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Sample records for biofilms microbial life

  1. Biofilms: Microbial Life on Surfaces

    PubMed Central

    2002-01-01

    Microorganisms attach to surfaces and develop biofilms. Biofilm-associated cells can be differentiated from their suspended counterparts by generation of an extracellular polymeric substance (EPS) matrix, reduced growth rates, and the up- and down- regulation of specific genes. Attachment is a complex process regulated by diverse characteristics of the growth medium, substratum, and cell surface. An established biofilm structure comprises microbial cells and EPS, has a defined architecture, and provides an optimal environment for the exchange of genetic material between cells. Cells may also communicate via quorum sensing, which may in turn affect biofilm processes such as detachment. Biofilms have great importance for public health because of their role in certain infectious diseases and importance in a variety of device-related infections. A greater understanding of biofilm processes should lead to novel, effective control strategies for biofilm control and a resulting improvement in patient management. PMID:12194761

  2. Biofilms: A microbial home

    PubMed Central

    Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

    2011-01-01

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

  3. Manipulation of Biofilm Microbial Ecology

    SciTech Connect

    White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

    1998-08-15

    The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  4. Manipulatiaon of Biofilm Microbial Ecology

    SciTech Connect

    Burkhalter, R.; Macnaughton, S.J.; Palmer, R.J.; Smith, C.A.; Whitaker, K.W.; White, D.C.; Zinn, M.; kirkegaard, R.

    1998-08-09

    The Biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms by generated. The most effective monitoring of biofilm formation, succession and desquamation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in the distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  5. 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.

  6. Biofilm formation and microbial corrosion

    SciTech Connect

    Goldstein, R.; Porcella, D.

    1992-07-01

    Biofilms-colonies of microorganisms growing on surfaces - can greatly accelerate the corrosion rates of metals and alloys in utility water systems. Fundamental EPRI research is showing how mechanisms of biofilm formation, interactions between bacterial species, and metabolic activities control such biofilm properties as corrosive potential This research is identifying methods to control biofilm development and prevent microbially influenced corrosion. The results should also apply to the control of other processes involving biological consortia, including the bioremediation of contaminated groundwater and soil and the biodesulfurization of coal.

  7. Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities

    SciTech Connect

    Singer, Steven; Erickson, Brian K; Verberkmoes, Nathan C; Hwang, Mona; Shah, Manesh B; Hettich, Robert {Bob} L; Banfield, Jillian F.; Thelen, Michael P.

    2010-01-01

    Characterizing proteins recovered from natural microbial communities affords the opportunity to correlate protein expression and modification with environmental factors, including species composition and successional stage. Proteogenomic and biochemical studies of pellicle biofilms from subsurface acid mine drainage streams have shown abundant cytochromes from the dominant organism, Leptospirillum Group II. These cytochromes are proposed to be key proteins in aerobic Fe(II) oxidation, the dominant mode of cellular energy generation by the biofilms. In this study, we determined that posttranslational modification and expression of amino-acid sequence variants change as a function of biofilm maturation. For Cytochrome579 (Cyt579), the most abundant cytochrome in the biofilms, late developmental-stage biofilms differed from early-stage biofilms in N-terminal truncations and decreased redox potentials. Expression of sequence variants of two monoheme c-type cytochromes also depended on biofilm development. For Cyt572, an abundant membrane-bound cytochrome, the expression of multiple sequence variants was observed in both early and late developmental-stage biofilms; however, redox potentials of Cyt572 from these different sources did not vary significantly. These cytochrome analyses show a complex response of the Leptospirillum Group II electron transport chain to growth within a microbial community and illustrate the power of multiple proteomics techniques to define biochemistry in natural systems.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  9. Cooperation and conflict in microbial biofilms

    PubMed Central

    Xavier, Joao B.; Foster, Kevin R.

    2007-01-01

    Biofilms, in which cells attach to surfaces and secrete slime (polymeric substances), are central to microbial life. Biofilms are often thought to require high levels of cooperation because extracellular polymeric substances are a shared resource produced by one cell that can be used by others. Here we examine this hypothesis by using a detailed individual-based simulation of a biofilm to investigate the outcome of evolutionary competitions between strains that differ in their level of polymer production. Our model includes a biochemical description of the carbon fluxes for growth and polymer production, and it explicitly calculates diffusion–reaction effects and the resulting solute gradients in the biofilm. An emergent property of these simple but realistic mechanistic assumptions is a strong evolutionary advantage to extracellular polymer production. Polymer secretion is altruistic to cells above a focal cell: it pushes later generations in their lineage up and out into better oxygen conditions, but it harms others; polymer production suffocates neighboring nonpolymer producers. This property, analogous to vertical growth in plants, suggests that polymer secretion provides a strong competitive advantage to cell lineages within mixed-genotype biofilms: global cooperation is not required. Our model fundamentally changes how biofilms are expected to respond to changing social conditions; the presence of multiple strains in a biofilm should promote rather than inhibit polymer secretion. PMID:17210916

  10. Microbial biofilms and gastrointestinal diseases

    PubMed Central

    von Rosenvinge, Erik C.; OMay, Graeme A.; Macfarlane, Sandra; Macfarlane, George T.; Shirtliff, Mark E.

    2014-01-01

    The majority of bacteria live not planktonically, but as residents of sessile biofilm communities. Such populations have been defined as matrix-enclosed microbial accretions, which adhere to both biological and nonbiological surfaces. Bacterial formation of biofilm is implicated in many chronic disease states. Growth in this mode promotes survival by increasing community recalcitrance to clearance by host immune effectors and therapeutic antimicrobials. The human gastrointestinal (GI) tract encompasses a plethora of nutritional and physicochemical environments, many of which are ideal for biofilm formation and survival. However, little is known of the nature, function, and clinical relevance of these communities. This review summarizes current knowledge of the composition and association with health and disease of biofilm communities in the GI tract. PMID:23620117

  11. Extracellular DNA in oral microbial biofilms.

    PubMed

    Jakubovics, Nicholas S; Burgess, J Grant

    2015-07-01

    The extracellular matrix of microbial biofilms is critical for surface adhesion and nutrient homeostasis. Evidence is accumulating that extracellular DNA plays a number of important roles in biofilm integrity and formation on hard and soft tissues in the oral cavity. Here, we summarise recent developments in the field and consider the potential of targeting DNA for oral biofilm control. PMID:25862975

  12. MICROBIAL BIOFILMS AS INDICATORS OF ESTUARINE CONDITION

    EPA Science Inventory

    Microbial biofilms are complex communities of bacteria, protozoa, microalgae, and micrometazoa which exist in a polymer matrix on submerged surfaces. Their development is integrative of environmental conditions and is affected by local biodiversity, the availability of organic ma...

  13. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

    Although several studies have shown that bacteria can deteriorate concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different microbial communities associated with concrete biofilms using 16S rRNA g...

  14. Microbial biofilms in intertidal systems: an overview

    NASA Astrophysics Data System (ADS)

    Decho, Alan W.

    2000-07-01

    Intertidal marine systems are highly dynamic systems which are characterized by periodic fluctuations in environmental parameters. Microbial processes play critical roles in the remineralization of nutrients and primary production in intertidal systems. Many of the geochemical and biological processes which are mediated by microorganisms occur within microenvironments which can be measured over micrometer spatial scales. These processes are localized by cells within a matrix of extracellular polymeric secretions (EPS), collectively called a "microbial biofilm". Recent examinations of intertidal systems by a range of investigators using new approaches show an abundance of biofilm communities. The purpose of this overview is to examine recent information concerning the roles of microbial biofilms in intertidal systems. The microbial biofilm is a common adaptation of natural bacteria and other microorganisms. In the fluctuating environments of intertidal systems, biofilms form protective microenvironments and may structure a range of microbial processes. The EPS matrix of biofilm forms sticky coatings on individual sediment particles and detrital surfaces, which act as a stabilizing anchor to buffer cells and their extracellular processes during the frequent physical stresses (e.g., changes in salinity and temperature, UV irradiation, dessication). EPS is an operational definition designed to encompass a range of large microbially-secreted molecules having widely varying physical and chemical properties, and a range of biological roles. Examinations of EPS using Raman and Fourier-transform infared spectroscopy, and atomic-force microscopy suggest that some EPS gels possess physical and chemical properties which may hasten the development of sharp geochemical gradients, and contribute a protective effect to cells. Biofilm polymers act as a sorptive sponge which binds and concentrates organic molecules and ions close to cells. Concurrently, the EPS appear to localize extracellular enzyme activities of bacteria, and hence contribute to the efficient biomineralization of organics. At larger spatial scales, the copious secretion of specific types of EPS by diatoms on the surfaces of intertidal mudflats may stabilize sediments against resuspension. Biofilms exert important roles in environmental- and public health processes occurring within intertidal systems. The sorptive properties of EPS effectively chelate toxic metals and other contaminants, which then act as an efficient trophic-transfer vehicle for the entry of contaminants into food webs. In the water column, biofilm microenvironments in suspended flocs may form a stabilizing refugia that enhances the survival and propagation of pathogenic (i.e., disease-causing) bacteria entering coastal waters from terrestrial and freshwater sources. The EPS matrix affords microbial cells a tremendous potential for resiliency during periods of stress, and may enhance the overall physiological activities of bacteria. It is emphasized here that the influences of small-scale microbial biofilms must be addressed in understanding larger-scale processes within intertidal systems.

