique and theoretical support for river water monitoring and water restoration.

From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

USGS Publications Warehouse

Verchot, Louis V.; Ward, Naomi L.; Belnap, Jayne; Bossio, Deborah; Coughenour, Michael; Gibson, John; Hanotte, Olivier; Muchiru, Andrew N.; Phillips, Susan L.; Steven, Blaire; Wall, Diana H.; Reid, Robin S.

2015-01-01

Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.

Disifin (sodium tosylchloramide) and Toll-like receptors (TLRs): evolving importance in health and diseases.

PubMed

Ofodile, Okom Nkili F C

2007-12-01

Disifin has emerged as a unique and very effective agent used in disinfection of wounds, disinfection of surfaces, materials and water, and other substances contaminated with almost every type of pathogenic microorganism ranging from viruses, bacteria, fungi and yeast, and, very possibly, protozoan parasites, as well. The major active component of Disifin is tosylchloramide sodium (chloramine T). However, the mechanism by which Disifin suppresses the activities of pathogenic microbial agents remains enigmatic. The molecular mechanisms, and the receptors and the signal transducing pathways responsible for the biological effects of Disifin are largely unknown. Despite considerable advances, enormous investigative efforts and large resources invested in the research on infectious diseases, microbial infection still remains a public health problem in many parts of the world. The exact nature of the pathogenic agents responsible for many infectious diseases, and the nature of the receptors mediating the associated inflammatory events are incompletely understood. Recent advances in understanding the molecular basis for mammalian host immune responses to microbial invasion suggest that the first line of defense against microbes is the recognition of pathogen-associated molecular patterns (PAMPs) by a family of transmembrane pattern-recognizing and signal transducing receptor proteins called Toll-like receptors (TLRs). The TLR family plays an instructive role in innate immune responses against microbial pathogens, as well as the subsequent induction of adaptive immune responses. TLRs mediate recognition and inflammatory responses to a wide range of microbial products and are crucial for effective host defense by eradication of the invading pathogens. Now, recent updates demonstrated the ability of Disifin-derived products, Disifin-Animal and Disifin-Pressant to effectively suppress the progression and activities of Chikungunya fever and that of avian influenza A virus [A/cardialis/Germany/72, H7N1: the agent of a highly pathogenic avian influenza (HPAI)] infection, respectively. Overall, the above findings led me to suggest that Disifin and TLRs may mechanistically overlap in the processes of executing their functions against pathogenic microbial organisms. Thus, elucidating and better understanding of the molecular underpinnings responsible for the biochemical effects of Disifin-products, and the nature and mode of the interaction(s) of Disifin with TLRs in the process of exerting their biological effects may open a novel dimension in the research of infectious diseases, which may provide novel therapeutic targets for the prevention and treatment of a wide range of infectious diseases.

Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

PubMed Central

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V.; Garcia-Trejo, Juan F.; Guevara-Gonzalez, Ramon G.

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems. PMID:26509157

Recognition of DHN-melanin by a C-type lectin receptor is required for immunity to Aspergillus.

PubMed

Stappers, Mark H T; Clark, Alexandra E; Aimanianda, Vishukumar; Bidula, Stefan; Reid, Delyth M; Asamaphan, Patawee; Hardison, Sarah E; Dambuza, Ivy M; Valsecchi, Isabel; Kerscher, Bernhard; Plato, Anthony; Wallace, Carol A; Yuecel, Raif; Hebecker, Betty; da Glória Teixeira Sousa, Maria; Cunha, Cristina; Liu, Yan; Feizi, Ten; Brakhage, Axel A; Kwon-Chung, Kyung J; Gow, Neil A R; Zanda, Matteo; Piras, Monica; Zanato, Chiara; Jaeger, Martin; Netea, Mihai G; van de Veerdonk, Frank L; Lacerda, João F; Campos, António; Carvalho, Agostinho; Willment, Janet A; Latgé, Jean-Paul; Brown, Gordon D

2018-03-15

Resistance to infection is critically dependent on the ability of pattern recognition receptors to recognize microbial invasion and induce protective immune responses. One such family of receptors are the C-type lectins, which are central to antifungal immunity. These receptors activate key effector mechanisms upon recognition of conserved fungal cell-wall carbohydrates. However, several other immunologically active fungal ligands have been described; these include melanin, for which the mechanism of recognition is hitherto undefined. Here we identify a C-type lectin receptor, melanin-sensing C-type lectin receptor (MelLec), that has an essential role in antifungal immunity through recognition of the naphthalene-diol unit of 1,8-dihydroxynaphthalene (DHN)-melanin. MelLec recognizes melanin in conidial spores of Aspergillus fumigatus as well as in other DHN-melanized fungi. MelLec is ubiquitously expressed by CD31 + endothelial cells in mice, and is also expressed by a sub-population of these cells that co-express epithelial cell adhesion molecule and are detected only in the lung and the liver. In mouse models, MelLec was required for protection against disseminated infection with A. fumigatus. In humans, MelLec is also expressed by myeloid cells, and we identified a single nucleotide polymorphism of this receptor that negatively affected myeloid inflammatory responses and significantly increased the susceptibility of stem-cell transplant recipients to disseminated Aspergillus infections. MelLec therefore recognizes an immunologically active component commonly found on fungi and has an essential role in protective antifungal immunity in both mice and humans.

Photodegradation of major soil microbial biomolecules is comparable to biodegradation: Insights from infrared and diffusion editing NMR spectroscopies

NASA Astrophysics Data System (ADS)

Spence, Adrian; Kelleher, Brian P.

2016-03-01

As a primary decomposition process in terrestrial biosystems, biodegradation has been extensively studied with regard to its impact on soil organic matter transformation. However, the biotransformation of soil microbial biomass (a primary source of soil organic carbon) remains poorly understood, and even less is known about the fate of microbial-derived carbon under photodegradation. Here, we combine infrared and diffusion editing NMR spectroscopies to provide molecular-level information on the photodegradation of major biochemical components in soil microbial biomass and leachates over time. Results indicate a considerable enrichment in aliphatic components, presumably polymethylenic-C [(C-H2)n] and the simultaneous loss of carbohydrate and protein structures in the biomass. An immediate conclusion is that photodegradation increased the conversion of macromolecular carbohydrates and proteins to smaller components. However, further analysis reveals that macromolecular carbohydrates and proteins may be more resistant to photodegradation than initially thought and are found in the leachates. Although attenuated, there is also evidence to suggest that some aliphatic structures persist in the leachates. Overall, the photodegradation pathway reported here is remarkably similar to that of biodegradation, suggesting that under rapidly expanding anthropogenic land disturbances, photodegradation could be an important driver of the transformation of microbial-derived organic matter in terrestrial biosystems.

The preliminary assessment of anti-microbial activity of HPLC separated components of Kirkia wilmsii.

PubMed

Chigayo, K; Mojapelo, P E L; Bessong, P; Gumbo, J R

2014-01-01

Most communities in developing countries rely on traditional medicines for the treatment of diseases. In South Africa, the Limpopo province, within the Lebowakgomo district, uses tuberous roots of Kirkia wilmsii, after infusion in water for the treatment of a wide range of diseases by Sotho communities. The main objective of the study was to assess the anti-microbial activity of separated aqueous components of the Kirkia wilmsii tuberous roots. The clear aqueous extracts that were obtained after a 0.45 µm membrane filtration (Millipore Millex-HV Hydrophillic PVDF filter), were then injected into a preparative high performance liquid chromatography instrument in which pure components, as shown by peaks, were collected and evaluated for anti-microbial activity against a range of microorganisms. The eight separated components were obtained, out of which four components showed anti-microbial activity (AMA). The freeze dried components were re-dissolved in deionised water and then evaluated for AMA against Vibrio cholerae, Shigella dysenteriae, Aeromonas hydrophilia, Salmonella typhi Proteus mirabilis, Escherichia coli, Staphylococcus aureus, Candida albicans and Enterobacter aerogenes. Component one exhibited antimicrobial activity against Shigella dysenteriae, Aeromonas hydrophilia, Salmonella typhi, Proteus mirabilis, Escherichia coli and Staphylococcus aureus with a minimum inhibitory concentration (MIC), of 3.445 mg/ml. Component five was only active against Proteus mirabilis with a MIC of 0.08 mg/ml. Component 7, was active against Shigella dysenteriae, Staphylococcus aureus and Escherichia coli with a MIC of 0.365 mg/ml against both Shigella dysenteriae and Staphylococcus aureus and 0.091 mg/ml against Escherichia coli. Component 8, was active against Shigella, Aeromonas hydrophilia, Salmonella, Proteus mirabilis, Escherichia coli with a MIC of 155 mg/ml. Only four out of eight aqueous extracts showed AMA against both gram negative and positive bacteria and showed no AMA against Candida albicans, Enterobacter aerogenes and Vibrio cholerae. Therefore the Kirkia wilmsii plant root may be used as a broad spectrum antibiotic.

Organic geochemical studies of the transformation of gymnospermous xylem during peatification and coalification to subbituminous coal

USGS Publications Warehouse

Hatcher, P.G.; Lerch, H. E.; Verheyen, T.V.

1990-01-01

It is generally recognized that xylem from trees that are buried in peat swamps is transformed first to huminite macerals in brown coal and then to vitrinite macerals in bituminous coal by processes collectively known as coalification. In order to understand the chemical nature of coalification of xylem and the chemical structures that eventually evolve in coal, we examined a series of gymnospermous xylem samples coalified to varying degrees. The samples included modern fresh xylem, modern degraded xylem in peat, and xylem coalified to ranks of brown coal (lignite B), lignite A, and subbituminous coal. The organic geochemical methods used in this study included solid-state 13C nuclear magnetic resonance (NMR) and pyrolysis/gas chromatography/mass spectrometry. The NMR method provided average compositional information, and the pyrolysis provided detailed molecular information. Although the samples examined include different plants of different geologic ages, they all share a common feature in that they are gymnospermous and presumably have or had a similar kind of lignin. The data obtained in this study provide enough details to allow delineation of specific coalification pathway for the xylem is microbial degradation in peat (peatification), leading to selective removal of cellulosic components. These components constitute a large fraction of the total mass of xylem, usually greater than 50%. Although cellulosic components can survive degradation under certain conditions, their loss during microbial degradation is the rule rather than exception during peatification. As these components of xylem are degraded and lost, lignin, another major component of xylem, is selectively enriched because it is more resistant to microbial degradation than the cellulosic components. Thus, lignin survives peatification in a practically unaltered state and becomes the major precursor of coalified xylem. During its transformation to brown coal and lignite A, lignin in xylem is altered by two important processes. The first involves loss of methoxyl groups, primarily by demethylation (Fig. 1A). The end products of demethylation are catechol-like structures as shown below in Figure 1B. The second transformation process involves increased cross-linking of the aromatic rings. This cross-linking induces increased carbon substitution of the aromatic rings such that the lignin-derived structures become more highly condensed. During its conversion to coalified xylem in subbituminous coal, lignitic xylem, composed primarily of condensed catechol-like structures, is transformed to a macromolecular material primarily composed of phenol-like structures. The catechol-like structures of lignitic xylem loose a hydroxyl group, which is replaced by a hydrogen to form the phenol-like structure as shown in the example in Figure 1B. The pyrolysis data provided only a few clues as to the fate of the C3-side chain of lignin during coalification. However, the NMR data suggest that this side chain is altered, probably by loss of the hydroxyl groups that are attached in modern lignin. Interference in the NMR analysis by aliphatic components of wood, such as resins, precludes definitive determinations of the fate of the C3-side chain during coalification. ?? 1990.

[Sanitary-hygienic assessment of microbial biofertilizer].

PubMed

Arkhipchenko, N A; Akhtemava, G A; Lebedeva, T V; Voronina, A A; Makhan'kova, T I; Pavlova, M M; Shteĭntsaĭg, T A

1991-10-01

Biological treatment of sewage from pig-breeding complexes allowed to produce microbial biomass and primary sediments. The mixture of these components (1:1) after rendering harmless and drying out become the high effective biofertilizer. The results of chronic experiment on sanitary status of soil (microbial and helminthological indexes) under this biofertilizer usage are discussed, and the harmlessness of it is demonstrated.

Sediment nitrification and denitrification rates in a Lake Superior estuary

EPA Science Inventory

Microbially-mediated nitrogen (N) cycling in aquatic sediments has been recognized as an ecosystem service due to mitigation of N-transport to receiving waters. In 2011 and 2012, we compared nitrification (NIT), unamended (DeNIT) and amended (DEA) denitrification rates among spat...

The chicken gastrointestinal microbiome

USDA-ARS?s Scientific Manuscript database

We are in the midst of what may, in retrospect, come to be referred to as the golden age of microbial ecology. Once considered as only a relatively few pathogens, the microorganisms and their genes (the microbiome) associated with higher organisms are now recognized as complex communities with impo...

Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface supports for high avidity microbial capture

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

Hansen, Ryan R; Hinestrosa Salazar, Juan P; Shubert, Katherine R

2013-01-01

Microbial exopolysaccharides (EPS) play a critical and dynamic role in shaping the interactions between microbial community members and their local environment. The capture of targeted microbes using surface immobilized lectins that recognize specific extracellular oligosaccharide moieties offers a non-destructive method for functional characterization based on EPS content. In this report, we evaluate the use of the block co-polymer, poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA), as a surface support for lectin-specific microbial capture. Arrays of circular polymer supports ten micron in diameter were generated on silicon substrates to provide discrete, covalent coupling sites for Triticum vulgare and Lens culinaris lectins. These supports promoted microbemore » adhesion and colony formation in a lectin-specific manner. Silicon posts with similar topography containing only physisorbed lectins showed significantly less activity. These results demonstrate that micropatterned PGMA-b-PVDMA supports provide a unique platform for microbial capture and screening based on EPS content by combining high avidity lectin surfaces with three-dimensional topography.« less

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics.

PubMed

Niederdorfer, Robert; Peter, Hannes; Battin, Tom J

2016-10-03

Small-scale hydraulics affects microbial behaviour at the cell level 1 , trophic interactions in marine aggregates 2 and the physical structure and function of stream biofilms 3,4 . However, it remains unclear how hydraulics, predictably changing from small streams to large rivers, impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we present experimental evidence unveiling hydraulics as a hitherto poorly recognized control of microbial lifestyle differentiation in fluvial ecosystems. Exposing planktonic source communities from stream and floodplain ecosystems to different hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Only a few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous resident taxa characterized aggregate communities. Our findings unveil fundamental differences between biofilms and aggregates and build the basis for a mechanistic understanding of how hydraulics drives the distribution of microbial diversity along the fluvial continuum 5-7 .

Sensory irritating potency of some microbial volatile organic compounds (MVOCs) and a mixture of five MVOCs.

PubMed

Korpi, A; Kasanen, J P; Alarie, Y; Kosma, V M; Pasanen, A L

1999-01-01

The authors investigated the ability/potencies of 3 microbial volatile organic compounds and a mixture of 5 microbial volatile organic compounds to cause eye and upper respiratory tract irritation (i.e., sensory irritation), with an animal bioassay. The authors estimated potencies by determining the concentration capable of decreasing the respiratory frequency of mice by 50% (i.e., the RD50 value). The RD50 values for 1-octen-3-ol, 3-octanol, and 3-octanone were 182 mg/m3 (35 ppm), 1359 mg/m3 (256 ppm), and 17586 mg/m3 (3360 ppm), respectively. Recommended indoor air levels calculated from the individual RD50 values for 1-octen-3-ol, 3-octanol, and 3-octanone were 100, 1000, and 13000 microg/m3, respectively-values considerably higher than the reported measured indoor air levels for these compounds. The RD50 value for a mixture of 5 microbial volatile organic compounds was also determined and found to be 3.6 times lower than estimated from the fractional concentrations and the respective RD50s of the individual components. The data support the conclusion that a variety of microbial volatile organic compounds may have some synergistic effects for the sensory irritation response, which constrains the interpretation and application of recommended indoor air levels of individual microbial volatile organic compounds. The results also showed that if a particular component of a mixture was much more potent than the other components, it may dominate the sensory irritation effect. With respect to irritation symptoms reported in moldy houses, the results of this study indicate that the contribution of microbial volatile organic compounds to these symptoms seems less than previously supposed.

Clinical applications of gut microbiota in cancer biology.

PubMed

Wong, Sunny H; Kwong, Thomas N Y; Wu, Chun-Ying; Yu, Jun

2018-05-18

The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation

PubMed Central

Teske, Andreas; de Beer, Dirk; McKay, Luke J.; Tivey, Margaret K.; Biddle, Jennifer F.; Hoer, Daniel; Lloyd, Karen G.; Lever, Mark A.; Røy, Hans; Albert, Daniel B.; Mendlovitz, Howard P.; MacGregor, Barbara J.

2016-01-01

The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region. PMID:26925032

Metagenomics: A new horizon in cancer research

PubMed Central

Banerjee, Joyita; Mishra, Neetu; Dhas, Yogita

2015-01-01

Metagenomics has broadened the scope of targeting microbes responsible for inducing various types of cancers. About 16.1% of cancers are associated with microbial infection. Metagenomics is an equitable way of identifying and studying micro-organisms within their habitat. In cancer research, this approach has revolutionized the way of identifying, analyzing and targeting the microbial diversity present in the tissue specimens of cancer patients. The genomic analyses of these micro-organisms through next generation sequencing techniques invariably facilitate in recognizing the microbial population in biopsies and their evolutionary relationships with each other. In this review an attempt has been made to generate current metagenomic view on cancer microbiota. Different types of micro-organisms have been found to be linked to various types of cancers, thus, contributing significantly in understanding the disease at molecular level. PMID:26110115

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

PubMed

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

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

Beck, Ashley; Hunt, Kristopher; Bernstein, Hans C.

Interest in microbial communities for bioprocessing has surged in recent years based on the potential to optimize multiple tasks simultaneously and to enhance process productivity and stability. The presence and magnitude of these desirable system properties often result from interactions between functionally distinct community members. The importance of interactions, while appreciated by some disciplines for decades, has gained interest recently due to the development of ‘omics techniques, polymicrobial culturing approaches, and computational methods which has made the systems-level analysis of interacting components more tractable. This review defines and categorizes natural and engineered system components, interactions, and emergent properties, as wellmore » as presents three ecological theories relevant to microbial communities. Case studies are interpreted to illustrate components, interactions, emergent properties and agreement with theoretical concepts. A general foundation is laid to facilitate interpretation of current systems and to aid in future design of microbial systems for the next generation of bioprocesses.« less

[Application and prospect of fungi elicitors in fermentation industry].

PubMed

Gu, Shaobin; Gong, Hui; Yang, Bin; Bu, Meiling

2013-11-01

Fungal elicitors are a group of chemicals that can stimulate the secondary metabolite production in plants and microbial cells. After being recognized, it could enhance the expression of related genes through the signal-transduction pathway; regulate the activity of the enzyme involved in the biosynthesis of secondary metabolites. In recent years, the inducible mechanism of fungal elicitors has been studied deeply worldwide. Meanwhile, it has acquired wide concern in the area of biological industry, especially in the fermentation industry. This paper addresses the application and prospect of fungal elicitors in the secondary metabolites of plant and microbial cells.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

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

Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism inmore » shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.« less

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea.

PubMed

Ziegler, Maren; Roik, Anna; Porter, Adam; Zubier, Khalid; Mudarris, Mohammed S; Ormond, Rupert; Voolstra, Christian R

2016-04-30

Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

USGS Publications Warehouse

Cloud, P.; Morrison, K.

1979-01-01

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

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

Konopka, Allan

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Similarities in Photodegradation of Cyanobacteria-Derived and Marine Fluorescent Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Ianiri, H. L.; Timko, S.; Gonsior, M.

2016-02-01

Marine dissolved organic matter (DOM) is one of the largest reduced carbon reservoirs on Earth, yet we only have a limited understanding of its production, cycling, degradation, and overall structure. It was previously believed that a significant portion of refractory dissolved organic carbon (RDOC) in the ocean was derived from terrestrial sources, however recent studies indicated that the majority of marine DOM might be produced in situ by marine biota. Previous research has found that terrestrial and microbial DOM fluorescent signatures are similar, complicating the identification of the origins of marine fluorescent DOM (FDOM). However, photodegradation kinetics of terrestrial and microbial-derived DOM are expected to be different due to their assumed different chemical compositions. In this study we analyzed for the first time the photodegradation kinetics of microbial-derived DOM originating from different cyanobacteria strains. Cyanobacterial-derived DOM were exposed to simulated sunlight for a total of 20 hours while recording excitation emission matrix (EEM) fluorescence every twenty minutes to observe the photodegradation of this specific FDOM. Parallel Factor Analysis (PARAFAC) was applied to deconvolute the EEM matrices into six separate components. The photodegradation kinetics was then calculated for each component and compared with previously obtained photodegradation data of marine and terrestrial FDOM. This six component PARAFAC model was similar to those generated from open ocean data and global DOM data sets. The "humic-like" FDOM was also found in cyanobacteria FDOM and showed similar fluorescence intensities and percent fluorescence loss when compared to marine DOM. The degradation kinetics of the "humic-like" component of microbial-derived DOM was faster than that of terrestrial-derived DOM, and marine FDOM samples showed degradation kinetics more similar to microbial-derived FDOM. This indicates marine FDOM is more similar in chemical composition to microbial-derived FDOM than terrestrial-derived FDOM, supporting the hypothesis that the majority of marine FDOM is produced in situ.

Mini-review of the chicken gastrointestinal microbiome

USDA-ARS?s Scientific Manuscript database

We are in the midst of what may, in retrospect, come to be referred to as the golden age of microbial ecology. The microorganisms and their genes associated with higher organisms (the microbiome) that were once viewed primarily as sources of human pathogens are now recognized as complex communities...

Microbial utilization of dissolved organic matter from leaves of the red mangrove, Rhizophora mangle, in the Fresh Creek estuary, Bahamas

NASA Astrophysics Data System (ADS)

Benner, Ronald; Peele, Emily R.; Hodson, Robert E.

1986-11-01

Dissolved organic matter was leached from [ 14C]labeled leaves of the red mangrove, Rhizophora mangle, and used in studies to determine the rates and efficiencies of microbial utilization of the water-soluble components of mangrove leaves in the Fresh Creek estuary, Bahamas. Rates of microbial utilization (assimilation plus mineralization) of mangrove leachate ranged from 0·022 to 4·675 μg ml -1 h -1 depending on the concentration of leachate and the size or diversity of microbial populations. Microflora associated with decaying mangrove leaves utilized mangrove leachate at rates up to 18-fold higher than rates of leachate utilization by planktonic microflora. Chemical analyses indicated that tannins and other potentially inhibitory phenolic compounds made up a major fraction (18%) of the dissolved organic matter in mangrove leachate. Mangrove leachate did not appear to be inhibitory to the microbial uptake of leachate or the microbial degradation of the lignocellulosic component of mangrove leaves except at high concentrations (mg ml -1). The availability of molecular oxygen also was an important parameter affecting rates of leachate utilization; rates of microbial utilization of leachate were up to 8-fold higher under aerobic rather than anaerobic conditions. The overall efficiency of conversion of mangrove leachate into microbial biomass was high and ranged from 64% to 94%. As much as 42% of the added leachate was utilized during 2 to 12 h incubations, indicating that a major fraction of the leachable material from mangrove leaves is incorporated into microbial biomass, and thus available to animals in the estuarine food web.

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.

PubMed

Mieczan, Tomasz; Tarkowska-Kukuryk, Monika

2017-08-01

Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.

Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

PubMed

Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

2007-09-01

In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis.

PubMed

Wyrsch, Ethan R; Roy Chowdhury, Piklu; Chapman, Toni A; Charles, Ian G; Hammond, Jeffrey M; Djordjevic, Steven P

2016-01-01

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities.

PubMed

Mumford, Adam C; Akob, Denise M; Klinges, J Grace; Cozzarelli, Isabelle M

2018-04-15

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills. IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of essential natural attenuation processes. These findings provide new insights into microbial responses following a release of UOG wastewaters and are critical for identifying strategies for the remediation and natural attenuation of impacted environments. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Interactions of Gut Microbiota, Endotoxemia, Immune Function, and Diet in Exertional Heatstroke

PubMed Central

Lee, Elaine C.; Armstrong, Elizabeth M.

2018-01-01

Exertional heatstroke (EHS) is a medical emergency that cannot be predicted, requires immediate whole-body cooling to reduce elevated internal body temperature, and is influenced by numerous host and environmental factors. Widely accepted predisposing factors (PDF) include prolonged or intense exercise, lack of heat acclimatization, sleep deprivation, dehydration, diet, alcohol abuse, drug use, chronic inflammation, febrile illness, older age, and nonsteroidal anti-inflammatory drug use. The present review links these factors to the human intestinal microbiota (IM) and diet, which previously have not been appreciated as PDF. This review also describes plausible mechanisms by which these PDF lead to EHS: endotoxemia resulting from elevated plasma lipopolysaccharide (i.e., a structural component of the outer membrane of Gram-negative bacteria) and tissue injury from oxygen free radicals. We propose that recognizing the lifestyle and host factors which are influenced by intestine-microbial interactions, and modifying habitual dietary patterns to alter the IM ecosystem, will encourage efficient immune function, optimize the intestinal epithelial barrier, and reduce EHS morbidity and mortality. PMID:29850597

CD14 Deficiency Impacts Glucose Homeostasis in Mice through Altered Adrenal Tone

PubMed Central

Young, James L.; Mora, Alfonso; Cerny, Anna; Czech, Michael P.; Woda, Bruce; Kurt-Jones, Evelyn A.; Finberg, Robert W.; Corvera, Silvia

2012-01-01

The toll-like receptors comprise one of the most conserved components of the innate immune system, signaling the presence of molecules of microbial origin. It has been proposed that signaling through TLR4, which requires CD14 to recognize bacterial lipopolysaccharide (LPS), may generate low-grade inflammation and thereby affect insulin sensitivity and glucose metabolism. To examine the long-term influence of partial innate immune signaling disruption on glucose homeostasis, we analyzed knockout mice deficient in CD14 backcrossed into the diabetes-prone C57BL6 background at 6 or 12 months of age. CD14-ko mice, fed either normal or high-fat diets, displayed significant glucose intolerance compared to wild type controls. They also displayed elevated norepinephrine urinary excretion and increased adrenal medullary volume, as well as an enhanced norepinephrine secretory response to insulin-induced hypoglycemia. These results point out a previously unappreciated crosstalk between innate immune- and sympathoadrenal- systems, which exerts a major long-term effect on glucose homeostasis. PMID:22253759

[Parasitosis and irritable bowel syndrome].

PubMed

Ibarra, Catalina; Herrera, Valentina; Pérez de Arce, Edith; Gil, Luis Carlos; Madrid, Ana María; Valenzuela, Lucía; Beltrán, Caroll J

2016-06-01

Irritable bowel syndrome (IBS) is a functional disorder of the gastrointestinal tract characterised by multi-factorial aetiology. In IBS physiopathology are involved diverse factors between them biological, psychosocial, and environmental components which affect the immune activation status of gut mucosa. Among these factors is recognized the intestinal parasitosis. Post-infection IBS (PI-IBS) is recognised as a subgroup of functional disorders whose symptoms onset appear after a symptomatic intestinal infection caused by microbial agents. There are few studies regarding of relationship between IBS and intestinal parasitosis in Chile. However, is has been well described a positive association between IBS and Blastocystis hominis infections, one of prevalent parasites in Chile. In other countries, is also described a relationship between IBS and amebiasis and giardiasis. Both, characterized by a common mode of transmission through water as well as contaminated food. Because the high prevalence of parasitosis in our country it is necessary to expand the association studies to clarify the strength of the parasites ethiology in IBS.

Carbohydrates as T-cell antigens with implications in health and disease.

PubMed

Sun, Lina; Middleton, Dustin R; Wantuch, Paeton L; Ozdilek, Ahmet; Avci, Fikri Y

2016-10-01

Glycosylation is arguably the most ubiquitous post-translational modification on proteins in microbial and mammalian cells. During the past few years, there has been intensive research demonstrating that carbohydrates, either in pure forms or in conjunction with proteins or lipids, evoke and modulate adaptive immune responses. We now know that carbohydrates can be directly recognized by T cells or participate in T-cell stimulation as components of T-cell epitopes. T-cell recognition of carbohydrate antigens takes place via their presentation by major histocompatibility complex pathways on antigen-presenting cells. In this review, we summarize studies on carbohydrates as T-cell antigens modulating adaptive immune responses. Through discussion of glycan-containing antigens, such as glycoproteins, glycolipids, zwitterionic polysaccharides and carbohydrate-based glycoconjugate vaccines, we will illustrate the key molecular and cellular interactions between carbohydrate antigens and T cells and the implications of these interactions in health and disease. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial polyesters: biosynthesis, biodegradable plastics and biotechnology.

PubMed

Lenz, Robert W; Marchessault, Robert H

2005-01-01

The discovery and chemical identification, in the 1920s, of the aliphatic polyester: poly(3-hydroxybutyrate), PHB, as a granular component in bacterial cells proceeded without any of the controversies which marked the recognition of macromolecules by Staudinger. Some thirty years after its discovery, PHB was recognized as the prototypical biodegradable thermoplastic to solve the waste disposal challenge. The development effort led by Imperial Chemical Industries Ltd., encouraged interdisciplinary research from genetic engineering and biotechnology to the study of enzymes involved in biosynthesis and biodegradation. From the simple PHB homopolyester discovered by Maurice Lemoigne in the mid-twenties, a family of over 100 different aliphatic polyesters of the same general structure has been discovered. Depending on bacterial species and substrates, these high molecular weight stereoregular polyesters have emerged as a new family of natural polymers ranking with nucleic acids, polyamides, polyisoprenoids, polyphenols, polyphosphates, and polysaccharides. In this historical review, the chemical, biochemical and microbial highlights are linked to personalities and locations involved with the events covering a discovery timespan of 75 years.

Rust preventive oil additives based on microbial fats

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

Salenko, V.I.; Fedorov, V.V.; Kazantsev, Yu.E.

1983-03-01

This article investigates the composition and lubricating properties of microbial fats obtained from microorganisms grown on various hydrocarbon substrates (n-paraffins, alcohols, natural gas, petroleum distillates, etc.). Focuses on the protective functions of the 4 main fractions (unsaponifiables, free fatty acids, glycerides, and phospholipids) which comprise the microbial fat from a yeast grown on purified liquid n-paraffins. Concludes that neutralized microbial fats can be used as preservative additives; that the principal components of the microbial fats have the properties necessary for oil-soluble corrosion inhibitors; that the phospholipids of the microbial fat can fulfill the functions of not only preservative additives, butmore » also highly effective operational/ preservative additives; and that fats of microbial origin can be used in the development of multipurpose polyfunctional additives.« less

An improved method to set significance thresholds for β diversity testing in microbial community comparisons.

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions

PubMed Central

Venkateswaran, Kasthuri; La Duc, Myron T.; Horneck, Gerda

2014-01-01

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space. PMID:25130881

Microbial existence in controlled habitats and their resistance to space conditions.

PubMed

Venkateswaran, Kasthuri; La Duc, Myron T; Horneck, Gerda

2014-09-17

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC's call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.

Oxidation-Specific Epitopes are Danger Associated Molecular Patterns Recognized by Pattern Recognition Receptors of Innate Immunity

PubMed Central

Miller, Yury I.; Choi, Soo-Ho; Wiesner, Philipp; Fang, Longhou; Harkewicz, Richard; Hartvigsen, Karsten; Boullier, Agnès; Gonen, Ayelet; Diehl, Cody J.; Que, Xuchu; Montano, Erica; Shaw, Peter X.; Tsimikas, Sotirios; Binder, Christoph J.; Witztum, Joseph L.

2010-01-01

Oxidation reactions are vital parts of metabolism and signal transduction. However, they also produce reactive oxygen species, which damage lipids, proteins and DNA, generating “oxidation-specific” epitopes. In this review, we will discuss the hypothesis that such common oxidation-specific epitopes are a major target of innate immunity, recognized by a variety of “pattern recognition receptors” (PRRs). By analogy with microbial “pathogen associated molecular patterns” (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent “danger (or damage) associated molecular patterns” (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Further, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation-specific epitopes, such PAMPs provided a strong secondary selecting pressure for the same set of oxidation-specific PRRs as well. Because lipid peroxidation is ubiquitous and a major component of the inflammatory state associated with atherosclerosis, the understanding that oxidation-specific epitopes are DAMPs, and thus the target of multiple arcs of innate immunity, provides novel insights into the pathogenesis of atherosclerosis. As examples, we show that both cellular and soluble PRRs, such as CD36, toll-like receptor-4, natural antibodies, and CRP recognize common oxidation-specific DAMPs, such as oxidized phospholipids and oxidized cholesteryl esters, and mediate a variety of immune responses, from expression of proinflammatory genes to excessive intracellular lipoprotein accumulation to atheroprotective humoral immunity. These insights may lead to improved understanding of inflammation and atherogenesis and suggest new approaches to diagnosis and therapy. PMID:21252151

Photosynthesis and early Earth.

PubMed

Shih, Patrick M

2015-10-05

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

Gut microbiota of liver transplantation recipients.

PubMed

Sun, Li-Ying; Yang, Yun-Sheng; Qu, Wei; Zhu, Zhi-Jun; Wei, Lin; Ye, Zhi-Sheng; Zhang, Jian-Rui; Sun, Xiao-Ye; Zeng, Zhi-Gui

2017-06-19

The characteristics of intestinal microbial communities may be affected by changes in the pathophysiology of patients with end-stage liver disease. Here, we focused on the characteristics of intestinal fecal microbial communities in post-liver transplantation (LT) patients in comparison with those in the same individuals pre-LT and in healthy individuals. The fecal microbial communities were analyzed via MiSeq-PE250 sequencing of the V4 region of 16S ribosomal RNA and were then compared between groups. We found that the gut microbiota of patients with severe liver disease who were awaiting LT was significantly different from that of healthy controls, as represented by the first principal component (p = 0.0066). Additionally, the second principal component represented a significant difference in the gut microbiota of patients between pre-LT and post-LT surgery (p = 0.03125). After LT, there was a significant decrease in the abundance of certain microbial species, such as Actinobacillus, Escherichia, and Shigella, and a significant increase in the abundance of other microbial species, such as Micromonosporaceae, Desulfobacterales, the Sarcina genus of Eubacteriaceae, and Akkermansia. Based on KEGG profiles, 15 functional modules were enriched and 21 functional modules were less represented in the post-LT samples compared with the pre-LT samples. Our study demonstrates that fecal microbial communities were significantly altered by LT.

Directed evolution of FLS2 towards novel flagellin peptide recognition

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

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

Directed evolution of FLS2 towards novel flagellin peptide recognition

DOE PAGES

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

2016-06-06

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

Controls on development and diversity of Early Archean stromatolites

PubMed Central

Allwood, Abigail C.; Grotzinger, John P.; Knoll, Andrew H.; Burch, Ian W.; Anderson, Mark S.; Coleman, Max L.; Kanik, Isik

2009-01-01

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans. PMID:19515817

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

PubMed

von Mutius, Erika

2016-03-01

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

Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

PubMed

Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

2012-12-01

Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbial solubilization of coal

DOEpatents

Strandberg, Gerald W.; Lewis, Susan N.

1990-01-01

This invention deals with the solubilization of coal using species of Streptomyces. Also disclosed is an extracellular component from a species of Streptomyces, said component being able to solubilize coal.

Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

PubMed

Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

2014-01-01

The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

Innate immunity in rice

PubMed Central

Chen, Xuewei; Ronald, Pamela C.

2011-01-01

Advances in studies of rice innate immunity have led to the identification and characterization of host sensors encoding receptor kinases that perceive conserved microbial signatures. The non-RD domain, a newly recognized hallmark of these receptor kinases is highly expanded in rice (Oryza sativa) compared with Arabidopsis (Arabidopsis thaliana). Researchers have also identified a diverse array of microbial effectors from bacterial and fungal pathogens that triggers immune responses upon perception. These include both, effectors that indirectly target host Nucleotide binding site/Leucine rice repeat (NBS-LRR) proteins and transcription activator-like (TAL) effectors that directly bind promoters of host genes. Here we review the recognition and signaling events that govern rice innate immunity. PMID:21602092

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Combining asymmetrical flow field-flow fractionation with on- and off-line fluorescence detection to examine biodegradation of riverine dissolved and particulate organic matter.

PubMed

Lee, Sang Tak; Yang, Boram; Kim, Jin-Yong; Park, Ji-Hyung; Moon, Myeong Hee

2015-08-28

This study demonstrated that asymmetrical flow field-flow fractionation (AF4) coupled with on-line UV and fluorescence detection (FLD) and off-line excitation-emission matrix (EEM) fluorescence spectroscopy can be employed to analyze the influence of microbial metabolic activity on the consumption and production of freshwater organic matter. With the AF4 system, organic matter is on-line enriched during a focusing/relaxation period, which is an essential process prior to separation. Size-fractionated chromophoric and fluorophoric organic materials were simultaneously monitored during the 30-min AF4 separation process. Two fractions of different sizes (dissolved organic matter (DOM) and particulate organic matter (POM)) of freshwater samples from three locations (up-, mid-, and downstream) along the Han River basin of Korea were incubated with the same inoculum for 14 days to analyze fraction-specific alterations in optical properties using AF4-UV-FLD. A comparison of AF4 fractograms obtained from pre- and post-incubation samples revealed that POM-derived DOM were more susceptible to microbial metabolic activity than was DOM. Preferential microbial consumption of protein-like DOM components concurred with enhanced peaks of chromophoric and humic-like fluorescent components, presumably formed as by-products of microbial processing. AF4-UV-FLD combined with off-line identification of microbially processed components using EEM fluorescence spectroscopy provides a powerful tool to study the relationship between microbial activity and composition as well as biodegradability of DOM and POM-derived DOM from different origins, especially for the analysis of chromophoric and fluorophoric organic matter that are consumed and produced by microbial metabolic activity. The proposed AF4 system can be applied to organic matter in freshwater samples having low concentration range (0.3-2.5ppm of total organic carbon) without a pre-concentration procedure. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of iron oxide nanoparticle films at the air–water interface in Arctic tundra waters

DOE PAGES

Jubb, Aaron M.; Eskelsen, Jeremy R.; Yin, Xiangping Lisa; ...

2018-04-04

Here, massive amounts of organic carbon have accumulated in Arctic permafrost and soils due to anoxic and low temperature conditions that limit aerobic microbial respiration. Alternative electron acceptors are thus required for microbes to degrade organic carbon in these soils. Iron or iron oxides have been recognized to play an important role in carbon cycle processes in Arctic soils, although the exact form and role as an electron acceptor or donor remain poorly understood. Here, Arctic biofilms collected during the summers of 2016 and 2017 from tundra surface waters on the Seward Peninsula of western Alaska were characterized with amore » suite of microscopic and spectroscopic methods. We hypothesized that these films contain redox-active minerals bound to biological polymers. The major components of the films were found to be iron oxide nanoparticle aggregates associated with extracellular polymeric substances. The observed mineral phases varied between films collected in different years with magnetite (Fe 2+Fe 2 3+O 4) nanoparticles (<5 nm) predominantly identified in the 2016 films, while for films collected in 2017 ferrihydrite-like amorphous iron oxyhydroxides were found. While the exact formation mechanism of these Artic iron oxide films remains to be explored, the presence of magnetite and other iron oxide/oxyhydroxide nanoparticles at the air–water interface may represent a previously unknown source of electron acceptors for continual anaerobic microbial respiration of organic carbon within poorly drained Arctic tundra.« less

New CRISPR-Cas systems from uncultivated microbes

NASA Astrophysics Data System (ADS)

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.