  15. Microbial Biofilms: from Ecology to Molecular Genetics

    PubMed Central

    Davey, Mary Ellen; O'toole, George A.

    2000-01-01

    Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development. PMID:11104821

  16. Modelling microbial competition in nitrifying biofilm reactors.

    PubMed

    Vannecke, T P W; Volcke, E I P

    2015-12-01

    A large variety of microbial parameter values for nitrifying microorganisms has been reported in literature and was revised in this study. Part of the variety was attributed to the variety of analysis methods applied; it also reflects the large biodiversity in nitrifying systems. This diversity is mostly neglected in conventional nitrifying biofilm models. In this contribution, a one-dimensional, multispecies nitrifying biofilm model was set up, taking into account the large variety of the maximum growth rate, the substrate affinity and the yield of nitrifiers reported in literature. Microbial diversity was implemented in the model by considering 60 species of ammonia-oxidizing bacteria (AOB) and 60 species of nitrite-oxidizing bacteria (NOB). A steady-state analysis showed that operational conditions such as the nitrogen loading rate and the bulk liquid oxygen concentration influence both the macroscopic output as well as the microbial composition of the biofilm through the prevailing concentration of substrates throughout the biofilm. Considering two limiting resources (nitrogen and oxygen), the coexistence of two species of the same functional guild (AOB or NOB) was possible at steady state. Their spatial distribution in the biofilm could be explained using the r- and K-selection theory. PMID:26084447

  17. Oral Biofilm Architecture at the Microbial Scale.

    PubMed

    Ferrer, Maria D; Mira, Alex

    2016-04-01

    The application of Spectral Imaging FISH to oral biofilm samples has permitted the direct, simultaneous observation of up to nine different bacterial taxa. This has revealed a complex yet organized microbial architecture, identifying the key microorganisms in the community and detecting the existing interspecies physical interactions at the micron scale. PMID:26962018

  18. Community Proteomics of a Natural Microbial Biofilm

    SciTech Connect

    Ram, Rachna J.; Verberkmoes, Nathan C; Thelen, Michael P.; Tyson, Gene W.; Baker, Brett J.; Shah, Manesh B; BlakeII, Robert C.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2005-06-01

    Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

  19. Microbial Biofilms: Persisters, Tolerance and Dosing

    NASA Astrophysics Data System (ADS)

    Cogan, N. G.

    2005-03-01

    Almost all moist surfaces are colonized by microbial biofilms. Biofilms are implicated in cross-contamination of food products, biofouling, medical implants and various human infections such as dental cavities, ulcerative colitis and chronic respiratory infections. Much of current research is focused on the recalcitrance of biofilms to typical antibiotic and antimicrobial treatments. Although the polymer component of biofilms impedes the penetration of antimicrobials through reaction-diffusion limitation, this does not explain the observed tolerance, it merely delays the action of the agent. Heterogeneities in growth-rate also slow the eradication of the bacteria since most antimicrobials are far less effective for non-growing, or slowly growing bacteria. This also does not fully describe biofilm tolerance, since heterogeneities arr primairly a result of nutrient consumption. In this investigation, we describe the formation of `persister' cells which neither grow nor die in the presence of antibiotics. We propose that the cells are of a different phenotype than typical bacterial cells and the expression of the phenotype is regulated by the growth rate and the antibiotic concentration. We describe several experiments which describe the dynamics of persister cells and which motivate a dosing protocol that calls for periodic dosing of the population. We then introduce a mathematical model, which describes the effect of such a dosing regiment and indicates that the relative dose/withdrawal times are important in determining the effectiveness of such a treatment. A reduced model is introduced and the similar behavior is demonstrated analytically.

  20. Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community

    PubMed Central

    2010-01-01

    Background Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Río Tinto (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum spp. (L. ferrooxidans and L. ferriphilum) and Acidithiobacillus ferrooxidans are abundant. These microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of Leptospirillum spp. as part of its natural extremely acidophilic community. Results Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of L. ferrooxidans. Genes up-regulated in the filamentous biofilm are involved in cellular functions related to biofilm formation and maintenance, such as: motility and quorum sensing (mqsR, cheAY, fliA, motAB), synthesis of cell wall structures (lnt, murA, murB), specific proteases (clpX/clpP), stress response chaperons (clpB, clpC, grpE-dnaKJ, groESL), etc. Additionally, genes involved in mixed acid fermentation (poxB, ackA) were up-regulated in the biofilm. This result, together with the presence of small organic acids like acetate and formate (1.36 mM and 0.06 mM respectively) in the acidic (pH 1.8) water stream, suggests that either L. ferrooxidans or other member of the microbial community are producing acetate in the acidophilic biofilm under microaerophilic conditions. Conclusions Our results indicate that the acidophilic filaments are dynamic structures in which different mechanisms for biofilm formation/dispersion are operating. Specific transcriptomic fingerprints can be inferred for both planktonic and sessile cells, having the former a more active TCA cycle, while the mixed acid fermentation process dominate in the latter. The excretion of acetate may play a relevant ecological role as a source of electron donor for heterotrophic Fe3+ reducers like some Alphaproteobacteria, Acidobacterium spp. and Sulfobacillus spp., also present in the biofilm. Additionally, acetate may have a negative effect on bioleaching by inhibiting the growth of chemolithotrophic bacteria. PMID:20576116

  1. Chitosan coupling makes microbial biofilms susceptible to antibiotics.

    PubMed

    Zhang, Amin; Mu, Haibo; Zhang, Wuxia; Cui, Guoting; Zhu, Jie; Duan, Jinyou

    2013-01-01

    Microbial biofilms, prevalent in nature and inherently resistant to both antimicrobial agents and host defenses, can cause serious problems in the chemical, medical and pharmaceutical industries. Herein we demonstrated that conjugation of an aminoglycoside antibiotic (streptomycin) to chitosan could efficiently damage established biofilms and inhibit biofilm formation. This method was suitable to eradiate biofilms formed by Gram-positive organisms, and it appeared that antibiotic contents, molecular size and positive charges of the conjugate were the key to retain this anti-biofilm activity. Mechanistic insight demonstrated chitosan conjugation rendered streptomycin more accessible into biofilms, thereby available to interact with biofilm bacteria. Thus, this work represent an innovative strategy that antibiotic covalently linked to carbohydrate carriers can overcome antibiotic resistance of microbial biofilms, and might provide a comprehensive solution to combat biofilms in industrial and medical settings. PMID:24284335

  2. Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments.

    PubMed

    Hödl, Iris; Mari, Lorenzo; Bertuzzo, Enrico; Suweis, Samir; Besemer, Katharina; Rinaldo, Andrea; Battin, Tom J

    2014-03-01

    Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in 'ripple-like' and 'star-like' architectures--as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms. PMID:23879839

  3. Microbial biofilm formation and its consequences for the CELSS program

    NASA Technical Reports Server (NTRS)

    Mitchell, R.

    1994-01-01

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

  4. Microbial diversity and interactions in subgingival biofilm communities.

    PubMed

    Diaz, Patricia I

    2012-01-01

    The human subgingival environment is a complex environmental niche where microorganisms from the three domains of life meet to form diverse biofilm communities that exist in close proximity to the host. Bacteria constitute the most abundant, diverse and ultimately well-studied component of these communities with about 500 bacterial taxa reported to occur in this niche. Cultivation and molecular approaches are revealing the breadth and depth of subgingival biofilm diversity as part of an effort to understand the subgingival microbiome, the collection of microorganisms that inhabit the gingival crevices. Although these investigations are constructing a pretty detailed taxonomical census of subgingival microbial communities, including inter-subject and temporal variability in community structure, as well as differences according to periodontal health status, we are still at the front steps in terms of understanding community function. Clinical studies that evaluate community structure need to be coupled with biologically relevant models that allow evaluation of the ecological determinants of subgingival biofilm maturation. Functional characteristics of subgingival biofilm communities that still need to be clarified include main metabolic processes that support microbial communities, identification of keystone species, microbial interactions and signaling events that lead to community maturation and the relationship of different communities with the host. This manuscript presents a summary of our current understanding of subgingival microbial diversity and an overview of experimental models used to dissect the functional characteristics of subgingival communities. Future coupling of 'omics'-based approaches with such models will facilitate a better understanding of subgingival ecology opening opportunities for community manipulation. PMID:22142955

  5. MICROBIAL BIOFILMS AS INTEGRATIVE SENSORS OF ENVIRONMENTAL QUALITY

    EPA Science Inventory

    Snyder, Richard A., Michael A. Lewis, Andreas Nocker and Joe E. Lepo. In press. Microbial Biofilms as Integrative Sensors of Environmental Quality. In: Estuarine Indicators Workshop Proceedings. CRC Press, Boca Raton, FL. 34 p. (ERL,GB 1198).

    Microbial biofilms are comple...

  6. Microbial biofilm as a smart material.

    PubMed

    Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper; Sams, Thomas

    2015-01-01

    Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa. PMID:25686310

  7. Microbial Biofilm as a Smart Material

    PubMed Central

    Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper; Sams, Thomas

    2015-01-01

    Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa. PMID:25686310

  8. Microbial composition and antibiotic resistance of biofilms recovered from endotracheal tubes of mechanically ventilated patients.