New CRISPR–Cas systems from uncultivated microbes

DOE PAGES

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; ...

2016-12-22

We present that 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 DNAmore » 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. Lastly, 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.« less

New CRISPR–Cas systems from uncultivated microbes

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

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.

We present that 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 DNAmore » 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. Lastly, 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.« less

Characterization of iron oxide nanoparticle films at the air–water interface in Arctic tundra waters

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

Jubb, Aaron M.; Eskelsen, Jeremy R.; Yin, Xiangping Lisa

Here, massive amounts of organic carbon have accumulated in Arctic permafrost and soils due to anoxic and low temperature conditions that limit aerobic microbial respiration. Alternative electron acceptors are thus required for microbes to degrade organic carbon in these soils. Iron or iron oxides have been recognized to play an important role in carbon cycle processes in Arctic soils, although the exact form and role as an electron acceptor or donor remain poorly understood. Here, Arctic biofilms collected during the summers of 2016 and 2017 from tundra surface waters on the Seward Peninsula of western Alaska were characterized with amore » suite of microscopic and spectroscopic methods. We hypothesized that these films contain redox-active minerals bound to biological polymers. The major components of the films were found to be iron oxide nanoparticle aggregates associated with extracellular polymeric substances. The observed mineral phases varied between films collected in different years with magnetite (Fe 2+Fe 2 3+O 4) nanoparticles (<5 nm) predominantly identified in the 2016 films, while for films collected in 2017 ferrihydrite-like amorphous iron oxyhydroxides were found. While the exact formation mechanism of these Artic iron oxide films remains to be explored, the presence of magnetite and other iron oxide/oxyhydroxide nanoparticles at the air–water interface may represent a previously unknown source of electron acceptors for continual anaerobic microbial respiration of organic carbon within poorly drained Arctic tundra.« less

TEMPORAL VARIABILITY OF MICROBIAL INDICATORS OF FECAL CONTAMINATION OF MARINE AND FRESHWATER BEACHES

EPA Science Inventory

Monitoring methods for microbial indicators of fecal contamination are an integral component for protecting the health of swimmers exposed to potentially contaminated bathing beach waters. The design of monitoring systems which will accurately characterize the quality of water is...

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

Nitrogen Addition Altered the Effect of Belowground C Allocation on Soil Respiration in a Subtropical Forest

PubMed Central

He, Tongxin; Wang, Qingkui; Wang, Silong; Zhang, Fangyue

2016-01-01

The availabilities of carbon (C) and nitrogen (N) in soil play an important role in soil carbon dioxide (CO2) emission. However, the variation in the soil respiration (Rs) and response of microbial community to the combined changes in belowground C and N inputs in forest ecosystems are not yet fully understood. Stem girdling and N addition were performed in this study to evaluate the effects of C supply and N availability on Rs and soil microbial community in a subtropical forest. The trees were girdled on 1 July 2012. Rs was monitored from July 2012 to November 2013, and soil microbial community composition was also examined by phospholipid fatty acids (PLFAs) 1 year after girdling. Results showed that Rs decreased by 40.5% with girdling alone, but N addition only did not change Rs. Interestingly, Rs decreased by 62.7% under the girdling with N addition treatment. The reducing effect of girdling and N addition on Rs differed between dormant and growing seasons. Girdling alone reduced Rs by 33.9% in the dormant season and 54.8% in the growing season compared with the control. By contrast, girdling with N addition decreased Rs by 59.5% in the dormant season and 65.4% in the growing season. Girdling and N addition significantly decreased the total and bacterial PLFAs. Moreover, the effect of N addition was greater than girdling. Both girdling and N addition treatments separated the microbial groups on the basis of the first principal component through principal component analysis compared with control. This indicated that girdling and N addition changed the soil microbial community composition. However, the effect of girdling with N addition treatment separated the microbial groups on the basis of the second principal component compared to N addition treatment, which suggested N addition altered the effect of girdling on soil microbial community composition. These results suggest that the increase in soil N availability by N deposition alters the effect of belowground C allocation on the decomposition of soil organic matter by altering the composition of the soil microbial community. PMID:27213934

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea).

PubMed

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

PubMed Central

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin. PMID:26485717

Turnover of microbial groups and cell components in soil: 13C analysis of cellular biomarkers

NASA Astrophysics Data System (ADS)

Gunina, Anna; Dippold, Michaela; Glaser, Bruno; Kuzyakov, Yakov

2017-01-01

Microorganisms regulate the carbon (C) cycle in soil, controlling the utilization and recycling of organic substances. To reveal the contribution of particular microbial groups to C utilization and turnover within the microbial cells, the fate of 13C-labelled glucose was studied under field conditions. Glucose-derived 13C was traced in cytosol, amino sugars and phospholipid fatty acid (PLFA) pools at intervals of 3, 10 and 50 days after glucose addition into the soil. 13C enrichment in PLFAs ( ˜ 1.5 % of PLFA C at day 3) was an order of magnitude greater than in cytosol, showing the importance of cell membranes for initial C utilization. The 13C enrichment in amino sugars of living microorganisms at day 3 accounted for 0.57 % of total C pool; as a result, we infer that the replacement of C in cell wall components is 3 times slower than that of cell membranes. The C turnover time in the cytosol (150 days) was 3 times longer than in PLFAs (47 days). Consequently, even though the cytosol pool has the fastest processing rates compared to other cellular compartments, intensive recycling of components here leads to a long C turnover time. Both PLFA and amino-sugar profiles indicated that bacteria dominated in glucose utilization. 13C enrichment decreased with time for bacterial cell membrane components, but it remained constant or even increased for filamentous microorganisms. 13C enrichment of muramic acid was the 3.5 times greater than for galactosamine, showing a more rapid turnover of bacterial cell wall components compared to fungal. Thus, bacteria utilize a greater proportion of low-molecular-weight organic substances, whereas filamentous microorganisms are responsible for further C transformations. Thus, tracing 13C in cellular compounds with contrasting turnover rates elucidated the role of microbial groups and their cellular compartments in C utilization and recycling in soil. The results also reflect that microbial C turnover is not restricted to the death or growth of new cells. Indeed, even within living cells, highly polymeric cell compounds are constantly replaced and renewed. This is especially important for assessing C fluxes in soil and the contribution of C from microbial residues to soil organic matter.

Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions.

PubMed

Koyle, Melinda L; Veloz, Madeline; Judd, Alec M; Wong, Adam C-N; Newell, Peter D; Douglas, Angela E; Chaston, John M

2016-07-30

The influence of microbes on myriad animal traits and behaviors has been increasingly recognized in recent years. The fruit fly Drosophila melanogaster is a model for understanding microbial interactions with animal hosts, facilitated by approaches to rear large sample sizes of Drosophila under microorganism-free (axenic) conditions, or with defined microbial communities (gnotobiotic). This work outlines a method for collection of Drosophila embryos, hypochlorite dechorionation and sterilization, and transfer to sterile diet. Sterilized embryos are transferred to sterile diet in 50 ml centrifuge tubes, and developing larvae and adults remain free of any exogenous microbes until the vials are opened. Alternatively, flies with a defined microbiota can be reared by inoculating sterile diet and embryos with microbial species of interest. We describe the introduction of 4 bacterial species to establish a representative gnotobiotic microbiota in Drosophila. Finally, we describe approaches for confirming bacterial community composition, including testing if axenic Drosophila remain bacteria-free into adulthood.

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

PubMed

Fishman, J A; Thomson, A W

2015-07-01

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

The plastid genome as a platform for the expression of microbial resistance genes

USDA-ARS?s Scientific Manuscript database

In recent years, our fundamental understanding of host-microbe interaction has developed considerably. We have begun to tease out the genetic components that influence host resistance to microbial colonization. The use of advancing molecular technologies such as microarray expression profiling and...

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Microbial ecology studies at two coal mine refuse sites in Illinois

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

Miller, R. M.; Cameron, R. E.

An investigation was made of the microflora associated with coal refuse at two abandoned mines in the midwestern United States. Information was gathered for both the edaphic and the biotic composition of the refuse material. Emphasis was placed on heterotrophic and autotrophic components as to numbers, kinds, and physiological groups. The presence of chemolithotrophs was also investigated. The relationship between abiotic and biotic components in regard to distribution of bacteria, fungi, and algae is discussed. Information presented in this report will be utilized in assessing trends and changes in microbial numbers and composition related to manipulations of the edaphic andmore » biotic ecosystem components associated with reclamation of the refuse piles.« less

Effects of substrate mineralogy on the biodegradability of fuel components

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

Apitz, S.E.; Meyers-Schulte, K.J.

1996-11-01

Experiments were carried out to determine the effects of mineralogy on the biodegradability of components of a whole fuel by a soil microbial consortium. Samples of quartz sand (Fischer Sea Sand) and illite clay (API 35) were spiked with marine diesel fuel, aged, slurried, and inoculated, and concentrations of fuel components were monitored over time. To help distinguish biotic from abiotic processes, identical samples were poisoned with mercuric chloride and were run in parallel. While there was a chromatographic and biomarker evidence of n-alkane biodegradation in the sand samples, illite samples showed no evidence of biogenic loss of aliphatic components.more » Polycyclic aromatic hydrocarbons, on the other hand, were lost equivalently on both minerals and in both cases were lost to a much greater extent than were total petroleum hydrocarbons (TPHs). These results suggest that under experimental conditions, illite inhibited the bioavailability of some TPH components to the soil microbial consortium.« less

Accounting for microbial habitats in modeling soil organic matter dynamics

NASA Astrophysics Data System (ADS)

Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

2017-04-01

The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

Microbial Signatures of Cadaver Gravesoil During Decomposition.

PubMed

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Vertical distribution of the subsurface microorganisms in Sagara oil reservoir

NASA Astrophysics Data System (ADS)

Nunoura, T.; Oida, H.; Masui, N.; Ingaki, F.; Takai, K.; Nealson, K. H.; Horikoshi, K.

2002-12-01

The recent microbiological studies reported that active microbial habitat for methanogen, sulfate reducers (Archaeoglobus, d-Proteobacteria, gram positives), fermenters (Thermococcus, Thermotogales, gram positives etc.) and other heterotrophs (g-Proteobacteria etc.) are in subsurface petroleum oil reservoirs. However, microbial distribution at vertical distances in depth has not been demonstrated since the samples in previous studies are only to use oil and the formation water. Here, we show the vertical profile of microbial community structure in Japanese terrestrial oil reservoir by a combination of molecular ecological analyses and culture dependent studies. The sequential WRC (Whole Round Core) samples (200 mbsf) were recovered from a drilling project for Sagara oil reservoir, Shizuoka Prefecture, Japan, conducted in Jar. -Mar. 2002. The lithology of the core samples was composed of siltstone, sandstone, or partially oil containing sand. The major oil components were gasoline, kerosene and light oil, that is a unique feature observed in the Sagara oil reservoir. The direct count of DAPI-stained cells suggested that the biomass was relatively constant, 1.0x104cells/g through the core of the non-oil layers, whereas the oil-bearing layers had quite higher population density at a range of 1.0x105 ? 3.7x107cells/g. The vertical profile of microbial community structures was analyzed by the sequence similarity analysis, phylogenetic analysis and T-RFLP fingerprinting of PCR-amplified 16S rDNA. From bacterial rDNA clone libraries, most of the examined rDNA were similar with the sequence of genera Pseudomanas, Stenotrophomonas and Sphingomonas within g-Proteobacteria. Especially, Pseudomonas stutzeri was predominantly present in all oil-bearing layers. From archaeal rDNA clone libraries, all rDNA clone sequences were phylogenetically associated with uncultured soil group in Crenarchaeota. We detected none of the sequences of sulfate reducers, sulfur dependent fermenters and methanogens that have been previously detected as dominant microbial components in other oil reservoir environments. The absence of methanogen was consistent with the results from the stable isotopic analysis that major hydrocarbon components including methane in Sagara oil reservoir are thermogenic origin. In this presentation, we will also show the activity of the subsurface microbial components by the cultivation assays and discuss about the relationship between the microbial community structure and the formation process of petroleum in Sagara oil reservoir.

46 CFR 164.019-17 - Recognized laboratory.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Recognized laboratory. 164.019-17 Section 164.019-17...: SPECIFICATIONS AND APPROVAL MATERIALS Personal Flotation Device Components § 164.019-17 Recognized laboratory. (a) General. A laboratory may be designated as a recognized laboratory under this subpart if it is— (1...

46 CFR 164.019-17 - Recognized laboratory.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Recognized laboratory. 164.019-17 Section 164.019-17...: SPECIFICATIONS AND APPROVAL MATERIALS Personal Flotation Device Components § 164.019-17 Recognized laboratory. (a) General. A laboratory may be designated as a recognized laboratory under this subpart if it is— (1...

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

PubMed Central

Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A.; Charles, Ian G.; Hammond, Jeffrey M.; Djordjevic, Steven P.

2016-01-01

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance. PMID:27379026

Understanding and Modulating Mammalian-Microbial Communication for Improved Human Health

PubMed Central

Mani, Sridhar; Boelsterli, Urs A.; Redinbo, Matthew R.

2013-01-01

The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. Detailed examinations of GI symbiotic bacteria that started in the early 2000s and the first phases of the Human Microbiome Project that were completed in 2012 have ushered in an exciting period of granularity with respect to the ecology, genetics, and chemistry of the mammalian-microbial axes of communication. Here we review aspects of the biochemical pathways at play between commensal GI bacteria and several mammalian systems, including both local-epithelia and nonlocal responses including inflammation, immunology, metabolism, and neurobiology. Finally, we discuss how the microbial biotransformation of therapeutic compounds, such as anticancer or nonsteroidal anti-inflammatory drugs, can be modulated to reduce toxicity and potentially improve therapeutic efficacy. PMID:24160697

Impact of antiretroviral drugs on the microbiome: unknown answers to important questions

PubMed Central

Pinto-Cardoso, Sandra; Klatt, Nichole R.; Reyes-Terán, Gustavo

2018-01-01

Purpose of review Little is known on how different antiretroviral (ARV) drugs affect the gut microbiome in HIV infection; and conflicting data exists on the effect of ARV drugs on residual inflammation/immune activation and microbial translocation. Recent findings Gut microbiome involvement in the transmission and pathogenesis of HIV infection is increasingly being recognized. Various studies have shown that antiretroviral therapy (ART) is unable to restore gut health despite effective suppression of plasma HIV viremia. Indeed, the resolution of residual inflammation and gut microbial translocation is partial under ART. Very recent studies have provided new evidence that ARV combinations can differentially affect the gut microbiome, immune activation and microbial translocation. Furthermore, a recent article uncovered a link between drug metabolism and specific microbial species indicating that microbes can directly metabolically degrade ARV drugs when administered topically. Summary There are still many unanswered questions regarding ARVs and the gut microbiome. It is, therefore, critical for researchers to address the effect of distinct ARV drugs on the microbiome and vice versa: the effects of the microbiome on ARV drug metabolism, and speculate about possible therapeutic avenues. PMID:29028667

Progress of air-breathing cathode in microbial fuel cells

NASA Astrophysics Data System (ADS)

Wang, Zejie; Mahadevan, Gurumurthy Dummi; Wu, Yicheng; Zhao, Feng

2017-07-01

Microbial fuel cell (MFC) is an emerging technology to produce green energy and vanquish the effects of environmental contaminants. Cathodic reactions are vital for high electrical power density generated from MFCs. Recently tremendous attentions were paid towards developing high performance air-breathing cathodes. A typical air-breathing cathode comprises of electrode substrate, catalyst layer, and air-diffusion layer. Prior researches demonstrated that each component influenced the performance of air-breathing cathode MFCs. This review summarized the progress in development of the individual component and elaborated main factors to the performance of air-breathing cathode.

Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis

NASA Astrophysics Data System (ADS)

Brangarí, Albert C.; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier; Manzoni, Stefano

2018-06-01

A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.

21 CFR 111.10 - What requirements apply for preventing microbial contamination from sick or infected personnel...

Code of Federal Regulations, 2014 CFR

2014-04-01

... FOR DIETARY SUPPLEMENTS Personnel § 111.10 What requirements apply for preventing microbial... components, dietary supplements, and contact surfaces used in the manufacture, packaging, labeling, or holding of a dietary supplement. Such measures include the following: (1) Excluding from working in any...

21 CFR 111.10 - What requirements apply for preventing microbial contamination from sick or infected personnel...

Code of Federal Regulations, 2012 CFR

2012-04-01

... FOR DIETARY SUPPLEMENTS Personnel § 111.10 What requirements apply for preventing microbial... components, dietary supplements, and contact surfaces used in the manufacture, packaging, labeling, or holding of a dietary supplement. Such measures include the following: (1) Excluding from working in any...

EVALUATION OF COMMERCIAL, MICROBIAL-BASED PRODUCTS TO TREAT PARAFFIN DEPOSITION IN TANK BOTTOMS AND OIL PRODUCTION EQUIPMENT

EPA Science Inventory

Introduction:

Paraffins are naturally-occurring components of crude oils, but often form solids within oil reservoirs and on oil production equipment when oil is harvested from hot subsurface temperatures to the cooler surface environments. Microbial t...

Compositions and methods of use of constructed microbial mats

DOEpatents

Bender, Judith A.; Phillips, Peter C.

2000-01-01

Compositions, methods and devices for bioremediation that comprise components of constructed microbial mats with organic and inorganic materials are described. The compositions, methods and devices can be used for bioremediation of different individual contaminants and for mixed or multiple contaminants, and for production of beneficial compositions and molecules.

Deriving site-specific soil clean-up values for metals and metalloids: Rationale for including protection of soil microbial processes

PubMed Central

Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen

2014-01-01

Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of microbial processes in contaminated soils. PMID:24376192

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2012 CFR

2012-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

Remote Sensing of a Manipulated Prairie Grassland Experiment to Predict Belowground Processes

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Schweiger, A. K.; Hobbie, S. E.; Madritch, M. D.; Wang, Z.; Couture, J. J.; Gamon, J. A.; Townsend, P. A.

2017-12-01

Given the importance of plant biodiversity for providing the ecosystem functions and services on which humans depend, rapid and remote methods of monitoring plant biodiversity across large spatial extents and biological scales are increasingly critical. In North American prairie systems, the ecosystem benefits of diversity are a subject of ongoing investigation and relevance to policy. However, detecting belowground components of ecosystem biodiversity, composition and associated functions are not possible directly through remote sensing. Nevertheless, belowground components of diversity may be linked to aboveground components allowing indirect inferences. Here we test a series of hypotheses about how aboveground functional and chemical diversity and composition of plant communities drive belowground functions, including N mineralization, enzyme activity and microbial biomass, as well as microbial diversity and composition. We hypothesize that the quantity and chemical composition of aboveground inputs to soil drive belowground processes, including decomposition and microbial enzyme activity. We use plant spectra (400 nm to 2500 nm) measured at the leaf and airborne level to determine chemical and functional composition of leaves and canopies in a long-term grassland experiment where diversity is manipulated at the Cedar Creek Ecosystem Science Reserve. We then assess the extent to which belowground chemistry, microbial diversity and composition are predicted from aboveground plant diversity, biomass and chemical composition. We find strong associations between aboveground inputs and belowground enzyme activity and microbial biomass but only weak linkages between aboveground diversity and belowground diversity. We discuss the potential for such approaches and the caveats related to the spatial scale of measurements and spatial resolution of airborne detection.

Incubation of Aquilaria subintegra with Microbial Culture Supernatants Enhances Production of Volatile Compounds and Improves Quality of Agarwood Oil.

PubMed

Monggoot, Sakon; Kulsing, Chadin; Wong, Yong Foo; Pripdeevech, Patcharee

2018-06-01

Incubation with microbial culture supernatants improved essential oil yield from Aquilaria subintegra woodchips. The harvested woodchips were incubated with de man, rogosa and sharpe (MRS) agar, yeast mold (YM) agar medium and six different microbial culture supernatants obtained from Lactobacillus bulgaricus , L. acidophilus , Streptococcus thermophilus , Lactococcus lactis , Saccharomyces carlsbergensis and S. cerevisiae prior to hydrodistillation. Incubation with lactic acid bacteria supernatants provided higher yield of agarwood oil (0.45% w/w) than that obtained from yeast (0.25% w/w), agar media (0.23% w/w) and water (0.22% w/w). The composition of agarwood oil from all media and microbial supernatant incubations was investigated by using gas chromatography-mass spectrometry. Overall, three major volatile profiles were obtained, which corresponded to water soaking (control), as well as, both YM and MRS media, lactic acid bacteria, and yeast supernatant incubations. Sesquiterpenes and their oxygenated derivatives were key components of agarwood oil. Fifty-two volatile components were tentatively identified in all samples. Beta-agarofuran, α-eudesmol, karanone, α-agarofuran and agarospirol were major components present in most of the incubated samples, while S. cerevisiae -incubated A. subintegra provided higher amount of phenyl acetaldehyde. Microbial culture supernatant incubation numerically provided the highest yield of agarwood oil compared to water soaking traditional method, possibly resulting from activity of extracellular enzymes produced by the microbes. Incubation of agarwood with lactic acid bacteria supernatant significantly enhanced oil yields without changing volatile profile/composition of agarwood essential oil, thus this is a promising method for future use.

Host- and microbe determinants that may influence the success of S. aureus colonization

PubMed Central

Johannessen, Mona; Sollid, Johanna E.; Hanssen, Anne-Merethe

2012-01-01

Staphylococcus aureus may cause serious skin and soft tissue infections, deep abscesses, endocarditis, osteomyelitis, pneumonia, and sepsis. S. aureus persistently colonizes 25–30% of the adult human population, and S. aureus carriers have an increased risk for infections caused by the bacterium. The major site of colonization is the nose, i.e., the vestibulum nasi, which is covered with ordinary skin and hair follicles. Several host and microbe determinants are assumed to be associated with colonization. These include the presence and expression level of bacterial adhesins, which can adhere to various proteins in the extracellular matrix or on the cellular surface of human skin. The host expresses several antimicrobial peptides and lipids. The level of β-defensin 3, free sphingosine, and cis-6-hexadecenoic acid are found to be associated with nasal carriage of S. aureus. Other host factors are certain polymorphisms in Toll-like receptor 2, mannose-binding lectin, C-reactive protein, glucocorticoid-, and vitamin D receptor. Additional putative determinants for carriage include genetic variation and expression of microbial surface components recognizing adhesive matrix molecules and their interaction partners, as well as variation among humans in the ability of recognizing and responding appropriately to the bacteria. Moreover, the available microflora may influence the success of S. aureus colonization. In conclusion, colonization is a complex interplay between the bacteria and its host. Several bacterial and host factors are involved, and an increased molecular understanding of these are needed. PMID:22919647

Host- and microbe determinants that may influence the success of S. aureus colonization.

PubMed

Johannessen, Mona; Sollid, Johanna E; Hanssen, Anne-Merethe

2012-01-01

Staphylococcus aureus may cause serious skin and soft tissue infections, deep abscesses, endocarditis, osteomyelitis, pneumonia, and sepsis. S. aureus persistently colonizes 25-30% of the adult human population, and S. aureus carriers have an increased risk for infections caused by the bacterium. The major site of colonization is the nose, i.e., the vestibulum nasi, which is covered with ordinary skin and hair follicles. Several host and microbe determinants are assumed to be associated with colonization. These include the presence and expression level of bacterial adhesins, which can adhere to various proteins in the extracellular matrix or on the cellular surface of human skin. The host expresses several antimicrobial peptides and lipids. The level of β-defensin 3, free sphingosine, and cis-6-hexadecenoic acid are found to be associated with nasal carriage of S. aureus. Other host factors are certain polymorphisms in Toll-like receptor 2, mannose-binding lectin, C-reactive protein, glucocorticoid-, and vitamin D receptor. Additional putative determinants for carriage include genetic variation and expression of microbial surface components recognizing adhesive matrix molecules and their interaction partners, as well as variation among humans in the ability of recognizing and responding appropriately to the bacteria. Moreover, the available microflora may influence the success of S. aureus colonization. In conclusion, colonization is a complex interplay between the bacteria and its host. Several bacterial and host factors are involved, and an increased molecular understanding of these are needed.

Characterization and Applications of Marine Microbial Enzymes in Biotechnology and Probiotics for Animal Health.

PubMed

Nguyen, T H; Nguyen, V D

Marine microorganisms have been recognized as potential sources of novel enzymes because they are relatively more stable than the corresponding enzymes derived from plants and animals. Enzymes from marine microorganisms also differ from homologous enzymes in terrestrial microorganisms based on salinity, pressure, temperature, and lighting conditions. Marine microbial enzymes can be used in diverse industrial applications. This chapter will focus on the biotechnological applications of marine enzymes and also their use as a tool of marine probiotics to improve host digestion (food digestion, food absorption, and mucus utilization) and cleave molecular signals involved in quorum sensing in pathogens to control disease in aquaculture. © 2017 Elsevier Inc. All rights reserved.

Microbial diversity in Brazilian mangrove sediments – a mini review

PubMed Central

Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

[Effects of plateau zokor disturbance and restoration years on soil nutrients and microbial functional diversity in alpine meadow].

PubMed

Hu, Lei; Ade, Lu-ji; Zi, Hong-biao; Wang, Chang-ting

2015-09-01

To explore the dynamic process of restoration succession in degraded alpine meadow that had been disturbed by plateau zokors in the eastern Tibetan Plateau, we examined soil nutrients and microbial functional diversity using conventional laboratory analysis and the Biolog-ECO microplate method. Our study showed that: 1) The zokors disturbance significantly reduced soil organic matter, total nitrogen, available nitrogen and phosphorus contents, but had no significant effects on soil total phosphorus and potassium contents; 2) Soil microbial carbon utilization efficiency, values of Shannon, Pielou and McIntosh indexes increased with alpine meadow restoration years; 3) Principal component analysis (PCA) showed that carbohydrates and amino acids were the main carbon sources for maintaining soil microbial community; 4) Redundancy analysis ( RDA) indicated that soil pH, soil organic matter, total nitrogen, available nitrogen, and total potassium were the main factors influencing the metabolic rate of soil microbial community and microbial functional diversity. In summary, variations in soil microbial functional diversity at different recovery stages reflected the microbial response to aboveground vegetation, soil microbial composition and soil nutrients.

Fate and Effects of Crude Oil Spilled on Subarctic Permafrost Terrain in Interior Alaska: Fifteen Years Later

DTIC Science & Technology

1993-08-01

tundra ecosystems of Alas- (75 m2) having surface oil visible. In contrast, most ka and northern Canada (Deneke et al. 1974, Atlas of the crude oil...Overall soil microbial activity was growing black spruce (Picea mariana) forest with an increased, with some components of the microbial understory of...terrestrial environments, in the heavily affected portions of the site; they 3. Determine the effect of crude oil spills on soil found that microbial

Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

PubMed

Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

2016-06-01

To detect the changes of microbial community functional diversity of corpses with different postmortem interval （PMI） and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components （accumulative contribution ratio >90%）.The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI （0=240 h） of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

Relationship between soluble microbial products (SMP) and effluent organic matter (EfOM): characterized by fluorescence excitation emission matrix coupled with parallel factor analysis.

PubMed

Yu, Huarong; Qu, Fangshu; Sun, Lianpeng; Liang, Heng; Han, Zhengshuang; Chang, Haiqing; Shao, Senlin; Li, Guibai

2015-02-01

Effluent organic matter (EfOM) originating from wastewater treatment plant (WWTP) is of significant concern, as it not only influences the discharge quality of WWTP but also exerts a significant effect on the efficiency of the downstream advanced treatment facilities. Soluble microbial products (SMP) is a major part of EfOM. In order to further understand the relationship between soluble microbial products (SMP) and EfOM, and in turn, to propose measures for EfOM control, the formation of SMP and EfOM in identical activated sludge sequencing batch reactors (SBR) with different feed water was investigated using fluorescence excitation and emission spectroscopy matrix coupled with parallel factor analysis (EEM-PARAFAC) as well as other organic matter quantification tools. Results showed that EfOM contained not only SMP but also a considerable amount of allochthonous organic matter that derived not merely from natural organic matter (NOM). Four components in EfOM/SMP were identified by EEM-PARAFAC. Tyrosine-like substances in EfOM (Component 3, λex/em=270/316 nm) were mainly originated from utilization associated products (UAP) of SMP. Tryptophan-like substances (Component 2, λex/em=280/336 nm) as well as fulvic-like and humic-like substances in EfOM (Component 1, λex/em=240(290)/392 nm and Component 4, λex/em=260(365)/444 nm) were majorly derived from the refractory substances introduced along with the influent, among which Component 2 was stemmed from sources other than NOM. As solid retention time (SRT) increased, Component 2 and polysaccharides in SMP/EfOM decreased, while Component 4 in SMP increased. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

DOE PAGES

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

2015-06-19

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

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

PubMed Central

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

2015-01-01

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

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

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

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

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

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

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

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

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

STUDY OF SOIL AND LEAF LITTER MICROBIAL FATTY ACID PROFILES IN TABONUCO FOREST IN THE LUQUILLO EXPERIMENTAL FOREST IN PUERTO RICO

EPA Science Inventory

The results of this study suggests that there are two significantly distinct microbial communities in the leaf litter and soil components of this tropical forest. Fungi are more abundant in the leaf litter while bacteria are more abundant in the soil.

Planetary quarantine

NASA Technical Reports Server (NTRS)

1971-01-01

Developed methodologies and procedures for the reduction of microbial burden on an assembled spacecraft at the time of encapsulation or terminal sterilization are reported. This technology is required for reducing excessive microbial burden on spacecraft components for the purposes of either decreasing planetary contamination probabilities for an orbiter or minimizing the duration of a sterilization process for a lander.

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California

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

Mueller, Ryan S.; Bryson, Sam; Kieft, Brandon

Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. Here we present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.

Cover cropping frequency is the main driver of soil microbial changes during six years of organic vegetable production

USDA-ARS?s Scientific Manuscript database

Soil microbes play a key role in soil health, and understanding the functional role of this living component of soil organic matter is critical to developing sustainable systems in major vegetable production regions like Salinas, California. Soil microbial community size and composition was evaluat...

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California

DOE PAGES

Mueller, Ryan S.; Bryson, Sam; Kieft, Brandon; ...

2015-04-30

Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. Here we present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microbial ecology that can play a role in animal health and productivity, but the magnitude of these changes remains unknown. The objective of this study was ...

IDENTIFYING THE SIGNATURE OF THE NATURAL ATTENUATION IN THE MICROBIAL ECOLOGY OF HYDROCARBON CONTAMINATED GROUNDWATER USING MOLECULAR METHODS AND &LDQUO;BUG TRAPS&RDQUO;

EPA Science Inventory

These related projects have combined biological molecular methods and a novel passive sampling system (bio-trap) to produce a technology that will allow the active component of any contaminated groundwater microbial community to be investigated. Conventional sampling methods c...

Gut microbiota and cardiometabolic outcomes: influence of dietary patterns and their associated components.

PubMed

Wong, Julia M W

2014-07-01

Many dietary patterns have been associated with cardiometabolic risk reduction. A commonality between these dietary patterns is the emphasis on plant-based foods. Studies in individuals who consume vegetarian and vegan diets have shown a reduced risk of cardiovascular events and incidence of diabetes. Plant-based dietary patterns may promote a more favorable gut microbial profile. Such diets are high in dietary fiber and fermentable substrate (ie, nondigestible or undigested carbohydrates), which are sources of metabolic fuel for gut microbial fermentation and, in turn, result in end products that may be used by the host (eg, short-chain fatty acids). These end products may have direct or indirect effects on modulating the health of their host. Modulation of the gut microbiota is an area of growing interest, and it has been suggested to have the potential to reduce risk factors associated with chronic diseases. Examples of dietary components that alter the gut microbial composition include prebiotics and resistant starches. Emerging evidence also suggests a potential link between interindividual differences in the gut microbiota and variations in physiology or predisposition to certain chronic disease risk factors. Alterations in the gut microbiota may also stimulate certain populations and may assist in biotransformation of bioactive components found in plant foods. Strategies to modify microbial communities may therefore provide a novel approach in the treatment and management of chronic diseases. © 2014 American Society for Nutrition.

Modeling microbial products in activated sludge under feast-famine conditions.

PubMed

Ni, Bing-Jie; Fang, Fang; Rittmann, Bruce E; Yu, Han-Qing

2009-04-01

We develop an expanded unified model that integrates production and consumption of internal storage products (X(STO)) into a unified model for extracellular polymeric substances (EPS), soluble microbial products (SMP), and active and inert biomass in activated sludge. We also conducted independent experiments to find needed parameter values and to test the ability of the expanded unified model to describe all the microbial products, along with original substrate and oxygen uptake. The model simulations match all experimental measurements and provide insights into the dynamics of soluble and solid components in activated sludge exposed to dynamic feast-and-famine conditions in two batch experiments and in one cycle of a sequencing batch reactor. In particular, the model illustrates how X(STO) cycles up and down rapidly during feast and famine periods, while EPS and biomass components are relatively stable despite feast and famine. The agreement between model outputs and experimental EPS, SMP, and X(STO) data from distinctly different experiments supports that the expanded unified model properly captures the relationships among the forms of microbial products.

In situ microbial detection in Mojave Desert soil using native fluorescence.

PubMed

Smith, H D; Duncan, A G; Neary, P L; Lloyd, C R; Anderson, A J; Sims, R C; McKay, C P

2012-03-01

We report on the use of a portable instrument for microbial detection in the Mojave Desert soil and the potential for its use on Mars. The instrument is based on native fluorescence and employs four excitation wavelengths combined with four emission wavelengths. A soil dilution series in which known numbers of Bacillus subtilis spores were added to soil was used to determine the sensitivity of the instrument. We found that the fluorescence of the biological and organic components of the desert soil samples studied can be as strong as the fluorescence of the mineral component of these soils. Using the calibration derived from B. subtilis spores, we estimated that microbial content at our primary sampling site was 10(7) bacteria per gram of soil, a level confirmed by phospholipid fatty acid analysis. At a nearby site, but in a slightly different geological setting, we tested the instrument's ability to map out microbial concentrations in situ. Over a ∼50 m diameter circle, soil microbial concentrations determined with the B. subtilis calibration indicate that the concentrations of microorganisms detected varies from 10(4) to 10(7) cells per gram of soil. We conclude that fluorescence is a promising method for detecting soil microbes in noncontact applications in extreme environments on Earth and may have applications on future missions to Mars.

Toward real time detection of the basic living activity in home using a wearable sensor and smart home sensors.

PubMed

Bang, Sunlee; Kim, Minho; Song, Sa-Kwang; Park, Soo-Jun

2008-01-01

As the elderly people living alone are enormously increasing recently, we need the system inferring activities of daily living (ADL) for maintaining healthy life and recognizing emergency. The system should be constructed with sensors, which are used to associate with people's living while remaining as non intrusive views as possible. To do this, the proposed system use a triaxial accelerometer sensor and environment sensors indicating contact with subject in home. Particularly, in order to robustly infer ADLs, we present component ADL, which is decided with conjunction of human motion together, not just only contacted object identification. It is an important component in inferring ADL. In special, component ADL decision firstly refines misclassified initial activities, which improves the accuracy of recognizing ADL. Preliminary experiments results for proposed system provides overall recognition rate of over 97% over 8 component ADLs, which can be effectively applicable to recognize the final ADLs.

Research advances on microbial genetics in China in 2015.

PubMed

Xie, Jian-ping; Han, Yu-bo; Liu, Gang; Bai, Lin-quan

2016-09-01

In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum.

Development of lower Triassic wrinkle structures: implications for the search for life on other planets.

PubMed

Mata, Scott A; Bottjer, David J

2009-11-01

Wrinkle structures are microbially mediated sedimentary structures that are a common feature of Proterozoic and earliest Phanerozoic siliciclastic seafloors on Earth and occur only rarely in post-Cambrian strata. These macroscopic microbially induced sedimentary structures are readily identifiable at the outcrop scale, and their recognition on other planetary bodies by landed missions may suggest the presence of past microbial life. Wrinkle structures of the Lower Triassic (Spathian) Virgin Limestone Member of the Moenkopi Formation in the western United States record an occurrence of widespread microbialite formation in the wake of the end-Permian mass extinction, the largest biotic crisis of the Phanerozoic. Wrinkle structures occur on proximal sandy tempestites deposited within the offshore transition. Storm layers appear to have been rapidly colonized by microbial mats and were subsequently buried by mud during fair-weather conditions. Wrinkle structures exhibit flat-topped crests and sinuous troughs, with associated mica grains oriented parallel to bedding, suggestive of trapping and binding activity. Although Lower Triassic wrinkle structures postdate the widespread occurrence of these features during the Proterozoic and Cambrian, they exhibit many of the same characteristics and environmental trends, which suggests a conservation of microbial formational and preservational processes in subtidal siliciclastic settings on Earth from the Precambrian into the Phanerozoic. In the search for extraterrestrial life, it may be these conservative characteristics that prove to be the most useful and robust for recognizing microbial features on other planetary bodies, and may add to an ever-growing foundation of knowledge for directing future explorations aimed at seeking out macroscopic microbial signatures.

Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments.

PubMed

Rousk, Kathrin; Michelsen, Anders; Rousk, Johannes

2016-12-01

Half the global soil carbon (C) is held in high-latitude systems. Climate change will expose these to warming and a shift towards plant communities with more labile C input. Labile C can also increase the rate of loss of native soil organic matter (SOM); a phenomenon termed 'priming'. We investigated how warming (+1.1 °C over ambient using open top chambers) and litter addition (90 g m -2  yr -1 ) treatments in the subarctic influenced the susceptibility of SOM mineralization to priming, and its microbial underpinnings. Labile C appeared to inhibit the mineralization of C from SOM by up to 60% within hours. In contrast, the mineralization of N from SOM was stimulated by up to 300%. These responses occurred rapidly and were unrelated to microbial successional dynamics, suggesting catabolic responses. Considered separately, the labile C inhibited C mineralization is compatible with previously reported findings termed 'preferential substrate utilization' or 'negative apparent priming', while the stimulated N mineralization responses echo recent reports of 'real priming' of SOM mineralization. However, C and N mineralization responses derived from the same SOM source must be interpreted together: This suggested that the microbial SOM-use decreased in magnitude and shifted to components richer in N. This finding highlights that only considering SOM in terms of C may be simplistic, and will not capture all changes in SOM decomposition. The selective mining for N increased in climate change treatments with higher fungal dominance. In conclusion, labile C appeared to trigger catabolic responses of the resident microbial community that shifted the SOM mining to N-rich components; an effect that increased with higher fungal dominance. Extrapolating from these findings, the predicted shrub expansion in the subarctic could result in an altered microbial use of SOM, selectively mining it for N-rich components, and leading to a reduced total SOM-use. © 2016 John Wiley & Sons Ltd.

Phenazines in the environment: microbes, habitats, and ecological relevance. In: Chincholkar, S., Thomashow, L., editors. Microbial phenazines: biosynthesis, agriculture and health. New York, NY; Springer

USDA-ARS?s Scientific Manuscript database

Phenazines, the pigmented, redox-active metabolites produced by certain fluorescent pseudomonads, streptomycetes, and members of a few other bacterial genera, have long been recognized for their broad-spectrum antibiotic activity. Much has been learned in recent years about the synthesis of these co...

Microbial facies distribution and its geological and geochemical controls at the Hanford 300 area

NASA Astrophysics Data System (ADS)

Hou, Z.; Nelson, W.; Stegen, J.; Murray, C. J.; Arntzen, E.

2015-12-01

Efforts have been made by various scientific disciplines to study hyporheic zones and characterize their associated processes. One way to approach the study of the hyporheic zone is to define facies, which are elements of a (hydrobio) geologic classification scheme that groups components of a complex system with high variability into a manageable set of discrete classes. In this study, we try to classify the hyporheic zone based on the geology, geochemistry, microbiology, and understand their interactive influences on the integrated biogeochemical distributions and processes. A number of measurements have been taken for 21 freeze core samples along the Columbia River bank in the Hanford 300 Area, and unique datasets have been obtained on biomass, pH, number of microbial taxa, percentage of N/C/H/S, microbial activity parameters, as well as microbial community attributes/modules. In order to gain a complete understanding of the geological control on these variables and processes, the explanatory variables are set to include quantitative gravel/sand/mud/silt/clay percentages, statistical moments of grain size distributions, as well as geological (e.g., Folk-Wentworth) and statistical (e.g., hierarchical) clusters. The dominant factors for major microbial and geochemical variables are identified and summarized using exploratory data analysis approaches (e.g., principal component analysis, hierarchical clustering, factor analysis, multivariate analysis of variance). The feasibility of extending the facies definition and its control of microbial and geochemical properties to larger scales is discussed.

On the Functional Overlap between Complement and Anti-Microbial Peptides.

PubMed

Zimmer, Jana; Hobkirk, James; Mohamed, Fatima; Browning, Michael J; Stover, Cordula M

2014-01-01

Intriguingly, activated complement and anti-microbial peptides share certain functionalities; lytic, phagocytic, and chemo-attractant activities and each may, in addition, exert cell instructive roles. Each has been shown to have distinct LPS detoxifying activity and may play a role in the development of endotoxin tolerance. In search of the origin of complement, a functional homolog of complement C3 involved in opsonization has been identified in horseshoe crabs. Horseshoe crabs possess anti-microbial peptides able to bind to acyl chains or phosphate groups/saccharides of endotoxin, LPS. Complement activity as a whole is detectable in marine invertebrates. These are also a source of anti-microbial peptides with potential pharmaceutical applicability. Investigating the locality for the production of complement pathway proteins and their role in modulating cellular immune responses are emerging fields. The significance of local synthesis of complement components is becoming clearer from in vivo studies of parenchymatous disease involving specifically generated, complement-deficient mouse lines. Complement C3 is a central component of complement activation. Its provision by cells of the myeloid lineage varies. Their effector functions in turn are increased in the presence of anti-microbial peptides. This may point to a potentiating range of activities, which should serve the maintenance of health but may also cause disease. Because of the therapeutic implications, this review will consider closely studies dealing with complement activation and anti-microbial peptide activity in acute inflammation (e.g., dialysis-related peritonitis, appendicitis, and ischemia).

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOEpatents

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

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

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

Wang, Gangsheng; Post, Wilfred M

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

Scavenger Receptors: Emerging Roles in Cancer Biology and Immunology

PubMed Central

Yu, Xiaofei; Guo, Chunqing; Fisher, Paul B.; Subjeck, John R.; Wang, Xiang-Yang

2015-01-01

Scavenger receptors constitute a large family of evolutionally conserved protein molecules that are structurally and functionally diverse. Although scavenger receptors were originally identified based on their capacity to scavenge modified lipoproteins, these molecules have been shown to recognize and bind to a broad spectrum of ligands, including modified and unmodified host-derived molecules or microbial components. As a major subset of innate pattern recognition receptors, scavenger receptors are mainly expressed on myeloid cells and function in a wide range of biological processes, such as endocytosis, adhesion, lipid transport, antigen presentation, and pathogen clearance. In addition to playing a crucial role in maintenance of host homeostasis, scavenger receptors have been implicated in the pathogenesis of a number of diseases, e.g., atherosclerosis, neurodegeneration, or metabolic disorders. Emerging evidence has begun to reveal these receptor molecules as important regulators of tumor behavior and host immune responses to cancer. This review summarizes our current understanding on the newly identified, distinct functions of scavenger receptors in cancer biology and immunology. The potential of scavenger receptors as diagnostic biomarkers and novel targets for therapeutic interventions to treat malignancies is also highlighted. PMID:26216637

Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control.

PubMed

Dai, Dongjuan; Prussin, Aaron J; Marr, Linsey C; Vikesland, Peter J; Edwards, Marc A; Pruden, Amy

2017-07-18

The "exposome" is a term describing the summation of one's lifetime exposure to microbes and chemicals. Such exposures are now recognized as major drivers of human health and disease. Because humans spend ∼90% of their time indoors, the built environment exposome merits particular attention. Herein we utilize an engineering perspective to advance understanding of the factors that shape the built environment exposome and its influence on human wellness and disease, while simultaneously informing development of a framework for intentionally controlling the exposome to protect public health. Historically, engineers have been focused on controlling chemical and physical contaminants and on eradicating microbes; however, there is a growing awareness of the role of "beneficial" microbes. Here we consider the potential to selectively control the materials and chemistry of the built environment to positively influence the microbial and chemical components of the indoor exposome. Finally, we discuss research gaps that must be addressed to enable intentional engineering design, including the need to define a "healthy" built environment exposome and how to control it.

Serine-Aspartate Repeat Protein D Increases Staphylococcus aureus Virulence and Survival in Blood

PubMed Central

Uchiyama, Satoshi; Valderrama, J. Andrés; Ajayi, Clement; Sollid, Johanna U. E.; van Sorge, Nina M.; Nizet, Victor; van Strijp, Jos A. G.

2016-01-01

ABSTRACT Staphylococcus aureus expresses a panel of cell wall-anchored adhesins, including proteins belonging to the microbial surface components recognizing adhesive matrix molecule (MSCRAMM) family, exemplified by the serine-aspartate repeat protein D (SdrD), which serve key roles in colonization and infection. Deletion of sdrD from S. aureus subsp. aureus strain NCTC8325-4 attenuated bacterial survival in human whole blood ex vivo, which was associated with increased killing by human neutrophils. Remarkably, SdrD was able to inhibit innate immune-mediated bacterial killing independently of other S. aureus proteins, since addition of recombinant SdrD protein and heterologous expression of SdrD in Lactococcus lactis promoted bacterial survival in human blood. SdrD contributes to bacterial virulence in vivo, since fewer S. aureus subsp. aureus NCTC8325-4 ΔsdrD bacteria than bacteria of the parent strain were recovered from blood and several organs using a murine intravenous infection model. Collectively, our findings reveal a new property of SdrD as an important key contributor to S. aureus survival and the ability to escape the innate immune system in blood. PMID:27795358

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities

PubMed Central

Bridier, Arnaud; Piard, Jean-Christophe; Pandin, Caroline; Labarthe, Simon; Dubois-Brissonnet, Florence; Briandet, Romain

2017-01-01

Biofilms are dynamic habitats which constantly evolve in response to environmental fluctuations and thereby constitute remarkable survival strategies for microorganisms. The modulation of biofilm functional properties is largely governed by the active remodeling of their three-dimensional structure and involves an arsenal of microbial self-produced components and interconnected mechanisms. The production of matrix components, the spatial reorganization of ecological interactions, the generation of physiological heterogeneity, the regulation of motility, the production of actives enzymes are for instance some of the processes enabling such spatial organization plasticity. In this contribution, we discussed the foundations of architectural plasticity as an adaptive driver of biofilms through the review of the different microbial strategies involved. Moreover, the possibility to harness such characteristics to sculpt biofilm structure as an attractive approach to control their functional properties, whether beneficial or deleterious, is also discussed. PMID:28775718

Evidence of synsedimentary microbial activity and iron deposition in ferruginous crusts of the Late Cenomanian Utrillas Formation (Iberian Basin, central Spain)

NASA Astrophysics Data System (ADS)

García-Hidalgo, José F.; Elorza, Javier; Gil-Gil, Javier; Herrero, José M.; Segura, Manuel

2018-02-01

Ferruginous sandstones and crusts are prominent sedimentary features throughout the continental (braided)-coastal siliciclastic (estuarine-tidal) wedges of the Late Cenomanian Utrillas Formation in the Iberian Basin. Crust types recognized are: Ferruginous sandy crusts (Fsc) with oxides-oxyhydroxides (hematite and goethite) concentrated on sandstone tops presenting a fibro-radial internal structure reminding organic structures that penetrate different mineral phases, suggesting the existence of bacterial activity in crust development; Ferruginous muddy crusts (Fmc) consisting of wavy, laminated, microbial mats, being composed mainly of hematite. On the other hand, a more dispersed and broader mineralization included as Ferruginous sandstones with iron oxides and oxyhydroxides (hematite and goethite) representing a limited cement phase on these sediments. The presence of microbial remains, ferruginous minerals, Microbially-induced sedimentary structures, microbial laminites and vertebrate tracks preserved due to the presence of biofilms suggest firstly a direct evidence of syn-depositional microbial activity in these sediments; and, secondly, that iron accumulation and ferruginous crusts development occurred immediately after deposition of the host, still soft sediments. Ferruginous crusts cap sedimentary cycles and they represent the gradual development of hard substrate conditions, and the development of a discontinuity surface at the top of the parasequence sets, related to very low sedimentary rates; the overlying sediments record subsequent flooding of underlying shallower environments; crusts are, consequently, interpreted as boundaries for these higher-order cycles in the Iberian Basin.

Cryptic carbon and sulfur cycling between surface ocean plankton.

PubMed

Durham, Bryndan P; Sharma, Shalabh; Luo, Haiwei; Smith, Christa B; Amin, Shady A; Bender, Sara J; Dearth, Stephen P; Van Mooy, Benjamin A S; Campagna, Shawn R; Kujawinski, Elizabeth B; Armbrust, E Virginia; Moran, Mary Ann

2015-01-13

About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly up-regulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when cocultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3-dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a previously unidentified and likely sizeable link in both the marine carbon and sulfur cycles.

Antibody for the prevention of neonatal noscocomial staphylococcal infection: a review of the literature.

PubMed

Weisman, L E

2007-09-01

Staphylococci, especially coagulase negative staphylococci (CONS), are responsible for over 75 % of late-onset infections in very low birth weight infants. These infections cause increased length of hospital stay, need for antibiotics, and cost of medical care. Several drug companies have developed and evaluated hyperimmune polyclonal and monoclonal antibodies for the prevention of neonatal staphylococcal infection including 1) Altastaph by North American Biologics Inc., 2) Veronate by Inhibitex Inc., and 3) Pagibaximab by Biosynexus Inc, and Glaxo Smith Kline Inc. We will review the development and status of these potential products. Altastaph is a S. aureus serotype 5 and 8 vaccine induced hyperimmune polyclonal antibody whose development has been placed on hold due to its failure to demonstrate any trend toward efficacy in a recently completed Phase II study. Veronate is a polyclonal antibody obtained by plasmapheresis from donors with high titers of MSCRAMM (microbial surface components recognizing adhesion matrix molecules) activity against CONS whose development has been placed on hold due to its failure to demonstrate effectiveness in a recently completed Phase III study. Pagibaximab is a humanized mouse chimeric monoclonal antibody (previously known as BSYX-A110) directed against lipoteichoic acid (LTA), a major cell wall component of gram-positive bacteria, that has recently completed a Phase II study suggesting efficacy and is being developed further for clinical investigation.

Corrosion of Iron by Sulfate-Reducing Bacteria: New Views of an Old Problem

PubMed Central

Garrelfs, Julia

2014-01-01

About a century ago, researchers first recognized a connection between the activity of environmental microorganisms and cases of anaerobic iron corrosion. Since then, such microbially influenced corrosion (MIC) has gained prominence and its technical and economic implications are now widely recognized. Under anoxic conditions (e.g., in oil and gas pipelines), sulfate-reducing bacteria (SRB) are commonly considered the main culprits of MIC. This perception largely stems from three recurrent observations. First, anoxic sulfate-rich environments (e.g., anoxic seawater) are particularly corrosive. Second, SRB and their characteristic corrosion product iron sulfide are ubiquitously associated with anaerobic corrosion damage, and third, no other physiological group produces comparably severe corrosion damage in laboratory-grown pure cultures. However, there remain many open questions as to the underlying mechanisms and their relative contributions to corrosion. On the one hand, SRB damage iron constructions indirectly through a corrosive chemical agent, hydrogen sulfide, formed by the organisms as a dissimilatory product from sulfate reduction with organic compounds or hydrogen (“chemical microbially influenced corrosion”; CMIC). On the other hand, certain SRB can also attack iron via withdrawal of electrons (“electrical microbially influenced corrosion”; EMIC), viz., directly by metabolic coupling. Corrosion of iron by SRB is typically associated with the formation of iron sulfides (FeS) which, paradoxically, may reduce corrosion in some cases while they increase it in others. This brief review traces the historical twists in the perception of SRB-induced corrosion, considering the presently most plausible explanations as well as possible early misconceptions in the understanding of severe corrosion in anoxic, sulfate-rich environments. PMID:24317078

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes

PubMed Central

Martens, Eric C.; Kelly, Amelia G.; Tauzin, Alexandra S.; Brumer, Harry

2014-01-01

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on time scales as short as several hours, due to the ability of the gut microbial community to rapidly alter its physiology from meal-to-meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. PMID:25026064

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

PubMed Central

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

2016-01-01

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

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.

PubMed

Martens, Eric C; Kelly, Amelia G; Tauzin, Alexandra S; Brumer, Harry

2014-11-25

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-02-01

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

Pathways and mechanisms for removal of dissolved organic carbon from leaf leachate in streams

Treesearch

Clifford N. Dahm

1981-01-01

Removal of dissolved organic carbon (DOC) from water resulting from adsorption and microbial uptake was examined to determine the importance of biotic and abiotic pathways. Physical–chemical adsorption to components of the stream sediment or water and biotic assimilation associated with the microbial population was determined in recirculating chambers utilizing...

An Inquiry-Based Laboratory Design for Microbial Ecology

ERIC Educational Resources Information Center

Tessier, Jack T.; Penniman, Clayton A.

2006-01-01

There is a collective need to increase the use of inquiry-based instruction at the college level. This paper provides of an example of how inquiry was successfully used in the laboratory component of an undergraduate course in microbial ecology. Students were offered a collection of field and laboratory methods to choose from, and they developed a…

Substrate-induced respiration in Puerto Rican soils: minimum glucose amendment

Treesearch

Marcela Zalamea; Grizelle Gonzalez

2007-01-01

Soil microbiota –usually quantified as microbial biomass –is a key component of terrestrial ecosystems, regulating nutrient cycling and organic matter turnover. Among the several methods developed for estimating soil microbial biomass, Substrate-Induced Respiration (SIR) is considered reliable and easy to implement; once the maximum respiratory response is determined...

Principal Component Analysis of Microbial Community Data from an Accelerated Decay Cellar Test

Treesearch

Grant T. Kirker; Patricia K. Lebow

2014-01-01

Analysis of microbial communities is a valuable tool for characterization and identification of microbes in a myriad of environments. We are currently using the molecular method terminal restriction fragment length polymorphism (T-RFLP) analysis to characterize changes in bacterial and fungal communities on treated and untreated wood in soil. T-RFLP uses fluorescently...

Microbial Ecology in Vineyards

USDA-ARS?s Scientific Manuscript database

Soil health affects grapevine health, which, in turn, affects fruit quality. Soil health has chemical, physical, and biological components. The chemical components are the best understood, and there are relatively convenient methods to both evaluate and amend chemical soil fertility. The physical...

Salivary Biomarkers for Caries Risk Assessment

PubMed Central

Guo, Lihong; Shi, Wenyuan

2013-01-01

Saliva contains various microbes and host biological components that could be used for caries risk assessment. This review focuses on the research topics that connect dental caries with saliva, including both the microbial and host components within saliva. PMID:23505756

Are biological effects of desert shrubs more important than physical effects on soil microorganisms?

PubMed

Berg, Naama; Steinberger, Yosef

2010-01-01

Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a longterm research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO2 evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.

Coupled Spatiotemporal Dynamics of Microbial Community Ecology, Biogeochemistry, and Hydrologic Mixing

NASA Astrophysics Data System (ADS)

Stegen, J.; Johnson, T. C.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

2015-12-01

The hyporheic zone (HZ) is a critical ecosystem component that links terrestrial, surface water, and groundwater ecosystems. A dominant feature of the HZ is groundwater-surface water mixing and the input of terrestrially—as well as aquatically—derived organic carbon. In many systems the HZ has a relatively small spatial extent, but in larger riverine systems groundwater-surface water mixing can occur 100s of meters beyond the surface water shoreline; we consider these more distal locations to be within the 'subsurface interaction zone' (SIZ) as they are beyond the traditional HZ. Microbial communities in the HZ and SIZ drive biogeochemical processes in these system components, yet relatively little is known about the ecological processes that drive HZ and SIZ microbial communities. Here, we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected through space (400m spatial extent) and time (7 month temporal extent) within the Hanford Site 300 Area. These data streams were integrated to evaluate how the influence of groundwater-surface water mixing on microbial communities changes when moving from the HZ to the broader SIZ. Our results indicate that groundwater-surface water mixing (i) consistently stimulated heterotrophic respiration, but only above a threshold of surface water intrusion, (ii) did not stimulate denitrification, (iii) caused deterministic shifts in HZ microbial communities due to changes in organic carbon composition, and (iv) did not cause shifts in SIZ microbial communities. These results suggest that microbial communities and the biogeochemical processes they drive are impacted by groundwater-surface water mixing primarily in the HZ and to a lesser extent in the SIZ.

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

USGS Publications Warehouse

Mumford, Adam C.; Akob, Denise M.; Klinges, J. Grace; Cozzarelli, Isabelle M.

2018-01-01

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

Microbial protein: future sustainable food supply route with low environmental footprint.

PubMed

Matassa, Silvio; Boon, Nico; Pikaar, Ilje; Verstraete, Willy

2016-09-01

Microbial biotechnology has a long history of producing feeds and foods. The key feature of today's market economy is that protein production by conventional agriculture based food supply chains is becoming a major issue in terms of global environmental pollution such as diffuse nutrient and greenhouse gas emissions, land use and water footprint. Time has come to re-assess the current potentials of producing protein-rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass, producible with a lower environmental footprint compared with other plant or animal-based alternatives. A major driver is the need to no longer disintegrate but rather upgrade a variety of low-value organic and inorganic side streams in our current non-cyclic economy. In this context, microbial bioconversions of such valuable matters to nutritive microbial cells and cell components are a powerful asset. The worldwide market of animal protein is of the order of several hundred million tons per year, that of plant protein several billion tons of protein per year; hence, the expansion of the production of microbial protein does not pose disruptive challenges towards the process of the latter. Besides protein as nutritive compounds, also other cellular components such as lipids (single cell oil), polyhydroxybuthyrate, exopolymeric saccharides, carotenoids, ectorines, (pro)vitamins and essential amino acids can be of value for the growing domain of novel nutrition. In order for microbial protein as feed or food to become a major and sustainable alternative, addressing the challenges of creating awareness and achieving public and broader regulatory acceptance are real and need to be addressed with care and expedience. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

The influence of gut microbiota on drug metabolism and toxicity

PubMed Central

Li, Houkai; He, Jiaojiao; Jia, Wei

2017-01-01

Introduction Gut microbiota plays critical roles in drug metabolism. The individual variation of gut microbiota contributes to the interindividual differences towards drug therapy including drug-induced toxicity and efficacy. Accordingly, the investigation and elucidation of gut microbial impacts on drug metabolism and toxicity will not only facilitate the way of personalized medicine, but also improve the rational drug design. Areas covered This review provide an overview on the microbiota-host cometabolism on drug metabolism and summarize 30 clinical drugs which are co-metabolized by host and gut microbiota. Moreover, this review is specifically focused on elucidating the gut microbial modulation on some clinical drugs, in which the gut microbial influences on drug metabolism, drug-induced toxicity and efficacy are intensively discussed. Expert opinion The gut microbial contribution to drug metabolism and toxicity is increasingly recognized, but remains largely unexplored due to the extremely complex relationship between gut microbiota and host. The mechanistic elucidation of gut microbiota in drug metabolism is critical before any practical progress in drug design or personalized medicine could be made by modulating human gut microbiota, which is predominantly relied on the technical innovations such as metagenomics and metabolomics, as well as the integration of multi-disciplinary knowledge. PMID:26569070

Type II NKT Cells in Inflammation, Autoimmunity, Microbial Immunity, and Cancer

PubMed Central

Marrero, Idania; Ware, Randle; Kumar, Vipin

2015-01-01

Natural killer T cells (NKT) recognize self and microbial lipid antigens presented by non-polymorphic CD1d molecules. Two major NKT cell subsets, type I and II, express different types of antigen receptors (TCR) with distinct mode of CD1d/lipid recognition. Though type II NKT cells are less frequent in mice and difficult to study, they are predominant in human. One of the major subsets of type II NKT cells reactive to the self-glycolipid sulfatide is the best characterized and has been shown to induce a dominant immune regulatory mechanism that controls inflammation in autoimmunity and in anti-cancer immunity. Recently, type II NKT cells reactive to other self-glycolipids and phospholipids have been identified suggesting both promiscuous and specific TCR recognition in microbial immunity as well. Since the CD1d pathway is highly conserved, a detailed understanding of the biology and function of type II NKT cells as well as their interplay with type I NKT cells or other innate and adaptive T cells will have major implications for potential novel interventions in inflammatory and autoimmune diseases, microbial immunity, and cancer. PMID:26136748

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

PubMed

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

2015-09-01

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Electron shuttles in biotechnology.

PubMed

Watanabe, Kazuya; Manefield, Mike; Lee, Matthew; Kouzuma, Atsushi

2009-12-01

Electron-shuttling compounds (electron shuttles [ESs], or redox mediators) are essential components in intracellular electron transfer, while microbes also utilize self-produced and naturally present ESs for extracellular electron transfer. These compounds assist in microbial energy metabolism by facilitating electron transfer between microbes, from electron-donating substances to microbes, and/or from microbes to electron-accepting substances. Artificially supplemented ESs can create new routes of electron flow in the microbial energy metabolism, thereby opening up new possibilities for the application of microbes to biotechnology processes. Typical examples of such processes include halogenated-organics bioremediation, azo-dye decolorization, and microbial fuel cells. Herein we suggest that ESs can be applied widely to create new microbial biotechnology processes.

Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells.

PubMed

Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

2017-01-01

The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter , which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

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

Roux, Simon; Hallam, Steven J.; Woyke, Tanja

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 newmore » viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.« less

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.

PubMed

Roux, Simon; Hallam, Steven J; Woyke, Tanja; Sullivan, Matthew B

2015-07-22

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

DOE PAGES

Roux, Simon; Hallam, Steven J.; Woyke, Tanja; ...

2015-07-22

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 newmore » viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.« less

Invited review: Essential oils as modifiers of rumen microbial fermentation.

PubMed

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial. Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance.

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

PubMed Central

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergey N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; Karnachuk, Olga V.; Bonch-Osmolovskaya, Elizaveta A.

2016-01-01

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles. PMID:28082967

Silage review: Using molecular approaches to define the microbial ecology of silage.

PubMed

McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

2018-05-01

Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors can also lead to biases in the interpretation of sequence data. Bioinformatic analyses are reliant on the integrity and presence of sequence data within established databases and can be subject to low taxonomic resolution. Despite these limitations, advancements in molecular biology are poised to revolutionize our current understanding of the microbial ecology of silage. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. All rights reserved.

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

PubMed

Fernandez-Ricaud, Luciano; Kourtchenko, Olga; Zackrisson, Martin; Warringer, Jonas; Blomberg, Anders

2016-06-23

Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology. To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis. PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.

Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

PubMed

Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

2010-07-15

Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. 2010 Elsevier B.V. All rights reserved.

Paleobiological Perspectives on Early Microbial Evolution

PubMed Central

Knoll, Andrew H.

2015-01-01

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles. PMID:26134315

Effect of a prolonged stay in a locked environment on the microbial flora in dogs

NASA Technical Reports Server (NTRS)

Balish, E.; Shih, C.-N.; Yale, C. E.; Mandel, A. D.

1974-01-01

Ten purebred Beagle dogs (all males) were used to determine the effect of a prolonged stay in a locked environment (i.e., no exogenous microbial contamination) on the microbial flora. At monthly intervals the microbial profile (feces, nose, and throat) of each dog was assessed. After 12 months it was found there was no drastic alteration or simplification of the microbial profile of isolated or control dogs. Although isolated dogs had slightly higher levels of anaerobic bacteria and somewhat lower levels of enterococci, the major groups of anaerobic, aerobic, and facultative bacteria remained qualitatively and quantitatively similar for the 12-month study period. Although they were only minor components of the fecal flora, Candida albicans and Shigella sonnei were consistently isolated in larger numbers from the dogs in the locked environment.

Lunar and Planetary Science XXXV: Astrobiology: Analogs and Applications to the Search for Life

NASA Technical Reports Server (NTRS)

2004-01-01

The session "Astrobiology: Analogs and Applications to the Search for Life" included the folowing reports:The Search for Life on Mars Using Macroscopically Visible Microbial Mats (Stromatolites) in 3.5/3.3 Ga Cherts from the Pilbara in Australia and Barberton in South Africa as Analogues; Life in a Mars Analog: Microbial Activity Associated with Carbonate Cemented Lava Breccias from NW Spitsbergen; Groundwater-fed Iron-rich Microbial Mats in a Freshwater Creek: Growth Cycles and Fossilization Potential of Microbial Features; Episodic Fossilization of Microorganisms on an Annual Timescale in an Anthropogenically Modified Natural Environment: Geochemical Controls and Implications for Astrobiology; Proterozoic Microfossils and Their Implications for Recognizing Life on Mars; Microbial Alteration of Volcanic Glass in Modern and Ancient Oceanic Crust as a Proxy for Studies of Extraterrestrial Material ; Olivine Alteration on Earth and Mars; Searching for an Acidic Aquifer in the R!o Tinto Basin. First Geobiology Results of MARTE Project; In-Field Testing of Life Detection Instruments and Protocols in a Mars Analogue Arctic Environment; Habitability of the Shallow Subsurface on Mars: Clues from the Meteorites; Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain; Characterization of the Organic Matter in an Archean Chert (Warrawoona, Australia); and The Solfatara Crater, Italy: Characterization of Hydrothermal Deposits, Biosignatures and Their Astrobiological Implication.

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

PubMed Central

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L−1. PMID:28102316

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

NASA Astrophysics Data System (ADS)

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L-1.

[Influence of Different Straws Returning with Landfill on Soil Microbial Community Structure Under Dry and Water Farming].

PubMed

Lan, Mu-ling; Gao, Ming

2015-11-01

Based on rice, wheat, corn straw and rape, broad bean green stalk as the research object, using phospholipid fatty acid (PLFA) method, combining principal component analysis method to study the soil microbial quantity, distribution of flora, community structure characteristics under dry and water farming as two different cultivated land use types. The PLFA analysis results showed that: under dry farming, total PLFA quantity ranged 8.35-25.15 nmol x g(-1), showed rape > broad bean > corn > rice > wheat, rape and broad bean significantly increased total PLFA quantity by 1.18 and 1.08 times compared to the treatment without straw; PLFA quantity of bacterial flora in treatments with straws was higher than that without straw, and fungal biomass was significantly increased, so was the species richness of microbial community. Under water faming, the treatments of different straws returning with landfill have improved the PLFA quantity of total soil microbial and flora comparing with the treatment without straw, fungi significantly increased, and species richness of microbial communities value also increased significantly. Total PLFA quantity ranged 4.04-22.19 nmol x g(-1), showed rice > corn > wheat > broad bean > rape, which in rape and broad bean treatments were lower than the treatment without straw; fungal PLFA amount in 5 kinds of straw except broad bean treatment was significantly higher than that of the treatment without straw, bacteria and total PLFA quantity in broad bean processing were significantly lower than those of other treatments, actinomycetes, G+, G- had no significant difference between all treatments; rice, wheat, corn, rape could significantly increase the soil microbial species richness index and dominance index under water faming. The results of principal component analysis showed that broad bean green stalk had the greatest impact on the microbial community structure in the dry soil, rape green stalk and wheat straw had the biggest influence on soil microbial community structure in water soil.

A microbial survey of the International Space Station (ISS)

PubMed Central

Lang, Jenna M.; Coil, David A.; Neches, Russell Y.; Brown, Wendy E.; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T.; Gilbert, Jack A.

2017-01-01

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the “buildings” in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Results Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. Conclusions While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036–4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain. PMID:29492330

A microbial survey of the International Space Station (ISS).

PubMed

Lang, Jenna M; Coil, David A; Neches, Russell Y; Brown, Wendy E; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T; Gilbert, Jack A; Eisen, Jonathan A

2017-01-01

Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Both IIC and IID Components of Mannose Phosphotransferase System Are Involved in the Specific Recognition between Immunity Protein PedB and Bacteriocin-Receptor Complex.

PubMed

Zhou, Wanli; Wang, Guohong; Wang, Chunmei; Ren, Fazheng; Hao, Yanling

2016-01-01

Upon exposure to exogenous pediocin-like bacteriocins, immunity proteins specifically bind to the target receptor of the mannose phosphotransferase system components (man-PTS IIC and IID), therefore preventing bacterial cell death. However, the specific recognition of immunity proteins and its associated target receptors remains poorly understood. In this study, we constructed hybrid receptors to identify the domains of IIC and/or IID recognized by the immunity protein PedB, which confers immunity to pediocin PA-1. Using Lactobacillus plantarum man-PTS EII mutant W903, the IICD components of four pediocin PA-1-sensitive strains (L. plantarum WQ0815, Leuconostoc mesenteroides 05-43, Lactobacillus salivarius REN and Lactobacillus acidophilus 05-172) were respectively co-expressed with the immunity protein PedB. Well-diffusions assays showed that only the complex formed by LpIICD from L. plantarum WQ0815 with pediocin PA-1 could be recognized by PedB. In addition, a two-step PCR approach was used to construct hybrid receptors by combining LpIIC or LpIID recognized by PedB with the other three heterologous IID or IIC compounds unrecognized by PedB, respectively. The results showed that all six hybrid receptors were recognized by pediocin PA-1. However, when IIC or IID of L. plantarum WQ0815 was replaced with any corresponding IIC or IID component from L. mesenteroides 05-43, L. salivarius REN and L. acidophilus 05-172, all the hybrid receptors could not be recognized by PedB. Taken altogether, we concluded that both IIC and IID components of the mannose phosphotransferase system play an important role in the specific recognition between the bacteriocin-receptor complex and the immunity protein PedB.

Cave speleothems as repositories of microbial biosignatures

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

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

Wilson, B.; Mordensky, S.; Verba, Circe

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO 2) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO 2 levels is a goal for many nations and carbon sequestration which traps CO 2 in the Earth’s subsurface is one method to reduce atmospheric CO 2 levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role inmore » biogeochemistry and accordingly may determine how CO 2 is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO 2 sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO 2 sequestration could be most efficiently implemented.« less

Microbial processing of carbon in hydrothermal systems (Invited)

NASA Astrophysics Data System (ADS)

LaRowe, D.; Amend, J. P.

2013-12-01

Microorganisms are known to be active in hydrothermal systems. They catalyze reactions that consume and produce carbon compounds as a result of their efforts to gain energy, grow and replace biomass. However, the rates of these processes, as well as the size of the active component of microbial populations, are poorly constrained in hydrothermal environments. In order to better characterize biogeochemical processes in these settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size is presented. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into biomass - either new microorganisms or the replacement of existing cell components - and the amount of energy that is required to synthesize biomass. The constraints that hydrothermal conditions place on power supply and demand are explicitly taken into account. The chemical composition, including the concentrations of organic compounds, of diffuse and focused flow hydrothermal fluids, hydrothermally influenced sediment pore water and fluids from the oceanic lithosphere are used in conjunction with cell count data and the model described above to constrain the rates of microbial processes that influence the carbon cycle in the Juan de Fuca hydrothermal system.

Isotopic Evidence for Microbial Activity in Crystalline Bedrock Fractures - a Case Study from Olkiluoto, SW Finland

NASA Astrophysics Data System (ADS)

Sahlstedt, E. K.; Karhu, J.; Pitkänen, P.

2015-12-01

Changes in the geochemical environment in crystalline bedrock fractures were investigated using the stable isotopes of C, O and S in fracture filling minerals as tracers. Of special interest were the possible changes which may occur in the subsurface at low temperatures. Especially, the influence of microbial activity was recognized as a catalyst for inducing changes in the geochemical environment. The study site is the Olkiluoto island located on the western coast of Finland, planned to host a geological repository for nuclear waste. Fracture surfaces were investigated to recognize the latest mineralizations at the site. These fillings were comprised of thin plates or small euhedral crystals of calcite and pyrite. The carbon and sulfur isotope compositions of calcite and pyrite were measured from bulk material by conventional IRMS, and in situ by secondary ion mass spectrometry. A notable feature of the late-stage fillings was high variabilities in the δ13C values of calcite and the δ34S values of pyrite, which ranged from -53.8 ‰ to +31.6 ‰ and from -50.4 ‰ to +77.7 ‰, respectively. Based on the isotopic compositions of the fillings, several features in the past hydrogeochemical environment could be recognized. The isotopic composition of the fracture fillings indicate an environment which was stratified with respect to depth. Characteristic features include bacterial sulfate reduction (BSR) occurring at depths <111 m (bsl), and a methanogenetic environment at depths >50 m. It appears that methanic conditions were replaced by sulfate reduction at depths >50 m likely due to infiltration of SO42--rich brackish waters. Sulfate reducing bacteria used mainly surface derived organic carbon as electron donors. Some indication of minor methanotrophic activity was recognized in anomalously low δ13C values of calcite, down to -53.8 ‰, at the depth range of 34-54 m. This methanotrophic activity may have been related to bacteria using CH4 as an electron donor in BSR.

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

PubMed

Wang, Gangsheng; Post, Wilfred M

2012-09-01

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

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

PubMed

Zhou, Jizhong; Ning, Daliang

2017-12-01

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)].

PubMed

Dinesh, R; Srinivasan, V; Hamza, S; Manjusha, A

2010-06-01

The study was conducted to determine whether short-term incorporation of organic manures and biofertilizers influence biochemical and microbial variables reflecting soil quality. For the study, soils were collected from a field experiment conducted on turmeric (Curcuma longa L.) involving organic nutrient management (ONM), chemical nutrient management (CNM) and integrated nutrient management (INM). The findings revealed that application of organic manures and biofertilizers (ONM and INM) positively influenced microbial biomass C, N mineralization, soil respiration and enzymes activities. Contrarily, greater metabolic quotient levels in CNM indicated a stressed soil microbial community. Principal component analysis indicated the strong relationship between microbial activity and the availability of labile and easily mineralizable organic matter. The findings imply that even short-term incorporation of organic manures and biofertilizers promoted soil microbial and enzyme activities and these parameters are sensitive enough to detect changes in soil quality due to short-term incorporation of biological fertilizers. (c) 2010 Elsevier Ltd. All rights reserved.

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

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

Elucidating carbon sources driving microbial metabolism during oil sands reclamation.

PubMed

Bradford, Lauren M; Ziolkowski, Lori A; Goad, Corey; Warren, Lesley A; Slater, Gregory F

2017-03-01

Microbial communities play key roles in remediation and reclamation of contaminated environments via biogeochemical cycling of organic and inorganic components. Understanding the trends in in situ microbial community abundance, metabolism and carbon sources is therefore a crucial component of effective site management. The focus of this study was to use radiocarbon analysis to elucidate the carbon sources driving microbial metabolism within the first pilot wetland reclamation project in the Alberta oil sands region where the observation of H 2 S had indicated the occurrence of microbial sulphate reduction. The reclamation project involved construction of a three compartment system consisting of a freshwater wetland on top of a sand cap overlying a composite tailings (CT) deposit. Radiocarbon analysis demonstrated that both dissolved and sediment associated organic carbon associated with the deepest compartments (the CT and sand cap) was primarily fossil (Δ 14 C = -769 to -955‰) while organic carbon in the overlying peat was hundreds to thousands of years old (Δ 14 C = -250 to -350‰). Radiocarbon contents of sediment associated microbial phospholipid fatty acids (PLFA) were consistent with the sediment bulk organic carbon pools (Peat: Δ 14 C PLFA  = -257‰; Sand cap Δ 14 C PLFA  = -805‰) indicating that these microbes were using sediment associated carbon. In contrast, microbial PLFA grown on biofilm units installed in wells within the deepest compartments contained much more modern carbon that the associated bulk carbon pools. This implied that the transfer of relatively more modern carbon was stimulating the microbial community at depth within the system. Correlation between cellular abundance estimates based on PLFA concentrations and the Δ 14 C PLFA indicated that the utilization of this more modern carbon was stimulating the microbial community at depth. These results highlight the importance of understanding the occurrence and potential outcomes of the introduction of relatively bioavailable carbon to mine wastes in order to predict and manage the performance of reclamation strategies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events.

PubMed

Angly, Florent E; Heath, Candice; Morgan, Thomas C; Tonin, Hemerson; Rich, Virginia; Schaffelke, Britta; Bourne, David G; Tyson, Gene W

2016-01-01

The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010-11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

PubMed Central

Heath, Candice; Morgan, Thomas C.; Tonin, Hemerson; Rich, Virginia; Schaffelke, Britta; Bourne, David G.; Tyson, Gene W.

2016-01-01

The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics. PMID:26839738

Versatile microbial surface-display for environmental remediation and biofuels production

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

Wu, Cindy H.; Mulchandani, Ashok; Chen, wilfred

2008-02-14

Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

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

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji-Won

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component comprising at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes duringmore » consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.« less

Chromophoric and fluorescent dissolved organic matter in and above the oxygen minimum zone off Peru

NASA Astrophysics Data System (ADS)

Loginova, A. N.; Thomsen, S.; Engel, A.

2016-11-01

As a result of nutrient upwelling, the Peruvian coastal system is one of the most productive regions in the ocean. Sluggish ventilation of intermediate waters, characteristic for the Eastern Tropical South Pacific (ETSP) and microbial degradation of a high organic matter load promotes deoxygenation at depth. Dissolved organic matter (DOM) plays a key role in microbial respiration and carbon cycling, but little is known on DOM distribution and cycling in the ETSP. DOM optical properties give important insights on DOM sources, structure and biogeochemical reactivity. Here, we present data and a conceptual view on distribution and cycling of chromophoric (CDOM) and fluorescent (FDOM) DOM in and above the oxygen minimum zone (OMZ) off Peru. Five fluorescent components were identified during PARAFAC analysis. Highest intensities of CDOM and of the amino acid-like fluorescent component (C3) occurred above the OMZ and coincided with maximum chl a concentrations, suggesting phytoplankton productivity as major source. High intensities of a marine humic-like fluorescent component (C1), observed in subsurface waters, indicated in situ microbial reworking of DOM. FDOM release from inner shelf sediment was determined by seawater analysis and continuous glider sensor measurement and included a humic-like component (C2) with a signature typical for terrestrially derived humic acids. Upwelling supplied humic-like substances to the euphotic zone. Photo-reactions were likely involved in the production of a humic-like fluorescent component (C5). Our data show that variable biological and physical processes need to be considered for understanding DOM cycling in a highly dynamic coastal upwelling system like the ETSP off Peru.