    PubMed

    Vandecandelaere, Ilse; Coenye, Tom

    2015-01-01

    In critically ill patients, breathing is impaired and mechanical ventilation, using an endotracheal tube (ET) connected to a ventilator, is necessary. Although mechanical ventilation is a life-saving procedure, it is not without risk. Because of several reasons, a biofilm often forms at the distal end of the ET and this biofilm is a persistent source of bacteria which can infect the lungs, causing ventilator-associated pneumonia (VAP). There is a link between the microbial flora of ET biofilms and the microorganisms involved in the onset of VAP. Culture dependent and independent techniques were already used to identify the microbial flora of ET biofilms and also, the antibiotic resistance of microorganisms obtained from ET biofilms was determined. The ESKAPE pathogens play a dominant role in the onset of VAP and these organisms were frequently identified in ET biofilms. Also, antibiotic resistant microorganisms were frequently present in ET biofilms. Members of the normal oral flora were also identified in ET biofilms but it is thought that these organisms initiate ET biofilm formation and are not directly involved in the development of VAP. PMID:25366226

  9. Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

    EPA Science Inventory

    Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand...

  10. The Role of Microbial Biofilms as Ecosystem Engineers in Streams

    NASA Astrophysics Data System (ADS)

    Battin, T. I.; Battin, T. I.; Kaplan, L. A.; Newbold, J. D.

    2001-12-01

    Microbial biofilms growing on and through the surface of streambeds physically alter the interface between the water column and benthic zone and influence the biogeochemistry within the steambed and hyporheic zone. We monitored the development of biofilms within stream-side flumes, and were able to relate changes in biofilm structure to concomitant changes in hydrodynamics, particle deposition, and dissolved organic carbon (DOC) uptake. Biofilm development was assessed by measurements of ash free dry mass, bacterial density, concentrations of chlorophyll a and exopolysaccharides, and confocal microscopy of fluorescent-stained biotic and abiotic assemblages. The microbial biofilms were followed through an initial colonization period, the development of mm-thick mats that included streamers undulating in the current, and the eventual erosion and sloughing of these structural features. As the biofilms matured, hydrologic exchange rate, transient storage capacity, and particle deposition rates increased, reached a plateau, and eventually declined. The uptake of glucose and arabinose, added in nM concentrations to the flumes, showed a preferential uptake of glucose over arabinose. However, as the biofilms grew, the differences between the uptake of these two saccharides declined. This change is consistent with a shift in the rate-limiting step for DOC uptake from internal biofilm processes to greater diffusion-limitation as biofilm thickness, and thus the diffusion barrier, increased. We suggest that microscale processes, which alter biofilm structure, in turn alter large-scale physical and biogeochemical processes, including streamwater/subsurface hydrodynamics and organic matter fluxes.

  11. The biofilm ecology of microbial biofouling, biocide resistance and corrosion

    SciTech Connect

    White, D.C. |; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B.; Arrage, A.A. |

    1997-06-01

    In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. Heterogeneous distribution of microbes and/or their metabolic activity can promote microbially influenced corrosion (MIC) which is a multibillion dollar problem. Consequently, it is important that biofilm microbial ecology be understood so it can be manipulated rationally. It is usually simple to select organisms that form biofilms by flowing a considerably dilute media over a substratum, and propagating the organisms that attach. To examine the biofilm most expeditiously, the biomass accumulation, desquamation, and metabolic activities need to be monitored on-line and non-destructively. This on-line monitoring becomes even more valuable if the activities can be locally mapped in time and space within the biofilm. Herein the authors describe quantitative measures of microbial biofouling, the ecology of pathogens in drinking water distributions systems, and localization of microbial biofilms and activities with localized MIC.

  12. Method for studying microbial biofilms in flowing-water systems

    SciTech Connect

    Pedersen, K.

    1982-01-01

    A method for the study of microbial biofilms in flowing-water systems was developed with special reference to the flow conditions in electrochemical concentration cells. Seawater was circulated in a semiclosed flow system through biofilm reactors (3 cm s/sup -1/) with microscope cover slips arranged in lamellar piles parallel with the flow. At fixed time intervals cover slips with their biofilm were removed from the pile, stained with crystal violet, and mounted on microscope slides. The absorbances of the slides were measured at 590 nm and plotted against time to give microbial biofilm development. From calibration experiments a staining time of 1 min and a rinse time of 10 min in a tap water flow (3 cm s/sup -1/) were considered sufficient. When an analysis of variance was performed on biofilm development data, 78% of the total variance was found to be due to random natural effects; the rest could be explained by experimental effects. The absorbance values correlated well with protein N, dry weight, and organic weight in two biofilm experiments, one with a biofilm with a high (75%) and one with a low (approx.25%, normal) inorganic content. Comparisons of regression lines revealed that the absorbance of the stained biofilms was an estimate closely related to biofilm dry weight.

  13. Influence of microbial biofilms on reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Gerlach, Robin; Cunningham, Al.

    2012-05-01

    Microbial biofilms form in natural and engineered systems and can significantly affect the hydrodynamics in porous media. Subsurface remediation, enhanced oil recovery, abatement of saltwater intrusion, filtration, deep-subsurface sequestration of supercritical carbon dioxide, and biofouling of injection or recovery wells are examples of proposed or implemented beneficial porous media biofilm applications. The thickness of the desired biofilm depends on a number of factors including desirable groundwater flow velocity and residence time of contaminated groundwater within the biofilm barrier as well as the prevailing hydraulic gradient. In order to better understand the influence of biofilms on reactive transport in porous media and ultimately improve biofilm-based porous media technologies, bench and mesoscale studies have been ongoing in our laboratories. This manuscript summarizes some of our past, current, and future efforts in this area and gives an outlook and overview of research and development needs.

  14. Dynamic remodeling of microbial biofilms by functionally distinct exopolysaccharides.

    PubMed

    Chew, Su Chuen; Kundukad, Binu; Seviour, Thomas; van der Maarel, Johan R C; Yang, Liang; Rice, Scott A; Doyle, Patrick; Kjelleberg, Staffan

    2014-01-01

    Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. Importance: Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical and industrial settings. One of the defining features of a biofilm is its extracellular matrix. The matrix has a heterogeneous structure and is formed from a secretion of various biopolymers, including proteins, extracellular DNA, and polysaccharides. It is generally known to interact with biofilm cells, thus affecting cell physiology and cell-cell communication. Despite the fact that the matrix may comprise up to 90% of the biofilm dry weight, how the matrix properties affect biofilm structure, maturation, and interspecies interactions remain largely unexplored. This study reveals that bacteria can use specific extracellular polymers to modulate the physical properties of their microenvironment. This in turn impacts biofilm structure, differentiation, and interspecies interactions. PMID:25096883

  15. Microbial biofilm study by synchrotron X-ray microscopy

    NASA Astrophysics Data System (ADS)

    Pennafirme, S.; Lima, I.; Bitencourt, J. A.; Crapez, M. A. C.; Lopes, R. T.

    2015-11-01

    Microbial biofilm has already being used to remove metals and other pollutants from wastewater. In this sense, our proposal was to isolate and cultivate bacteria consortia from mangrove's sediment resistant to Zn (II) and Cu (II) at 50 mg L-1 and to observe, through synchrotron X-ray fluorescence microscopy (microXRF), whether the biofilm sequestered the metal. The biofilm area analyzed was 1 mm2 and a 2D map was generated (pixel size 20×20 μm2, counting time 5 s/point). The biofilm formation and retention followed the sequence Zn>Cu. Bacterial consortium zinc resistant formed dense biofilm and retained 63.83% of zinc, while the bacterial consortium copper resistant retained 3.21% of copper, with lower biofilm formation. Dehydrogenase activity of Zn resistant bacterial consortium was not negatively affect by 50 mg ml-1 zinc input, whereas copper resistant bacterial consortium showed a significant decrease on dehydrogenase activity (50 mg mL-1 of Cu input). In conclusion, biofilm may protect bacterial cells, acting as barrier against metal toxicity. The bacterial consortia Zn resistant, composed by Nitratireductor spp. and Pseudomonas spp formed dense biofilm and sequestered metal from water, decreasing the metal bioavailability. These bacterial consortia can be used in bioreactors and in bioremediation programs.

  16. The effects of disinfectant foam on microbial biofilms.

    PubMed

    Sreenivasan, Prem K; Chorny, Roberto C

    2005-01-01

    This investigation examined the effects of common aqueous biocides and disinfectant foams derived from them on Pseudomonas aeruginosa biofilms. Biofilms were grown on stainless steel coupons under standardised conditions in a reactor supplemented with low concentrations of organic matter to simulate conditions prevalent in industrial systems. Five-day-old biofilms formed under ambient conditions with continuous agitation demonstrated a low coefficient of variation (5.809%) amongst viable biofilm bacteria from independent trials. Scanning electron microscopy revealed biofilms on coupons with viable biofilm bacteria observed by confocal microscopy. An aqueous solution of a common foaming agent amine oxide (AO) produced negligible effects on bacterial viability in biofilms (p>0.05). However, significant biofilm inactivation was noted with aqueous solutions of common biocides (peracetic acid, sodium hypochlorite, sodium ethylenediaminetetraacetic acid) with or without AO (p<0.05). Aereation of a mixture of AO with each of these common biocides resulted in significant reductions in the viability of biofilm bacteria (p<0.05). In contrast, limited effects were noted by foam devoid of biocides. A relationship between microbial inactivation and the concentration of biocide in foam (ranging from 0.1-0.5%) and exposure period were noted (p<0.05). Although, lower numbers of viable biofilm bacteria were recovered after treatment with the disinfectant foam than by the cognate aqueous biocide, significant differences between these treatments were not evident (p>0.05). In summary, the studies revealed significant biofilm inactivation by biocidal foam prepared with common biocides. Validation of foam disinfectants in controlled trials at manufacturing sites may facilitate developments for clean in place applications. Advantages of foam disinfectants include reductions in the volumes of biocides for industrial disinfection and in their disposal after use. PMID:16167393

  17. Laser Microbial Killing and Biofilm Disruption

    NASA Astrophysics Data System (ADS)

    Krespi, Yosef P.; Kizhner, Victor

    2009-06-01

    Objectives: To analyze the ability of NIR lasers to reduce bacterial load and demonstrate the capability of fiber-based Q-switched Nd:YAG laser disrupting biofilm. Study Design: NIR diode laser was tested in vitro and in vivo using pathogenic microorganisms (S. aureus, S. pneumoniae, P. aeruginosa). In addition biofilms were grown from clinical Pseudomonas isolates and placed in culture plates, screws, tympanostomy tubes and PET sutures. Methods: In the animal experiments acute rhinosinusitis model was created by packing the rabbit nose with bacteria soaked solution. The nasal pack was removed in two days and nose was exposed to laser irradiation. A 940 nm diode laser with fiber diffuser was used. Nasal cultures were obtained before and after the laser treatments. Animals were sacrificed fifteen days following laser treatment and bacteriologic/histologic results analyzed. Q-switched Nd:YAG laser generated shockwave pulses were delivered on biofilm using special probes over culture plates, screws, tubes, and PET sutures for the biofilm experiments. Results: Average of two log bacteria reduction was achieved with NIR laser compared to controls. Histologic studies demonstrated preservation of tissue integrity without significant damage to mucosa. Biofilms were imaged before, during and after treatment using a confocal microscope. During laser-generated shockwave application, biofilm was initially seen to oscillate and eventually break off. Large and small pieces of biofilm were totally and instantly removed from the surface to which they were attached in seconds. Conclusions: Significant bacterial reduction was achieved with NIR laser therapy in this experimental in vitro and animal study. In addition we disrupted Pseudomonas aeruginosa biofilms using Q-switched Nd:YAG laser and special probes generating plasma and shockwave. This new and innovative method of bacteria killing and biofilm disruption without injuring host tissue may have clinical application in the future.

  18. Embryo fossilization is a biological process mediated by microbial biofilms

    PubMed Central

    Raff, Elizabeth C.; Schollaert, Kaila L.; Nelson, David E.; Donoghue, Philip C. J.; Thomas, Ceri-Wyn; Turner, F. Rudolf; Stein, Barry D.; Dong, Xiping; Bengtson, Stefan; Huldtgren, Therese; Stampanoni, Marco; Chongyu, Yin; Raff, Rudolf A.

    2008-01-01

    Fossilized embryos with extraordinary cellular preservation appear in the Late Neoproterozoic and Cambrian, coincident with the appearance of animal body fossils. It has been hypothesized that microbial processes are responsible for preservation and mineralization of organic tissues. However, the actions of microbes in preservation of embryos have not been demonstrated experimentally. Here, we show that bacterial biofilms assemble rapidly in dead marine embryos and form remarkable pseudomorphs in which the bacterial biofilm replaces and exquisitely models details of cellular organization and structure. The experimental model was the decay of cleavage stage embryos similar in size and morphology to fossil embryos. The data show that embryo preservation takes place in 3 distinct steps: (i) blockage of autolysis by reducing or anaerobic conditions, (ii) rapid formation of microbial biofilms that consume the embryo but form a replica that retains cell organization and morphology, and (iii) bacterially catalyzed mineralization. Major bacterial taxa in embryo decay biofilms were identified by using 16S rDNA sequencing. Decay processes were similar in different taphonomic conditions, but the composition of bacterial populations depended on specific conditions. Experimental taphonomy generates preservation states similar to those in fossil embryos. The data show how fossilization of soft tissues in sediments can be mediated by bacterial replacement and mineralization, providing a foundation for experimentally creating biofilms from defined microbial species to model fossilization as a biological process. PMID:19047625

  19. Molecular Survey of Concrete Sewer Biofilm Microbial Communities

    EPA Science Inventory

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

  20. Molecular Analysis of Microbial Communities in Endotracheal Tube Biofilms

    PubMed Central

    Cairns, Scott; Thomas, John Gilbert; Hooper, Samuel James; Wise, Matthew Peter; Frost, Paul John; Wilson, Melanie Julia; Lewis, Michael Alexander Oxenham; Williams, David Wynne

    2011-01-01

    Background Ventilator-associated pneumonia is the most prevalent acquired infection of patients on intensive care units and is associated with considerable morbidity and mortality. Evidence suggests that an improved understanding of the composition of the biofilm communities that form on endotracheal tubes may result in the development of improved preventative strategies for ventilator-associated pneumonia. Methodology/Principal Findings The aim of this study was to characterise microbial biofilms on the inner luminal surface of extubated endotracheal tubes from ICU patients using PCR and molecular profiling. Twenty-four endotracheal tubes were obtained from twenty mechanically ventilated patients. Denaturing gradient gel electrophoresis (DGGE) profiling of 16S rRNA gene amplicons was used to assess the diversity of the bacterial population, together with species specific PCR of key marker oral microorganisms and a quantitative assessment of culturable aerobic bacteria. Analysis of culturable aerobic bacteria revealed a range of colonisation from no growth to 2.1108 colony forming units (cfu)/cm2 of endotracheal tube (mean 1.4107 cfu/cm2). PCR targeting of specific bacterial species detected the oral bacteria Streptococcus mutans (n?=?5) and Porphyromonas gingivalis (n?=?5). DGGE profiling of the endotracheal biofilms revealed complex banding patterns containing between 3 and 22 (mean 6) bands per tube, thus demonstrating the marked complexity of the constituent biofilms. Significant inter-patient diversity was evident. The number of DGGE bands detected was not related to total viable microbial counts or the duration of intubation. Conclusions/Significance Molecular profiling using DGGE demonstrated considerable biofilm compositional complexity and inter-patient diversity and provides a rapid method for the further study of biofilm composition in longitudinal and interventional studies. The presence of oral microorganisms in endotracheal tube biofilms suggests that these may be important in biofilm development and may provide a therapeutic target for the prevention of ventilator-associated pneumonia. PMID:21423727

  1. Utilization of microbial biofilms as monitors of bioremediation

    SciTech Connect

    Peacock, Aaron D.; IstokD., Jonathan; Krumholz, Lee R.; Geyer, Roland; Kinsall, Barry Lee; Watson, David B; Sublette, K.; White, David C.

    2004-03-01

    A down-well aquifer microbial sampling system was developed using glass wool or Bio-Sep beads as a solid-phase support matrix. Here we describe the use of these devices to monitor the groundwater microbial community dynamics during field bioremediation experiments at the U.S. Department of Energy Natural and Accelerated Bioremediation Research Programs Field Research Center at the Oak Ridge National Laboratory. During the 6-week deployment, microbial biofilms colonized glass wool and bead internal surfaces. Changes in viable biomass, community composition, metabolic status, and respiratory state were reflected in sampler composition, type of donor, and groundwater pH. Biofilms that formed on Bio-Sep beads had 2-13 times greater viable biomass; however, the bead communities were less metabolically active [higher cyclopropane/monoenoic phospholipid fatty acid (PLFA) ratios] and had a lower aerobic respiratory state (lower total respiratory quinone/PLFA ratio and ubiquinone/menaquinone ratio) than the biofilms formed on glass wool. Anaerobic growth in these systems was characterized by plasmalogen phospholipids and was greater in the wells that received electron donor additions. Partial 16S rDNA sequences indicated that Geobacter and nitrate-reducing organisms were induced by the acetate, ethanol, or glucose additions. DNA and lipid biomarkers were extracted and recovered without the complications that commonly plague sediment samples due to the presence of clay or dissolved organic matter. Although microbial community composition in the groundwater or adjacent sediments may differ from those formed on down-well biofilm samplers, the metabolic activity responses of the biofilms to modifications in groundwater geochemistry record the responses of the microbial community to biostimulation while providing integrative sampling and ease of recovery for biomarker analysis.

  2. Microbial Surface Colonization and Biofilm Development in Marine Environments.

    PubMed

    Dang, Hongyue; Lovell, Charles R

    2016-03-01

    Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. PMID:26700108

  3. Microbial genomes: Blueprints for life

    SciTech Connect

    Relman, David A.; Strauss, Evelyn

    2000-12-31

    Complete microbial genome sequences hold the promise of profound new insights into microbial pathogenesis, evolution, diagnostics, and therapeutics. From these insights will come a new foundation for understanding the evolution of single-celled life, as well as the evolution of more complex life forms. This report is an in-depth analysis of scientific issues that provides recommendations and will be widely disseminated to the scientific community, federal agencies, industry and the public.

  4. Life Support Systems Microbial Challenges

    NASA Technical Reports Server (NTRS)

    Roman, Monserrate C.

    2009-01-01

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

  5. Physicochemical characteristics and microbial community evolution of biofilms during the start-up period in a moving bed biofilm reactor.