Galectins as self/non-self recognition receptors in innate and adaptive immunity: an unresolved paradox

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Nita-Lazar, Mihai; Banerjee, Aditi; Pasek, Marta; Shridhar, Surekha; Guha, Prasun; Fernández-Robledo, José A.

2012-01-01

Galectins are characterized by their binding affinity for β-galactosides, a unique binding site sequence motif, and wide taxonomic distribution and structural conservation in vertebrates, invertebrates, protista, and fungi. Since their initial description, galectins were considered to bind endogenous (“self”) glycans and mediate developmental processes and cancer. In the past few years, however, numerous studies have described the diverse effects of galectins on cells involved in both innate and adaptive immune responses, and the mechanistic aspects of their regulatory roles in immune homeostasis. More recently, however, evidence has accumulated to suggest that galectins also bind exogenous (“non-self”) glycans on the surface of potentially pathogenic microbes, parasites, and fungi, suggesting that galectins can function as pattern recognition receptors (PRRs) in innate immunity. Thus, a perplexing paradox arises by the fact that galectins also recognize lactosamine-containing glycans on the host cell surface during developmental processes and regulation of immune responses. According to the currently accepted model for non-self recognition, PRRs recognize pathogens via highly conserved microbial surface molecules of wide distribution such as LPS or peptidoglycan (pathogen-associated molecular patterns; PAMPs), which are absent in the host. Hence, this would not apply to galectins, which apparently bind similar self/non-self molecular patterns on host and microbial cells. This paradox underscores first, an oversimplification in the use of the PRR/PAMP terminology. Second, and most importantly, it reveals significant gaps in our knowledge about the diversity of the host galectin repertoire, and the subcellular targeting, localization, and secretion. Furthermore, our knowledge about the structural and biophysical aspects of their interactions with the host and microbial carbohydrate moieties is fragmentary, and warrants further investigation. PMID:22811679

Stenian Estuarine System and Early Neoproterozoic Microbial Records of Capiru Formation, Southern Ribeira Belt.

NASA Astrophysics Data System (ADS)

Cury, L. F.; Santos, L. D. R.; Leandro, R.; Lange, L.; Bahniuk Rumbelsperger, A.

2017-12-01

The Capiru formation is a low-grade metasedimentary sequence composed by slates, rhythmic phyllites, quartzites and marbles, disposed and disrupted in tectonic blocks delimited by thrust and strike-slip faults related to oblique collisions in the southern Ribeira Belt, Curitiba terrane, southern Brazil. The rocks of the Capiru formation crops out as a thrust-folded belt, delimited on the north by the transcurrent faults of Lancinha Shear Zone (LSZ), and to the south by thrust faults with large isograde variation. Three lithological sequences are recognized mainly by their compositional and stratigraphic records, including a (i) ferruginous sequence with quartzites, metasandstones and metaconglomerates with goethite/hematite cements and phyllites with magnetite; ii) metadolomites with stromatolites, interbeded with pelitic layers and iii) a metapelitic sequence with metarhythmites and metasandstones with well preserved organic-rich material. The records of two tectonic-metamorphic events related to thrust and transpressive tectonics are heterogeneously developed in all sequences, still been recognized sections with the original stratigraphic succession. The stratigraphic record suggests an estuarine environment with rising sea level developing tidal flats and tidal channels. U-Pb detrital zircon analyses characterizes Rhyacian ages (between 2.2-2.1 Ga) as the main sources, and Stenian ages (between 1.08-1.20 Ga) as maximum age for sedimentation. The metapelites mineral assemblage is composed by quartz, muscovite, sericite, illite, kaolinite, sepiolite, magnetite, goethite, hematite and carbonaceous material with bulk organic carbon content (BOC) ranging from 0.09 to 1.21 (%), a precambrian microbial activity record. The metadolomites are characterized by the presence of stromatolites in different types and dimensions, with microbial activity records supported by SEM-EDS (up to 91% C), with EPS-like morphologies within microporosity, NaCl compounds and clay minerals, probably indicative of microorganism contribution during the deposition.

The MICROBE Project, A Report from the Interagency Working Group on Microbial Genomics

DTIC Science & Technology

2001-01-01

including targeting of genes related to pathogenesis, possibilities for acquired pathogen resistance, industrial and food -grade enzymes, and probiotics ...safety, food security, biotechnology, value-added products , human nutrition and functional foods , plant and animal protection and furthering fundamental...supports a number of microbial studies, which are integral components of the USDA national programs in animal health, food animal production , food

Enzyme Amplified Detection of Microbial Cell Wall Components

NASA Technical Reports Server (NTRS)

Wainwright, Norman R.

2004-01-01

This proposal is MBL's portion of NASA's Johnson Space Center's Astrobiology Center led by Principal Investigator, Dr. David McKay, entitled: 'Institute for the Study of Biomarkers in Astromaterials.' Dr. Norman Wainwright is the principal investigator at MBL and is responsible for developing methods to detect trace quantities of microbial cell wall chemicals using the enzyme amplification system of Limulus polyphemus and other related methods.

Borrelia burgdorferi protein interactions critical for microbial persistence in mammals.

PubMed

Bernard, Quentin; Thakur, Meghna; Smith, Alexis A; Kitsou, Chrysoula; Yang, Xiuli; Pal, Utpal

2018-06-22

Borrelia burgdorferi is the causative agent of Lyme disease that persists in a complex enzootic life cycle, involving Ixodes ticks and vertebrate hosts. The microbe invades ticks and vertebrate hosts in spite of active immune surveillance and potent microbicidal responses, and establishes long-term infection utilizing mechanisms that are yet to be unraveled. The pathogen can cause multi-system disorders when transmitted to susceptible mammalian hosts, including in humans. In the past decades, several studies identified a limited number of B. burgdorferi gene-products critical for pathogen persistence, transmission between the vectors and the host, and host-pathogen interactions. This review will focus on the interactions between B. burgdorferi proteins, as well between microbial proteins and host components, protein and non-protein components, highlighting their roles in pathogen persistence in the mammalian host. A better understanding of the contributions of protein interactions in the microbial virulence and persistence of B. burgdorferi would support development of novel therapeutics against the infection. This article is protected by copyright. All rights reserved.

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

Yerington Paiute Tribe Energy Plan Version 1

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

Consulting, BB9; Director, Environmental

The Yerington Paiute Tribe has made energy management and planning a priority. The Tribal Council has recognized that energy is an important component of their goal of self-sufficiency. Recognizing energy development as a component of the Tribe’s natural resources provides for needed economic development.A number of priorities have been identified for energy development. These range from immediate housing needs such as weatherization and solar to interest in energy as economic development.

Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

PubMed

Tepper, Naama; Shlomi, Tomer

2011-01-21

Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).

Are variations in heterotrophic soil respiration related to changes in substrate availability and microbial biomass carbon in the subtropical forests?

PubMed

Wei, Hui; Chen, Xiaomei; Xiao, Guoliang; Guenet, Bertrand; Vicca, Sara; Shen, Weijun

2015-12-16

Soil temperature and moisture are widely-recognized controlling factors on heterotrophic soil respiration (Rh), although they often explain only a portion of Rh variability. How other soil physicochemical and microbial properties may contribute to Rh variability has been less studied. We conducted field measurements on Rh half-monthly and associated soil properties monthly for two years in four subtropical forests of southern China to assess influences of carbon availability and microbial properties on Rh. Rh in coniferous forest was significantly lower than that in the other three broadleaf species-dominated forests and exhibited obvious seasonal variations in the four forests (P < 0.05). Temperature was the primary factor influencing the seasonal variability of Rh while moisture was not in these humid subtropical forests. The quantity and decomposability of dissolved organic carbon (DOC) were significantly important to Rh variations, but the effect of DOC content on Rh was confounded with temperature, as revealed by partial mantel test. Microbial biomass carbon (MBC) was significantly related to Rh variations across forests during the warm season (P = 0.043). Our results suggest that DOC and MBC may be important when predicting Rh under some conditions, and highlight the complexity by mutual effects of them with environmental factors on Rh variations.

The Microbial Resource Research Infrastructure MIRRI: Strength through Coordination

PubMed Central

Stackebrandt, Erko; Schüngel, Manuela; Martin, Dunja; Smith, David

2015-01-01

Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain biological resource centres (mBRC) provide live cultures and associated data to foster and support the development of basic and applied science in countries worldwide and especially in Europe, where the density of highly advanced mBRCs is high. The not-for-profit and distributed project MIRRI (Microbial Resource Research Infrastructure) aims to coordinate access to hitherto individually managed resources by developing a pan-European platform which takes the interoperability and accessibility of resources and data to a higher level. Providing a wealth of additional information and linking to datasets such as literature, environmental data, sequences and chemistry will enable researchers to select organisms suitable for their research and enable innovative solutions to be developed. The current independent policies and managed processes will be adapted by partner mBRCs to harmonize holdings, services, training, and accession policy and to share expertise. The infrastructure will improve access to enhanced quality microorganisms in an appropriate legal framework and to resource-associated data in a more interoperable way. PMID:27682123

The Microbial Resource Research Infrastructure MIRRI: Strength through Coordination.

PubMed

Stackebrandt, Erko; Schüngel, Manuela; Martin, Dunja; Smith, David

2015-11-18

Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain biological resource centres (mBRC) provide live cultures and associated data to foster and support the development of basic and applied science in countries worldwide and especially in Europe, where the density of highly advanced mBRCs is high. The not-for-profit and distributed project MIRRI (Microbial Resource Research Infrastructure) aims to coordinate access to hitherto individually managed resources by developing a pan-European platform which takes the interoperability and accessibility of resources and data to a higher level. Providing a wealth of additional information and linking to datasets such as literature, environmental data, sequences and chemistry will enable researchers to select organisms suitable for their research and enable innovative solutions to be developed. The current independent policies and managed processes will be adapted by partner mBRCs to harmonize holdings, services, training, and accession policy and to share expertise. The infrastructure will improve access to enhanced quality microorganisms in an appropriate legal framework and to resource-associated data in a more interoperable way.

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

PubMed

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

2017-01-01

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

Microbial transformation of elements: the case of arsenic and selenium

USGS Publications Warehouse

Stolz, J.; Basu, P.; Oremland, R.

2002-01-01

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.

Microbial transformation of elements: the case of arsenic and selenium.

PubMed

Stolz, J F; Basu, P; Oremland, R S

2002-12-01

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.

Multi-technique approach to assess the effects of microbial biofilms involved in copper plumbing corrosion.

PubMed

Vargas, Ignacio T; Alsina, Marco A; Pavissich, Juan P; Jeria, Gustavo A; Pastén, Pablo A; Walczak, Magdalena; Pizarro, Gonzalo E

2014-06-01

Microbially influenced corrosion (MIC) is recognized as an unusual and severe type of corrosion that causes costly failures around the world. A microbial biofilm could enhance the copper release from copper plumbing into the water by forming a reactive interface. The biofilm increases the corrosion rate, the mobility of labile copper from its matrix and the detachment of particles enriched with copper under variable shear stress due to flow conditions. MIC is currently considered as a series of interdependent processes occurring at the metal-liquid interface. The presence of a biofilm results in the following effects: (a) the formation of localized microenvironments with distinct pH, dissolved oxygen concentrations, and redox conditions; (b) sorption and desorption of labile copper bonded to organic compounds under changing water chemistry conditions; (c) change in morphology by deposition of solid corrosion by-products; (d) diffusive transport of reactive chemical species from or towards the metal surface; and (e) detachment of scale particles under flow conditions. Using a multi-technique approach that combines pipe and coupon experiments this paper reviews the effects of microbial biofilms on the corrosion of copper plumbing systems, and proposes an integrated conceptual model for this phenomenon supported by new experimental data. Copyright © 2013 Elsevier B.V. All rights reserved.

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

PubMed Central

2013-01-01

Background Understanding the biological mechanisms used by microorganisms for plant biomass degradation is of considerable biotechnological interest. Despite of the growing number of sequenced (meta)genomes of plant biomass-degrading microbes, there is currently no technique for the systematic determination of the genomic components of this process from these data. Results We describe a computational method for the discovery of the protein domains and CAZy families involved in microbial plant biomass degradation. Our method furthermore accurately predicts the capability to degrade plant biomass for microbial species from their genome sequences. Application to a large, manually curated data set of microbial degraders and non-degraders identified gene families of enzymes known by physiological and biochemical tests to be implicated in cellulose degradation, such as GH5 and GH6. Additionally, genes of enzymes that degrade other plant polysaccharides, such as hemicellulose, pectins and oligosaccharides, were found, as well as gene families which have not previously been related to the process. For draft genomes reconstructed from a cow rumen metagenome our method predicted Bacteroidetes-affiliated species and a relative to a known plant biomass degrader to be plant biomass degraders. This was supported by the presence of genes encoding enzymatically active glycoside hydrolases in these genomes. Conclusions Our results show the potential of the method for generating novel insights into microbial plant biomass degradation from (meta-)genome data, where there is an increasing production of genome assemblages for uncultured microbes. PMID:23414703

Chemical Structure and Molecular Dimension As Controls on the Inherent Stability of Charcoal in Boreal Forest Soil

NASA Astrophysics Data System (ADS)

Hockaday, W. C.; Kane, E. S.; Ohlson, M.; Huang, R.; Von Bargen, J.; Davis, R.

2014-12-01

Efforts have been made by various scientific disciplines to study hyporheic zones and characterize their associated processes. One way to approach the study of the hyporheic zone is to define facies, which are elements of a (hydrobio) geologic classification scheme that groups components of a complex system with high variability into a manageable set of discrete classes. In this study, we try to classify the hyporheic zone based on the geology, geochemistry, microbiology, and understand their interactive influences on the integrated biogeochemical distributions and processes. A number of measurements have been taken for 21 freeze core samples along the Columbia River bank in the Hanford 300 Area, and unique datasets have been obtained on biomass, pH, number of microbial taxa, percentage of N/C/H/S, microbial activity parameters, as well as microbial community attributes/modules. In order to gain a complete understanding of the geological control on these variables and processes, the explanatory variables are set to include quantitative gravel/sand/mud/silt/clay percentages, statistical moments of grain size distributions, as well as geological (e.g., Folk-Wentworth) and statistical (e.g., hierarchical) clusters. The dominant factors for major microbial and geochemical variables are identified and summarized using exploratory data analysis approaches (e.g., principal component analysis, hierarchical clustering, factor analysis, multivariate analysis of variance). The feasibility of extending the facies definition and its control of microbial and geochemical properties to larger scales is discussed.

Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying.

PubMed

Zhang, Junya; Cai, Xing; Qi, Lu; Shao, Chunyan; Lin, Yang; Zhang, Jin; Zhang, Yuanli; Shen, Peihong; Wei, Yuansong

2015-09-01

Sludge bio-drying in which sludge is dried by means of the heat generated by the aerobic degradation of its own organic substances has been widely used for sludge treatment. A better understanding of the evolution of dissolved organic matter (DOM) and its degradation drivers during sludge bio-drying could facilitate its control. Aeration is one of the key factors that affect sludge bio-drying performance. In this study, two aeration strategies (pile I-the optimized and pile II-the current) were established to investigate their impacts on the evolution of DOM and the microbial community in a full-scale sludge bio-drying plant. A higher pile temperature in pile I caused pile I to enter the DOM and microbiology stable stage approximately2 days earlier than pile II. The degradation of easily degradable components in the DOM primarily occurred in the thermophilic phase; after that degradation, the DOM components changed a little. Along with the evolution of the DOM, its main degradation driver, the microbial community, changed considerably. Phyla Firmicutes and Proteobacteria were dominant in the thermophilic stage, and genus Ureibacillus, which was the primary thermophilic bacteria, was closely associated with the degradation of the DOM. In the mesophilic stage, the microbial community changed significantly at first and subsequently stabilized, and the genus Parapedobacter, which belongs to Bacteriodetes, became dominant. This study elucidates the interplay between the DOM and microbial community during sludge bio-drying.

Molecular and Imaging Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

NASA Astrophysics Data System (ADS)

Dohnalkova, A.; Tfaily, M.; Smith, A. P.; Chu, R. K.; Crump, A.; Brislawn, C.; Varga, T.; Shi, Z.; Thomashow, L. S.; Harsh, J. B.; Balogh-Brunstad, Z.; Keller, C. K.

2017-12-01

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is limited. The objective of this study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix. We hypothesized that nutrient limitation would cause formation of microbially-produced C constituents that would contribute to SOM stabilization. We focused on the processes of rhizodeposition in the rhizosphere, and we utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of the microbial community and the newly-formed SOM compounds in the rhizosphere and the bulk soil. We considered implications regarding their degree of long-term stability. The microbes in this controlled, nutrient-limited system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. These findings provide insight into the various degrees of stability of microbial SOM products in ecosystems and evidence that the residual biogenic material associated with mineral matrices may be important components in current carbon cycle models.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

PubMed

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

2012-03-24

Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

PubMed Central

2012-01-01

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. PMID:22443485

Planktonic trophic structure in a coral reef ecosystem - Grazing versus microbial food webs and the production of mesozooplankton

NASA Astrophysics Data System (ADS)

Nakajima, Ryota; Yamazaki, Haruka; Lewis, Levi S.; Khen, Adi; Smith, Jennifer E.; Nakatomi, Nobuyuki; Kurihara, Haruko

2017-08-01

The relative contributions of grazing versus microbial food webs to the production of mesozooplankton communities in coral reef ecosystems remains an important and understudied field of inquiry. Here, we investigated the biomass and production of component organisms within these two food webs, and compared them to those of mesozooplankton on a coral reef in Okinawa, Japan throughout four seasons in 2011-2012. The relative production of grazing (phytoplankton) and microbial (nano and microzooplankton) food webs were on average 39% (7-77%) and 37% (19-57%), respectively, of the food requirements of particle-feeding mesozooplankton. Carbon flows within this planktonic food web suggested that primary production from the grazing food web could not satisfy the nutritional demands of mesozooplankton, and that the microbial food web contributed a significant amount of nutrition to their diets. These results also show that the heterotrophic components of the microbial food web (nano and microzooplankton) and mesozooplankton consume the equivalent of the entire phytoplankton production (particulate net production) each day, while the microzooplankton were almost entirely eaten by higher trophic levels (mesozooplankton) each day. However, even the combined production from both the grazing and microbial food webs did not fulfill mesozooplankton food requirements in some seasons, explaining 26-53%, suggesting that detritus was used to compensate for nutritional deficiencies during these periods. Understanding the flow of energy throughout coral reefs requires a detailed accounting of pelagic sources and sinks of carbon. Our results provide such an assessment and indicate that detailed investigation on the origin and production of detritus is necessary to better understand pelagic trophodynamics in coral ecosystems.

Can Phlorotannins Purified Extracts Constitute a Novel Pharmacological Alternative for Microbial Infections with Associated Inflammatory Conditions?

PubMed Central

Lopes, Graciliana; Sousa, Carla; Silva, Luís R.; Pinto, Eugénia; Andrade, Paula B.; Bernardo, João; Mouga, Teresa; Valentão, Patrícia

2012-01-01

Bacterial and fungal infections and the emerging multidrug resistance are driving interest in fighting these microorganisms with natural products, which have generally been considered complementary to pharmacological therapies. Phlorotannins are polyphenols restricted to brown seaweeds, recognized for their biological capacity. This study represents the first research on the antibacterial, antifungal, anti-inflammatory and antioxidant activity of phlorotannins purified extracts, which were obtained from ten dominant brown seaweeds of the occidental Portuguese coast. Phlorotannins content was determined by the specific dimethoxybenzaldehyde (DMBA) method and a yield between 75 and 969 mg/Kg phloroglucinol units (dry matter) was obtained. Fucus spiralis ranked first, followed by three Cystoseira species. The anti-inflammatory potential of the purified extracts was assessed via inhibitory effect on nitric oxide (NO) production by lipopolysaccharide-stimulated RAW 264.7 macrophage cells, Cystoseira tamariscifolia being the one showing promising activity for the treatment of inflammation. NO scavenging ability was also addressed in cell free systems, F. spiralis being the species with highest capacity. The antimicrobial potential of the extracts was checked against five Gram-positive and four Gram-negative bacteria and three fungi strains, that commonly colonize skin and mucosa and are responsible for food contamination. The different extracts were more effective against Gram-positive bacteria, Staphylococcus epidermidis being the most susceptible species. Concerning antifungal activity, Trichophyton rubrum was the most sensitive species. Although the molecular mechanisms underlying these properties remain poorly understood, the results obtained turn phlorotannins purified extracts a novel and potent pharmacological alternative for the treatment of a wide range of microbial infections, which usually also present an inflammatory component. In addition to the biological properties demonstrated herein, phlorotannins extracts may also be preferred, in order to avoid side effects and allergic reactions commonly associated with synthetic drugs. PMID:22319609

Anthropogenic Carbon Pump in an Urbanized Estuary

NASA Astrophysics Data System (ADS)

Park, J. H.; Yoon, T. K.; Jin, H.; Begum, M. S.

2015-12-01

The importance of estuaries as a carbon source has been increasingly recognized over the recent decades. However, constraining sources of CO2 evasion from urbanized estuaries remains incomplete, particularly in densely populated river systems receiving high loads of organic carbon from anthropogenic sources. To account for major factors regulating carbon fluxes the tidal reach of the Han River estuary along the metropolitan Seoul, characterization of organic carbon in the main stem and major urban tributaries were combined with continuous, submersible sensor measurements of pCO2 at a mid-channel location over a year and continuous underway measurements using a submersible sensor and two equilibrator sytems across the estuarine section receiving urban streams. Single-site continuous measurements exhibited large seasonal and diurnal variations in pCO2, ranging from sub-ambient air levels to exceptionally high values approaching 10,000 ppm. Diurnal variations of pCO2 were pronounced in summer and had an inverse relationship with dissolved oxygen, pointing to a potential role of day-time algal consumption of CO2. Cruise measurements displayed sharp pCO2 pulses along the confluences of urban streams as compared with relatively low values along the upper estuary receiving low-CO2 outflows from upstream dams. Large downstream increases in pCO2, concurrent with increases in DOC concentrations and fluorescence intensities indicative of microbially processed organic components, imply a translocation and subsequent dilution of CO2 carried by urban streams and/or fast transformations of labile C during transit along downstream reaches. The unique combination of spatial and temporal continuous measurements of pCO2 provide insights on estuarine CO2 pulses that might have resulted from the interplay between high loads of CO2 and organic C of anthropogenic origin and their priming effects on estuarine microbial processing of terrigenous and algal organic matter.

Microbial Efflux Pump Inhibition: Tactics and Strategies

PubMed Central

Tegos, George P.; Haynes, Mark; Strouse, J. Jacob; Khan, Mohiuddin Md. T.; Bologa, Cristian G.; Oprea, Tudor I.; Sklar, Larry A.

2013-01-01

Traditional antimicrobials are increasingly suffering from the emergence of multidrug resistance among pathogenic microorganisms. To overcome these deficiencies, a range of novel approaches to control microbial infections are under investigation as potential alternative treatments. Multidrug efflux is a key target of these efforts. Efflux mechanisms are broadly recognized as major components of resistance to many classes of chemotherapeutic agents as well as antimicrobials. Efflux occurs due to the activity of membrane transporter proteins widely known as Multidrug Efflux Systems (MES). They are implicated in a variety of physiological roles other than efflux and identifying natural substrates and inhibitors is an active and expanding research discipline. One plausible alternative is the combination of conventional antimicrobial agents/antibiotics with small molecules that block MES known as multidrug efflux pump inhibitors (EPIs). An array of approaches in academic and industrial research settings, varying from high-throughput screening (HTS) ventures to bioassay guided purification and determination, have yielded a number of promising EPIs in a series of pathogenic systems. This synergistic discovery platform has been exploited in translational directions beyond the potentiation of conventional antimicrobial treatments. This venture attempts to highlight different tactical elements of this platform, identifying the need for highly informative and comprehensive EPI-discovery strategies. Advances in assay development genomics, proteomics as well as the accumulation of bioactivity and structural information regarding MES facilitates the basis for a new discovery era. This platform is expanding drastically. A combination of chemogenomics and chemoinformatics approaches will integrate data mining with virtual and physical HTS ventures and populate the chemical-biological interface with a plethora of novel chemotypes. This comprehensive step will expedite the preclinical development of lead EPIs. PMID:21470111

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

NASA Astrophysics Data System (ADS)

Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

2013-07-01

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations) was nearly constant (250 μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (⩾38 μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of ΣNH3, NO2- and NO3- of the stream water. The δ15N value of ΣNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial ΣNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of ΣNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of ΣNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

TBK1-targeted suppression of TRIF-dependent signaling pathway of Toll-like receptors by 6-shogaol, an active component of ginger.

PubMed

Park, Se-Jeong; Lee, Mi-Young; Son, Bu-Soon; Youn, Hyung-Sun

2009-07-01

Toll-like receptors (TLRs) are primary sensors that detect a wide variety of microbial components involving induction of innate immune responses. After recognition of microbial components, TLRs trigger the activation of myeloid differential factor 88 (MyD88) and Toll-interleukin-1 (IL-1) receptor domain-containing adapter inducing interferon-beta (TRIF)-dependent downstream signaling pathways. 6-Shoagol, an active ingredient of ginger, inhibits the MyD88-dependent signaling pathway by inhibiting inhibitor-kappaB kinase activity. Inhibitor-kappaB kinase is a key kinase in nuclear factor kappaB (NF-kappaB) activation. However, it is not known whether 6-shogaol inhibits the TRIF-dependent signaling pathway. Our goal was to identify the molecular target of 6-shogaol in the TRIF-dependent pathway of TLRs. 6-Shogaol inhibited the activation of interferon-regulatory factor 3 (IRF3) induced by lipopolysaccharide (LPS) and by polyriboinosinic polyribocytidylic acid (poly[I:C]), overexpression of TRIF, TANK-binding kinase1 (TBK1), and IRF3. Furthermore, 6-shogaol inhibited TBK1 activity in vitro. Together, these results suggest that 6-shogaol inhibits the TRIF-dependent signaling pathway of TLRs by targeting TBK1, and, they imply that 6-shogaol can modulate TLR-derived immune/inflammatory target gene expression induced by microbial infection.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Review of Concrete Biodeterioration in Relation to Buried Nuclear Waste

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

Turick, C; Berry, C.

Long-term storage of low level radioactive material in below ground concrete disposal units (DUs) (Saltstone Disposal Facility) is a means of depositing wastes generated from nuclear operations of the U.S. Department of Energy. Based on the currently modeled degradation mechanisms, possible microbial induced effects on the structural integrity of buried low level wastes must be addressed. Previous international efforts related to microbial impacts on concrete structures that house low level radioactive waste showed that microbial activity can play a significant role in the process of concrete degradation and ultimately structural deterioration. This literature review examines the recent research in thismore » field and is focused on specific parameters that are applicable to modeling and prediction of the fate of concrete vaults housing stored wastes and the wastes themselves. Rates of concrete biodegradation vary with the environmental conditions, illustrating a need to understand the bioavailability of key compounds involved in microbial activity. Specific parameters require pH and osmotic pressure to be within a certain range to allow for microbial growth as well as the availability and abundance of energy sources like components involved in sulfur, iron and nitrogen oxidation. Carbon flow and availability are also factors to consider in predicting concrete biodegradation. The results of this review suggest that microbial activity in Saltstone, (grouted low level radioactive waste) is unlikely due to very high pH and osmotic pressure. Biodegradation of the concrete vaults housing the radioactive waste however, is a possibility. The rate and degree of concrete biodegradation is dependent on numerous physical, chemical and biological parameters. Results from this review point to parameters to focus on for modeling activities and also, possible options for mitigation that would minimize concrete biodegradation. In addition, key chemical components that drive microbial activity on concrete surfaces are discussed.« less

Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition

PubMed Central

Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

2015-01-01

The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m−2 yr−1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m−2 yr−1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m−2 yr−1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration. PMID:26678303

Using fluorescence spectroscopy coupled with chemometric analysis to investigate the origin, composition, and dynamics of dissolved organic matter in leachate-polluted groundwater.

PubMed

He, Xiao-Song; Xi, Bei-Dou; Gao, Ru-Tai; Wang, Lei; Ma, Yan; Cui, Dong-Yu; Tan, Wen-Bing

2015-06-01

Groundwater was collected in 2011 and 2012, and fluorescence spectroscopy coupled with chemometric analysis was employed to investigate the composition, origin, and dynamics of dissolved organic matter (DOM) in the groundwater. The results showed that the groundwater DOM comprised protein-, fulvic-, and humic-like substances, and the protein-like component originated predominantly from microbial production. The groundwater pollution by landfill leachate enhanced microbial activity and thereby increased microbial by-product-like material such as protein-like component in the groundwater. Excitation-emission matrix fluorescence spectra combined with parallel factor analysis showed that the protein-like matter content increased from 2011 to 2012 in the groundwater, whereas the fulvic- and humic-like matter concentration exhibited no significant changes. In addition, synchronous-scan fluorescence spectra coupled with two-dimensional correlation analysis showed that the change of the fulvic- and humic-like matter was faster than that of the protein-like substances, as the groundwater flowed from upstream to downstream in 2011, but slower than that of the protein-like substance in 2012 due to the enhancement of microbial activity. Fluorescence spectroscopy combined with chemometric analysis can investigate groundwater pollution characteristics and monitor DOM dynamics in groundwater.

Synergism between Trichuris suis and the microbial flora of the large intestine causing dysentery in pigs.

PubMed

Rutter, J M; Beer, R J

1975-02-01

The role of the microbial flora of the large intestine in experimental Trichuris suis infection was studied by comparing the clinical syndrome in conventionally reared (CR) pigs, specific pathogen-free pigs, and gnotobiotic pigs. Thedisease in CR pigs was characterized by a severe mucohemorrhagic enteritis; in contrast, a mild catarrhal enteritis was observed in specific pathogen-free and gnotobiotic pigs. Spirochaetes and vibrio-like organisms were observed only in CR pigs and increased during the clinical phase of the disease. The clinical syndrome was not transmitted by oral administration of intestinal or fecal material from infected CR pigs to CR pigs free of T. suis. Smaller numbers of T. suis produced diarrhea in CR pigs and significantly reduced the growth rates of infected animals; clinical signs and the reduction in growth rate was prevented by incorporating an antibacterial substance (dimetridazole) in the food. Although clinical trichuriasis closely resembles swin dysentery, the two syndromes seem to be distinct. The present results suggest that a microbial component acts synergistically with T. suis to produce the severe clinical syndrome in CR pigs, but identification of the microbial component and the mechanism by which clinical signs are produced await further studies of the bacterial flora of the large intestine of pigs.

Recognition of bacterial plant pathogens: local, systemic and transgenerational immunity.

PubMed

Henry, Elizabeth; Yadeta, Koste A; Coaker, Gitta

2013-09-01

Bacterial pathogens can cause multiple plant diseases and plants rely on their innate immune system to recognize and actively respond to these microbes. The plant innate immune system comprises extracellular pattern recognition receptors that recognize conserved microbial patterns and intracellular nucleotide binding leucine-rich repeat (NLR) proteins that recognize specific bacterial effectors delivered into host cells. Plants lack the adaptive immune branch present in animals, but still afford flexibility to pathogen attack through systemic and transgenerational resistance. Here, we focus on current research in plant immune responses against bacterial pathogens. Recent studies shed light onto the activation and inactivation of pattern recognition receptors and systemic acquired resistance. New research has also uncovered additional layers of complexity surrounding NLR immune receptor activation, cooperation and sub-cellular localizations. Taken together, these recent advances bring us closer to understanding the web of molecular interactions responsible for coordinating defense responses and ultimately resistance. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Human NOD2 Recognizes Structurally Unique Muramyl Dipeptides from Mycobacterium leprae

PubMed Central

Schenk, Mirjam; Mahapatra, Sebabrata; Le, Phuonganh; Kim, Hee Jin; Choi, Aaron W.; Brennan, Patrick J.; Belisle, John T.

2016-01-01

The innate immune system recognizes microbial pathogens via pattern recognition receptors. One such receptor, NOD2, via recognition of muramyl dipeptide (MDP), triggers a distinct network of innate immune responses, including the production of interleukin-32 (IL-32), which leads to the differentiation of monocytes into dendritic cells (DC). NOD2 has been implicated in the pathogenesis of human leprosy, yet it is not clear whether Mycobacterium leprae, which has a distinct MDP structure, can activate this pathway. We investigated the effect of MDP structure on the innate immune response, finding that infection of monocytes with M. leprae induces IL-32 and DC differentiation in a NOD2-dependent manner. The presence of the proximal l-Ala instead of Gly in the common configuration of the peptide side chain of M. leprae did not affect recognition by NOD2 or cytokine production. Furthermore, amidation of the d-Glu residue did not alter NOD2 activation. These data provide experimental evidence that NOD2 recognizes naturally occurring structural variants of MDP. PMID:27297389

Microbiota-host interplay at the gut epithelial level, health and nutrition.

PubMed

Lallès, Jean-Paul

2016-01-01

Growing evidence suggests the implication of the gut microbiota in various facets of health and disease. In this review, the focus is put on microbiota-host molecular cross-talk at the gut epithelial level with special emphasis on two defense systems: intestinal alkaline phosphatase (IAP) and inducible heat shock proteins (iHSPs). Both IAP and iHSPs are induced by various microbial structural components (e.g. lipopolysaccharide, flagellin, CpG DNA motifs), metabolites (e.g. n-butyrate) or secreted signal molecules (e.g., toxins, various peptides, polyphosphate). IAP is produced in the small intestine and secreted into the lumen and in the interior milieu. It detoxifies microbial components by dephosphorylation and, therefore, down-regulates microbe-induced inflammation mainly by inhibiting NF-κB pro-inflammatory pathway in enterocytes. IAP gene expression and enzyme activity are influenced by the gut microbiota. Conversely, IAP controls gut microbiota composition both directly, and indirectly though the detoxification of pro-inflammatory free luminal adenosine triphosphate and inflammation inhibition. Inducible HSPs are expressed by gut epithelial cells in proportion to the microbial load along the gastro-intestinal tract. They are also induced by various microbial components, metabolites and secreted molecules. Whether iHSPs contribute to shape the gut microbiota is presently unknown. Both systems display strong anti-inflammatory and anti-oxidant properties that are protective to the gut and the host. Importantly, epithelial gene expressions and protein concentrations of IAP and iHSPs can be stimulated by probiotics, prebiotics and a large variety of dietary components, including macronutrients (protein and amino acids, especially L-glutamine, fat, fiber), and specific minerals (e.g. calcium) and vitamins (e.g. vitamins K1 and K2). Some food components (e.g. lectins, soybean proteins, various polyphenols) may inhibit or disturb these systems. The general cellular and molecular mechanisms involved in the microbiota-host epithelial crosstalk and subsequent gut protection through IAP and iHSPs are reviewed along with their nutritional modulation. Special emphasis is also given to the pig, an economically important species and valuable biomedical model.

MODELING MICROBIAL TRANSPORT IN SOIL AND GROUNDWATER: MICROBIOLOGISTS CAN ASSIST IN THE DEVELOPMENT OF MODELS OF CONTAMINANT TRANSPORT

EPA Science Inventory

A large body of literature describes the processes affecting the fate of microorganisms in the subsurface environment (i.e., soil and groundwater). The fate of microorganisms depends on two main components: survival and transport. other components must be considered when determin...

Microbiome involved in microbial electrochemical systems (MESs): A review.

PubMed

Saratale, Rijuta Ganesh; Saratale, Ganesh Dattatraya; Pugazhendhi, Arivalagan; Zhen, Guangyin; Kumar, Gopalakrishnan; Kadier, Abudukeremu; Sivagurunathan, Periyasamy

2017-06-01

Microbial electrochemical systems (MESs) are an attracting technology for the disposal of wastewater treatment and simultaneous energy production. In MESs, at the anode microorganisms through the catalytic activity generates electrons that can be converted into electricity or other valuable chemical compounds. Microorganisms those having ability to donate and accept electrons to and from anode and cathode electrodes, respectively are recognized as 'exoelectrogens'. In the MESs, it renders an important function for its performance. In the present mini-review, we have discussed the role of microbiome including pure culture, enriched culture and mixed culture in different BESs application. The effects of operational and biological factors on microbiome development have been discussed. Further discussion about the molecular techniques for the evaluation of microbial community analysis is addressed. In addition different electrochemical techniques for extracellular electron transfer (EET) mechanism of electroactive biofilms have been discussed. This review highlights the importance of microbiome in the development of MESs, effective operational factors for exo-electrogens activities as well their key challenges and future technological aspects are also briefly discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Textural and Carbon Isotopic Analyses of Modern Carbonate Microbialites: Possible Ancient and Martian Analogs

NASA Technical Reports Server (NTRS)

Thompson, Joel B.

1998-01-01

Many modem and ancient carbonate deposits around the world have been recognized as microbial buildups or microbialites. Ancient microbialite structures have been divided into two basic categories based on their internal fabric or texture. They include stromatolites which have a predominantly laminated internal fabric and thrombolites which have an open-porous clotted fabric, that lacks laminae. The origin of these two basic microbial fabrics is still being debated in the literature. Understanding the origin and the various microorganisms involved in forming these modem fabrics is the key to the interpretation of similar fabrics in ancient and possibly Martian rocks. Therefore, detailed studies are needed on the microbiological makeup and origin of the fabrics in modem microbialites. Such studies may serve as analogs for ancient and Martian microbialites in the future. The purpose of this study is to examine the textures and carbon isotopic signatures of the following modem microbialites from the Bahamas: 1) a modem subtidal microbialite from Iguana Cay, Bahamas and 2) a modem microbial mat (stromatolite) from a hypersaline pond on Lee Stocking Island, Bahamas.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

PubMed Central

Roux, Simon; Hallam, Steven J; Woyke, Tanja; Sullivan, Matthew B

2015-01-01

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI: http://dx.doi.org/10.7554/eLife.08490.001 PMID:26200428

Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss)

USGS Publications Warehouse

Palti, Y.; Rodriguez, M.F.; Gahr, S.A.; Purcell, M.K.; Rexroad, C. E.; Wiens, G.D.

2010-01-01

Induction of innate immune pathways is critical for early anti-microbial defense but there is limited understanding of how teleosts recognize microbial molecules and activate these pathways. In mammals, Toll-like receptors (TLR) 1 and 2 form a heterodimer involved in recognizing peptidoglycans and lipoproteins of microbial origin. Herein, we identify and describe the rainbow trout (Oncorhynchus mykiss) TLR1 gene ortholog and its mRNA expression. Two TLR1 loci were identified from a rainbow trout bacterial artificial chromosome (BAC) library using DNA sequencing and genetic linkage analyses. Full length cDNA clone and direct sequencing of four BACs revealed an intact omTLR1 open reading frame (ORF) located on chromosome 14 and a second locus on chromosome 25 that contains a TLR1 pseudogene. The duplicated trout loci exhibit conserved synteny with other fish genomes that extends beyond the TLR1 gene sequences. The omTLR1 gene includes a single large coding exon similar to all other described TLR1 genes, but unlike other teleosts it also has a 5??? UTR exon and intron preceding the large coding exon. The omTLR1 ORF is predicted to encode an 808 amino-acid protein with 69% similarity to the Fugu TLR1 and a conserved pattern of predicted leucine-rich repeats (LRR). Phylogenetic analysis grouped omTLR1 with other fish TLR1 genes on a separate branch from the avian TLR1 and mammalian TLR1, 6 and 10. omTLR1 expression levels in rainbow trout anterior kidney leukocytes were not affected by the human TLR2/6 and TLR2/1 agonists diacylated lipoprotein (Pam2CSK4) and triacylated lipoprotein (Pam3CSK4). However, due to the lack of TLR6 and 10 genes in teleost genomes and up-regulation of TLR1 mRNA in response to LPS and bacterial infection in other fish species we hypothesize an important role for omTLR1 in anti-microbial immunity. Therefore, the identification of a TLR2 ortholog in rainbow trout and the development of assays to measure ligand binding and downstream signaling are critical for future elucidation of omTLR1 functions.

Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss)

USGS Publications Warehouse

Palti, Yniv; Rodriguez, M. Fernanda; Gahr, Scott A.; Purcell, Maureen K.; Rexroad, Caird E.; Wiens, Gregory D.

2010-01-01

Induction of innate immune pathways is critical for early anti-microbial defense but there is limited understanding of how teleosts recognize microbial molecules and activate these pathways. In mammals, Toll-like receptors (TLR) 1 and 2 form a heterodimer involved in recognizing peptidoglycans and lipoproteins of microbial origin. Herein, we identify and describe the rainbow trout (Oncorhynchus mykiss) TLR1 gene ortholog and its mRNA expression. Two TLR1 loci were identified from a rainbow trout bacterial artificial chromosome (BAC) library using DNA sequencing and genetic linkage analyses. Full length cDNA clone and direct sequencing of four BACs revealed an intact omTLR1 open reading frame (ORF) located on chromosome 14 and a second locus on chromosome 25 that contains a TLR1 pseudogene. The duplicated trout loci exhibit conserved synteny with other fish genomes that extends beyond the TLR1 gene sequences. The omTLR1 gene includes a single large coding exon similar to all other described TLR1 genes, but unlike other teleosts it also has a 5' UTR exon and intron preceding the large coding exon. The omTLR1 ORF is predicted to encode an 808 amino-acid protein with 69% similarity to the Fugu TLR1 and a conserved pattern of predicted leucine-rich repeats (LRR). Phylogenetic analysis grouped omTLR1 with other fish TLR1 genes on a separate branch from the avian TLR1 and mammalian TLR1, 6 and 10. omTLR1 expression levels in rainbow trout anterior kidney leukocytes were not affected by the human TLR2/6 and TLR2/1 agonists diacylated lipoprotein (Pam2CSK4) and triacylated lipoprotein (Pam3CSK4). However, due to the lack of TLR6 and 10 genes in teleost genomes and up-regulation of TLR1 mRNA in response to LPS and bacterial infection in other fish species we hypothesize an important role for omTLR1 in anti-microbial immunity. Therefore, the identification of a TLR2 ortholog in rainbow trout and the development of assays to measure ligand binding and downstream signaling are critical for future elucidation of omTLR1 functions.

EPS in Environmental Microbial Biofilms as Examined by Advanced Imaging Techniques

NASA Astrophysics Data System (ADS)

Neu, T. R.; Lawrence, J. R.

2006-12-01

Biofilm communities are highly structured associations of cellular and polymeric components which are involved in biogenic and geogenic environmental processes. Furthermore, biofilms are also important in medical (infection), industrial (biofouling) and technological (biofilm engineering) processes. The interfacial microbial communities in a specific habitat are highly dynamic and change according to the environmental parameters affecting not only the cellular but also the polymeric constituents of the system. Through their EPS biofilms interact with dissolved, colloidal and particulate compounds from the bulk water phase. For a long time the focus in biofilm research was on the cellular constituents in biofilms and the polymer matrix in biofilms has been rather neglected. The polymer matrix is produced not only by different bacteria and archaea but also by eukaryotic micro-organisms such as algae and fungi. The mostly unidentified mixture of EPS compounds is responsible for many biofilm properties and is involved in biofilm functionality. The chemistry of the EPS matrix represents a mixture of polymers including polysaccharides, proteins, nucleic acids, neutral polymers, charged polymers, amphiphilic polymers and refractory microbial polymers. The analysis of the EPS may be done destructively by means of extraction and subsequent chemical analysis or in situ by means of specific probes in combination with advanced imaging. In the last 15 years laser scanning microscopy (LSM) has been established as an indispensable technique for studying microbial communities. LSM with 1-photon and 2-photon excitation in combination with fluorescence techniques allows 3-dimensional investigation of fully hydrated, living biofilm systems. This approach is able to reveal data on biofilm structural features as well as biofilm processes and interactions. The fluorescent probes available allow the quantitative assessment of cellular as well as polymer distribution. For this purpose lectin-binding- analysis has been suggested as a suitable approach to image glycoconjugates within the polymer matrix of biofilm communities. More recently synchrotron radiation is increasingly recognized as a powerful tool for studying biological samples. Hard X-ray excitation can be used to map elemental composition whereas IR imaging allows examination of biological macromolecules. A further technique called soft X-ray scanning transmission microscopy (STXM) has the advantage of both techniques and may be employed to detect elements as well as biomolecules. Using the appropriate spectra, near edge X-ray absorption fine structure (NEXAFS) microscopy allows quantitative chemical mapping at 50 nm resolution. In this presentation the applicability of LSM and STXM will be demonstrated using several examples of different environmental biofilm systems. The techniques in combination provide a new view of complex microbial communities and their interaction with the environment. These advanced imaging techniques offer the possibility to study the spatial structure of cellular and polymeric compounds in biofilms as well as biofilm microhabitats, biofilm functionality and biofilm processes.

Rapid detection of microbial cell abundance in aquatic systems

DOE PAGES

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.; ...

2016-06-01

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less

Rapid detection of microbial cell abundance in aquatic systems

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

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

PubMed Central

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

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

Pan, Donald; Nolan, Jason; Williams, Kenneth H.

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE PAGES

Pan, Donald; Nolan, Jason; Williams, Kenneth H.; ...

2017-07-11

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Compositions and Methods for the Treatment of Pierce's Disease

DOEpatents

Gupta, Goutam

2008-10-07

Chimeric anti-microbial proteins, compositions, and methods for the therapeutic and prophylactic treatment of plant diseases caused by the bacterial pathogen Xylella fastidiosa are provided. The anti-microbial proteins of the invention generally comprise a surface recognition domain polypeptide, capable of binding to a bacterial membrane component, fused to a bacterial lysis domain polypeptide, capable of affecting lysis or rupture of the bacterial membrane, typically via a fused polypeptide linker. In particular, methods and compositions for the treatment or prevention of Pierce's disease of grapevines are provided. Methods for the generation of transgenic Vitus vinefera plants expressing xylem-secreted anti-microbial chimeras are also provided.

Low Water Activity Packaged White Bread.

DTIC Science & Technology

1985-12-31

this method is different in quality from the normal white pan bread. It has been well recognized that water activity is a key factor in controlling ...important in controlling microbial growth. The purpose of this project was to develop a shelf-stable white pan bread in a flexible pouch by utilizing...coded and randomized in order of presentation. Each judge was presented five samples: control , 5% sorbitol, 20% sorbitol, 8% glycerol, and 10% sorbitol-5

Parameters of microbial respiration in soils of the impact zone of a mineral fertilizer factory

NASA Astrophysics Data System (ADS)

Zhukova, A. D.; Khomyakov, D. M.

2015-08-01

The carbon content in the microbial biomass and the microbial production of CO2 (the biological component of soil respiration) were determined in the upper layer (0-10 cm) of soils in the impact zone of the OJSC Voskresensk Mineral Fertilizers, one of the largest factories manufacturing mineral fertilizers in Russia. Statistical characteristics and schematic distribution of the biological parameters in the soil cover of the impact zone were analyzed. The degree of disturbance of microbial communities in the studied objects varied from weak to medium. The maximum value (0.44) was observed on the sampling plot 4 km away from the factory and 0.5 km away from the place of waste (phosphogypsum) storage. Significantly lower carbon content in the microbial biomass and its specific respiration were recorded in the agrosoddy-podzolic soil as compared with the alluvial soil sampled at the same distance from the plant. The effects of potential soil pollutants (fluorine, sulfur, cadmium, and stable strontium) on the characteristics of soil microbial communities were described with reliable regression equations.

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell

NASA Astrophysics Data System (ADS)

Aleksandrovich Yuriev, Denis; Viktorovna Zaitseva, Svetlana; Olegovna Zhdanova, Galina; Yurievich Tolstoy, Mikhail; Dondokovna Barkhutova, Darima; Feodorovna Vyatchina, Olga; Yuryevna Konovalova, Elena; Iosifovich Stom, Devard

2018-02-01

Electrogenic, molecular and some other properties of a microbial mat isolated from the Kuchiger hot spring (Kurumkansky District, Republic of Buryatia) were studied. Molecular analysis showed that representatives of Proteobacteria (85.5 % of the number of classified bacterial sequences) prevailed in the microbial mat of the Kuchiger springs, among which sulfur bacteria of the genus Thiothrix were the most numerous. In the microbial mat there were bacteria from the families Rhodocyclaceae, Comamonadaceae and Flavobacteriaceae. Phylum Bacteroidetes, Cyanobacteria/Chloroplast, Fusobacteria, Fibrobacteres, Acidobacteria, Chlorobi, Spirochaetes, Verrucomicrobia, Firmicutes, Deinococcus-Thermus, Chloroflexi and Actinobacteria are also noted in the composition of the microbial mat. Under the experimental conditions using Kuchiger-mat 16 as bioagents, glucose and peptone as substrates, the power of BFC was 240 and 221 mW / m2, respectively. When replacing the substrate with sodium acetate, the efficiency of the BFC was reduced by a factor of 10 (20 mW / m2). The prospects of using a microbial mat “Kuchiger-16” as an electrogen in BFC when utilizing alkaline waste water components to generate electricity are discussed.

Identification of microorganisms associated with corrosion of offshore oil production systems

NASA Astrophysics Data System (ADS)

Sørensen, Ketil; Grigoryan, Aleksandr; Holmkvist, Lars; Skovhus, Torben; Thomsen, Uffe; Lundgaard, Thomas

2010-05-01

Microbiologically influenced corrosion (MIC) poses a major challenge to oil producers and distributors. The annual cost associated with MIC-related pipeline failures and general maintenance and surveillance of installations amounts to several billion dollar in the oil production sector alone. Hence, large efforts are undertaken by some producers to control and monitor microbial growth in pipelines and other installations, and extensive surveillance programs are carried out in order to detect and quantify potential MIC-promoting microorganisms. Traditionally, efforts to mitigate and survey microbial growth in oil production systems have focused on sulfate-reducing Bacteria (SRB), and microorganisms have usually been enumerated by the culture-dependent MPN (most probable number) -technique. Culture-independent molecular tools yielding much more detailed information about the microbial communities have now been implemented as a reliable tool for routine surveillance of oil production systems in the North Sea. This has resulted in new and hitherto unattainable information regarding the distribution of different microorganisms in hot reservoirs and associated oil production systems. This presentation will provide a review of recent insights regarding thermophilic microbial communities and their implication for steel corrosion in offshore oil production systems. Data collected from solids and biofilms in different corroded pipelines and tubes indicate that in addition to SRB, other groups such as methanogens and sulfate-reducing Archaea (SRA) are also involved in MIC. In the hot parts of the system where the temperature approaches 80 ⁰C, SRA closely related to Archaeoglobus fulgidus outnumber SRB by several orders of magnitude. Methanogens affiliated with the genus Methanothermococcus were shown to completely dominate the microbial community at the metal surface in a sample of highly corroded piping. Thus, the microbial communities associated with MIC appear to be more complex than previously recognized by the industry.

Development of the human infant intestinal microbiota.

PubMed

Palmer, Chana; Bik, Elisabeth M; DiGiulio, Daniel B; Relman, David A; Brown, Patrick O

2007-07-01

Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human biology, the temporal progression of this process, the sources of the microbes that make up the ecosystem, how and why it varies from one infant to another, and how the composition of this ecosystem influences human physiology, development, and disease are still poorly understood. As a step toward systematically investigating these questions, we designed a microarray to detect and quantitate the small subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria. We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life. To investigate possible origins of the infant microbiota, we also profiled vaginal and milk samples from most of the mothers, and stool samples from all of the mothers, most of the fathers, and two siblings. The composition and temporal patterns of the microbial communities varied widely from baby to baby. Despite considerable temporal variation, the distinct features of each baby's microbial community were recognizable for intervals of weeks to months. The strikingly parallel temporal patterns of the twins suggested that incidental environmental exposures play a major role in determining the distinctive characteristics of the microbial community in each baby. By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract.

Finding the best windows: An apparent environmental threshold determines which diffuse flows are dominated by subsurface microbes

NASA Astrophysics Data System (ADS)

Olins, H. C.; Rogers, D.; Scholin, C. A.; Preston, C. J.; Vidoudez, C.; Ussler, W.; Pargett, D.; Jensen, S.; Roman, B.; Birch, J. M.; Girguis, P. R.

2014-12-01

Hydrothermal vents are hotspots of microbial primary productivity often described as "windows into the subsurface biosphere." High temperature vents have received the majority of research attention, but cooler diffuse flows are as, if not more, important a source of heat and chemicals to the overlying ocean. We studied patterns of in situ gene expression and co-registered geochemistry in order to 1) describe the diversity and physiological poise of active microbial communities that span thermal and geochemical gradients from active diffuse flow to background vent field seawater, and 2) determine to what extent seawater or subsurface microbes were active throughout this environment. Analyses of multiple metatranscriptomes from 5 geochemically distinct sites (some from samples preserved in situ) show that proximate diffuse flows showed strikingly different transcription profiles. Specifically, caldera background and some diffuse flows were similar, both dominated by seawater-derived Gammaproteobacteria despite having distinct geochemistries. Intra-field community shows evidence of increased primary productivity throughout the entire vent field and not just at individual diffuse flows. In contrast, a more spatially limited, Epsilonproteobacteria-dominated transcription profile from the most hydrothermally-influenced diffuse flow appeared to be driven by the activity of vent-endemic microbes, likely reflecting subsurface microbial activity. We suggest that the microbial activity within many diffuse flow vents is primarily attributable to seawater derived Gammaproteobacterial sulfur oxidizers, while in certain other flows vent-endemic Epsilonproteobactiera are most active. These data reveal a diversity in microbial activity at diffuse flows that has not previously been recognized, and reshapes our thinking about the relative influence that different microbial communities may have on local processes (such as primary production) and potentially global biogeochemical cycles.

Changes in the dissolved organic matter leaching from soil under severe temperature and N-deposition.

PubMed

Nguyen, Hang Vo-Minh; Choi, Jung Hyun

2015-06-01

In this study, we conducted growth chamber experiments using three types of soil (wetland, rice paddy, and forest) under the conditions of a severe increase in the temperature and N-deposition in order to investigate how extreme weather influences the characteristics of the dissolved organic matter (DOM) leaching from different soil types. This leachate controls the quantity and quality of DOM in surface water systems. After 5 months of incubation, the dissolved organic carbon (DOC) concentrations decreased in the range of 21.1 to 88.9 %, while the specific UV absorption (SUVA) values increased substantially in the range of 19.9 to 319.9 % for all of the samples. Higher increases in the SUVA values were observed at higher temperatures, whereas the opposite trend was observed for samples with N-addition. The parallel factor analysis (PARAFAC) results showed that four fluorescence components: terrestrial humic-like (component 1 (C1)), microbial humic-like (component 2 (C2)), protein-like (component 3 (C3)), and anthropogenic humic-like (component 4 (C4)) constituted the fluorescence matrices of soil samples. During the experiment, labile DOM from the soils was consumed and transformed into resistant aromatic carbon structures and less biodegradable components via microbial processes. The principle component analysis (PCA) results indicated that severe temperatures and N-deposition could enhance the contribution of the aromatic carbon compounds and humic-like components in the soil samples.

Advances in cholangiocyte immunobiology

PubMed Central

Syal, Gaurav; Fausther, Michel

2012-01-01

Cholangiocytes, or bile duct epithelia, were once thought to be the simple lining of the conduit system comprising the intra- and extrahepatic bile ducts. Growing experimental evidence demonstrated that cholangiocytes are in fact the first line of defense of the biliary system against foreign substances. Experimental advances in recent years have unveiled previously unknown roles of cholangiocytes in both innate and adaptive immune responses. Cholangiocytes can release inflammatory modulators in a regulated fashion. Moreover, they express specialized pattern-recognizing molecules that identify microbial components and activate intracellular signaling cascades leading to a variety of downstream responses. The cytokines secreted by cholangiocytes, in conjunction with the adhesion molecules expressed on their surface, play a role in recruitment, localization, and modulation of immune responses in the liver and biliary tract. Cholangiocyte survival and function is further modulated by cytokines and inflammatory mediators secreted by immune cells and cholangiocytes themselves. Because cholangiocytes act as professional APCs via expression of major histocompatibility complex antigens and secrete antimicrobial peptides in bile, their role in response to biliary infection is critical. Finally, because cholangiocytes release mediators critical to myofibroblastic differentiation of portal fibroblasts and hepatic stellate cells, cholangiocytes may be essential in the pathogenesis of biliary cirrhosis. PMID:22961800

Advances in cholangiocyte immunobiology.

PubMed

Syal, Gaurav; Fausther, Michel; Dranoff, Jonathan A

2012-11-15

Cholangiocytes, or bile duct epithelia, were once thought to be the simple lining of the conduit system comprising the intra- and extrahepatic bile ducts. Growing experimental evidence demonstrated that cholangiocytes are in fact the first line of defense of the biliary system against foreign substances. Experimental advances in recent years have unveiled previously unknown roles of cholangiocytes in both innate and adaptive immune responses. Cholangiocytes can release inflammatory modulators in a regulated fashion. Moreover, they express specialized pattern-recognizing molecules that identify microbial components and activate intracellular signaling cascades leading to a variety of downstream responses. The cytokines secreted by cholangiocytes, in conjunction with the adhesion molecules expressed on their surface, play a role in recruitment, localization, and modulation of immune responses in the liver and biliary tract. Cholangiocyte survival and function is further modulated by cytokines and inflammatory mediators secreted by immune cells and cholangiocytes themselves. Because cholangiocytes act as professional APCs via expression of major histocompatibility complex antigens and secrete antimicrobial peptides in bile, their role in response to biliary infection is critical. Finally, because cholangiocytes release mediators critical to myofibroblastic differentiation of portal fibroblasts and hepatic stellate cells, cholangiocytes may be essential in the pathogenesis of biliary cirrhosis.

Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor

NASA Astrophysics Data System (ADS)

Kumar, Amit; Delogu, Francesco

2017-02-01

The present work focuses on the dynamical aspects of cross-reactivity between myelin based protein (MBP) self-peptide and two microbial peptides (UL15, PMM) for Hy.1B11 T-cell receptor (TCR). This same TCR was isolated from a patient suffering from multiple sclerosis (MS). The study aims at highlighting the chemical interactions underlying recognition mechanisms between TCR and the peptides presented by Major Histocompatibility Complex (MHC) proteins, which form a crucial component in adaptive immune response against foreign antigens. Since the ability of a TCR to recognize different peptide antigens presented by MHC depends on its cross-reactivity, we used molecular dynamics methods to obtain atomistic detail on TCR-peptide-MHC complexes. Our results show how the dynamical basis of Hy.1B11 TCR’s cross-reactivity is rooted in a similar bridging interaction pattern across the TCR-peptide-MHC interface. Our simulations confirm the importance of TCR CDR3α E98 residue interaction with MHC and a predominant role of P6 peptide residue in MHC binding affinity. Altogether, our study provides energetic and dynamical insights into factors governing peptide recognition by the cross-reactive Hy.1B11 TCR, found in MS patient.

Serine-Aspartate Repeat Protein D Increases Staphylococcus aureus Virulence and Survival in Blood.

PubMed

Askarian, Fatemeh; Uchiyama, Satoshi; Valderrama, J Andrés; Ajayi, Clement; Sollid, Johanna U E; van Sorge, Nina M; Nizet, Victor; van Strijp, Jos A G; Johannessen, Mona

2017-01-01

Staphylococcus aureus expresses a panel of cell wall-anchored adhesins, including proteins belonging to the microbial surface components recognizing adhesive matrix molecule (MSCRAMM) family, exemplified by the serine-aspartate repeat protein D (SdrD), which serve key roles in colonization and infection. Deletion of sdrD from S. aureus subsp. aureus strain NCTC8325-4 attenuated bacterial survival in human whole blood ex vivo, which was associated with increased killing by human neutrophils. Remarkably, SdrD was able to inhibit innate immune-mediated bacterial killing independently of other S. aureus proteins, since addition of recombinant SdrD protein and heterologous expression of SdrD in Lactococcus lactis promoted bacterial survival in human blood. SdrD contributes to bacterial virulence in vivo, since fewer S. aureus subsp. aureus NCTC8325-4 ΔsdrD bacteria than bacteria of the parent strain were recovered from blood and several organs using a murine intravenous infection model. Collectively, our findings reveal a new property of SdrD as an important key contributor to S. aureus survival and the ability to escape the innate immune system in blood. Copyright © 2016 Askarian et al.

Environment polluting conventional chemical control compared to an environmentally friendly IPM approach for control of diamondback moth, Plutella xylostella (L.), in China: a review.

PubMed

Shakeel, Muhammad; Farooq, Muhammad; Nasim, Wajid; Akram, Waseem; Khan, Fawad Zafar Ahmad; Jaleel, Waqar; Zhu, Xun; Yin, Haichen; Li, Shuzhong; Fahad, Shah; Hussain, Saddam; Chauhan, Bhagirath Singh; Jin, Fengliang

2017-06-01

The diamondback moth, Plutella xylostella, is recognized as a widely distributed destructive insect pest of Brassica worldwide. The management of this pest is a serious issue, and an estimated annual cost of its management has reached approximately US$4 billion. Despite the fact that chemicals are a serious threat to the environment, lots of chemicals are applied for controlling various insect pests especially P. xylostella. An overreliance on chemical control has not only led to the evolution of resistance to insecticides and to a reduction of natural enemies but also has polluted various components of water, air, and soil ecosystem. In the present scenario, there is a need to implement an environmentally friendly integrated pest management (IPM) approach with new management tactics (microbial control, biological control, cultural control, mating disruption, insecticide rotation strategies, and plant resistance) for an alternative to chemical control. The IPM approach is not only economically beneficial but also reduces the environmental and health risks. The present review synthesizes published information on the insecticide resistance against P. xylostella and emphasizes on adopting an alternative environmentally friendly IPM approach for controlling P. xylostella in China.

The role of polymorphonuclear neutrophils during HIV-1 infection.

PubMed

Yaseen, Mahmoud Mohammad; Abuharfeil, Nizar Mohammad; Yaseen, Mohammad Mahmoud; Shabsoug, Barakat Mohammad

2018-01-01

It is well-recognized that human immunodeficiency virus type-1 (HIV-1) mainly targets CD4 + T cells and macrophages. Nonetheless, during the past three decades, a huge number of studies have reported that HIV-1 can directly or indirectly target other cellular components of the immune system including CD8 + T cells, B cells, dendritic cells, natural killer cells, and polymorphonuclear neutrophils (PMNs), among others. PMNs are the most abundant leukocytes in the human circulation, and are known to play principal roles in the elimination of invading pathogens, regulating different immune responses, healing of injured tissues, and maintaining mucosal homeostasis. Until recently, little was known about the impact of HIV-1 infection on PMNs as well as the impact of PMNs on HIV-1 disease progression. This is because early studies focused on neutropenia and recurrent microbial infections, particularly, during advanced disease. However, recent studies have extended the investigation area to cover new aspects of the interactions between HIV-1 and PMNs. This review aims to summarize these advances and address the impact of HIV-1 infection on PMNs as well as the impact of PMNs on HIV-1 disease progression to better understand the pathophysiology of HIV-1 infection.

['Specificity' in microbiology and immunochemistry between 1880 and 1930].

PubMed

Corbellini, Gilberto

2010-01-01

During the second half of the XIX Century, microbiological sciences acquired a set of conceptual, methodological and technological tools that radically transformed theoretical and empirical knowledge of the microorganisms, with particular regard to their biochemical properties and their etiopathological role in infectious diseases. During that period, theoretical and experimental researches in general microbiology and immunochemistry addressed the nature and empirical appearances of microbes, both pathogens and not, and the origins of chemical properties of immune sera. In other words, microbiologists tried operatively explaining the origins of the morphological, physiological, and pathogenetic differences between the microbial species. At the same time physiologists and biochemists investigated the chemical basis of the selective or specific interactions between microorganisms or their chemical components and humoral factors contained into the sera produced by the body in response to the contact with microbes. During the half a century, between 1880 and 1930, qualitative and quantitative experimental studies demonstrated that the specificity of microbiological phenomena depended on the biology of microbes and that the specificity of immune reactions hinged upon the biochemical properties of special molecules synthesized by some physiological system which can recognize and react against any foreign substance.

Relational and item-specific influences on generate-recognize processes in recall.

PubMed

Guynn, Melissa J; McDaniel, Mark A; Strosser, Garrett L; Ramirez, Juan M; Castleberry, Erica H; Arnett, Kristen H

2014-02-01

The generate-recognize model and the relational-item-specific distinction are two approaches to explaining recall. In this study, we consider the two approaches in concert. Following Jacoby and Hollingshead (Journal of Memory and Language 29:433-454, 1990), we implemented a production task and a recognition task following production (1) to evaluate whether generation and recognition components were evident in cued recall and (2) to gauge the effects of relational and item-specific processing on these components. An encoding task designed to augment item-specific processing (anagram-transposition) produced a benefit on the recognition component (Experiments 1-3) but no significant benefit on the generation component (Experiments 1-3), in the context of a significant benefit to cued recall. By contrast, an encoding task designed to augment relational processing (category-sorting) did produce a benefit on the generation component (Experiment 3). These results converge on the idea that in recall, item-specific processing impacts a recognition component, whereas relational processing impacts a generation component.

Immunity by equilibrium.

PubMed

Eberl, Gérard

2016-08-01

The classical model of immunity posits that the immune system reacts to pathogens and injury and restores homeostasis. Indeed, a century of research has uncovered the means and mechanisms by which the immune system recognizes danger and regulates its own activity. However, this classical model does not fully explain complex phenomena, such as tolerance, allergy, the increased prevalence of inflammatory pathologies in industrialized nations and immunity to multiple infections. In this Essay, I propose a model of immunity that is based on equilibrium, in which the healthy immune system is always active and in a state of dynamic equilibrium between antagonistic types of response. This equilibrium is regulated both by the internal milieu and by the microbial environment. As a result, alteration of the internal milieu or microbial environment leads to immune disequilibrium, which determines tolerance, protective immunity and inflammatory pathology.

Antibodies Encoded by FCRL4-Bearing Memory B Cells Preferentially Recognize Commensal Microbial Antigens.

PubMed

Liu, Yanling; McDaniel, Jonathan R; Khan, Srijit; Campisi, Paolo; Propst, Evan J; Holler, Theresa; Grunebaum, Eyal; Georgiou, George; Ippolito, Gregory C; Ehrhardt, Götz R A

2018-06-15

FCRL4, a low-affinity IgA Ab receptor with strong immunoregulatory potential, is an identifying feature of a tissue-based population of memory B cells (Bmem). We used two independent approaches to perform a comparative analysis of the Ag receptor repertoires of FCRL4 + and FCRL4 - Bmem in human tonsils. We determined that FCRL4 + Bmem displayed lower levels of somatic mutations in their Ag receptors compared with FCRL4 - Bmem but had similar frequencies of variable gene family usage. Importantly, Abs with reactivity to commensal microbiota were enriched in FCRL4 + cells, a phenotype not due to polyreactive binding characteristics. Our study links expression of the immunoregulatory FCRL4 molecule with increased recognition of commensal microbial Ags. Copyright © 2018 by The American Association of Immunologists, Inc.

Deciphering microbial landscapes of fish eggs to mitigate emerging diseases

PubMed Central

Liu, Yiying; de Bruijn, Irene; Jack, Allison LH; Drynan, Keith; van den Berg, Albert H; Thoen, Even; Sandoval-Sierra, Vladimir; Skaar, Ida; van West, Pieter; Diéguez-Uribeondo, Javier; van der Voort, Menno; Mendes, Rodrigo; Mazzola, Mark; Raaijmakers, Jos M

2014-01-01

Animals and plants are increasingly suffering from diseases caused by fungi and oomycetes. These emerging pathogens are now recognized as a global threat to biodiversity and food security. Among oomycetes, Saprolegnia species cause significant declines in fish and amphibian populations. Fish eggs have an immature adaptive immune system and depend on nonspecific innate defences to ward off pathogens. Here, meta-taxonomic analyses revealed that Atlantic salmon eggs are home to diverse fungal, oomycete and bacterial communities. Although virulent Saprolegnia isolates were found in all salmon egg samples, a low incidence of Saprolegniosis was strongly correlated with a high richness and abundance of specific commensal Actinobacteria, with the genus Frondihabitans (Microbacteriaceae) effectively inhibiting attachment of Saprolegniato salmon eggs. These results highlight that fundamental insights into microbial landscapes of fish eggs may provide new sustainable means to mitigate emerging diseases. PMID:24671087

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems.

PubMed

Kokko, Marika; Epple, Stefanie; Gescher, Johannes; Kerzenmacher, Sven

2018-06-01

Over the last decade, there has been an ever-growing interest in bioelectrochemical systems (BES) as a sustainable technology enabling simultaneous wastewater treatment and biological production of, e.g. electricity, hydrogen, and further commodities. A key component of any BES degrading organic matter is the anode where electric current is biologically generated from the oxidation of organic compounds. The performance of BES depends on the interactions of the anodic microbial communities. To optimize the operational parameters and process design of BES a better comprehension of the microbial community dynamics and interactions at the anode is required. This paper reviews the abundance of different microorganisms in anodic biofilms and discusses their roles and possible side reactions with respect to their implications on the performance of BES utilizing wastewaters. The most important operational parameters affecting anodic microbial communities grown with wastewaters are highlighted and guidelines for controlling the composition of microbial communities are given. Copyright © 2018 Elsevier Ltd. All rights reserved.

Correcting names of bacteria deposited in National Microbial Repositories: an analysed sequence data necessary for taxonomic re-categorization of misclassified bacteria-ONE example, genus Lysinibacillus.

PubMed

Rekadwad, Bhagwan N; Gonzalez, Juan M

2017-08-01

A report on 16S rRNA gene sequence re-analysis and digitalization is presented using Lysinibacillus species (one example) deposited in National Microbial Repositories in India. Lysinibacillus species 16S rRNA gene sequences were digitalized to provide quick response (QR) codes, Chaose Game Representation (CGR) and Frequency of Chaose Game Representation (FCGR). GC percentage, phylogenetic analysis, and principal component analysis (PCA) are tools used for the differentiation and reclassification of the strains under investigation. The seven reasons supporting the statements made by us as misclassified Lysinibacillus species deposited in National Microbial Depositories are given in this paper. Based on seven reasons, bacteria deposited in National Microbial Repositories such as Lysinibacillus and many other needs reanalyses for their exact identity. Leaves of identity with type strains of related species shows difference 2 to 8 % suggesting that reclassification is needed to correctly assign species names to the analyzed Lysinibacillus strains available in National Microbial Repositories.

Integrated microbial processes for biofuels and high value-added products: the way to improve the cost effectiveness of biofuel production.

PubMed

da Silva, Teresa Lopes; Gouveia, Luísa; Reis, Alberto

2014-02-01

The production of microbial biofuels is currently under investigation, as they are alternative sources to fossil fuels, which are diminishing and their use has a negative impact on the environment. However, so far, biofuels derived from microbes are not economically competitive. One way to overcome this bottleneck is the use of microorganisms to transform substrates into biofuels and high value-added products, and simultaneously taking advantage of the various microbial biomass components to produce other products of interest, as an integrated process. In this way, it is possible to maximize the economic value of the whole process, with the desired reduction of the waste streams produced. It is expected that this integrated system makes the biofuel production economically sustainable and competitive in the near future. This review describes the investigation on integrated microbial processes (based on bacteria, yeast, and microalgal cultivations) that have been experimentally developed, highlighting the importance of this approach as a way to optimize microbial biofuel production process.

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

Phytoplankton biomass and microbial abundances during the spring upwelling season in the coastal area off Concepción, central-southern Chile: Variability around a time series station

NASA Astrophysics Data System (ADS)

Morales, Carmen E.; Anabalón, Valeria

2012-01-01

In the coastal system off Concepción, time series observations at a fixed station (St. 18) have shown strong seasonal changes in the oceanographic environment of the upper layer (<35 m depth), accompanied by large increases in phytoplankton biomass during the spring-summer upwelling season. These blooms, dominated by microplanktonic diatoms, have usually overshadowed the relevance of the smaller microbial components during upwelling. This study focuses on the variability of oceanographic conditions and their association with the structure of the planktonic community (size fractionated chlorophyll-a and microbial abundances) in the upper layer during the upwelling season, examining the extent to which St. 18 is representative of the coastal system off Concepción during springtime. For this purpose, data from three consecutive springs (2004, 2005, 2006) were compared, which included cruises for all years (8 stations around St. 18) as well as monthly sampling at St. 18. Most of the spatial (submesoscale) variability in chlorophyll-a and the microbial components was not significant, but data dispersion around mean values was high. Water column structure (temperature and salinity) in the upper layer explained a significant fraction (25-65%) of the spatial variability in most of the planktonic components; their responses to oceanographic variability were linear in some cases and non-linear in others. For the most part, St. 18 appears to adequately represent mean oceanographic conditions and the structure of planktonic communities in the coastal waters off Concepción during springtime, however spatial variability needs to be taken into account in the interpretations of temporal changes at this fixed station as well as in assessments of carbon flow within, and exportation processes from, this upwelling system.

Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

NASA Astrophysics Data System (ADS)

Boston, P. J.

2016-12-01

In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial metabolism occurs against a complex backdrop of hydrology, geochemistry, and geological structures of subsurface environments. These are not static but change in response to both short term and much longer geological time scales thus presenting significant challenges in interpretation.

Gut microbiota functions: metabolism of nutrients and other food components.

PubMed

Rowland, Ian; Gibson, Glenn; Heinken, Almut; Scott, Karen; Swann, Jonathan; Thiele, Ines; Tuohy, Kieran

2018-02-01

The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.

Brain angiogenesis inhibitor 1 (BAI1) is a pattern recognition receptor that mediates macrophage binding and engulfment of Gram-negative bacteria

PubMed Central

Das, Soumita; Owen, Katherine A.; Ly, Kim T.; Park, Daeho; Black, Steven G.; Wilson, Jeffrey M.; Sifri, Costi D.; Ravichandran, Kodi S.; Ernst, Peter B.; Casanova, James E.

2011-01-01

Bacterial recognition by host cells is essential for initiation of infection and the host response. Bacteria interact with host cells via multiple pattern recognition receptors that recognize microbial products or pathogen-associated molecular patterns. In response to this interaction, host cell signaling cascades are activated that lead to inflammatory responses and/or phagocytic clearance of attached bacteria. Brain angiogenesis inhibitor 1 (BAI1) is a receptor that recognizes apoptotic cells through its conserved type I thrombospondin repeats and triggers their engulfment through an ELMO1/Dock/Rac1 signaling module. Because thrombospondin repeats in other proteins have been shown to bind bacterial surface components, we hypothesized that BAI1 may also mediate the recognition and clearance of pathogenic bacteria. We found that preincubation of bacteria with recombinant soluble BAI1 ectodomain or knockdown of endogenous BAI1 in primary macrophages significantly reduced binding and internalization of the Gram-negative pathogen Salmonella typhimurium. Conversely, overexpression of BAI1 enhanced attachment and engulfment of Salmonella in macrophages and in heterologous nonphagocytic cells. Bacterial uptake is triggered by the BAI1-mediated activation of Rac through an ELMO/Dock-dependent mechanism, and inhibition of the BAI1/ELMO1 interaction prevents both Rac activation and bacterial uptake. Moreover, inhibition of ELMO1 or Rac function significantly impairs the proinflammatory response to infection. Finally, we show that BAI1 interacts with a variety of Gram-negative, but not Gram-positive, bacteria through recognition of their surface lipopolysaccharide. Together these findings identify BAI1 as a pattern recognition receptor that mediates nonopsonic phagocytosis of Gram-negative bacteria by macrophages and directly affects the host response to infection. PMID:21245295

Xanthomonas campestris cell-cell signalling molecule DSF (diffusible signal factor) elicits innate immunity in plants and is suppressed by the exopolysaccharide xanthan.

PubMed

Kakkar, Akanksha; Nizampatnam, Narasimha Rao; Kondreddy, Anil; Pradhan, Binod Bihari; Chatterjee, Subhadeep

2015-11-01

Several secreted and surface-associated conserved microbial molecules are recognized by the host to mount the defence response. One such evolutionarily well-conserved bacterial process is the production of cell-cell signalling molecules which regulate production of multiple virulence functions by a process known as quorum sensing. Here it is shown that a bacterial fatty acid cell-cell signalling molecule, DSF (diffusible signal factor), elicits innate immunity in plants. The DSF family of signalling molecules are highly conserved among many phytopathogenic bacteria belonging to the genus Xanthomonas as well as in opportunistic animal pathogens. Using Arabidopsis, Nicotiana benthamiana, and rice as model systems, it is shown that DSF induces a hypersensitivity reaction (HR)-like response, programmed cell death, the accumulation of autofluorescent compounds, hydrogen peroxide production, and the expression of the PATHOGENESIS-RELATED1 (PR-1) gene. Furthermore, production of the DSF signalling molecule in Pseudomonas syringae, a non-DSF-producing plant pathogen, induces the innate immune response in the N. benthamiana host plant and also affects pathogen growth. By pre- and co-inoculation of DSF, it was demonstrated that the DSF-induced plant defence reduces disease severity and pathogen growth in the host plant. In this study, it was further demonstrated that wild-type Xanthomonas campestris suppresses the DSF-induced innate immunity by secreting xanthan, the main component of extracellular polysaccharide. The results indicate that plants have evolved to recognize a widely conserved bacterial communication system and may have played a role in the co-evolution of host recognition of the pathogen and the communication machinery. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Xanthomonas campestris cell–cell signalling molecule DSF (diffusible signal factor) elicits innate immunity in plants and is suppressed by the exopolysaccharide xanthan

PubMed Central

Kakkar, Akanksha; Nizampatnam, Narasimha Rao; Kondreddy, Anil; Pradhan, Binod Bihari; Chatterjee, Subhadeep

2015-01-01

Several secreted and surface-associated conserved microbial molecules are recognized by the host to mount the defence response. One such evolutionarily well-conserved bacterial process is the production of cell–cell signalling molecules which regulate production of multiple virulence functions by a process known as quorum sensing. Here it is shown that a bacterial fatty acid cell–cell signalling molecule, DSF (diffusible signal factor), elicits innate immunity in plants. The DSF family of signalling molecules are highly conserved among many phytopathogenic bacteria belonging to the genus Xanthomonas as well as in opportunistic animal pathogens. Using Arabidopsis, Nicotiana benthamiana, and rice as model systems, it is shown that DSF induces a hypersensitivity reaction (HR)-like response, programmed cell death, the accumulation of autofluorescent compounds, hydrogen peroxide production, and the expression of the PATHOGENESIS-RELATED1 (PR-1) gene. Furthermore, production of the DSF signalling molecule in Pseudomonas syringae, a non-DSF-producing plant pathogen, induces the innate immune response in the N. benthamiana host plant and also affects pathogen growth. By pre- and co-inoculation of DSF, it was demonstrated that the DSF-induced plant defence reduces disease severity and pathogen growth in the host plant. In this study, it was further demonstrated that wild-type Xanthomonas campestris suppresses the DSF-induced innate immunity by secreting xanthan, the main component of extracellular polysaccharide. The results indicate that plants have evolved to recognize a widely conserved bacterial communication system and may have played a role in the co-evolution of host recognition of the pathogen and the communication machinery. PMID:26248667

Tomato Prenylated RAB Acceptor Protein 1 Modulates Trafficking and Degradation of the Pattern Recognition Receptor LeEIX2, Affecting the Innate Immune Response

PubMed Central

Pizarro, Lorena; Leibman-Markus, Meirav; Schuster, Silvia; Bar, Maya; Meltz, Tal; Avni, Adi

2018-01-01

Plants recognize microbial/pathogen associated molecular patterns (MAMP/PAMP) through pattern recognition receptors (PRRs) triggering an immune response against pathogen progression. MAMP/PAMP triggered immune response requires PRR endocytosis and trafficking for proper deployment. LeEIX2 is a well-known Solanum lycopersicum RLP-PRR, able to recognize and respond to the fungal MAMP/PAMP ethylene-inducing xylanase (EIX), and its function is highly dependent on intracellular trafficking. Identifying protein machinery components regulating LeEIX2 intracellular trafficking is crucial to our understanding of LeEIX2 mediated immune responses. In this work, we identified a novel trafficking protein, SlPRA1A, a predicted regulator of RAB, as an interactor of LeEIX2. Overexpression of SlPRA1A strongly decreases LeEIX2 endosomal localization, as well as LeEIX2 protein levels. Accordingly, the innate immune responses to EIX are markedly reduced by SlPRA1A overexpression, presumably due to a decreased LeEIX2 availability. Studies into the role of SlPRA1A in LeEIX2 trafficking revealed that LeEIX2 localization in multivesicular bodies/late endosomes is augmented by SlPRA1A. Furthermore, inhibiting vacuolar function prevents the LeEIX2 protein level reduction mediated by SlPRA1A, suggesting that SlPRA1A may redirect LeEIX2 trafficking to the vacuole for degradation. Interestingly, SlPRA1A overexpression reduces the amount of several RLP-PRRs, but does not affect the protein level of receptor-like kinase PRRs, suggesting a specific role of SlPRA1A in RLP-PRR trafficking and degradation. PMID:29545816

Pathogen profiling for disease management and surveillance.