    PubMed

    Zhu, Yan; Zhang, Yan; Ren, Hong-Qiang; Geng, Jin-Ju; Xu, Ke; Huang, Hui; Ding, Li-Li

    2015-03-01

    This study aimed to investigate biofilm properties evolution coupled with different ages during the start-up period in a moving bed biofilm reactor system. Physicochemical characteristics including adhesion force, extracellular polymeric substances (EPS), morphology as well as volatile solid and microbial community were studied. Results showed that the formation and development of biofilms exhibited four stages, including (I) initial attachment and young biofilm formation, (II) biofilms accumulation, (III) biofilm sloughing and updating, and (IV) biofilm maturation. During the whole start-up period, adhesion force was positively and significantly correlated with the contents of EPS, especially the content of polysaccharide. In addition, increased adhesion force and EPS were beneficial for biofilm retention. Gram-negative bacteria mainly including Sphaerotilus, Zoogloea and Haliscomenobacter were predominant in the initial stage. Actinobacteria was beneficial to resist sloughing. Furthermore, filamentous bacteria were dominant in maturation biofilm. PMID:25636169

  6. Microbial diversity of biofilms in dental unit water systems.

    PubMed

    Singh, Ruby; Stine, O Colin; Smith, David L; Spitznagel, John K; Labib, Mohamed E; Williams, Henry N

    2003-06-01

    We investigated the microbial diversity of biofilms found in dental unit water systems (DUWS) by three methods. The first was microscopic examination by scanning electron microscopy (SEM), acridine orange staining, and fluorescent in situ hybridization (FISH). Most bacteria present in the biofilm were viable. FISH detected the beta and gamma, but not the alpha, subclasses of Proteobacteria: In the second method, 55 cultivated biofilm isolates were identified with the Biolog system, fatty acid analysis, and 16S ribosomal DNA (rDNA) sequencing. Only 16S identified all 55 isolates, which represented 13 genera. The most common organisms, as shown by analyses of 16S rDNA, belonged to the genera Afipia (28%) and Sphingomonas (16%). The third method was a culture-independent direct amplification and sequencing of 165 subclones from community biofilm 16S rDNA. This method revealed 40 genera: the most common ones included Leptospira (20%), Sphingomonas (14%), Bacillus (7%), Escherichia (6%), Geobacter (5%), and Pseudomonas (5%). Some of these organisms may be opportunistic pathogens. Our results have demonstrated that a biofilm in a health care setting may harbor a vast diversity of organisms. The results also reflect the limitations of culture-based techniques to detect and identify bacteria. Although this is the greatest diversity reported in DUWS biofilms, other genera may have been missed. Using a technique based on jackknife subsampling, we projected that a 25-fold increase in the number of subclones sequenced would approximately double the number of genera observed, reflecting the richness and high diversity of microbial communities in these biofilms. PMID:12788744

  7. Adhesion and formation of microbial biofilms in complex microfluidic devices

    SciTech Connect

    Kumar, Aloke; Karig, David K; Neethirajan, Suresh; Suresh, Anil K; Srijanto, Bernadeta R; Mukherjee, Partha P; Retterer, Scott T; Doktycz, Mitchel John

    2012-01-01

    Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles in the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.

  8. Microbial biofilm growth on irradiated, spent nuclear fuel cladding

    NASA Astrophysics Data System (ADS)

    Bruhn, D. F.; Frank, S. M.; Roberto, F. F.; Pinhero, P. J.; Johnson, S. G.

    2009-02-01

    A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 × 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments.

  9. Microbial Biofilm Growth on Irradiated, Spent Nuclear Fuel Cladding

    SciTech Connect

    S.M. Frank

    2009-02-01

    A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 × 103 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments.

  10. Sponge larval settlement cues: the role of microbial biofilms in a warming ocean

    PubMed Central

    Whalan, S.; Webster, N. S.

    2014-01-01

    Microbial biofilms play important roles in initiating settlement of marine invertebrate larvae. Given the importance of habitat selection by the motile larval phase, understanding settlement choices is critical if we are to successfully predict the population dynamics of sessile adults. Marine microbial biofilms show remarkable variability in community composition, often mediated by environmental conditions and biofilm age. To determine if biofilm communities were influenced by the time allowed to establish (age) and/or seawater temperature, we manipulated experimental surfaces to firstly determine biofilm community composition and secondly test larval settlement responses for the abundant coral reef sponge Rhopaloeides odorabile. Microbial profiling of biofilms revealed different communities according to both age and temperature. Biofilm community composition, as a result of both elevated seawater temperature and biofilm age, contributed to settlement for sponge larvae with markedly higher numbers of larvae settling to biofilms developed over longer periods (10?d) and at temperatures 26C above ambient. PMID:24518965

  11. Molecular survey of concrete sewer biofilm microbial communities.

    PubMed

    Santo Domingo, Jorge W; Revetta, Randy P; Iker, Brandon; Gomez-Alvarez, Vicente; Garcia, Jarissa; Sullivan, John; Weast, James

    2011-10-01

    The microbial composition of concrete biofilms within wastewater collection systems was studied using molecular assays. SSU rDNA clone libraries were generated from 16 concrete surfaces of manholes, a combined sewer overflow, and sections of a corroded sewer pipe. Of the 2457 sequences analyzed, ?-, ?-, ?-, and ?-Proteobacteria represented 15%, 22%, 11%, and 4% of the clones, respectively. ?-Proteobacteria (47%) sequences were more abundant in the pipe crown than any of the other concrete surfaces. While 178 to 493 Operational Taxonomic Units (OTUs) were associated with the different concrete samples, only four sequences were shared among the different clone libraries. Bacteria implicated in concrete corrosion were found in the clone libraries while archaea, fungi, and several bacterial groups were also detected using group-specific assays. The results showed that concrete sewer biofilms are more diverse than previously reported. A more comprehensive molecular database will be needed to better study the dynamics of concrete biofilms. PMID:21981064

  12. Changes in Microbial Biofilm Communities during Colonization of Sewer Systems.

    PubMed

    Auguet, O; Pijuan, M; Batista, J; Borrego, C M; Gutierrez, O

    2015-10-01

    The coexistence of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) in anaerobic biofilms developed in sewer inner pipe surfaces favors the accumulation of sulfide (H2S) and methane (CH4) as metabolic end products, causing severe impacts on sewerage systems. In this study, we investigated the time course of H2S and CH4 production and emission rates during different stages of biofilm development in relation to changes in the composition of microbial biofilm communities. The study was carried out in a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer using a combination of process data and molecular techniques (e.g., quantitative PCR [qPCR], denaturing gradient gel electrophoresis [DGGE], and 16S rRNA gene pyrotag sequencing). After 2 weeks of biofilm growth, H2S emission was notably high (290.7±72.3 mg S-H2S liter(-1) day(-1)), whereas emissions of CH4 remained low (17.9±15.9 mg COD-CH4 liter(-1) day(-1)). This contrasting trend coincided with a stable SRB community and an archaeal community composed solely of methanogens derived from the human gut (i.e., Methanobrevibacter and Methanosphaera). In turn, CH4 emissions increased after 1 year of biofilm growth (327.6±16.6 mg COD-CH4 liter(-1) day(-1)), coinciding with the replacement of methanogenic colonizers by species more adapted to sewer conditions (i.e., Methanosaeta spp.). Our study provides data that confirm the capacity of our laboratory experimental system to mimic the functioning of full-scale sewers both microbiologically and operationally in terms of sulfide and methane production, gaining insight into the complex dynamics of key microbial groups during biofilm development. PMID:26253681

  13. Life Support Systems Microbial Challenges

    NASA Technical Reports Server (NTRS)

    Roman, Monsi C.

    2010-01-01

    Many microbiological studies were performed during the development of the Space Station Water Recovery and Management System from1990-2009. Studies include assessments of: (1) bulk phase (planktonic) microbial population (2) biofilms, (3) microbially influenced corrosion (4) biofouling treatments. This slide presentation summarizes the studies performed to assess the bulk phase microbial community during the Space Station Water Recovery Tests (WRT) from 1990 to 1998. This report provides an overview of some of the microbiological analyses performed during the Space Station WRT program. These tests not only integrated several technologies with the goal of producing water that met NASA s potable water specifications, but also integrated humans, and therefore human flora into the protocols. At the time these tests were performed, not much was known (or published) about the microbial composition of these types of wastewater. It is important to note that design changes to the WRS have been implemented over the years and results discussed in this report might be directly related to test configurations that were not chosen for the final flight configuration. Results microbiological analyses performed Conclusion from the during the WRT showed that it was possible to recycle water from different sources, including urine, and produce water that can exceed the quality of municipally produced water.

  14. Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

    NASA Astrophysics Data System (ADS)

    Davis, C. A.; Pyrak-Nolte, L. J.; Atekwana, E. A.; Werkema, D. D.; Haugen, M. E.