PubMed

Sintchenko, Vitali; Iredell, Jonathan R; Gilbert, Gwendolyn L

2007-06-01

The usefulness of rapid pathogen genotyping is widely recognized, but its effective interpretation and application requires integration into clinical and public health decision-making. How can pathogen genotyping data best be translated to inform disease management and surveillance? Pathogen profiling integrates microbial genomics data into communicable disease control by consolidating phenotypic identity-based methods with DNA microarrays, proteomics, metabolomics and sequence-based typing. Sharing data on pathogen profiles should facilitate our understanding of transmission patterns and the dynamics of epidemics.

[Soil microbial community structure of monoculture and mixed plantation stands of native tree species in south subtropical China].

PubMed

Luo, Da; Shi, Zuo-Min; Tang, Jing-Chao; Liu, Shi-Rong; Lu, Li-Hua

2014-09-01

The effects of three plantation stands, Erythrophleumf ordii (EF), Pinus massoniana (PM), and their mixed plantation (MP), on soil microbial biomass and microbial community structure in south subtropical China were studied by the method of phospholipid fatty acids (PLFAs) analysis. The results showed that the amounts of microbial total PLFAs and PLFAs of each microbial group in these three plantation stand soils were significantly higher in dry season than in rainy season. In dry season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and actinomycetes PLFAs were the highest in the PM soil, moderate in the MP soil, and the lowest in the EF soil. But in rainy season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and arbuscular mycorrhizal fungi (AMF) PLFAs in the EF soil were higher than in the MP soil, and were significantly higher than in the PM soil. Principal component analysis (PCA) indicated that the variations in soil microbial community structure composition were affected by both plantation types and seasons. Redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil temperature and moisture, pH, total nitrogen content, and ammonium nitrogen content had significant correlations with PLFA signatures. In addition, the ratio of fungi PLFAs to bacteria PLFAs in the MP soil was the highest among the three stand soils within the whole year, indicating that mixed plantation stands could facilitate the stability of the soil ecosystem.

Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables.

PubMed

Wang, Ya-Fen; Tam, Nora Fung-Yee

2012-04-15

Changes of microbial community structure and its relationship with various environmental variables in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. Temporal variations in the microbial community structure were clearly revealed by principal component analysis (PCA) of the microbial ester-linked fatty acid methyl ester (EL-FAME) profiles. The most obvious shift in microbial community structure was detected 6 months after the removal of the dock, although no significant decline in the levels of pollutants could be detected. As determined by EL-FAME profiles, the microbial diversity recovered and the predominance of gram-negative bacteria was gradually replaced by gram-positive bacteria and fungi in the impacted stations. With redundancy analysis (RDA), the concentration of total polycyclic aromatic hydrocarbons (PAHs) was found to be the second important determinant of microbial community structure, next to Time. The relative abundance of 18:1ω9c and hydroxyl fatty acids enriched in the PAH hot spots, whereas 16:1ω9 and 18:1ω9t were negatively correlated to total PAH concentration. The significant relationships observed between microbial EL-FAME profiles and pollutants, exampled by PAHs in the present study, suggested the potential of microbial community analysis in the assessment of the natural attenuation process in contaminated environments. Copyright © 2012 Elsevier B.V. All rights reserved.

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

NASA Astrophysics Data System (ADS)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

Plankton communities in the five Iles Eparses (Western Indian Ocean) considered to be pristine ecosystems

NASA Astrophysics Data System (ADS)

Bouvy, M.; Got, P.; Domaizon, I.; Pagano, M.; Leboulanger, C.; Bouvier, C.; Carré, C.; Roques, C.; Dupuy, C.

2016-04-01

Coral reef environments are generally recognized as being the most threatened of marine ecosystems. However, it is extremely difficult to distinguish the effects of climate change from other forcing factors, mainly because it is difficult to study ecosystems that are isolated from human pressure. The five Iles Eparses (Scattered Islands) are located in the Western Indian Ocean (WIO) and can be considered to be "pristine" ecosystems not subject to anthropogenic pressure. This study characterized their plankton assemblages for the first time, by determining the abundances of microbial (virus, bacteria, heterotrophic protists and phytoplankton) and metazooplankton communities in various lagoon and ocean sites around each island. The Europa lagoon has extensive, productive mangrove forests, which have the highest nutrient concentrations (nitrogen forms, dissolved organic carbon) and whose microbial communities present a peculiar structure and functioning. By means of bioassay experiments, we observed that bacterial production and growth rates are higher in Europa than those reported for the other islands. Tromelin, which lies outside the Mozambique Channel, had the lowest biological productivity, nutrient concentrations, and bacterial growth rates. Multivariate analysis indicated that distinct microbial assemblages occur in association to varying nutrient concentrations. Molecular fingerprinting showed clear discrimination of the structure of the archaea, bacteria and eukaryotes community between the sites. Our results suggest that the geographical distance can influence the diversity of dominant microbial taxa in the WIO.

[Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

PubMed

Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

2018-01-25

Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

PubMed

Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

2016-02-01

Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review.

PubMed

Grengg, Cyrill; Mittermayr, Florian; Ukrainczyk, Neven; Koraimann, Günther; Kienesberger, Sabine; Dietzel, Martin

2018-05-01

Microbial induced concrete corrosion (MICC) is recognized as one of the main degradation mechanisms of subsurface infrastructure worldwide, raising the demand for sustainable construction materials in corrosive environments. This review aims to summarize the key research progress acquired during the last decade regarding the understanding of MICC reaction mechanisms and the development of durable materials from an interdisciplinary perspective. Special focus was laid on aspects governing concrete - micoorganisms interaction since being the central process steering biogenic acid corrosion. The insufficient knowledge regarding the latter is proposed as a central reason for insufficient progress in tailored material development for aggressive wastewater systems. To date no cement-based material exists, suitable to withstand the aggressive conditions related to MICC over its entire service life. Research is in particular needed on the impact of physiochemical material parameters on microbial community structure, growth characteristics and limitations within individual concrete speciation. Herein an interdisciplinary approach is presented by combining results from material sciences, microbiology, mineralogy and hydrochemistry to stimulate the development of novel and sustainable materials and mitigation strategies for MICC. For instance, the application of antibacteriostatic agents is introduced as an effective instrument to limit microbial growth on concrete surfaces in aggressive sewer environments. Additionally, geopolymer concretes are introduced as highly resistent in acid environments, thus representing a possible green alternative to conventional cement-based construction materials. Copyright © 2018 Elsevier Ltd. All rights reserved.

An integrative view of microbiome-host interactions in inflammatory bowel diseases

PubMed Central

Wlodarska, Marta; Kostic, Aleksandar D.; Xavier, Ramnik J.

2015-01-01

Summary The intestinal microbiota, which is composed of bacteria, viruses, and micro-eukaryotes, acts as an accessory organ system with distinct functions along the intestinal tract that are critical for health. This review focuses on how the microbiota drives intestinal disease through alterations in microbial community architecture, disruption of the mucosal barrier, modulation of innate and adaptive immunity, and dysfunction of the enteric nervous system. Inflammatory bowel disease is used as a model system to understand these microbial-driven pathologies, but the knowledge gained in this space is extended to less well studied intestinal diseases that may also have an important microbial component, including environmental enteropathy and chronic colitis-associated colorectal cancer. PMID:25974300

Final Report Real Time Monitoring of Rates of Subsurface Microbial Activity Associated with Natural Attenuation and Electron Donor Availability

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

Lovley, Derek R.

The project was successful in developing new sensing technologies for monitoring rates of microbial activity in soils and sediments and also developed a novel proof-of-concept for monitoring the presence of bioavailable concentrations of a diversity of metabolites and toxic components in sedimentary environments. These studies led not only to publications in the peer-reviewed literature, but also two patent applications and a start-up company.

Comparative evaluation of the indigenous microbial diversity vs. drilling fluid contaminants in the NEEM Greenland ice core.

PubMed

Miteva, Vanya; Burlingame, Caroline; Sowers, Todd; Brenchley, Jean

2014-08-01

Demonstrating that the detected microbial diversity in nonaseptically drilled deep ice cores is truly indigenous is challenging because of potential contamination with exogenous microbial cells. The NEEM Greenland ice core project provided a first-time opportunity to determine the origin and extent of contamination throughout drilling. We performed multiple parallel cultivation and culture-independent analyses of five decontaminated ice core samples from different depths (100-2051 m), the drilling fluid and its components Estisol and Coasol, and the drilling chips collected during drilling. We created a collection of diverse bacterial and fungal isolates (84 from the drilling fluid and its components, 45 from decontaminated ice, and 66 from drilling chips). Their categorization as contaminants or intrinsic glacial ice microorganisms was based on several criteria, including phylogenetic analyses, genomic fingerprinting, phenotypic characteristics, and presence in drilling fluid, chips, and/or ice. Firmicutes and fungi comprised the dominant group of contaminants among isolates and cloned rRNA genes. Conversely, most Proteobacteria and Actinobacteria originating from the ice were identified as intrinsic. This study provides a database of potential contaminants useful for future studies of NEEM cores and can contribute toward developing standardized protocols for contamination detection and ensuring the authenticity of the microbial diversity in deep glacial ice. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Greenhouse gas, animal performance, and bacterial population structure responses to dietary monensin fed to dairy cows.

PubMed

Hamilton, Scott W; DePeters, Edward J; McGarvey, Jeffery A; Lathrop, Jeremy; Mitloehner, Frank M

2010-01-01

The present study investigated the effects of a feed additive and rumen microbial modifier, monensin sodium (monensin), on selected variables in lactating dairy cows. Monensin fed cows (MON, 600 mg d(-1)) were compared with untreated control cows (CON, 0 mg d(-1)) with respect to the effects of monensin on the production of three greenhouse gases (GHG), methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)), along with animal performance (dry matter intake; DMI), milk production, milk components, plasma urea nitrogen (PUN), milk urea nitrogen (MUN), and the microbial population structure of fresh feces. Measurements of GHG were collected at Days 14 and 60 in an environmental chamber simulating commercial dairy freestall housing conditions. Milk production and DMI measurements were collected twice daily over the 60-d experimental period; milk components, PUN, and MUN were measured on Days 14 and 60. The microbial population structure of feces from 6 MON and 6 CON cows was examined on three different occasions (Days 14, 30, and 60). Monensin did not affect emissions of methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)). Over a 24-h period, emissions of CH(4), N(2)O, and CO(2) decreased in both MON and CON groups. Animal performance and the microbial population structure of the animal fresh waste were also unaffected for MON vs. CON cows.

The effect of essential oils on microbial composition and quality of grass carp (Ctenopharyngodon idellus) fillets during chilled storage.

PubMed

Huang, Zhan; Liu, Xiaochang; Jia, Shiliang; Zhang, Longteng; Luo, Yongkang

2018-02-02

Antimicrobial and antioxidant effects of essential oils (oregano, thyme, and star anise) on microbial composition and quality of grass carp fillets were investigated. Essential oils treatment was found to be effective in inhibiting microbial growth, delaying lipid oxidation, and retarding the increase of TVB-N, putrescine, hypoxanthine, and K-value. Based on sensory analysis, shelf-life of grass carp fillets was 6days for control and 8days for treatment groups. Among the essential oils, oregano essential oil exhibited the highest antimicrobial and antioxidant activities. GC-MS analysis of essential oils components revealed that carvacrol (88.64%) was the major component of oregano essential oil. According to the results of high-throughput sequencing, Aeromonas, Glutamicibacter, and Aequorivita were the predominant microbiota in fresh control samples. However, oregano essential oil decreased the relative abundance of Aeromonas, while thyme and star anise essential oils decreased the relative abundance of Glutamicibacter and Aequorivita in fresh treated samples. The microbial composition of both control and treatment groups became less diverse as storage time increased. Aeromonas and Pseudomonas were dominant in spoiled samples and contributed to fish spoilage. Compared to the control, essential oils effectively inhibited the growth of Aeromonas and Shewanella in grass carp fillets during chilled storage. Copyright © 2017 Elsevier B.V. All rights reserved.

Reproduction allocation and potential mechanism of individual allelopathic rice plants in the presence of competing barnyardgrass.

PubMed

Kong, Chui-Hua; Wang, Ming-Li; Wang, Peng; Ni, Han-Wen; Meng, Xiang-Rui

2013-01-01

In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism. At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root-zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples. Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system. Copyright © 2012 Society of Chemical Industry.

The influence of nickel on the bioremediation of multi-component contaminated tropical soil: microcosm and batch bioreactor studies.

PubMed

Taketani, Natália Franco; Taketani, Rodrigo Gouvêa; Leite, Selma Gomes Ferreira; Rizzo, Andrea Camardella de Lima; Tsai, Siu Mui; da Cunha, Cláudia Duarte

2015-07-01

Large petrochemical discharges are responsible for organic and inorganic pollutants in the environment. The purpose of this study was to evaluate the influence of nickel, one of the most abundant inorganic element in crude oil and the main component of hydrogen catalysts for oil refining, on the microbial community structure in artificially petroleum-contaminated microcosms and in solid phase bioreactor studies. In the presence of metals, the oil biodegradation in microcosms was significantly delayed during the first 7 days of operation. Also, increasing amounts of moisture generated a positive influence on the biodegradation processes. The oil concentration, exhibiting the most negative influence at the end of the treatment period. Molecular fingerprinting analyses (denaturing gradient gel electrophoresis--DGGE) indicated that the inclusion of nickel into the contaminated soil promoted direct changes to the microbial community structure. By the end of the experiments, the results of the total petroleum hydrocarbons removal in the bioreactor and the microcosm were similar, but reductions in the treatment times were observed with the bioreactor experiments. An analysis of the microbial community structure by DGGE using various markers showed distinct behaviors between two treatments containing high nickel concentrations. The main conclusion of this study was that Nickel promotes a significant delay in oil biodegradation, despite having only a minor effect over the microbial community.

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine.

PubMed

Liu, Zhibin; Wang, Zhiyao; Lv, Xucong; Zhu, Xiaoping; Chen, Liling; Ni, Li

2018-02-01

Hong Qu, which mainly contains Monascus sp. and other microorganisms, as well as numerous microbial metabolites, is used as the fermentation starter of Hong Qu glutinous rice wine, a traditional alcoholic beverage. Two widely-used types of Hong Qu, namely Wuyi Qu (WYQ) and Gutian Qu (GTQ), were thoroughly compared for their fermentation properties, volatile profiles, and microbiota structures in this study. Significantly higher color value, glucoamylase and α-amylase activities were discovered in WYQ. And substantial variation in volatile components and microbial communities were also observed between them. It was identified that bacterial genus Burkholderia dominated GTQ (71.62%) and Bacillus dominated WYQ (44.73%), while Monascus purpureus was the most abundant fungal species in both types of starters (76.99%). In addition, 213 bacterial genera and 150 fungal species with low-abundance were also detected. Since the Linear Discriminant Analysis Effect Size algorithm, 14 genus-level bacterial taxa and 10 species-level fungal taxa could be utilized to distinguish these two types of starters. Moreover, the potential correlation of the volatile components and microbiota within WYQ and GTQ were further analyzed, by utilizing Partial Least Squares Discriminant Analysis. Ultimately, this study provides detailed insight into the volatile profiles and microbial communities presented in Hong Qu. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial transformation of the Deepwater Horizon oil spill—past, present, and future perspectives

PubMed Central

Kimes, Nikole E.; Callaghan, Amy V.; Suflita, Joseph M.; Morris, Pamela J.

2014-01-01

The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components. PMID:25477866

Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools.

PubMed

Shabarova, Tanja; Widmer, Franco; Pernthaler, Jakob

2013-09-01

We investigated the transformations of the microbial communities in epiphreatic karst cave pools with different flooding frequencies. Fingerprinting of 16S rRNA genes was combined with microscopic and sequence analysis to examine if source water would transport comparable microbial inocula into the pools at consecutive flood events, and to assess possible effects of residence time on the microbial assemblages during stagnant periods. Variability in the concentrations of dissolved organic carbon and conductivity indicated differences between floods and changes of pool water over time. High numbers of Betaproteobacteria affiliated with Methylophilaceae and Comamonadaceae were introduced into the pools during floodings. While the former persisted in the pools, the latter exhibited considerable microdiversification. These Betaproteobacteria might thus represent core microbial groups in karst water. A decrease in the estimated total diversity of the remaining bacterial taxa was apparent after a few weeks of residence: Some were favoured by stagnant conditions, whereas the majority was rapidly outcompeted. Thus, the microbial communities consisted of different components governed by complementary assembly mechanisms (dispersal versus environmental filtering) upon introduction into the pools. High overlap of temporary and persistent community members between samplings from two winters, moreover, reflected the seasonal recurrence of the studied microbial assemblages. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Effects of simulated acid rain on microbial characteristics in a lateritic red soil.

PubMed

Xu, Hua-qin; Zhang, Jia-en; Ouyang, Ying; Lin, Ling; Quan, Guo-ming; Zhao, Ben-liang; Yu, Jia-yu

2015-11-01

A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

NASA Astrophysics Data System (ADS)

Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

2013-08-01

The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

[Soil microbial functional diversity of different altitude Pinus koraiensis forests].

PubMed

Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

2015-12-01

In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

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

Zak, Donald R.

A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO 2 in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use ofmore » genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.« less

Preferential flow in the vadose zone and interface dynamics: Impact of microbial exudates

NASA Astrophysics Data System (ADS)

Li, Biting; Pales, Ashley R.; Clifford, Heather M.; Kupis, Shyla; Hennessy, Sarah; Liang, Wei-Zhen; Moysey, Stephen; Powell, Brian; Finneran, Kevin T.; Darnault, Christophe J. G.

2018-03-01

In the hydrological cycle, the infiltration process is a critical component in the distribution of water into the soil and in the groundwater system. The nonlinear dynamics of the soil infiltration process yield preferential flow which affects the water distribution in soil. Preferential flow is influenced by the interactions between water, soil, plants, and microorganisms. Although the relationship among the plant roots, their rhizodeposits and water transport in soil has been the subject of extensive study, the effect of microbial exudates has been studied in only a few cases. Here the authors investigated the influence of two artificial microbial exudates-catechol and riboflavin-on the infiltration process, particularly unstable fingered flow, one form of preferential flow. Flow experiments investigating the effects of types and concentrations of microbial exudates on unstable fingered flow were conducted in a two-dimensional tank that was filled with ASTM

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

PubMed Central

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

2016-01-01

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. PMID:27052662

Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

PubMed

Stegen, James C; Fredrickson, James K; Wilkins, Michael J; Konopka, Allan E; Nelson, William C; Arntzen, Evan V; Chrisler, William B; Chu, Rosalie K; Danczak, Robert E; Fansler, Sarah J; Kennedy, David W; Resch, Charles T; Tfaily, Malak

2016-04-07

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis

PubMed Central

He, Baokun; Nohara, Kazunari; Ajami, Nadim J.; Michalek, Ryan D.; Tian, Xiangjun; Wong, Matthew; Losee-Olson, Susan H.; Petrosino, Joseph F.; Yoo, Seung-Hee; Shimomura, Kazuhiro; Chen, Zheng

2015-01-01

Dietary fibers are increasingly appreciated as beneficial nutritional components. However, a requisite role of gut microbiota in fiber function and the overall impact of fibers on metabolomic flux remain unclear. We herein showed enhancing effects of a soluble resistant maltodextrin (RM) on glucose homeostasis in mouse metabolic disease models. Remarkably, fecal microbiota transplantation (FMT) caused pronounced and time-dependent improvement in glucose tolerance in RM recipient mice, indicating a causal relationship between microbial remodeling and metabolic efficacy. Microbial 16S sequencing revealed transmissible taxonomic changes correlated with improved metabolism, notably enrichment of probiotics and reduction of Alistipes and Bacteroides known to associate with high fat/protein diets. Metabolomic profiling further illustrated broad changes, including enrichment of phenylpropionates and decreases in key intermediates of glucose utilization, cholesterol biosynthesis and amino acid fermentation. These studies elucidate beneficial roles of RM-dependent microbial remodeling in metabolic homeostasis, and showcase prevalent health-promoting potentials of dietary fibers. PMID:26040234

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments

PubMed Central

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan DW

2008-01-01

Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments. PMID:18717988

Relationship between diet, the gut microbiota, and brain function.

PubMed

Tengeler, Anouk C; Kozicz, Tamas; Kiliaan, Amanda J

2018-04-28

The human intestinal microbiota, comprising trillions of microorganisms, exerts a substantial effect on the host. The microbiota plays essential roles in the function and development of several physiological processes, including those in the brain. A disruption in the microbial composition of the gut has been associated with many metabolic, inflammatory, neurodevelopmental, and neurodegenerative disorders. Nutrition is one of several key factors that shape the microbial composition during infancy and throughout life, thereby affecting brain structure and function. This review examines the effect of the gut microbiota on brain function. The ability of external factors, such as diet, to influence the microbial composition implies a certain vulnerability of the gut microbiota. However, it also offers a potential therapeutic strategy for ameliorating symptoms of mental and physical disorders. Therefore, this review examines the potential effect of nutritional components on gut microbial composition and brain function.

21 CFR 864.2360 - Mycoplasma detection media and components.

Code of Federal Regulations, 2010 CFR

2010-04-01

... SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Cell And Tissue Culture Products... microbial contaminant in cell cultures. (b) Classification. Class I (general controls). These devices are...

[Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere].

PubMed

Zhou, Quan; Wang, Long Chang; Xing, Yi; Ma, Shu Min; Zhang, Xiao Duan; Chen, Jiao; Shi, Chao

2018-03-01

The application of green manure is facing serious problems in purple soil region of southwest China. With the aim to explore the potential application of green manure, we examined the functional characteristics of soil microbial community in a system of Chinese milk vetch intercropped with rape. The innovations are the application of Chinese milk vetch in dry land of the southwest China and the establishment of new planting pattern of rape by providing empirical data. Results showed that the intercropping with Chinese milk vetch decreased the carbon resource use efficiency of microbial community in rape rhizosphere, especially for the utilization of carbohydrates. At the same time, Shannon index, Simpson index, and richness were reduced, but evenness index was increased by intercropping. Those results from cluster analysis and principal component analysis suggest that the soil microbial community composition was significantly different between monocropping and intercropping. The carbohydrates, amino acids and carboxylic acids were the sensitive carbon sources for differentiating the changes of the microbial community induced by monocropping and intercropping. Intercropping Chinese milk vetch could decrease functional activity, change community composition, and reduce diversity of soil microbial community in rape rhizosphere.

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments.

PubMed

Smith, H J; Dieser, M; McKnight, D M; SanClements, M D; Foreman, C M

2018-05-14

Vast expanses of Earth's surface are covered by ice, with microorganisms in these systems affecting local and global biogeochemical cycles. We examined microbial assemblages from habitats fed by glacial meltwater within the McMurdo Dry Valleys, Antarctica, and on the west Greenland Ice Sheet, (GrIS) evaluating potential physicochemical factors explaining trends in community structure. Microbial assemblages present in the different Antarctic dry valley habitats were dominated by Sphingobacteria and Flavobacteria, while Gammaproteobacteria and Sphingobacteria prevailed in west GrIS supraglacial environments. Microbial assemblages clustered by location (Canada Glacier, Cotton Glacier, west GrIS) and were separated by habitat type (i.e. ice, cryoconite holes, supraglacial lakes, sediment, and stream water). Community dissimilarities were strongly correlated with dissolved organic matter (DOM) quality. Microbial meltwater assemblages were most closely associated with different protein-like components of the DOM pool. Microbes in environments with mineral particles (i.e. stream sediments, cryoconite holes) were linked to DOM containing more humic-like fluorescence. Our results demonstrate the establishment of distinct microbial communities within ephemeral glacial meltwater habitats, with DOM-microbe interactions playing an integral role in shaping communities on local and polar spatial scales.

Optimization of biomass composition explains microbial growth-stoichiometry relationships

USGS Publications Warehouse

Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

2011-01-01

Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

Predictors of microbial agents in dust and respiratory health in the Ecrhs.

PubMed

Tischer, Christina; Zock, Jan-Paul; Valkonen, Maria; Doekes, Gert; Guerra, Stefano; Heederik, Dick; Jarvis, Deborah; Norbäck, Dan; Olivieri, Mario; Sunyer, Jordi; Svanes, Cecilie; Täubel, Martin; Thiering, Elisabeth; Verlato, Giuseppe; Hyvärinen, Anne; Heinrich, Joachim

2015-05-02

Dampness and mould exposure have been repeatedly associated with respiratory health. However, less is known about the specific agents provoking or arresting health effects in adult populations. We aimed to assess predictors of microbial agents in mattress dust throughout Europe and to investigate associations between microbial exposures, home characteristics and respiratory health. Seven different fungal and bacterial parameters were assessed in mattress dust from 956 adult ECRHS II participants in addition to interview based home characteristics. Associations between microbial parameters and the asthma score and lung function were examined using mixed negative binomial regression and linear mixed models, respectively. Indoor dampness and pet keeping were significant predictors for higher microbial agent concentrations in mattress dust. Current mould and condensation in the bedroom were significantly associated with lung function decline and current mould at home was positively associated with the asthma score. Higher concentrations of muramic acid were associated with higher mean ratios of the asthma score (aMR 1.37, 95%CI 1.17-1.61). There was no evidence for any association between fungal and bacterial components and lung function. Indoor dampness was associated with microbial levels in mattress dust which in turn was positively associated with asthma symptoms.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen.

PubMed

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V; Sanchez, Laura M; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A; Cichewicz, Robert H; Alexandrov, Theodore; Dorrestein, Pieter C

2016-01-01

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

PubMed Central

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V.; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A.; Cichewicz, Robert H.; Alexandrov, Theodore

2016-01-01

ABSTRACT Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level. PMID:28028548

From Stool Transplants to Next-generation Microbiota Therapeutics

PubMed Central

2014-01-01

The epidemic of Clostridium difficile infection fueled by new virulent strains of the organism has led to increased use of fecal microbiota transplantation (FMT). The procedure is effective for even the most desperate cases, after failure of multiple courses of antibiotics. The approach recognizes microbiota to be integral to normal human physiology, and microbiota being used in FMT represents a new class of therapeutics. Imbalance in the composition and altered activity of the microbiota are associated with many diseases. Consequently, there is growing interest in applying FMT to non-C. difficile indications. However, this may succeed only if microbiota therapeutics are developed systematically, based on mechanistic understanding, and applying updo-date principles of microbial ecology. We discuss two pathways in development of this new therapeutic class: whole microbial communities separated from donor stool and an assembly of specific fecal microorganisms grown in vitro. PMID:24412527

What Does Tympanostomy Tube Placement in Children Teach Us About the Association Between Atopic Conditions and Otitis Media?

PubMed Central

Juhn, Young J.; Wi, Chung-Il

2014-01-01

Otitis media is the most common infection second only to viral upper respiratory infection in the outpatient setting. Tympanostomy tube insertion (TTI) is the most common ambulatory surgical procedure in the United States. While many risk factors for otitis media have been identified, atopic conditions have been under-recognized as risk factors for recurrent and persistent otitis media. Given that asthma and other atopic conditions are the most common chronic conditions during childhood, it is worth examining the association between atopic conditions and risk of otitis media, which can provide insight into how atopic conditions influence the risk of microbial infections. This paper focuses its discussion on otitis media, however it is important that the association between atopic conditions and risk of otitis media be interpreted in the context of the association of atopic conditions with increased risks of various microbial infections. PMID:24816652

Microbiota as a mediator of cancer progression and therapy.

PubMed

Pope, Jillian L; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiota as a mediator of cancer progression and therapy

PubMed Central

Pope, Jillian L.; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. PMID:27554797

Gut microbiota in autoimmunity: potential for clinical applications.

PubMed

Kim, Donghyun; Yoo, Seung-Ah; Kim, Wan-Uk

2016-11-01

Microbial habitation in the human body begins immediately after birth, and adults are colonized by microbes outnumbering human cells by a factor of ten. Especially, intestinal track is a living space for diverse microbial species that have coevolved symbiotically. A principal function of the gut microbiota is to protect the host from harmful bacteria and to provide benefits for the host through several mechanisms, including direct competition for limited nutrients, training of host immune systems to recognize specifically foreign materials and conversion of otherwise indigestible food into energy and absorbable nutrients. Therefore, gut dysbiosis, a bacterial imbalance state, is related with the pathogenesis of various host diseases including autoimmune diseases. In the current review, we highlight the importance of gut microbiota in the normal health and autoimmune diseases. We also discuss regulation of gut dysbiosis and future direction for potential clinical applications, including treatment and diagnostics of autoimmune diseases.

Metalworking fluid-associated hypersensitivity pneumonitis: a workshop summary.

PubMed

Kreiss, K; Cox-Ganser, J

1997-10-01

A workshop discussing eight clusters of hypersensitivity pneumonitis in the automotive industry among metalworking fluid-exposed workers concluded that a risk exists for this granulomatous lung disease where water-based fluids are used and unusual microbial contaminants predominate. Strong candidates for microbial etiology are nontuberculous mycobacteria and fungi. Cases of hypersensitivity pneumonitis occur among cases with other work-related respiratory symptoms and chest diseases. Reversibility of disease has occurred in many cases with exposure cessation, allowing return to work to jobs without metalworking fluid exposures or, in some situations, to jobs without the same metalworking fluid exposures. Cases have been recognized with metalworking fluid exposures generally less than 0.5 mg/m3. The workshop participants identified knowledge gaps regarding risk factors, exposure-response relationships, intervention efficacy, and natural history, as well as surveillance needs to define the extent of the problem in this industry. In the absence of answers to these questions, guidance for prevention is necessarily limited.

Interfacing microbiology and biotechnology. Conference abstracts

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

Maupin, Julia A.

2001-05-19

The Interfacing Microbiology and Biotechnology Conference was attended by over 100 faculty, post-docs, students, and research scientists from the US, Europe, and Latin America. The conference successfully stimulated communication and the dissemination of knowledge among scientists involved in basic and applied research. The focus of the conference was on microbial physiology and genetics and included sessions on C1 metabolism, archaeal metabolism, proteases and chaperones, gene arrays, and metabolic engineering. The meeting provided the setting for in-depth discussions between scientists who are internationally recognized for their research in these fields. The following objectives were met: (1) The promotion of interaction andmore » future collaborative projects among scientists involved in basic and applied research which incorporates microbial physiology, genetics, and biochemistry; (2) the facilitation of communication of new research findings through seminars, posters, and abstracts; (3 ) the stimulation of enthusiasm and education among participants including graduate and undergraduate students.« less

Unrelated facultative endosymbionts protect aphids against a fungal pathogen.

PubMed

Łukasik, Piotr; van Asch, Margriet; Guo, Huifang; Ferrari, Julia; Godfray, H Charles J

2013-02-01

The importance of microbial facultative endosymbionts to insects is increasingly being recognized, but our understanding of how the fitness effects of infection are distributed across symbiont taxa is limited. In the pea aphid, some of the seven known species of facultative symbionts influence their host's resistance to natural enemies, including parasitoid wasps and a pathogenic fungus. Here we show that protection against this entomopathogen, Pandora neoaphidis, can be conferred by strains of four distantly related symbionts (in the genera Regiella, Rickettsia, Rickettsiella and Spiroplasma). They reduce mortality and also decrease fungal sporulation on dead aphids which may help protect nearby genetically identical insects. Pea aphids thus obtain protection from natural enemies through association with a wider range of microbial associates than has previously been thought. Providing resistance against natural enemies appears to be a particularly common way for facultative endosymbionts to increase in frequency within host populations. © 2012 Blackwell Publishing Ltd/CNRS.

Control of adaptive immunity by the innate immune system.

PubMed

Iwasaki, Akiko; Medzhitov, Ruslan

2015-04-01

Microbial infections are recognized by the innate immune system both to elicit immediate defense and to generate long-lasting adaptive immunity. To detect and respond to vastly different groups of pathogens, the innate immune system uses several recognition systems that rely on sensing common structural and functional features associated with different classes of microorganisms. These recognition systems determine microbial location, viability, replication and pathogenicity. Detection of these features by recognition pathways of the innate immune system is translated into different classes of effector responses though specialized populations of dendritic cells. Multiple mechanisms for the induction of immune responses are variations on a common design principle wherein the cells that sense infections produce one set of cytokines to induce lymphocytes to produce another set of cytokines, which in turn activate effector responses. Here we discuss these emerging principles of innate control of adaptive immunity.

Extraterrestrial Life in the Microbial Age

NASA Astrophysics Data System (ADS)

Gronstal, Aaron L.

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

Bacteria beneath the West Antarctic ice sheet.

PubMed

Lanoil, Brian; Skidmore, Mark; Priscu, John C; Han, Sukkyun; Foo, Wilson; Vogel, Stefan W; Tulaczyk, Slawek; Engelhardt, Hermann

2009-03-01

Subglacial environments, particularly those that lie beneath polar ice sheets, are beginning to be recognized as an important part of Earth's biosphere. However, except for indirect indications of microbial assemblages in subglacial Lake Vostok, Antarctica, no sub-ice sheet environments have been shown to support microbial ecosystems. Here we report 16S rRNA gene and isolate diversity in sediments collected from beneath the Kamb Ice Stream, West Antarctic Ice Sheet and stored for 15 months at 4 degrees C. This is the first report of microbes in samples from the sediment environment beneath the Antarctic Ice Sheet. The cells were abundant ( approximately 10(7) cells g(-1)) but displayed low diversity (only five phylotypes), likely as a result of enrichment during storage. Isolates were cold tolerant and the 16S rRNA gene diversity was a simplified version of that found in subglacial alpine and Arctic sediments and water. Although in situ cell abundance and the extent of wet sediments beneath the Antarctic ice sheet can only be roughly extrapolated on the basis of this sample, it is clear that the subglacial ecosystem contains a significant and previously unrecognized pool of microbial cells and associated organic carbon that could potentially have significant implications for global geochemical processes.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

γδ T cells recognize a microbial encoded B cell antigen to initiate a rapid antigen specific Interleukin 17 response

PubMed Central

Zeng, Xun; Wei, Yu-ling; Huang, Jun; Newell, Evan W.; Yu, Hongxiang; Kidd, Brian A.; Kuhns, Michael S.; Waters, Ray W.; Davis, Mark M.; Weaver, Casey T.; Chien, Yueh-hsiu

2012-01-01

Summary γδ T cells contribute uniquely to host immune defense. However, how they function remains an enigma. Although it is unclear what most γδ T cells recognize, common dogma asserts that they recognize self-antigens. While they are the major initial Interleukin-17 (IL-17) producers in infections, it is unclear what is required to trigger these cells to act. Here, we report that a noted B cell antigen, the algae protein-phycoerythrin (PE) is an antigen for murine and human γδ T cells. PE also stained specific bovine γδ T cells. Employing this specificity, we demonstrated that antigen recognition, but not extensive clonal expansion, was required to activate naïve γδ T cells to make IL-17. In this activated state, γδ T cells gained the ability to respond to cytokine signals that perpetuated the IL-17 production. These results underscore the adaptability of lymphocyte antigen receptors and suggest a previously unrecognized antigen-driven rapid response in protective immunity prior to the maturation of classical adaptive immunity. PMID:22960222

Human NOD2 Recognizes Structurally Unique Muramyl Dipeptides from Mycobacterium leprae.

PubMed

Schenk, Mirjam; Mahapatra, Sebabrata; Le, Phuonganh; Kim, Hee Jin; Choi, Aaron W; Brennan, Patrick J; Belisle, John T; Modlin, Robert L

2016-09-01

The innate immune system recognizes microbial pathogens via pattern recognition receptors. One such receptor, NOD2, via recognition of muramyl dipeptide (MDP), triggers a distinct network of innate immune responses, including the production of interleukin-32 (IL-32), which leads to the differentiation of monocytes into dendritic cells (DC). NOD2 has been implicated in the pathogenesis of human leprosy, yet it is not clear whether Mycobacterium leprae, which has a distinct MDP structure, can activate this pathway. We investigated the effect of MDP structure on the innate immune response, finding that infection of monocytes with M. leprae induces IL-32 and DC differentiation in a NOD2-dependent manner. The presence of the proximal l-Ala instead of Gly in the common configuration of the peptide side chain of M. leprae did not affect recognition by NOD2 or cytokine production. Furthermore, amidation of the d-Glu residue did not alter NOD2 activation. These data provide experimental evidence that NOD2 recognizes naturally occurring structural variants of MDP. Copyright © 2016 Schenk et al.

Defining the mRNA recognition signature of a bacterial toxin protein

DOE PAGES

Schureck, Marc A.; Dunkle, Jack A.; Maehigashi, Tatsuya; ...

2015-10-27

Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. In this paper, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop tomore » recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Finally, our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.« less

Defining the mRNA recognition signature of a bacterial toxin protein

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

Schureck, Marc A.; Dunkle, Jack A.; Maehigashi, Tatsuya

Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. In this paper, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop tomore » recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Finally, our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.« less

[Effects of re-vegetation on soil microbial functional diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China.

PubMed

Wen, Dong Xin; Yang, Ning; Yang, Man Yuan

2016-08-01

The aim of the study was to explore the effects of re-vegetation on soil microbial functio-nal diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China. By using the spatial series to replace time series, four typical sampling plots, grass (Setaria viridi, GS), frutex and grass (Lagerstroemia indica-Setaria viridi, FG), frutex (Vitex negundo var. cannabifolia+Robinia pseudoacacia, FX), as well as arbor and frutex (Liquidamdar formosana+Melia azedarach-Vitex negundo var. cannabifolia, AF) community were selected to study the soil microbial functional diversity by using the Biolog-ECO micro-plate technique. The four communities in purple soils on sloping-land were similar and denoted four different re-vegetation stages. The results showed that the soil microbial metabolic activity increased after re-vegetation significantly, and the average well color development (AWCD) which represented soil microbial activity and functional diversity followed the order of AF community＞FX community＞FG community＞GS community at different re-vegetation stages, and followed the order of 0-10 cm ＞10-20 cm in different soil layers. Principal component analysis (PCA) identified that FG and FX community had similar C sources utilization mode and metabolic function, and GS and AF community were diffe-rent. The carbohydrates, amino acids, intermediate metabolites, and secondary metabolites were the main carbon sources separating the two principal component factors. The Shannon species richness index (H), Shannon evenness index (E), Simpson dominance index (D), McIntosh index (U) at four re-vegetation stages were the highest in AF community, the second in FG and FX community, and the lowest in GS community. The results of correlation analysis indicated that the content of soil water content (SWC), soil total organic carbon (STOC), total nitrogen (TN), total phospho-rus (TP) and available phosphorus (AP) had important influence on the soil microbial metabolic function and functional diversity indices. There existed significant correlation between the activities of urease (URE), alk-phosphatase (APE), invertase (INV), catalase (CAT) and the soil microbial metabolic function and functional diversity indices. All the results indicated that re-vegetation could enhance the soil microbial metabolic function, which was beneficial to the reproduction of soil micro-organisms, thereby promoting an increase of soil carbon source utilization intensity.

Microbial Enrichment from Six Hydraulic Fracturing Fluids and Biogeochemical Characteristics of Flowback Waters in Oklahoma Shale Formations

NASA Astrophysics Data System (ADS)

Krzmarzick, M. J.; McCutchan, A.; Carroll, J.; Lozano, T.

2017-12-01

Hydraulic fracturing of oil and gas formations has revolutionized the industry, but little is known regarding the interactions of the microbiology in formations and the hydraulic fracturing chemicals used. In the first part of this study, six representative hydraulic fracturing fluids were incubated in bench scale microcosms with surface soils over six months at 1× concentrations used in the field. These fluids differed greatly in terms of biocide, surfactants, corrosion inhibitors and crosslinking agents (if any). The changes in microbial communities were measured by Illumina 16S rRNA gene analysis and quantitative-PCR. As a whole, the microbial communities enriched were significantly varied between fluids, with the magnitude of the difference tightly linked to the total organic carbon of each fluid. Most enriched bacteria heavily grew within just the first couple of weeks, and belonged to genera well-linked to xenobiotic degradation, such as Azospirillum, Ralstonia, and Comamonas. This, combined with bulk parameters such as chemical oxygen demand of the water, indicates that a significant fraction of these fluids are readily degradable, though individual chemicals were not monitored for recalcitrance. In the second component of this work, the flowback waters from sixteen newly completed wells in south-central Oklahoma were monitored over two months for compositions of boron, dissolved solids, BTEX, chloride, and their microbial communities. As expected, dissolved solids increased over time as the flowback waters became more characteristic of the formation waters. In these wells, boron, a carefully measured component of the fracturing fluid for cross-linking applications, was either stable or increased over time. The microbial community characteristics are pending but will be compared between formations, to the chemical data, and to the results in the bench-top degradation study.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE PAGES

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; ...

2015-07-21

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

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

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Origins of species: acquired genomes and individuality

NASA Technical Reports Server (NTRS)

Margulis, L.

1993-01-01

Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky ("Symbiogenesis" in Russian, 1909) and by Wallin ("Symbionticism", see p. 181, this issue).

The role of lipids in host microbe interactions.

PubMed

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.

Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

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

Firestone, Mary

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbonmore » decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.« less

Microbial Transformation of Esters of Chlorinated Carboxylic Acids

PubMed Central

Paris, D. F.; Wolfe, N. L.; Steen, W. C.

1984-01-01

Two groups of compounds were selected for microbial transformation studies. In the first group were carboxylic acid esters having a fixed aromatic moiety and an increasing length of the alkyl component. Ethyl esters of chlorine-substituted carboxylic acids were in the second group. Microorganisms from environmental waters and a pure culture of Pseudomonas putida U were used. The bacterial populations were monitored by plate counts, and disappearance of the parent compound was followed by gas-liquid chromatography as a function of time. The products of microbial hydrolysis were the respective carboxylic acids. Octanol-water partition coefficients (Kow) for the compounds were measured. These values spanned three orders of magnitude, whereas microbial transformation rate constants (kb) varied only 50-fold. The microbial rate constants of the carboxylic acid esters with a fixed aromatic moiety increased with an increasing length of alkyl substituents. The regression coefficient for the linear relationships between log kb and log Kow was high for group 1 compounds, indicating that these parameters correlated well. The regression coefficient for the linear relationships for group 2 compounds, however, was low, indicating that these parameters correlated poorly. PMID:16346459

The Lectin Pathway of Complement and Rheumatic Heart Disease

PubMed Central

Beltrame, Marcia Holsbach; Catarino, Sandra Jeremias; Goeldner, Isabela; Boldt, Angelica Beate Winter; de Messias-Reason, Iara José

2014-01-01

The innate immune system is the first line of host defense against infection and is comprised of humoral and cellular mechanisms that recognize potential pathogens within minutes or hours of entry. The effector components of innate immunity include epithelial barriers, phagocytes, and natural killer cells, as well as cytokines and the complement system. Complement plays an important role in the immediate response against microorganisms, including Streptococcus sp. The lectin pathway is one of three pathways by which the complement system can be activated. This pathway is initiated by the binding of mannose-binding lectin (MBL), collectin 11 (CL-K1), and ficolins (Ficolin-1, Ficolin-2, and Ficolin-3) to microbial surface oligosaccharides and acetylated residues, respectively. Upon binding to target molecules, MBL, CL-K1, and ficolins form complexes with MBL-associated serine proteases 1 and 2 (MASP-1 and MASP-2), which cleave C4 and C2 forming the C3 convertase (C4b2a). Subsequent activation of complement cascade leads to opsonization, phagocytosis, and lysis of target microorganisms through the formation of the membrane-attack complex. In addition, activation of complement may induce several inflammatory effects, such as expression of adhesion molecules, chemotaxis and activation of leukocytes, release of reactive oxygen species, and secretion of cytokines and chemokines. In this chapter, we review the general aspects of the structure, function, and genetic polymorphism of lectin-pathway components and discuss most recent understanding on the role of the lectin pathway in the predisposition and clinical progression of Rheumatic Fever. PMID:25654073

Students' Abstraction in Recognizing, Building with and Constructing a Quadrilateral

ERIC Educational Resources Information Center

Budiarto, Mega Teguh; Rahaju, Endah Budi; Hartono, Sugi

2017-01-01

This study aims to implement empirically students' abstraction with socio-cultural background of Indonesia. Abstraction is an activity that involves a vertical reorganization of previously constructed mathematics into a new mathematical structure. The principal components of the model are three dynamic nested epistemic actions: recognizing,…

Hydrolytic microbial communities in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

2014-05-01

Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional time), the most significant one is moisture. Moisture levels providing maximum activity of a hydrolytic microbial complex depend on the soil type. Development of a hydrolytic microbial complex occurs in a very wide moisture range - from values close to field capacity to those close to the wilting moisture point. The functional role of mycelial actinobacteria in the metabolism of chitin consists, on the one hand, in active decomposition of this biopolymer, and on the other hand, in the regulation of microbial hydrolytic complex activity through the production of biologically active regulatory metabolites, which occurs in a wide range of environmental parameters (moisture, temperature, organic matter, successional time). Experimental design is applicable to identify in situ optimal values of environmental factors that considerably affect the functional parameters of hydrolytic microbial complexes.

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

USGS Publications Warehouse

Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

2011-01-01

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

Imaging and Analytical Approaches for Characterization of Soil Mineral Weathering

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

Dohnalkova, Alice; Arey, Bruce; Varga, Tamas

Soil minerals weathering is the primary natural source of nutrients necessary to sustain productivity in terrestrial ecosystems. Soil microbial communities increase soil mineral weathering and mineral-derived nutrient availability through physical and chemical processes. Rhizosphere, the zone immediately surrounding plant roots, is a biogeochemical hotspot with microbial activity, soil organic matter production, mineral weathering, and secondary phase formation all happening in a small temporally ephemeral zone of steep geochemical gradients. The detailed exploration of the micro-scale rhizosphere is essential to our better understanding of large-scale processes in soils, such as nutrient cycling, transport and fate of soil components, microbial-mineral interactions, soilmore » erosion, soil organic matter turnover and its molecular-level characterization, and predictive modeling.« less

Microbial innovations in the world of food.

PubMed

Kawasaki, Hisashi; Ueda, Kenji

2017-01-01

Technological developments in Japan based on the results of microbial research were a major pillar supporting the postwar industrial revolution. The wellspring of these advancements was the sophisticated technology used in traditional brewing, a foundation of the characteristic Japanese food culture. In this manuscript, we will describe the fermentative production of amino acids and nucleic acids following the discovery of the umami component so distinct in Japanese cuisine, which finally revealed the true power of microbial production. Thereafter, we will describe acetic acid production stemming from brewed vinegar production and the fermentative production of some other organic acids. Finally, we will delve into the massive scale of innovations achieved by the discovery of valuable micro-organisms and how they have affected the field of food.

Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

PubMed Central

Matsen IV, Frederick A.; Evans, Steven N.

2013-01-01

Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome. PMID:23505415

Fresh squeezed orange juice odor: a review.

PubMed

Perez-Cacho, Pilar Ruiz; Rouseff, Russell L

2008-08-01

Fresh orange juice is a highly desirable but unstable product. This review examines analytical findings, odor activity, and variations due to cultivar, sampling methods, manner of juicing, plus possible enzymatic and microbial artifacts. Initial attempts to characterize orange juice odor were based on volatile quantitation and overemphasized the importance of high concentration volatiles. Although over 300 volatiles have been reported from GC-MS analytical studies, this review presents 36 consensus aroma active components from GC-olfactometry studies consisting of 14 aldehydes, 7 esters, 5 terpenes, 6 alcohols, and 4 ketones. Most are trace (microg/L) components. (+)-Limonene is an essential component in orange juice odor although its exact function is still uncertain. Total amounts of volatiles in mechanically squeezed juices are three to 10 times greater than hand-squeezed juices because of elevated peel oil levels. Elevated peel oil changes the relative proportion of several key odorants. Odor active components from solvent extraction studies differ from those collected using headspace techniques as they include volatiles with low vapor pressure such as vanillin. Some reported odorants such as 2,3-butanedione are microbial contamination artifacts. Orange juice odor models confirm that fresh orange aroma is complex as the most successful models contain 23 odorants.

Effect of rice straw application on microbial community and activity in paddy soil under different water status.

PubMed

Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Yao, Huaiying

2016-03-01

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

PubMed

Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

2012-09-01

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

Calibration procedure of Hukseflux SR25 to Establish the Diffuse Reference for the Outdoor Broadband Radiometer Calibration

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

Reda, Ibrahim M.; Andreas, Afshin M.

2017-08-01

Accurate pyranometer calibrations, traceable to internationally recognized standards, are critical for solar irradiance measurements. One calibration method is the component summation method, where the pyranometers are calibrated outdoors under clear sky conditions, and the reference global solar irradiance is calculated as the sum of two reference components, the diffuse horizontal and subtended beam solar irradiances. The beam component is measured with pyrheliometers traceable to the World Radiometric Reference, while there is no internationally recognized reference for the diffuse component. In the absence of such a reference, we present a method to consistently calibrate pyranometers for measuring the diffuse component. Themore » method is based on using a modified shade/unshade method and a pyranometer with less than 0.5 W/m2 thermal offset. The calibration result shows that the responsivity of Hukseflux SR25 pyranometer equals 10.98 uV/(W/m2) with +/-0.86 percent uncertainty.« less

Pyrosequencing analysis of the microbial diversity of airag, khoormog and tarag, traditional fermented dairy products of mongolia.

PubMed

Oki, Kaihei; Dugersuren, Jamyan; Demberel, Shirchin; Watanabe, Koichi

2014-01-01

Here, we used pyrosequencing to obtain a detailed analysis of the microbial diversities of traditional fermented dairy products of Mongolia. From 22 Airag (fermented mare's milk), 5 Khoormog (fermented camel's milk) and 26 Tarag (fermented milk of cows, goats and yaks) samples collected in the Mongolian provinces of Arhangai, Bulgan, Dundgobi, Tov, Uburhangai and Umnugobi, we obtained a total of 81 operational taxonomic units, which were assigned to 15 families, 21 genera and 41 species in 3 phyla. The genus Lactobacillus is a core bacterial component of Mongolian fermented milks, and Lactobacillus helveticus, Lactobacillus kefiranofaciens and Lactobacillus delbrueckii were the predominant species of lactic acid bacteria (LAB) in the Airag, Khoormog and Tarag samples, respectively. By using this pyrosequencing approach, we successfully detected most LAB species that have been isolated as well as seven LAB species that have not been found in our previous culture-based study. A subsequent analysis of the principal components of the samples revealed that L. delbrueckii, L. helveticus, L. kefiranofaciens and Streptococcus thermophilus were the main factors influencing the microbial diversity of these Mongolian traditional fermented dairy products and that this diversity correlated with the animal species from which the milk was sourced.

[Spring water quality assessment regarding the problem of endemic fluorosis].

PubMed

Leshchenko, D V; Mialo, O A; Beliakova, M B; Beliaeva, E A; Samoukina, A M; Chervinets, Iu V; Ivanova, O V

2013-01-01

A possible variant for reducing the consumption of fluoride by population of Tver region is the use of water with low fluoride content, such as spring water. Assessment of drinking suitability of spring water (the content of physiologically important mineral elements and microbial purity) is relevant to our region. Water samples from 6 spring-water source of Tver region were studied during the year. The content of fluoride and calcium were measured by using an ion-selective electrodes. Microbiological purity tested by the presence of total coliform bacteria, thermotolerant coliform bacteria, coliphages and total microbial numbers. The analysis of some mineral components in spring water of Tver region showed that calcium content was in range 33-88 mg/l, that satisfied the recommended value; fluoride concentration is less then 0.5 mg/l. In all spring water samples total coliforms, thermotolerant coliforms and coliphages were absent. The total microbial number was in standard range, except of two spring-water source in the autumn and summer. The data suppose that spring water of Tver region can be used as a component of diet normalizing the fluoride consumption at risk of dental fluorosis in children.

Gut epithelial inducible heat-shock proteins and their modulation by diet and the microbiota

PubMed Central

Arnal, Marie-Edith

2016-01-01

The epidemic of metabolic diseases has raised questions about the interplay between the human diet and the gut and its microbiota. The gut has two vital roles: nutrient absorption and intestinal barrier function. Gut barrier defects are involved in many diseases. Excess energy intake disturbs the gut microbiota and favors body entry of microbial compounds that stimulate chronic metabolic inflammation. In this context, the natural defense mechanisms of gut epithelial cells and the potential to boost them nutritionally warrant further study. One such important defense system is the activation of inducible heat-shock proteins (iHSPs) which protect the gut epithelium against oxidative stress and inflammation. Importantly, various microbial components can induce the expression of iHSPs. This review examines gut epithelial iHSPs as the main targets of microbial signals and nutrients and presents data on diseases involving disturbances of gut epithelial iHSPs. In addition, a broad literature analysis of dietary modulation of gut epithelial iHSPs is provided. Future research aims should include the identification of gut microbes that can optimize gut-protective iHSPs and the evaluation of iHSP-mediated health benefits of nutrients and food components. PMID:26883882

Antimicrobial activity and determination of bioactive components from marine Alcaligenes faecalis extract against a sulfate-reducing bacteria

NASA Astrophysics Data System (ADS)

AbdSharad, Ali; Usup, Gires; Sahrani, Fathul Karim; Ahmad, Asmat

2016-11-01

Biogenic souring and microbial-influenced corrosion is a common scenario in petroleum reservoir. The serious threat normally comes from sulfate-reducing bacteria (SRB). Alcaligenes faecalis was tested in this study for the ability to inhibit the growth of SRB. Ethyl acetate extraction of A. faecalis grown in marine broth was carried out to produce crude ethyl acetate of A. faecalis (CEAF). CEAF was diluted at concentrations 0.2-12.8 mg/mL and was tested for anti-microbial activity by microdilution susceptibility tests in 96-wells plate. CEAF was then analyzed by Gas Chromatography Mass Spectrometry (GC-MS). The microdilution susceptibility tests showed that the crude have anti- microbial activities on SRB. CEAF showed immediate killing effect against SRB in liquid medium which suggest the presence of active chemical compounds with antimicrobial activity. The GC-MS analysis showed the presence of 20 different chemical compounds in CEAF, The major components in CEAF can be related to antimicrobial, antifungal, antioxidant, pesticide, metabolism, toxicity, anticancer and corrosion inhibition activities. In conclusion, crude ethyl acetate extract of A. faecalis has the ability to inhibit SRB growth.

Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review.

PubMed

Mosele, Juana I; Macià, Alba; Motilva, Maria-José

2015-09-18

Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced diets are associated with undesirable changes in gut metabolism that could be detrimental to intestinal health. In terms of explaining the possible effects of non-absorbed phenolic compounds, we have also gathered information regarded their influence on the local metabolism. For this purpose, a number of issues are discussed. Firstly, we consider the possible implications of phenolic compounds in the metabolism of colonic products, such as short chain fatty acids (SCFA), sterols (cholesterol and bile acids), and microbial products of non-absorbed proteins. Due to their being recognized as affective antioxidant and anti-inflammatory agents, the ability of phenolic compounds to counteract or suppress pro-oxidant and/or pro-inflammatory responses, triggered by bowel diseases, is also presented. The modulation of gut microbiota through dietetic maneuvers including phenolic compounds is also commented on. Although the available data seems to assume positive effects in terms of gut health protection, it is still insufficient for solid conclusions to be extracted, basically due to the lack of human trials to confirm the results obtained by the in vitro and animal studies. We consider that more emphasis should be focused on the study of phenolic compounds, particularly in their microbial metabolites, and their power to influence different aspects of gut health.

Remote Sensing between Liver and Intestine: Importance of Microbial Metabolites

PubMed Central

Fu, Zidong Donna; Cui, Julia Yue

2017-01-01

Recent technological advancements including metagenomics sequencing and metabolomics have allowed the discovery of critical functions of gut microbiota in obesity, malnutrition, neurological disorders, asthma, and xenobiotic metabolism. Classification of the human gut microbiome into distinct “enterotypes” has been proposed to serve as a new paradigm for understanding the interplay between microbial variation and human disease phenotypes, as many organs are affected by gut microbiota modifications during the pathogenesis of diseases. Gut microbiota remotely interacts with liver and other metabolic organs of the host through various microbial metabolites that are absorbed into the systemic circulation. Purpose of review The present review summarizes recent literature regarding the importance of gut microbiota in modulating the physiological and pathological responses of various host organs, and describes the functions of the known microbial metabolites that are involved in this remote sensing process, with a primary focus on the gut microbiota-liver axis. Recent findings Under physiological conditions, gut microbiota modulates the hepatic transcriptome, proteome, and metabolome, most notably down-regulating cytochrome P450 3a mediated xenobiotic metabolism. Gut microbiome also modulates the rhythmicity in liver gene expression, likely through microbial metabolites, such as butyrate and propionate that serve as epigenetic modifiers. Additionally, the production of host hormones such as primary bile acids and glucagon like peptide 1 is altered by gut microbiota to modify intermediary metabolism of the host. Summary Dysregulation of gut microbiota is implicated in various liver diseases such as alcoholic liver disease, non-alcoholic steatohepatitis, liver cirrhosis, cholangitis, and liver cancer. Gut microbiota modifiers such as probiotics and prebiotics are increasingly recognized as novel therapeutic modalities for liver and other types of human diseases. PMID:28983453

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept

PubMed Central

Kristoffersen, Jon B.; Oulas, Anastasis; De Troch, Marleen; Arvanitidis, Christos

2017-01-01

Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane’s Artenminimum (“species minimum”) concept. It was developed for the Baltic Sea, one of the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane’s. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane’s concept. PMID:29043106

Linking Sediment Microbial Communities to Carbon Cycling in High-Latitude Lakes

NASA Astrophysics Data System (ADS)

Emerson, J. B.; Varner, R. K.; Johnson, J. E.; Owusu-Dommey, A.; Binder, M.; Woodcroft, B. J.; Wik, M.; Freitas, N. L.; Boyd, J. A.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

2015-12-01

It is well recognized that thawing permafrost peatlands are likely to provide a positive feedback to climate change via CH4 and CO2 emissions. High-latitude lakes in these landscapes have also been identified as sources of CH4 and CO2 loss to the atmosphere. To investigate microbial contributions to carbon loss from high-latitude lakes, we characterized sediment geochemistry and microbiota via cores collected from deep and shallow regions of two lakes (Inre Harrsjön and Mellersta Harrsjön) in Arctic Sweden in July, 2012. These lakes are within the Stordalen Mire long-term ecological area, a focal site for investigating the impacts of climate change-related permafrost thaw, and the lakes in this area are responsible for ~55% of the CH4 loss from this hydrologically interconnected system. Across 40 samples from 4 to 40 cm deep within four sediment cores, Illumina 16S rRNA gene sequencing revealed that the sedimentary microbiota was dominated by candidate phyla OP9 and OP8 (Atribacteria and Aminicenantes, respectively, including putative fermenters and anaerobic respirers), predicted methanotrophic Gammaproteobacteria, and predicted methanogenic archaea from the Thermoplasmata Group E2 clade. We observed some overlap in community structure with nearby peatlands, which tend to be dominated by methanogens and Acidobacteria. Sediment microbial communities differed significantly between lakes, by overlying lake depth (shallow vs. deep), and by depth within a core, with each trend corresponding to parallel differences in biogeochemical measurements. Overall, our results support the potential for significant microbial controls on carbon cycling in high-latitude lakes associated with thawing permafrost, and ongoing metagenomic analyses of focal samples will yield further insight into the functional potential of these microbial communities and their dominant members.

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

PubMed Central

Ionescu, Danny; Siebert, Christian; Polerecky, Lubos; Munwes, Yaniv Y.; Lott, Christian; Häusler, Stefan; Bižić-Ionescu, Mina; Quast, Christian; Peplies, Jörg; Glöckner, Frank Oliver; Ramette, Alban; Rödiger, Tino; Dittmar, Thorsten; Oren, Aharon; Geyer, Stefan; Stärk, Hans-Joachim; Sauter, Martin; Licha, Tobias; Laronne, Jonathan B.; de Beer, Dirk

2012-01-01

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit. PMID:22679498

Shape recognition of microbial cells by colloidal cell imprints

NASA Astrophysics Data System (ADS)

Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

2013-08-01

We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources.

PubMed

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe(2+) ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD(+) through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats.

Potable Water Reuse: What Are the Microbiological Risks?

PubMed

Nappier, Sharon P; Soller, Jeffrey A; Eftim, Sorina E

2018-06-01

With the increasing interest in recycling water for potable reuse purposes, it is important to understand the microbial risks associated with potable reuse. This review focuses on potable reuse systems that use high-level treatment and de facto reuse scenarios that include a quantifiable wastewater effluent component. In this article, we summarize the published human health studies related to potable reuse, including both epidemiology studies and quantitative microbial risk assessments (QMRA). Overall, there have been relatively few health-based studies evaluating the microbial risks associated with potable reuse. Several microbial risk assessments focused on risks associated with unplanned (or de facto) reuse, while others evaluated planned potable reuse, such as indirect potable reuse (IPR) or direct potable reuse (DPR). The reported QMRA-based risks for planned potable reuse varied substantially, indicating there is a need for risk assessors to use consistent input parameters and transparent assumptions, so that risk results are easily translated across studies. However, the current results overall indicate that predicted risks associated with planned potable reuse scenarios may be lower than those for de facto reuse scenarios. Overall, there is a clear need to carefully consider water treatment train choices when wastewater is a component of the drinking water supply (whether de facto, IPR, or DPR). More data from full-scale water treatment facilities would be helpful to quantify levels of viruses in raw sewage and reductions across unit treatment processes for both culturable and molecular detection methods.

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources

PubMed Central

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe2+ ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD+ through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats. PMID:26500609

Microbial Incorporation of Fatty Acids Derived From n-Alkanes Into Glycerides and Waxes

PubMed Central

Davis, J. B.

1964-01-01

When n-alkanes with 13 to 20 carbon atoms were fed to a Nocardia closely related to N. salmonicolor, the produced cellular triglycerides and aliphatic waxes invariably contained fatty acids with an even or an odd number of carbon atoms subject to this feature of the n-alkane substrate. Beta-oxidation and C2 addition are both operative, as evidenced by the spectra of fatty acids incorporated into the cellular lipid components. There is no distinction in the rate of microbial incorporation of the odd-or even-numbered carbon chains. The fatty acids are apparently directly derived from the long chain n-alkanes, rather than synthesized via the classic C2-condensation route. The alcohol component of waxes produced by the Nocardia is invariably of the same chain length as the n-alkane substrate. PMID:14170957

Planetary quarantine

NASA Technical Reports Server (NTRS)

1971-01-01

Methods for presterilization cleaning or decontamination of spacecraft hardware to reduce microbial load, without harming materials or spacecraft components, are investigated. Three methods were considered: (1) chemicals in liquid form, relying on physical removal as well as bacterial or bacteriostatic action; (2) chemicals used in the gaseous phase, relying on bacterial activity; and (3) mechanical cleaning relying on physical removal of organisms. These methods were evaluated in terms of their effectiveness in microbial burden reduction and compatibility with spacecraft hardware. Results show chemical methods were effective against spore microorganisms but were harmful to spacecraft materials. Mechanical methods were also effective with the degree depending upon the type of instrument employed. Mechanical methods caused problems in handling the equipment, due to vacuum pressure damaging the very thin layered materials used for shielding, and the bristles used in the process caused streaks or abrasions on some spacecraft components.

Technological approaches to optimize colonial resistance control for humans in artificial environment

NASA Astrophysics Data System (ADS)

Viacheslav, Ilyin; Skedina, Marina; Muokhamedieva, Lana; Gegenava, Anna; Mardanov, Robert

Infectious safety of humans in confined habitat is one of the most important problems of contem-porary space medicine. It is known that together with increasing of space station exploration increases the risc of nosocomial-like strains formation. Investigations analyzing spaceflights on spaceships Spollo, Soyuz, Saljut, Mir revealed shifts in content of human microflora, decreas-ing of protective microflora and immunity, translocation of conventional pathogens, mainly, spaphylococci, to different biotopes. At present time, control on microbial state of cosmo-nauts is performed on Earth before and after the flight, and once in flight 5 days prior to landing. This seems to me not enough. Together with increasing of spaceflight duration it starts to be mostly actual to develop contemporary technological approaches to perform op-erative control on colonial resistance of cosmonauts. It is preferable that these means and measures should be simple and biologically safe, i.e. non-cultivating. One of such technologies is express-diagnostics of human disbiotic shifts with the aid of automatised method of digital treatment of microscopy microbial images. At present the standardized swab and automatised recognizing of microbial cells with calculation of quantitative rate of different microbial groups in tested materials and it's transformation via telecommunication channels. Knowing content and quantity of microbes in tested biotope, one can forecast risk of infection development and give countermeasures recommendation. Other prospective technology -gaseous chromatomass spectrometry which basing on analysis of different microbial volatile lipid acids can determine quantity and content of microbes. These markers are unique for different microbial specia and allow to isolate them from plenty of bioobjects. This technology was also successfully tested for space crewmembers in groundbase studies and in spaceflight. The data revealed increasing of pathogenicity potential on microflora in spaceflight, which was comparable to data obtained by classic bacteriology methods. The testings results allow to recommend this technology for colonial resistance control for humans in artificial environment.

Separation and characterization of the immunostimulatory components in unpolished rice black vinegar (kurozu).

PubMed

Hashimoto, Masahito; Obara, Kyoko; Ozono, Mami; Furuyashiki, Maiko; Ikeda, Tsuyoshi; Suda, Yasuo; Fukase, Koichi; Fujimoto, Yukari; Shigehisa, Hiroshi

2013-12-01

Unpolished rice black vinegar (kurozu), a traditional Japanese vinegar, is considered to have beneficial health effects. Kurozu is produced via a static fermentation process involving the saccharification of rice by Aspergillus oryzae, alcohol fermentation by Saccharomyces cerevisiae, and the oxidation of ethanol to acetic acid by acetic acid bacteria such as Acetobacter pasteurianus. Since this process requires about 6 months' fermentation and then over a year of aging, most of these organisms die during the production process and so microbial components, which might stimulate the innate immune system, are expected to be present in the vinegar. In this study, we investigated whether microbial components are present in kurozu, and after confirming this we characterized their immunostimulatory activities. Lyophilized kurozu stimulated murine spleen cells to produce tumor necrosis factor (TNF)-α, at least in part, via Toll-like receptor (TLR) 2 and the Nod-like receptors NOD1 and 2. The active components associated with TLR2 activation were concentrated by Triton X-114-water phase partitioning and hydrophobic interaction chromatography on Octyl Sepharose. TLR4-activating components were also enriched by these methods. The concentrated preparation stimulated murine spleen cells to produce TNF-α and interferon (IFN)-γ. These results indicate that long-term fermented kurozu contains immunostimulatory components and that the TLR2 and TLR4-activating immunostimulatory components of kurozu are hydrophobic. These components might be responsible for the beneficial health effects of kurozu. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The Gut Microbiota: Ecology and Function

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

Willing, B.P.; Jansson, J.K.

The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowelmore » diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms inhabiting the gut. Recent studies have revealed new insights into the membership of the gut microbial community, interactions within that community, as well as mechanisms of interaction with the host. This chapter focuses on the microbial ecology of the gut, with an emphasis on information gleaned from recent molecular studies.« less

Stable and non-competitive association of Saccharomyces cerevisiae, Candida milleri and Lactobacillus sanfranciscensis during manufacture of two traditional sourdough baked goods.

PubMed

Venturi, Manuel; Guerrini, Simona; Vincenzini, Massimo

2012-08-01

The microbiota occurring in all the manufacturing phases of two Italian sourdough sweet-leavened baked goods (a typical Genoese dry biscuit, Lagaccio, and a soft stuffed North Italian typical cake, Panettone) were investigated over a period of three years. The two sourdough mother sponges were characterized by the stable presence of three dominant microbial species in potential competition for carbohydrates: Lactobacillus sanfranciscensis, Candida milleri, and Saccharomyces cerevisiae. Genotypic and phenotypic characterizations of microbial isolates pointed out that each mother sponge harbored its own strains, well distinguishable by molecular methods of analysis but not differing in their main metabolic properties from those known for the corresponding species. The microbial and biochemical evolution during the whole production protocol of both manufactures demonstrated that the three microbial species grew at almost the same growth rates, without exhausting any of the main carbon substrates (maltose, glucose and fructose). The quite similar growth dynamics under practical conditions and the constant presence of all fermentable carbohydrates were recognized as responsible for the stable non competitive association of maltose-positive and maltose-negative species in both sourdoughs. However, the two sourdoughs were characterized by quite different LAB to yeast ratio, with values significantly higher in Panettone than in Lagaccio. The cause of this difference could mainly be ascribed to the temperature of the mother sponge regeneration phase, that, in the case of Panettone manufacture, occurred under conditions of moderate refrigeration. Copyright © 2012 Elsevier Ltd. All rights reserved.

Microbial endocrinology: Host-microbiota neuroendocrine interactions influencing brain and behavior.

PubMed

Lyte, Mark

2014-01-01

The ability of microorganisms, whether present as commensals within the microbiota or introduced as part of a therapeutic regimen, to influence behavior has been demonstrated by numerous laboratories over the last few years. Our understanding of the mechanisms that are responsible for microbiota-gut-brain interactions is, however, lacking. The complexity of the microbiota is, of course, a contributing factor. Nonetheless, while microbiologists approaching the issue of microbiota-gut-brain interactions in the behavior well recognize such complexity, what is often overlooked is the equal complexity of the host neurophysiological system, especially within the gut which is differentially innervated by the enteric nervous system. As such, in the search for common mechanisms by which the microbiota may influence behavior one may look for mechanisms which are shared by both host and microbiota. Such interkingdom signaling can be found in the shared production of neurochemical mediators that are found in both eukaryotes and prokaryotes. The study of the production and recognition of neurochemicals that are exactly the same in structure to those produced in the vertebrate organisms is known as microbial endocrinology. The examination of the microbiota from the vantage point of host-microbiota neuroendocrine interactions cannot only identify new microbial endocrinology-based mechanisms by which the microbiota can influence host behavior, but also lead to the design of interventions in which the composition of the microbiota may be modulated in order to achieve a specific microbial endocrinology-based profile beneficial to overall host behavior.

Sedimentary organic biomarkers suggest detrimental effects of PAHs on estuarine microbial biomass during the 20th century in San Francisco Bay, CA, USA

USGS Publications Warehouse

Nilsen, Elena B.; Rosenbauer, Robert J.; Fuller, Christopher C.; Jaffe, Bruce E.

2014-01-01

Hydrocarbon contaminants are ubiquitous in urban aquatic ecosystems, and the ability of some microbial strains to degrade certain polycyclic aromatic hydrocarbons (PAHs) is well established. However, detrimental effects of petroleum hydrocarbon contamination on nondegrader microbial populations and photosynthetic organisms have not often been considered. In the current study, fatty acid methyl ester (FAME) biomarkers in the sediment record were used to assess historical impacts of petroleum contamination on microbial and/or algal biomass in South San Francisco Bay, CA, USA. Profiles of saturated, branched, and monounsaturated fatty acids had similar concentrations and patterns downcore. Total PAHs in a sediment core were on average greater than 20× higher above ∼200 cm than below, which corresponds roughly to the year 1900. Isomer ratios were consistent with a predominant petroleum combustion source for PAHs. Several individual PAHs exceeded sediment quality screening values. Negative correlations between petroleum contaminants and microbial and algal biomarkers – along with high trans/cis ratios of unsaturated FA, and principle component analysis of the PAH and fatty acid records – suggest a negative impacts of petroleum contamination, appearing early in the 20th century, on microbial and/or algal ecology at the site.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

DAMPs, MAMPs, and NAMPs in plant innate immunity.

PubMed

Choi, Hyong Woo; Klessig, Daniel F

2016-10-26

Multicellular organisms have evolved systems/mechanisms to detect various forms of danger, including attack by microbial pathogens and a variety of pests, as well as tissue and cellular damage. Detection via cell-surface receptors activates an ancient and evolutionarily conserved innate immune system. Potentially harmful microorganisms are recognized by the presence of molecules or parts of molecules that have structures or chemical patterns unique to microbes and thus are perceived as non-self/foreign. They are referred to as Microbe-Associated Molecular Patterns (MAMPs). Recently, a class of small molecules that is made only by nematodes, and that functions as pheromones in these organisms, was shown to be recognized by a wide range of plants. In the presence of these molecules, termed Nematode-Associated Molecular Patterns (NAMPs), plants activate innate immune responses and display enhanced resistance to a broad spectrum of microbial and nematode pathogens. In addition to pathogen attack, the relocation of various endogenous molecules or parts of molecules, generally to the extracellular milieu, as a result of tissue or cellular damage is perceived as a danger signal, and it leads to the induction of innate immune responses. These relocated endogenous inducers are called Damage-Associated Molecular Patterns (DAMPs). This mini-review is focused on plant DAMPs, including the recently discovered Arabidopsis HMGB3, which is the counterpart of the prototypic animal DAMP HMGB1. The plant DAMPs will be presented in the context of plant MAMPs and NAMPs, as well as animal DAMPs.

The plant microbiome explored: implications for experimental botany

PubMed Central

Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

2017-01-01

The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies. PMID:26547794

Potential rainfall-intensity and pH-driven shifts in the apparent fluorescent composition of dissolved organic matter in rainwater.

PubMed

Zhou, Yongqiang; Yao, Xiaolong; Zhang, Yibo; Shi, Kun; Zhang, Yunlin; Jeppesen, Erik; Gao, Guang; Zhu, Guangwei; Qin, Boqiang

2017-05-01

Perturbations of rainwater chromophoric dissolved organic matter (CDOM) fluorescence induced by changes in rainfall intensity and pH were investigated by field observations and laboratory pH titrations. Microbial humic-like fluorophores dominated the rainwater CDOM pool, followed by tryptophan-like and tyrosine-like substances. Increased rainfall intensity had notable dilution effects on all six fluorescent components (C1-C6) identified using parallel factor (PARAFAC) analysis, the effect being especially pronounced for the microbial humic-like C1, tryptophan-like C3, and tyrosine-like C5. The results also indicated that increasing pH from 7 to 9 led to decreased fluorescence intensity (F max ) of all the six components, while a pH increase from 5 to 7, resulted in increasing F max of terrestrial humic-like C2, tyrosine-like C5, and tryptophan-like C6 and decreasing microbial humic-like C1, tryptophan-like C3, and fulvic-like C4. Two-dimensional correlation spectroscopy (2D-COS) demonstrated that synchronous fluorescence responded first to pH modifications at fulvic-like wavelength (λ Ex /λ Em  = ∼316/416 nm), followed by tyrosine-like wavelength (λ Ex /λ Em  = ∼204/304 nm), tryptophan-like wavelength (λ Ex /λ Em  = ∼226/326 nm), microbial humic-like wavelength (∼295/395 nm), and finally terrestrial humic-like wavelength (∼360/460 nm). Our results suggest that a decrease in areas affected by acid rain in South China occurring at present may possibly result in apparent compositional changes of CDOM fluorescence. The decreased rainfall in South-West China and increased rainfall in North-West China during the past five decades may possibly accordingly result in increased and decreased F max of all the six components identified in South-West and North-West China, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Virulence Genes of S. aureus from Dairy Cow Mastitis and Contagiousness Risk.

PubMed

Magro, Giada; Biffani, Stefano; Minozzi, Giulietta; Ehricht, Ralf; Monecke, Stefan; Luini, Mario; Piccinini, Renata

2017-06-21

Staphylococcus aureus ( S. aureus ) is a major agent of dairy cow intramammary infections: the different prevalences of mastitis reported might be related to a combination of S. aureus virulence factors beyond host factors. The present study considered 169 isolates from different Italian dairy herds that were classified into four groups based on the prevalence of S. aureus infection at the first testing: low prevalence (LP), medium-low (MLP), medium-high (MHP) and high (HP). We aimed to correlate the presence of virulence genes with the prevalence of intramammary infections in order to develop new strategies for the control of S. aureus mastitis. Microarray data were statistically evaluated using binary logistic regression and correspondence analysis to screen the risk factors and the relationship between prevalence group and gene. The analysis showed: (1) 24 genes at significant risk of being detected in all the herds with infection prevalence >5%, including genes belonging to microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), immune evasion and serine proteases; and (2) a significant correlation coefficient between the genes interacting with the host immune response and HP isolates against LP ones. These results support the hypothesis that virulence factors, in addition to cow management, could be related to strain contagiousness, offering new insights into vaccine development.