    2009-12-01

    Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand columns. A control column (non-biostimulated) and a biostimulated column were studied in a 2D acoustic scanning apparatus, and a second set of columns were constructed with Ag-AgCl electrodes for complex conductivity measurements. At the completion of the 29-day experiment, compressional wave amplitudes and arrival times for the control column were observed to be relatively uniform over the scanned 2D region. However, the biostimulated sample exhibited a high degree of spatial variability within the column for both the amplitude and arrival times. Furthermore, portions of the sample exhibited increased attenuation (~ 80%) concurrent with an increase in the arrival times, while other portions exhibited decreased attenuation (~ 45%) and decreased arrival time. The acoustic amplitude and arrival times changed significantly in the biostimulated column between Days 5 and 7 of the experiment and are consistent with a peak in the imaginary conductivity (σ”) values. The σ” response corresponds to different stages of biofilm development. That is, we interpret the peak σ” with the maximum biofilm thickness and decreasing σ” due to cell death or detachment. Environmental scanning electron microscope (ESEM) imaging confirmed microbial cell attachment to sand surfaces in the biostimulated columns, showed apparent differences in the morphology of attached biomass between regions of increased and decreased attenuation, and indicated no mineral precipitation or biomineralization. The heterogeneity in the elastic properties arises from the differences in the morphology and structure of attached biofilms. These results suggest that combining acoustic imaging and complex conductivity techniques can provide a powerful tool for assessing microbial growth or biofilm formation and the associated changes in porous media, such as those that occur during bioremediation and microbial enhanced oil recovery. Furthermore, this study suggests microbial growth and biofilm development can yield a detectable geophysical response without biomineralization effects. Acknowledgments: This material is based in part on work supported by the National Science Foundation under Grant No. OCE-0729642, EAR 0722410 (MRI), EAR 0525316, and REU Award # 0552918, and EPA Student Services Contract EP07D000660. LJPN would like to acknowledge support from Geosciences Research Program, Office of Basic Energy Sciences, US Department of Energy (DEFG02-97ER14785 08).

  15. Advances in Microbial Biofilm Prevention on Indwelling Medical Devices with Emphasis on Usage of Acoustic Energy

    PubMed Central

    Dror, Naama; Mandel, Mathilda; Hazan, Zadik; Lavie, Gad

    2009-01-01

    Microbial biofilms are a major impediment to the use of indwelling medical devices, generating device-related infections with high morbidity and mortality. Major efforts directed towards preventing and eradicating the biofilm problem face difficulties because biofilms protect themselves very effectively by producing a polysaccharide coating, reducing biofilm sensitivity to antimicrobial agents. Techniques applied to combating biofilms have been primarily chemical. These have met with partial and limited success rates, leading to current trends of eradicating biofilms through physico-mechanical strategies. Here we review the different approaches that have been developed to control biofilm formation and removal, focusing on the utilization of acoustic energy to achieve these objectives. PMID:22574031

  16. INVESTIGATING THE EFFECT OF MICROBIAL GROWTH AND BIOFILM FORMATION ON SEISMIC WAVE PROPAGATION IN SEDIMENT

    EPA Science Inventory

    Previous laboratory investigations have demonstrated that the seismic methods are sensitive to microbially-induced changes in porous media through the generation of biogenic gases and biomineralization. The seismic signatures associated with microbial growth and biofilm formation...

  17. Acoustic and Electrical Property Changes Due to Microbial Growth and Biofilm Formation in Porous Media

    EPA Science Inventory

    A laboratory study was conducted to investigate the effect of microbial growth and biofilm formation on compressional waves, and complex conductivity during stimulated microbial growth. Over the 29 day duration of the experiment, compressional wave amplitudes and arrival times f...

  18. Early microbial biofilm formation on marine plastic debris.

    PubMed

    Lobelle, Delphine; Cunliffe, Michael

    2011-01-01

    An important aspect of the global problem of plastic debris pollution is plastic buoyancy. There is some evidence that buoyancy is influenced by attached biofilms but as yet this is poorly understood. We submerged polyethylene plastic in seawater and sampled weekly for 3 weeks in order to study early stage processes. Microbial biofilms developed rapidly on the plastic and coincided with significant changes in the physicochemical properties of the plastic. Submerged plastic became less hydrophobic and more neutrally buoyant during the experiment. Bacteria readily colonised the plastic but there was no indication that plastic-degrading microorganisms were present. This study contributes to improved understanding of the fate of plastic debris in the marine environment. PMID:21093883

  19. Biofilms

    PubMed Central

    van Hoek, Monique L

    2013-01-01

    Our understanding of the virulence and pathogenesis of Francisella spp. has significantly advanced in recent years, including a new understanding that this organism can form biofilms. What is known so far about Francisella spp. biofilms is summarized here and future research questions are suggested. The molecular basis of biofilm production has begun to be studied, especially the role of extracellular carbohydrates and capsule, quorum sensing and two-component signaling systems. Further work has explored the contribution of amoebae, pili, outer-membrane vesicles, chitinases, and small molecules such as c-di-GMP to Francisella spp. biofilm formation. A role for Francisella spp. biofilm in feeding mosquito larvae has been suggested. As no strong role in virulence has been found yet, Francisella spp. biofilm formation is most likely a key mechanism for environmental survival and persistence. The significance and importance of Francisella spp.’s biofilm phenotype as a critical aspect of its microbial physiology is being developed. Areas for further studies include the potential role of Francisella spp. biofilms in the infection of mammalian hosts and virulence regulation. PMID:24225421

  20. Cathodic and anodic biofilms in Single Chamber Microbial Fuel Cells.

    PubMed

    Cristiani, P; Carvalho, M L; Guerrini, E; Daghio, M; Santoro, C; Li, B

    2013-08-01

    The oxygen reduction due to microaerophilic biofilms grown on graphite cathodes (biocathodes) in Single Chamber Microbial Fuel Cells (SCMFCs) is proved and analysed in this paper. Pt-free cathode performances are compared with those of different platinum-loaded cathodes, before and after the biofilm growth. Membraneless SCMFCs were operating in batch-mode, filled with wastewater. A substrate (fuel) of sodium acetate (0.03 M) was periodically added and the experiment lasted more than six months. A maximum of power densities, up to 0.5 W m(-2), were reached when biofilms developed on the electrodes and the cathodic potential decreased (open circuit potential of 50-200 mV vs. SHE). The power output was almost constant with an acetate concentration of 0.01-0.05 M and it fell down when the pH of the media exceeded 9.5, independently of the Pt-free/Pt-loading at the cathodes. Current densities varied in the range of 1-5 Am(-2) (cathode area of 5 cm(2)). Quasi-stationary polarization curves performed with a three-electrode configuration on cathodic and anodic electrodes showed that the anodic overpotential, more than the cathodic one, may limit the current density in the SCMFCs for a long-term operation. PMID:23474690

  1. Microbial biofilms: impact on the pathogenesis of periodontitis, cystic fibrosis, chronic wounds and medical device-related infections.

    PubMed

    Mihai, Mara Madalina; Holban, Alina Maria; Giurcaneanu, Calin; Popa, Liliana Gabriela; Oanea, Raluca Mihaela; Lazar, Veronica; Chifiriuc, Mariana Carmen; Popa, Marcela; Popa, Mircea Ioan

    2015-01-01

    The majority of chronic infections are associated with mono- or polymicrobial biofilms, having a significant impact on the patients' quality of life and survival rates. Although the use of medical devices revolutionized health care services and significantly improved patient outcomes, it also led to complications associated with biofilms and to the emergence of multidrug resistant bacteria. Immunocompromised patients, institutionalized or hospitalized individuals, elderly people are at greater risk due to life-threatening septic complications, but immunocompetent individuals with predisposing genetic or acquired diseases can also be affected, almost any body part being able to shelter persistent biofilms. Moreover, chronic biofilm-related infections can lead to the occurrence of systemic diseases, as in the case of chronic periodontitis, linked to atherosclerosis, cardiovascular disease and diabetes. The more researchers discover, new unknown issues add up to the complexity of biofilm infections, in which microbial species establish relationships of cooperation and competition, and elaborate phenotypic differentiation into functional, adapted communities. Their interaction with the host's immune system or with therapeutic agents contributes to the complex puzzle that still misses a lot of pieces. In this comprehensive review we aimed to highlight the microbial composition, developmental stages, architecture and properties of medical biofilms, as well as the diagnostic tools used in the management of biofilm related infections. Also, we present recently acquired knowledge on the etiopathogenesis, diagnosis and treatment of four chronic diseases associated with biofilm development in tissues (chronic periodontitis, chronic lung infection in cystic fibrosis, chronic wounds) and artificial substrata (medical devices-related infections). PMID:25877092

  2. Microbial Communities in Biofilms of an Acid Mine Drainage Site Determined by Phospholipid Analysis

    NASA Astrophysics Data System (ADS)

    Das Gupta, S.; Fang, J.

    2008-12-01

    Phospholipids were extracted to determine the microbial biomass and community structure of biofims from an acid mine drainage (AMD) at the Green Valley coal mine site (GVS) in western Indiana. The distribution of specific biomarkers indicated the presence of a variety of microorganisms. Phototrophic microeukaryotes, which include Euglena mutabilis, algae, and cyanobacteria were the most dominant organisms, as indicated by the presence of polyunsaturated fatty acids. The presence of terminally methyl branched fatty acids suggests the presence of Gram-positive bacteria, and the mid-methyl branched fatty acids indicates the presence of sulfate-reducing bacteria. Fungi appear to also be an important part of the AMD microbial communities as suggested by the presence of 18:2 fatty acid. The acidophilic microeukaryotes Euglena dominated the biofilm microbial communities. These microorganisms appear to play a prominent role in the formation and preservation of stromatolites and in releasing oxygen to the atmosphere by oxygenic photosynthesis. Thus, the AMD environment comprises a host of microorganisms spreading out within the phylogenetic tree of life. Novel insights on the roles of microbial consortia in the formation and preservation of stromatolites and the production of oxygen through photosynthesis in AMD systems may have significance in the understanding of the interaction of Precambrian microbial communities in environments that produced microbially-mediated sedimentary structures and that caused oxygenation of Earth's atmosphere.

  3. Detection of microbial Life in the Subsurface

    NASA Astrophysics Data System (ADS)

    Stan-Lotter, H.; Fendrihan, S.; Dornmayr-Pfaffenhuemer, M.; Legat, A.; Gruber, C.; Weidler, G.; Gerbl, F.

    2007-08-01

    In recent years microbial communities were detected, which dwell in rocks, soil and caves deep below the surface of the Earth. This has led to a new view of the diversity of the terrestrial biosphere and of the physico-chemical boundaries for life. Two types of subterranean environments are Permo-Triassic salt sediments and thermal radioactive springs from igneous rocks in the Alps. Viable extremely halophilic archaea were isolated from ancient salt sediments which are estimated to be about 250 million years old (1). Chemotaxonomic and molecular characterization showed that they represent novel species, e. g. Halococcus salifodinae, Hcc. dombrowskiiand Halobacterium noricense. Simulation experiments with artificial halite suggested that these microorganisms probably survived while embedded in fluid inclusions. In the thermal springs, evidence for numerous novel microorganisms was found by 16S rDNA sequencing and probing for some metabolic genes; in addition, scanning electron microscopy of biofilms on the rock surfaces revealed great diversity of morphotypes (2). These communities appear to be active and growing, although their energy and carbon sources are entirely unknown. The characterization of subsurface inhabitants is of astrobiological relevance since extraterrestrial halite has been detected (3) and since microbial life on Mars, if existent, may have retreated into the subsurface. As a long-term goal, a thorough census of terrestrial microorganisms should be taken and their survival potential be determined in view of future missions for the search for extraterrestrial life, including planning precautions against possible forward contamination by space probes. (1) Fendrihan, S., Legat, A., Gruber, C., Pfaffenhuemer, M., Weidler, G., Gerbl, F., Stan-Lotter, H. (2006) Extremely halophilic archaea and the issue of long term microbial survival. Reviews in Environmental Science and Bio/technology 5, 1569-1605. (2) Weidler, G.W., Dornmayr-Pfaffenhuemer, M., Gerbl, F.W., Heinen, W., Stan- Lotter, H. (2007) Communities of Archaea and Bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps and evidence for ammonia oxidizing Crenarchaeota. Appl. Environ. Microbiol. 73, 259-270. (3) Stan-Lotter, H., Radax, C., McGenity, T.J., Legat, A., Pfaffenhuemer, M.,Wieland, H., Gruber, C., Denner, E.B.M. (2004) From Intraterrestrials to Extraterrestrials - Viable haloarchaea in ancient salt deposits. In: Halophilic Microorganisms. Ventosa A. (Ed.), Springer Verlag, Berlin, Heidelberg, New York, pp. 89-102.

  4. Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China.

    PubMed

    Lin, Huirong; Zhang, Shuting; Gong, Song; Zhang, Shenghua; Yu, Xin

    2015-01-01

    The composition and microbial community structure of the drinking water system biofilms were investigated using microstructure analysis and 454 pyrosequencing technique in Xiamen city, southeast of China. SEM (scanning electron microscope) results showed different features of biofilm morphology in different fields of PVC pipe. Extracellular matrix material and sparse populations of bacteria (mainly rod-shaped and coccoid) were observed. CLSM (confocal laser scanning microscope) revealed different distributions of attached cells, extracellular proteins, ?-polysaccharides, and ?-polysaccharides. The biofilms had complex bacterial compositions. Differences in bacteria diversity and composition from different tap materials and ages were observed. Proteobacteria was the common and predominant group in all biofilms samples. Some potential pathogens (Legionellales, Enterobacteriales, Chromatiales, and Pseudomonadales) and corrosive microorganisms were also found in the biofilms. This study provides the information of characterization and visualization of the drinking water biofilms matrix, as well as the microbial community structure and opportunistic pathogens occurrence. PMID:26273617

  5. Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China

    PubMed Central

    Lin, Huirong; Zhang, Shuting; Gong, Song; Zhang, Shenghua; Yu, Xin

    2015-01-01

    The composition and microbial community structure of the drinking water system biofilms were investigated using microstructure analysis and 454 pyrosequencing technique in Xiamen city, southeast of China. SEM (scanning electron microscope) results showed different features of biofilm morphology in different fields of PVC pipe. Extracellular matrix material and sparse populations of bacteria (mainly rod-shaped and coccoid) were observed. CLSM (confocal laser scanning microscope) revealed different distributions of attached cells, extracellular proteins, α-polysaccharides, and β-polysaccharides. The biofilms had complex bacterial compositions. Differences in bacteria diversity and composition from different tap materials and ages were observed. Proteobacteria was the common and predominant group in all biofilms samples. Some potential pathogens (Legionellales, Enterobacteriales, Chromatiales, and Pseudomonadales) and corrosive microorganisms were also found in the biofilms. This study provides the information of characterization and visualization of the drinking water biofilms matrix, as well as the microbial community structure and opportunistic pathogens occurrence. PMID:26273617

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  7. Sunlight-Exposed Biofilm Microbial Communities Are Naturally Resistant to Chernobyl Ionizing-Radiation Levels

    PubMed Central

    Ragon, Marie; Restoux, Gwendal; Moreira, David; Møller, Anders Pape; López-García, Purificación

    2011-01-01

    Background The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well. Methodology/Principal Findings To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates. Conclusions/Significance Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation. PMID:21765911

  8. Microbial Community Analysis of Fresh and Old Microbial Biofilms on Bayon Temple Sandstone of Angkor Thom, Cambodia

    PubMed Central

    Lan, Wensheng; Li, Hui; Wang, Wei-Dong; Katayama, Yoko

    2010-01-01

    The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region. Electronic supplementary material The online version of this article (doi:10.1007/s00248-010-9707-5) contains supplementary material, which is available to authorized users. PMID:20593173

  9. Microbial diversity in biofilm infections of the urinary tract with the use of sonication techniques.

    PubMed

    Holá, Veronika; Ruzicka, Filip; Horka, Marie

    2010-08-01

    Infections of the urinary tract account for >40% of nosocomial infections; most of these are infections in catheterized patients. Bacterial colonization of the urinary tract and catheters causes not only the particular infection but also a number of complications, for example blockage of catheters with crystallic deposits of bacterial origin, generation of gravels and pyelonephritis. Infections of urinary catheters are only rarely single-species infections. The longer a patient is catheterized, the higher the diversity of biofilm microbial communities. The aims of this study were to investigate the microbial diversity on the catheters and to compare the ability to form biofilm among isolated microbial species. The next aim was to discriminate particular causative agents of infections of the urinary tract and their importance as biofilm formers in the microbial community on the urinary catheter. We examined catheters from 535 patients and isolated 1555 strains of microorganisms. Most of the catheters were infected by three or more microorganisms; only 12.5% showed monomicrobial infection. Among the microorganisms isolated from the urinary catheters, there were significant differences in biofilm-forming ability, and we therefore conclude that some microbial species have greater potential to cause a biofilm-based infection, whereas others can be only passive members of the biofilm community. PMID:20602639

  10. Complex conductivity response to microbial growth and biofilm formation on phenanthrene spiked medium

    NASA Astrophysics Data System (ADS)

    Albrecht, Remy; Gourry, Jean Christophe; Simonnot, Marie-Odile; Leyval, Corinne

    2011-11-01

    Several laboratory studies have recently demonstrated the utility of geophysical methods for the investigation of microbial-induced changes over contaminated sites. However, it remains difficult to distinguish the effects due to the new physical properties imparted by microbial processes, to bacterial growth, or to the development of bacterial biofilm. We chose to study the influence of biofilm formation on geophysical response using complex conductivity measurements (0.1-1000 Hz) in phenanthrene-contaminated media. Biotic assays were conducted with two phenanthrene (PHE) degrading bacterial strains: Burkholderia sp (NAH1), which produced biofilm and Stenophomonas maltophilia (MATE10), which did not, and an abiotic control. Results showed that bacterial densities for NAH1 and MATE10 strains continuously increased at the same rate during the experiment. However, the complex conductivity signature showed noticeable differences between the two bacteria, with a phase shift of 50 mrad at 4 Hz for NAH1, which produced biofilm. Biofilm volume was quantified by Scanning Confocal Laser Microscopy (SCLM). Significant correlations were established between phase shift decrease and biofilm volume for NAH1 assays. Results suggest that complex conductivity measurements, specifically phase shift, can be a useful indicator of biofilm formation inside the overall signal of microbial activity on contaminated sites.

  11. New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms.

    PubMed

    Almstrand, Robert; Daims, Holger; Persson, Frank; Srensson, Fred; Hermansson, Malte

    2013-10-01

    In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

  12. New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

    PubMed Central

    Almstrand, Robert; Daims, Holger; Persson, Frank; Srensson, Fred

    2013-01-01

    In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

  13. Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches.