Regulation of dendritic cell function through Toll-like receptors.

PubMed

Kaisho, Tsuneyasu; Akira, Shizuo

2003-06-01

Higher animals establish host defense by orchestrating innate and adaptive immunity. This is mediated by professional antigen presenting cells, i.e. dendritic cells (DCs). DCs can incorporate pathogens, produce a variety of cytokines, maturate, and present pathogen-derived peptides to T cells, thereby inducing T cell activation and differentiation. These responses are triggered by microbial recognition through type I transmembrane proteins, Toll-like receptors (TLRs) on DCs. TLRs consist of ten members and each TLR is involved in recognizing a variety of microorganism-derived molecular structures. TLR ligands include cell wall components, proteins, nucleic acids, and synthetic chemical compounds, all of which can activate DCs as immune adjuvants. Each TLR can activate DCs in a similar, but distinct manner. For example, TLRs can be divided into subgroups according to their type I interferon (IFN) inducing ability. TLR2 cannot induce IFN-alpha or IFN-beta, but TLR4 can lead to IFN-beta production. Meanwhile, TLR3, TLR7, and TLR9 can induce both IFN-alpha and IFN-beta. Recent evidences suggest that cytoplamic adapters for TLRs are especially crucial for this functional heterogeneity. Clarifying how DC function is regulated by TLRs should provide us with critical information for manipulating the host defense against a variety of diseases.

Neutrophil mobilization by surface-glycan altered Th17-skewing bacteria mitigates periodontal pathogen persistence and associated alveolar bone loss.

PubMed

Settem, Rajendra P; Honma, Kiyonobu; Sharma, Ashu

2014-01-01

Alveolar bone (tooth-supporting bone) erosion is a hallmark of periodontitis, an inflammatory disease that often leads to tooth loss. Periodontitis is caused by a select group of pathogens that form biofilms in subgingival crevices between the gums and teeth. It is well-recognized that the periodontal pathogen Porphyromonas gingivalis in these biofilms is responsible for modeling a microbial dysbiotic state, which then initiates an inflammatory response destructive to the periodontal tissues and bone. Eradication of this pathogen is thus critical for the treatment of periodontitis. Previous studies have shown that oral inoculation in mice with an attenuated strain of the periodontal pathogen Tannerella forsythia altered in O-glycan surface composition induces a Th17-linked mobilization of neutrophils to the gingival tissues. In this study, we sought to determine if immune priming with such a Th17-biasing strain would elicit a productive neutrophil response against P. gingivalis. Our data show that inoculation with a Th17-biasing T. forsythia strain is effective in blocking P. gingivalis-persistence and associated alveolar bone loss in mice. This work demonstrates the potential of O-glycan modified Tannerella strains or their O-glycan components for harnessing Th17-mediated immunity against periodontal and other mucosal pathogens.

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.

PubMed

Ransom-Jones, Emma; McCarthy, Alan J; Haldenby, Sam; Doonan, James; McDonald, James E

2017-01-01

The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, to address the paucity of information on biomass-degrading microbial diversity beyond the gastrointestinal tract, cellulose (cotton) "baits" were incubated in landfill leachate microcosms to enrich the landfill cellulolytic microbial community for taxonomic and functional characterization. Metagenome and 16S rRNA gene amplicon sequencing demonstrated the dominance of Firmicutes , Bacteroidetes , Spirochaetes , and Fibrobacteres in the landfill cellulolytic community. Functional metagenome analysis revealed 8,371 carbohydrate active enzymes (CAZymes) belonging to 244 CAZyme families. In addition to observing biomass-degrading enzymes of anaerobic bacterial "cellulosome" systems of members of the Firmicutes , we report the first detection of the Fibrobacter cellulase system and the Bacteroidetes polysaccharide utilization locus (PUL) in landfill sites. These data provide evidence for the presence of multiple mechanisms of biomass degradation in the landfill microbiome and highlight the extraordinary functional diversity of landfill microorganisms as a rich source of biomass-degrading enzymes of potential biotechnological significance. IMPORTANCE The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, we identified Firmicutes , Spirochaetes , and Fibrobacteres as key phyla in the landfill cellulolytic community, detecting 8,371 carbohydrate active enzymes (CAZymes) that represent at least three of the recognized strategies for cellulose decomposition. These data highlight substantial hydrolytic enzyme diversity in landfill sites as a source of new enzymes for biomass conversion.

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity

PubMed Central

Ransom-Jones, Emma; McCarthy, Alan J.; Haldenby, Sam; Doonan, James

2017-01-01

ABSTRACT The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, to address the paucity of information on biomass-degrading microbial diversity beyond the gastrointestinal tract, cellulose (cotton) “baits” were incubated in landfill leachate microcosms to enrich the landfill cellulolytic microbial community for taxonomic and functional characterization. Metagenome and 16S rRNA gene amplicon sequencing demonstrated the dominance of Firmicutes, Bacteroidetes, Spirochaetes, and Fibrobacteres in the landfill cellulolytic community. Functional metagenome analysis revealed 8,371 carbohydrate active enzymes (CAZymes) belonging to 244 CAZyme families. In addition to observing biomass-degrading enzymes of anaerobic bacterial “cellulosome” systems of members of the Firmicutes, we report the first detection of the Fibrobacter cellulase system and the Bacteroidetes polysaccharide utilization locus (PUL) in landfill sites. These data provide evidence for the presence of multiple mechanisms of biomass degradation in the landfill microbiome and highlight the extraordinary functional diversity of landfill microorganisms as a rich source of biomass-degrading enzymes of potential biotechnological significance. IMPORTANCE The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, we identified Firmicutes, Spirochaetes, and Fibrobacteres as key phyla in the landfill cellulolytic community, detecting 8,371 carbohydrate active enzymes (CAZymes) that represent at least three of the recognized strategies for cellulose decomposition. These data highlight substantial hydrolytic enzyme diversity in landfill sites as a source of new enzymes for biomass conversion. PMID:28776044

The Microbial Ferrous Wheel in a Neutral pH Groundwater Seep

PubMed Central

Roden, Eric E.; McBeth, Joyce M.; Blöthe, Marco; Percak-Dennett, Elizabeth M.; Fleming, Emily J.; Holyoke, Rebecca R.; Luther, George W.; Emerson, David; Schieber, Juergen

2012-01-01

Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II) at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II) just at its surface (∼5 cm depth), suggesting an internal Fe(II) source coupled to active Fe(III) reduction. Most probable number enumerations detected microaerophilic Fe(II)-oxidizing bacteria (FeOB) and dissimilatory Fe(III)-reducing bacteria (FeRB) at densities of 102 to 105 cells mL−1 in samples from both sites. In vitro Fe(III) reduction experiments revealed the potential for immediate reduction (no lag period) of native Fe(III) oxides. Conventional full-length 16S rRNA gene clone libraries were compared with high throughput barcode sequencing of the V1, V4, or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g., Gallionella, Sideroxydans, Aquabacterium). Sequences related to recognized FeRB (e.g., Rhodoferax, Aeromonas, Geobacter, Desulfovibrio) were also well-represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode libraries provided confirmation of key clone library results (e.g., the predominance of Betaproteobacteria) and an expanded view of lithotrophic microbial community composition. PMID:22783228

Automatic recognition of light source from color negative films using sorting classification techniques

NASA Astrophysics Data System (ADS)

Sanger, Demas S.; Haneishi, Hideaki; Miyake, Yoichi

1995-08-01

This paper proposed a simple and automatic method for recognizing the light sources from various color negative film brands by means of digital image processing. First, we stretched the image obtained from a negative based on the standardized scaling factors, then extracted the dominant color component among red, green, and blue components of the stretched image. The dominant color component became the discriminator for the recognition. The experimental results verified that any one of the three techniques could recognize the light source from negatives of any film brands and all brands greater than 93.2 and 96.6% correct recognitions, respectively. This method is significant for the automation of color quality control in color reproduction from color negative film in mass processing and printing machine.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

PubMed Central

Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-01-01

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide. PMID:18301735

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.

PubMed

Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong

2013-02-01

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.

Microbial ecology of four coral atolls in the Northern Line Islands.

PubMed

Dinsdale, Elizabeth A; Pantos, Olga; Smriga, Steven; Edwards, Robert A; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A; Thurber, Rebecca Vega; Willis, Bette L; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-02-27

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Comparative evaluation of microbial diversity and metabolite profiles in doenjang, a fermented soybean paste, during the two different industrial manufacturing processes.

PubMed

Lee, Sunmin; Lee, Sarah; Singh, Digar; Oh, Ji Young; Jeon, Eun Jung; Ryu, Hyung SeoK; Lee, Dong Wan; Kim, Beom Seok; Lee, Choong Hwan

2017-04-15

Two different doenjang manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for doenjang using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, meju fermentation, cooling, brining, and aging. Further, correlation analysis indicated that Aspergillus population was linked to sugar metabolism, Bacillus spp. with that of fatty acids, whereas Tetragenococcus and Zygosaccharomyces were found associated with amino acids. These results suggest that the components and quality of doenjang are critically influenced by the microbial assortments in each process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biological nutrient removal and molecular biological characteristics in an anaerobic-multistage anaerobic/oxic (A-MAO) process to treat municipal wastewater.

PubMed

Huang, Xiao; Dong, Wenyi; Wang, Hongjie; Jiang, Shilong

2017-10-01

This study aimed to present an anaerobic-multistage anaerobic/oxic (A-MAO) process to treat municipal wastewater. The average COD, NH 4 + -N, TN, and TP removal efficiency were 91.81%, 96.26%, 83.73% and 94.49%, respectively. Temperature plunge and C/N decrease have a certain impact on the modified process. Characteristics of microbial community, function microorganism, and correlation of microbial community with environmental variables in five compartments were carried out by Illumina Miseq high-throughput sequencing. The differences of microbial community were observed and Blastocatella, Flavobacterium and Pseudomonas were the dominant genus. Nitrosomonas and Nitrospira occupied a dominant position in AOB and NOB, respectively. Rhodospirillaceae and Rhodocyclaceae owned a considerable proportion in phosphorus removal bacteria. DO and COD played significant roles on affecting the microbial components. The A-MAO process in this study demonstrated a high potential for nutrient removal from municipal wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous microbial reduction of vanadium (V) and chromium (VI) by Shewanella loihica PV-4.

PubMed

Wang, Guangyu; Zhang, Baogang; Li, Shuang; Yang, Meng; Yin, Changcheng

2017-03-01

Toxic vanadium (V) and chromium (VI) often co-exist in wastewater from vanadium ore smelting and their reductions by bacterial strain Shewanella loihica PV-4 is realized simultaneously. After 27-d operation, 71.3% of V(V) and 91.2% of Cr(VI) were removed respectively, with citrate as organic carbon source. Enhancement of Cr(VI) bioreduction was observed with the suppressed V(V) reduction. V(IV) and Cr(III), the main reduction products, precipitated inside the organisms and attached on cell surfaces. Both membrane components containing cytochrome c and cytoplasmic fractions containing soluble proteins as well as NADH may contribute to these microbial reductions. Most Cr(VI) were reduced extracellularly and V(V) tended to be reduced through intracellular process, as revealed by mapping the microbial surface and a line scan across the cell, performed by scanning transmission electron microscopy. This study provides an efficient alternative for controlling combined pollution caused by these two metals based on microbial technology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

PubMed Central

Gründger, Friederike; Jiménez, Núria; Thielemann, Thomas; Straaten, Nontje; Lüders, Tillmann; Richnow, Hans-Hermann; Krüger, Martin

2015-01-01

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport. PMID:25852663

Targeting the gut microbiota by dietary nutrients: A new avenue for human health.

PubMed

Li, Daotong; Wang, Pan; Wang, Pengpu; Hu, Xiaosong; Chen, Fang

2017-08-28

The gut microbiota is a complex ecosystem consisted of trillions of microbes that have co-evolved with their host for hundreds of millions of years. During the last decade, a growing body of knowledge has suggested that there is a compelling set of connections among diet, gut microbiota and human health. Various physiological functions of the host, ranging from metabolic and immune regulation to nerve and endocrine development, are possibly mediated by the structural components of microbial cell or the products of microbial metabolism, which are greatly influenced by dietary macronutrients and micronutrients. Thus, governing the production and activity of these microbial-associated small molecules and metabolites through dietary intervention may provide promising strategies for the improvement of human health and disease. In this review article, we first provide an overview of current findings about the intimate interrelationships between diet and gut microbiota. We also introduce the physiological effects of some microbial-associated small molecules and metabolites on the host as well as the detailed signaling mechanisms.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

DOE PAGES

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; ...

2016-04-07

Environmental transition zones are associated with geochemical gradients that overcome energy limitations to microbial metabolism, resulting in biogeochemical hot spots and moments. Riverine systems where groundwater mixes with surface water (the hyporheic zone) are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. To investigate the coupling among groundwater-surface water mixing, microbial communities, and biogeochemistry we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected across times and locations representing amore » broad range of mixing conditions. Mixing of groundwater and surface water resulted in a shift from transport-driven stochastic dynamics to a deterministic microbial structure associated with elevated biogeochemical rates. While the dynamics of the hyporheic make predictive modeling a challenge, we provide new knowledge that can improve the tractability of such models.« less

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Metabolic heterogeneity in clonal microbial populations.

PubMed

Takhaveev, Vakil; Heinemann, Matthias

2018-02-21

In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in constant environments to molecular noise in gene expression that propagates into metabolism. Furthermore, we provide an overview of current methods to quantify the levels of metabolites and biomass components in single cells. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Production-related petroleum microbiology: progress and prospects.

PubMed

Voordouw, Gerrit

2011-06-01

Microbial activity in oil reservoirs is common. Methanogenic consortia hydrolyze low molecular weight components to methane and CO2, transforming light oil to heavy oil to bitumen. The presence of sulfate in injection water causes sulfate-reducing bacteria to produce sulfide. This souring can be reversed by nitrate, stimulating nitrate-reducing bacteria. Removing biogenic sulfide is important, because it contributes to pitting corrosion and resulting pipeline failures. Increased water production eventually makes oil production uneconomic. Microbial fermentation products can lower oil viscosity or interfacial tension and produced biomass can block undesired flow paths to produce more oil. These biotechnologies benefit from increased understanding of reservoir microbial ecology through new sequence technologies and help to decrease the environmental impact of oil production. Copyright © 2010 Elsevier Ltd. All rights reserved.

Characterizing fluorescent dissolved organic matter in a membrane bioreactor via excitation-emission matrix combined with parallel factor analysis.

PubMed

Maqbool, Tahir; Quang, Viet Ly; Cho, Jinwoo; Hur, Jin

2016-06-01

In this study, we successfully tracked the dynamic changes in different constitutes of bound extracellular polymeric substances (bEPS), soluble microbial products (SMP), and permeate during the operation of bench scale membrane bioreactors (MBRs) via fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (PARAFAC). Three fluorescent groups were identified, including two protein-like (tryptophan-like C1 and tyrosine-like C2) and one microbial humic-like components (C3). In bEPS, protein-like components were consistently more dominant than C3 during the MBR operation, while their relative abundance in SMP depended on aeration intensities. C1 of bEPS exhibited a linear correlation (R(2)=0.738; p<0.01) with bEPS amounts in sludge, and C2 was closely related to the stability of sludge. The protein-like components were more greatly responsible for membrane fouling. Our study suggests that EEM-PARAFAC can be a promising monitoring tool to provide further insight into process evaluation and membrane fouling during MBR operation. Copyright © 2016 Elsevier Ltd. All rights reserved.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

PubMed

Dick, Gregory J; Anantharaman, Karthik; Baker, Brett J; Li, Meng; Reed, Daniel C; Sheik, Cody S

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides) plantations on the structure and activity of soil microbial communities.

PubMed

Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

2015-01-01

This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4(+)) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+) content, nitrate content (NH3(-)), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

PubMed Central

Dick, Gregory J.; Anantharaman, Karthik; Baker, Brett J.; Li, Meng; Reed, Daniel C.; Sheik, Cody S.

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales. PMID:23720658

Release and Removal of Microorganisms from Land-Deposited Animal Waste and Animal Manures: A Review of Data and Models.

PubMed

Blaustein, Ryan A; Pachepsky, Yakov A; Shelton, Daniel R; Hill, Robert L

2015-09-01

Microbial pathogens present a leading cause of impairment to rivers, bays, and estuaries in the United States, and agriculture is often viewed as the major contributor to such contamination. Microbial indicators and pathogens are released from land-applied animal manure during precipitation and irrigation events and are carried in overland and subsurface flow that can reach and contaminate surface waters and ground water used for human recreation and food production. Simulating the release and removal of manure-borne pathogens and indicator microorganisms is an essential component of microbial fate and transport modeling regarding food safety and water quality. Although microbial release controls the quantities of available pathogens and indicators that move toward human exposure, a literature review on this topic is lacking. This critical review on microbial release and subsequent removal from manure and animal waste application areas includes sections on microbial release processes and release-affecting factors, such as differences in the release of microbial species or groups; bacterial attachment in turbid suspensions; animal source; animal waste composition; waste aging; manure application method; manure treatment effect; rainfall intensity, duration, and energy; rainfall recurrence; dissolved salts and temperature; vegetation and soil; and spatial and temporal scale. Differences in microbial release from liquid and solid manures are illustrated, and the influential processes are discussed. Models used for simulating release and removal and current knowledge gaps are presented, and avenues for future research are suggested. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Modern Microbial Ecosystems are a Key to Understanding Our Biosphere's Early Evolution and its Contributions To The Atmosphere and Rock Record

NASA Technical Reports Server (NTRS)

DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The survival of our early biosphere depended upon efficient coordination anion- diverse microbial populations. Microbial mats exhibit a 3.46-billion-year fossil record, thus they are the oldest known ecosystems. Photosynthetic microbial mats were key because, today, sunlight powers more than 99 percent of global primary productivity. Thus photosynthetic ecosystems have affected the atmosphere profoundly and have created the most pervasive, easily-detected fossils. Photosynthetic biospheres elsewhere will be most detectible via telescopes or spacecraft. As a part of the Astrobiology Institute, our Ames Microbial Ecosystems group examines the roles played by ecological processes in the early evolution of our biosphere, as recorded in geologic fossils and in the macromolecules of living cells: (1) We are defining the microbial mat microenvironment, which was an important milieu for early evolution. (2) We are comparing mats in contrasting environments to discern strategies of adaptation and diversification, traits that were key for long-term survival. (3) We have selected sites that mimic key environmental attributes of early Earth and thereby focus upon evolutionary adaptations to long-term changes in the global environment. (4) Our studies of gas exchange contribute to better estimates of biogenic gases in Earth's early atmosphere. This group therefore directly addresses the question: How have the Earth and its biosphere influenced each other over time Our studies strengthen the systematics for interpreting the microbial fossil record and thereby enhance astrobiological studies of martian samples. Our models of biogenic gas emissions will enhance models of atmospheres that might be detected on inhabited extrasolar planets. This work therefore also addresses the question: How can other biospheres be recogniZed" Our choice of field sites helps us explore Earth's evolving early environment. For example, modern mats that occupy thermal springs and certain freshwater environments experience conditions such as low O2 and sulfate and high inorganic carbon and sulfide levels that resemble those of ancient marine environments. Later in history, both biologically-induced carbonate precipitation and the trapping and binding of suspended grains of carbonate became a dominant mechanism for carbonate deposition. Modern marine carbonate platforms and alkaline offer good examples of microbiologically-induced calcification. Both marine platforms and solar salterns illustrate microbially-driven trapping and binding. We are also exploring the effects of water composition upon the exchange of biogenic gases with the atmosphere.

Systems Reliability Framework for Surface Water Sustainability and Risk Management

NASA Astrophysics Data System (ADS)

Myers, J. R.; Yeghiazarian, L.

2016-12-01

With microbial contamination posing a serious threat to the availability of clean water across the world, it is necessary to develop a framework that evaluates the safety and sustainability of water systems in respect to non-point source fecal microbial contamination. The concept of water safety is closely related to the concept of failure in reliability theory. In water quality problems, the event of failure can be defined as the concentration of microbial contamination exceeding a certain standard for usability of water. It is pertinent in watershed management to know the likelihood of such an event of failure occurring at a particular point in space and time. Microbial fate and transport are driven by environmental processes taking place in complex, multi-component, interdependent environmental systems that are dynamic and spatially heterogeneous, which means these processes and therefore their influences upon microbial transport must be considered stochastic and variable through space and time. A physics-based stochastic model of microbial dynamics is presented that propagates uncertainty using a unique sampling method based on artificial neural networks to produce a correlation between watershed characteristics and spatial-temporal probabilistic patterns of microbial contamination. These results are used to address the question of water safety through several sustainability metrics: reliability, vulnerability, resilience and a composite sustainability index. System reliability is described uniquely though the temporal evolution of risk along watershed points or pathways. Probabilistic resilience describes how long the system is above a certain probability of failure, and the vulnerability metric describes how the temporal evolution of risk changes throughout a hierarchy of failure levels. Additionally our approach allows for the identification of contributions in microbial contamination and uncertainty from specific pathways and sources. We expect that this framework will significantly improve the efficiency and precision of sustainable watershed management strategies through providing a better understanding of how watershed characteristics and environmental parameters affect surface water quality and sustainability. With microbial contamination posing a serious threat to the availability of clean water across the world, it is necessary to develop a framework that evaluates the safety and sustainability of water systems in respect to non-point source fecal microbial contamination. The concept of water safety is closely related to the concept of failure in reliability theory. In water quality problems, the event of failure can be defined as the concentration of microbial contamination exceeding a certain standard for usability of water. It is pertinent in watershed management to know the likelihood of such an event of failure occurring at a particular point in space and time. Microbial fate and transport are driven by environmental processes taking place in complex, multi-component, interdependent environmental systems that are dynamic and spatially heterogeneous, which means these processes and therefore their influences upon microbial transport must be considered stochastic and variable through space and time. A physics-based stochastic model of microbial dynamics is presented that propagates uncertainty using a unique sampling method based on artificial neural networks to produce a correlation between watershed characteristics and spatial-temporal probabilistic patterns of microbial contamination. These results are used to address the question of water safety through several sustainability metrics: reliability, vulnerability, resilience and a composite sustainability index. System reliability is described uniquely though the temporal evolution of risk along watershed points or pathways. Probabilistic resilience describes how long the system is above a certain probability of failure, and the vulnerability metric describes how the temporal evolution of risk changes throughout a hierarchy of failure levels. Additionally our approach allows for the identification of contributions in microbial contamination and uncertainty from specific pathways and sources. We expect that this framework will significantly improve the efficiency and precision of sustainable watershed management strategies through providing a better understanding of how watershed characteristics and environmental parameters affect surface water quality and sustainability.

[Microbial Community Structure on the Root Surface of Patients with Periodontitis.

PubMed

Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

2016-11-01

To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P <0.05),while the abundance of Prevotella,Selenomonas,Corynebacterium and Olsenella had a negative correlation with the depth of the collection site of samples ( P <0.05). There is region-specificity of microbial community structure on the root surface of patients with periodontitis.

Case Study: Microbial Ecology and Forensics of Chinese Drywall-Elemental Sulfur Disproportionation as Primary Generator of Hydrogen Sulfide.

PubMed

Tomei Torres, Francisco A

2017-06-21

Drywall manufactured in China released foul odors attributed to volatile sulfur compounds. These included hydrogen sulfide, methyl mercaptan, and sulfur dioxide. Given that calcium sulfate is the main component of drywall, one would suspect bacterial reduction of sulfate to sulfide as the primary culprit. However, when the forensics, i.e., the microbial and chemical signatures left in the drywall, are studied, the evidence suggests that, rather than dissimilatory sulfate reduction, disproportionation of elemental sulfur to hydrogen sulfide and sulfate was actually the primary cause of the malodors. Forensic evidence suggests that the transformation of elemental sulfur went through several abiological and microbial stages: (1) partial volatilization of elemental sulfur during the manufacture of plaster of Paris, (2) partial abiotic disproportionation of elemental sulfur to sulfide and thiosulfate during the manufacture of drywall, (3) microbial disproportionation of elemental sulfur to sulfide and sulfate resulting in neutralization of all alkalinity, and acidification below pH 4, (4) acidophilic microbial disproportionation of elemental sulfur to sulfide and sulfuric acid, and (5) hydrogen sulfide volatilization, coating of copper fixtures resulting in corrosion, and oxidation to sulfur dioxide.

Differences in carbon source usage by dental plaque in children with and without early childhood caries

PubMed Central

Zhao, Yan; Zhong, Wen-Jie; Xun, Zhe; Zhang, Qian; Song, Ye-Qing; Liu, Yun-Song; Chen, Feng

2017-01-01

Early childhood caries (ECC) is a considerable pediatric and public health problem worldwide. Preceding studies have focused primarily on bacterial diversity at the taxonomic level. Although these studies have provided significant information regarding the connection between dental caries and oral microbiomes, further comprehension of this microbial community’s ecological relevance is limited. This study identified the carbon source metabolic differences in dental plaque between children with and without ECC. We compared the microbial community functional diversity in 18 caries-free subjects with 18 severe ECC patients based on sole carbon source usage using a Biolog assay. The anaerobic microbial community in the ECC patients displayed greater metabolic activity than that of the control group. Specific carbon source metabolism differed significantly between the two groups. Subjects from the two groups were well distinguished by cluster and principal component analyses based on discriminative carbon sources. Our results implied that the microbial functional diversity between the ECC patients and healthy subjects differed significantly. In addition, the Biolog assay furthered our understanding of oral microbiomes as a composite of functional abilities, thus enabling us to identify the ecologically relevant functional differences among oral microbial communities.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

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

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

Living microorganisms change the information (Shannon) content of a geophysical system.

PubMed

Tang, Fiona H M; Maggi, Federico

2017-06-12

The detection of microbial colonization in geophysical systems is becoming of interest in various disciplines of Earth and planetary sciences, including microbial ecology, biogeochemistry, geomicrobiology, and astrobiology. Microorganisms are often observed to colonize mineral surfaces, modify the reactivity of minerals either through the attachment of their own biomass or the glueing of mineral particles with their mucilaginous metabolites, and alter both the physical and chemical components of a geophysical system. Here, we hypothesise that microorganisms engineer their habitat, causing a substantial change to the information content embedded in geophysical measures (e.g., particle size and space-filling capacity). After proving this hypothesis, we introduce and test a systematic method that exploits this change in information content to detect microbial colonization in geophysical systems. Effectiveness and robustness of this method are tested using a mineral sediment suspension as a model geophysical system; tests are carried out against 105 experiments conducted with different suspension types (i.e., pure mineral and microbially-colonized) subject to different abiotic conditions, including various nutrient and mineral concentrations, and different background entropy production rates. Results reveal that this method can systematically detect microbial colonization with less than 10% error in geophysical systems with low-entropy background production rate.

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

PubMed Central

Wasmund, Kenneth; Mußmann, Marc

2017-01-01

Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

DOE PAGES

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.; ...

2014-10-28

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

Environmental characteristics and changes of sediment pore water dissolved organic matter in four Chinese lakes.

PubMed

Mostofa, Khan M G; Li, Wen; Wu, Fengchang; Liu, Cong-Qiang; Liao, Haiqing; Zeng, Li; Xiao, Min

2018-01-01

Sediment pore waters were examined in four Chinese lakes (Bosten, Qinghai, Chenghai and Dianchi) to characterise the sources of dissolved organic matter (DOM) and their microbial changes in the sediment depth profiles. Parallel factor (PARAFAC) modelling on the sample fluorescence spectra confirmed that the pore water DOM was mostly composed of two components with a mixture of both allochthonous and autochthonous fulvic acid-like substances in three lakes, except Lake Dianchi, and protein-like components in Lake Bosten. However, DOM in Lake Dianchi was composed of three components, including a fulvic acid-like, and two unidentified components, which could originate from mixed sources of either sewerage-impacted allochthonous or autochthonous organic matter (OM). Dissolved organic carbon (DOC) concentrations were typically high (583-7410 μM C) and fluctuated and increased vertically in the depth profile. The fluorescence intensity of the fulvic acid-like substance and absorbance at 254 nm increased vertically in the sediment pore waters of three lakes. A significant relationship between DOC and the fluorescence intensity of the fulvic acid-like component in the sediment pore waters of three lakes, except Lake Dianchi, suggested that the fulvic acid-like component could significantly contribute to total DOM and could originate via complex microbial processes in early diagenesis on OM (ca. phytoplankton, terrestrial plant material) in these lakes. Pore water DOM components could therefore be a useful indicator to assess the DOM sources of the lake sediment during sedimentation over the past several decades, which have been heavily affected by ambient terrestrial vegetation and human activities.

6 CFR Appendix A to Part 5 - FOIA/Privacy Act Offices of the Department of Homeland Security

Code of Federal Regulations, 2010 CFR

2010-01-01

... development program. 5. The life sciences activities related to microbial pathogens of Biological and... and Infrastructure Protection Directorate of Science and Technology II. Requests made to components...

6 CFR Appendix A to Part 5 - FOIA/Privacy Act Offices of the Department of Homeland Security

Code of Federal Regulations, 2013 CFR

2013-01-01

... development program. 5. The life sciences activities related to microbial pathogens of Biological and... and Infrastructure Protection Directorate of Science and Technology II. Requests made to components...

6 CFR Appendix A to Part 5 - FOIA/Privacy Act Offices of the Department of Homeland Security

Code of Federal Regulations, 2012 CFR

2012-01-01

... development program. 5. The life sciences activities related to microbial pathogens of Biological and... and Infrastructure Protection Directorate of Science and Technology II. Requests made to components...

6 CFR Appendix A to Part 5 - FOIA/Privacy Act Offices of the Department of Homeland Security

Code of Federal Regulations, 2014 CFR

2014-01-01

... development program. 5. The life sciences activities related to microbial pathogens of Biological and... and Infrastructure Protection Directorate of Science and Technology II. Requests made to components...

6 CFR Appendix A to Part 5 - FOIA/Privacy Act Offices of the Department of Homeland Security

Code of Federal Regulations, 2011 CFR

2011-01-01

... development program. 5. The life sciences activities related to microbial pathogens of Biological and... and Infrastructure Protection Directorate of Science and Technology II. Requests made to components...

[Carbon sources metabolic characteristics of airborne microbial communities in constructed wetlands].

PubMed

Song, Zhi-Wen; Wang, Lin; Xu, Ai-Ling; Wu, Deng-Deng; Xia, Yan

2015-02-01

Using BIOLOG-GN plates, this article describes the carbon sources metabolic characteristics of airborne microbial communities in a free surface-flow constructed wetland in different seasons and clarify the correlation between airborne microbial metabolic functions and environmental factors. The average well color development (AWCD), carbon metabolic profiles and McIntosh values of airborne microbial communities in different seasons were quite different. Analysis of the variations showed that AWCD in spring and summer differed significantly from that in autumn and winter (P < 0.01). In the same season, the degree of utilization of different types of carbon by airborne microbes was different. Summer had a significant difference from other seasons (P < 0.05). Dominant communities of airborne microbes in four seasons were carboxylic acids metabolic community, carbohydrates metabolic community, polymers metabolic community and carboxylic acids metabolic community respectively. Principal component analysis showed that the carbon metabolic characteristics of airborne microbial community in autumn were similar to those in winter but different from those in spring and summer. The characteristics of carbon metabolism revealed differences between summer and spring, autumn, or winter. These differences were mainly caused by amines or amides while the differences between spring and autumn or winter were mainly caused by carboxylic acids. Environmental factors, including changes in wind speed, temperature, and humidity acted to influence the carbon sources metabolic properties of airborne microbial community. The dominant environmental factors that acted to influence the carbon sources metabolic properties of airborne microbial community varied between different seasons.

Functional effects of the bacterial insecticide Bacillus thuringiensis var. kurstaki on aquatic microbial communities.

PubMed

Kreutzweiser, D P; Gringorten, J L; Thomas, D R; Butcher, J T

1996-04-01

Epilithic microbial communities were colonized on leaf disks and exposed to commercial preparations of Bacillus thuringiensis var. kurstaki (Btk) in aquatic microcosms. Responses in terms of microbial respiration, bacterial cell density, protozoan density, and microbial decomposition activity were measured. Test concentrations for treatments with Dipel 64AF and Dipel 8AF in microcosms were the expected environmental concentration (EEC) of 20 IU/ml, 100x the EEC, and 1000x the EEC. Bacterial cell density in the biofilm of leaf disks was significantly increased at concentrations as low as the EEC. There were no concomitant alterations in protozoan density. Microbial respiration was significantly increased, and decomposition activity was significantly decreased, but only at the artificially high concentration of 1000x the EEC. This effect was attributed to the spore-crystal component rather than formulation ingredients. Microbial decomposition of leaf material was also determined in outdoor stream channels treated at concentrations ranging from the EEC to 100x the EEC. Although there tended to be reduced decomposition activity in treated channels, there were no significant differences in mass loss of leaf material between treated and control channels. Various regression, classification, and ordination procedures were applied to the experimental data, and none indicated significant treatment effects. These results from laboratory and controlled field experiments indicate that contamination of watercourses with Btk is unlikely to result in significant adverse effects on microbial community function in terms of detrital decomposition.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

PubMed

Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

2014-11-28

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

PubMed Central

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Systematic discovery of antiphage defense systems in the microbial pangenome.

PubMed

Doron, Shany; Melamed, Sarah; Ofir, Gal; Leavitt, Azita; Lopatina, Anna; Keren, Mai; Amitai, Gil; Sorek, Rotem

2018-03-02

The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in "defense islands" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

State of research: environmental pathways and food chain transfer.

PubMed Central

Vaughan, B E

1984-01-01

Data on the chemistry of biologically active components of petroleum, synthetic fuel oils, certain metal elements and pesticides provide valuable generic information needed for predicting the long-term fate of buried waste constituents and their likelihood of entering food chains. Components of such complex mixtures partition between solid and solution phases, influencing their mobility, volatility and susceptibility to microbial transformation. Estimating health hazards from indirect exposures to organic chemicals involves an ecosystem's approach to understanding the unique behavior of complex mixtures. Metabolism by microbial organisms fundamentally alters these complex mixtures as they move through food chains. Pathway modeling of organic chemicals must consider the nature and magnitude of food chain transfers to predict biological risk where metabolites may become more toxic than the parent compound. To obtain predictions, major areas are identified where data acquisition is essential to extend our radiological modeling experience to the field of organic chemical contamination. PMID:6428875

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

PubMed Central

Churchland, Carolyn; Grayston, Sue J.

2014-01-01

Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests. PMID:24917855

Metagenomic Analysis of Ammonia-Oxidizing Archaea Affiliated with the Soil Group

PubMed Central

Bartossek, Rita; Spang, Anja; Weidler, Gerhard; Lanzen, Anders; Schleper, Christa

2012-01-01

Ammonia-oxidizing archaea (AOA) have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C) in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of 16 fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, 5 were fully sequenced, 4 of which grouped with the soil/I.1b (Nitrososphaera-) lineage, and 1 with marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologs in currently available marine Thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of Thaumarchaeota. PMID:22723795

Slope failure as an upslope source of stream wood

Treesearch

Daniel Miller

2013-01-01

Large woody debris is recognized as an important component of stream geomorphology and stream ecosystem function, and forest-land management is recognized as an important control on the quantity (and size and species distributions) of wood available for recruitment to streams. Much of the wood present in streams comes from adjacent forests, and riparian management...

The Vulnerability of Female Body Image to Weight Related Feedback.

ERIC Educational Resources Information Center

Mori, DeAnna L.; Morey, Leslie

A central component of anorexia nervosa is a body image disturbance (BID). BID, as it is experienced in anorexia nervosa, is defined as an inability to recognize how thin one really is and is exhibited by a sense of feeling overweight in spite of severe emaciation. Several researchers have recognized a relationship between depressive personality…

Mixedwood management in the Northeastern United States

Treesearch

Laura S. Kenefic

2016-01-01

In the Northeast, we recognize mixedwood stands as hardwood- softwood mixtures in which neither component contributes more than 75% - 80% of stocking (usually assessed in terms of basal area). Such stands have long been recognized in regional forest type codes used by commercial land managers, i.e., SH for softwood-dominated mixedwoods and HS for hardwood-dominated...

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates

PubMed Central

McKay, Christopher P.; Rask, Jon C.; Detweiler, Angela M.; Bebout, Brad M.; Everroad, R. Craig; Lee, Jackson Z.; Chanton, Jeffrey P.; Mayer, Marisa H.; Caraballo, Adrian A. L.; Kapili, Bennett; Al-Awar, Meshgan; Al-Farraj, Asma

2016-01-01

Salt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat communities with the hypersaline layer at the top and freshwater layers below. We describe and characterize a rich photosynthetically-based microbial ecosystem that is protected from the arid outside environment by a translucent salt crust. Gases collected from sediments under shallow ponds in the sabkha contain methane in concentrations as high as 3400 ppm. The salt crust could preserve biomarkers and other evidence for life in the salt after it dries out. Chloride-filled depressions have been identified on Mars and although surface flow of water is unlikely on Mars today, ground water is possible. Such a near surface system with modern groundwater flowing under ancient salt deposits could be present on Mars and could be accessed by surface rovers. PMID:26982497

Microbial Extremophiles in Evolutionary Aspect

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.

2007-01-01

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

Microbial Mechanisms Underlying Acidity-induced Reduction in Soil Respiration Under Nitrogen Fertilization

NASA Astrophysics Data System (ADS)

Niu, S.; Li, Y.

2016-12-01

Terrestrial ecosystems are receiving increasing amounts of reactive nitrogen (N) due to anthropogenic activities, which largely changes soil respiration and its feedback to climate change. N enrichment can not only increase N availability but also induce soil acidification, both may affect soil microbial activity and root growth with a consequent impact on soil respiration. However, it remains unclear whether elevated N availability or soil acidity has greater impact on soil respiration (Rs). We conducted a manipulative experiment to simulate N enrichment (10 g m-2 yr-1 NH4NO3) and soil acidity (0.552 mol H+ m-2 yr-1 sulfuric acid) and studied their effects on Rs and its components in a temperate forest. Our results showed that soil pH was reduced by 0.2 under N addition or acid addition treatment. Acid addition significantly decreased autotrophic respiration (Ra) and heterotrophic respiration (Rh) by 21.5% and 22.7% in 2014, 34.8% and 21.9% in 2015, respectively, resulting in a reduction of Rs by 22.2% in 2014 and 26.1% in 2015. Nitrogen enrichment reduced Ra, Rh, Rs by 21.9%, 16.2%, 18.6% in 2014 and 22.1%, 5.9%, 11.7% in 2015, respectively. The reductions of Rs and its components were attributable to decrease of fine root biomass, microbial biomass, and cellulose degrading enzymes. N addition did not change microbial community but acid addition increased both fungal and arbuscular mycorrhiza fungi PLFAs, and N plus acid addition significantly enhanced fungal to bacterial ratio. All the hydrolase enzymes were reduced more by soil acidity (43-50%) than nitrogen addition (30-39%). Structural equation model showed that soil acidity played more important role than N availability in reducing soil respiration mainly by changing microbial extracellular enzymes. We therefore suggest that N deposition induced indirect effect of soil acidification on microbial properties is critical and should be taken into account to better understand and predict ecosystem C cycling in the future scenarios of anthropogenic N deposition and acid enrichment.