    PubMed

    Beltrán, Yislem; Cerqueda-García, Daniel; Taş, Neslihan; Thomé, Patricia E; Iglesias-Prieto, Roberto; Falcón, Luisa I

    2016-01-01

    Coral reefs are among the most productive ecosystems on the planet, but are rapidly declining due to global-warming-mediated changes in the oceans. Particularly for the Caribbean region, Acropora sp. stony corals have lost ∼80% of their original coverage, resulting in vast extensions of dead coral rubble. We analyzed the microbial composition of biofilms that colonize and lithify dead Acropora palmata rubble in the Mexican Caribbean and identified the microbial assemblages that can persist under scenarios of global change, including high temperature and low pH. Lithifying biofilms have a mineral composition that includes aragonite and magnesium calcite (16 mole% MgCO3) and calcite, while the mineral phase corresponding to coral skeleton is basically aragonite. Microbial composition of the lithifying biofilms are different in comparison to surrounding biotopes, including a microbial mat, water column, sediments and live A. palmata microbiome. Significant shifts in biofilm composition were detected in samples incubated in mesocosms. The combined effect of low pH and increased temperature showed a strong effect after two-week incubations for biofilm composition. Findings suggest that lithifying biofilms could remain as a secondary structure on reef rubble possibly impacting the functional role of coral reefs. PMID:26705570

  14. How to Study Biofilms after Microbial Colonization of Materials Used in Orthopaedic Implants.

    PubMed

    Drago, Lorenzo; Agrappi, Serse; Bortolin, Monica; Toscano, Marco; Romanò, Carlo Luca; De Vecchi, Elena

    2016-01-01

    Over the years, various techniques have been proposed for the quantitative evaluation of microbial biofilms. Spectrophotometry after crystal violet staining is a widespread method for biofilm evaluation, but several data indicate that it does not guarantee a good specificity, although it is rather easy to use and cost saving. Confocal laser microscopy is one of the most sensitive and specific tools to study biofilms, and it is largely used for research. However, in some cases, no quantitative measurement of the matrix thickness or of the amount of embedded microorganisms has been performed, due to limitation in availability of dedicated software. For this reason, we have developed a protocol to evaluate the microbial biofilm formed on sandblasted titanium used for orthopaedic implants, that allows measurement of biomass volume and the amount of included cells. Results indicate good reproducibility in terms of measurement of biomass and microbial cells. Moreover, this protocol has proved to be applicable for evaluation of the efficacy of different anti-biofilm treatments used in the orthopaedic setting. Summing up, the protocol here described is a valid and inexpensive method for the study of microbial biofilm on prosthetic implant materials. PMID:26927075

  15. Microbial interactions in marine water amended by eroded benthic biofilm: A case study from an intertidal mudflat

    NASA Astrophysics Data System (ADS)

    Montanié, Hélène; Ory, Pascaline; Orvain, Francis; Delmas, Daniel; Dupuy, Christine; Hartmann, Hans J.

    2014-09-01

    In shallow macrotidal ecosystems with large intertidal mudflats, the sediment-water coupling plays a crucial role in structuring the pelagic microbial food web functioning, since inorganic and organic matter and microbial components (viruses and microbes) of the microphytobenthic biofilm can be suspended toward the water column. Two experimental bioassays were conducted in March and July 2008 to investigate the importance of biofilm input for the pelagic microbial and viral loops. Pelagic inocula (< 0.6 μ- and < 10 μ filtrates) were diluted either with < 30 kDa-ultrafiltered seawater or with this ultrafiltrate enriched with the respective size-fractionated benthic biofilm or with < 30 kDa-benthic compounds (BC). The kinetics of heterotrophic nanoflagellates (HNF), bacteria and viruses were assessed together with bacterial and viral genomic fingerprints, bacterial enzymatic activities and viral life strategies. The experimental design allowed us to evaluate the effect of BC modulated by those of benthic size-fractionated microorganisms (virus + bacteria, + HNF). BC presented (1) in March, a positive effect on viruses and bacteria weakened by pelagic HNF. Benthic microorganisms consolidated this negative effect and sustained the viral production together with a relatively diverse and uneven bacterial assemblage structure; (2) in July, no direct impact on viruses but a positive effect on bacteria modulated by HNF, which indirectly enhanced viral multiplication. Both effects were intensified by benthic microorganisms and bacterial assemblage structure became more even. HNF indirectly profited from BC more in March than in July. The microbial loop would be stimulated by biofilm during periods of high resources (March) and the viral loop during periods of depleted resources (July).

  16. Microbial biofilms are able to destroy hydroxyapatite in the absence of host immunity in vitro

    PubMed Central

    Junka, Adam Feliks; Szymczyk, Patrycja; Smutnicka, Danuta; Kos, Marcin; Smolina, Iryna; Bartoszewicz, Marzenna; Chlebus, Edward; Turniak, Michal; Sedghizadeh, Parish P.

    2014-01-01

    Introduction It is widely thought that inflammation and osteoclastogenesis result in hydroxyapatite (HA) resorption and sequestra formation during osseous infections, and microbial biofilm pathogens induce the inflammatory destruction of HA. We hypothesized that biofilms associated with infectious bone disease can directly resorb HA in the absence of host inflammation or osteoclastogenesis. Therefore, we developed an in vitro model to test this hypothesis. Materials and Methods Customized HA discs were manufactured as a substrate for growing clinically relevant biofilm pathogens. Single-species biofilms of S.mutans, S.aureus, P.aeruginosa and C.albicans, and mixed-species biofilms of C.albicans + S.mutans were incubated on HA discs for 72 hours to grow mature biofilms. Three different non-biofilm control groups were also established for testing. HA discs were then evaluated by means of scanning electron microscopy, micro-CT metrotomography, x-ray spectroscopy and confocal microscopy with planimetric analysis. Additionally, quantitative cultures and pH assessment were performed. ANOVA was used to test for significance between treatment and control groups. Results All investigated biofilms were able to cause significant (P<0.05) and morphologically characteristic alterations in HA structure as compared to controls. The highest number of alterations observed was caused by mixed biofilms of C.albicans + S.mutans. S. mutans biofilm incubated in medium with additional sucrose content was the most detrimental to HA surfaces among single-species biofilms. Conclusion These findings suggest that direct microbial resorption of bone is possible in addition to immune-mediated destruction, which has important translational implications for the pathogenesis of chronic bone infections and for targeted antimicrobial therapeutics. PMID:25544303

  17. Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.

    PubMed

    Ren, Z; Steinberg, L M; Regan, J M

    2008-01-01

    Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion. PMID:18725730

  18. Electrochemical and microbial monitoring of multi-generational electroactive biofilms formed from mangrove sediment.

    PubMed

    Rivalland, Caroline; Madhkour, Sonia; Salvin, Paule; Robert, Florent

    2015-12-01

    Electroactive biofilms were formed from French Guiana mangrove sediments for the analysis of bacterial communities' composition. The electrochemical monitoring of three biofilm generations revealed that the bacterial selection occurring at the anode, supposedly leading microbial electrochemical systems (MESs) to be more efficient, was not the only parameter to be taken into account so as to get the best electrical performance (maximum current density). Indeed, first biofilm generations produced a stable current density reaching about 18 A/m(2) while second and third generations produced current densities of about 10 A/m(2). MES bacterial consortia were characterized thanks to molecular biology techniques: DGGE and MiSeq sequencing (Illumina). High-throughput sequencing data statistical analysis confirmed preliminary DGGE data analysis, showing strong similarities between electroactive biofilms of second and third generations, but also revealing both selection and stabilization of the biofilms. PMID:26055041

  19. A framework for modeling electroactive microbial biofilms performing direct electron transfer.

    PubMed

    Korth, Benjamin; Rosa, Luis F M; Harnisch, Falk; Picioreanu, Cristian

    2015-12-01

    A modeling platform for microbial electrodes based on electroactive microbial biofilms performing direct electron transfer (DET) is presented. Microbial catabolism and anabolism were coupled with intracellular and extracellular electron transfer, leading to biofilm growth and current generation. The model includes homogeneous electron transfer from cells to a conductive biofilm component, biofilm matrix conduction, and heterogeneous electron transfer to the electrode. Model results for Geobacter based anodes, both at constant electrode potential and in voltammetric (dynamic electrode potential) conditions, were compared to experimental data from different sources. The model can satisfactorily describe microscale (concentration, pH and redox gradients) and macroscale (electric currents, biofilm thickness) properties of Geobacter biofilms. The concentration of electrochemically accessible redox centers, here denominated as cytochromes, involved in the extracellular electron transfer, plays the key role and may differ between constant potential (300 mM) and dynamic potential (3mM) conditions. Model results also indicate that the homogeneous and heterogeneous electron transfer rates have to be within the same order of magnitude (1.2 s(-1)) for reversible extracellular electron transfer. PMID:25921352

  20. Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond.

    PubMed

    Golby, Susanne; Ceri, Howard; Gieg, Lisa M; Chatterjee, Indranil; Marques, Lyriam L R; Turner, Raymond J

    2012-01-01

    Bitumen extraction from the oil sands of Alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. Unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. We considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. Culturing of mixed species biofilms in vitro using the Calgary Biofilm Device (CBD) under aerobic, microaerobic, and anaerobic growth conditions was successful both with and without the addition of various growth nutrients. Denaturant gradient gel electrophoresis and 16S rRNA gene pyrotag sequencing revealed that unique mixed biofilm communities were recovered under each incubation condition, with the dominant species belonging to Pseudomonas, Thauera, Hydrogenophaga, Rhodoferax, and Acidovorax. This work used an approach that allowed organisms to grow as a biofilm directly from a sample collected of their environment, and the biofilms cultivated in vitro were representative of the endogenous environmental community. For the first time, representative environmental mixed species biofilms have been isolated and grown under laboratory conditions from an oil sands tailings pond environment and a description of their composition is provided. PMID:22029695

  1. Microbial biofilms in seafood: a food-hygiene challenge.

    PubMed

    Mizan, Md Furkanur Rahaman; Jahid, Iqbal Kabir; Ha, Sang-Do

    2015-08-01

    Seafood forms a part of a healthy diet. However, seafood can be contaminated with foodborne pathogens, resulting in disease outbreaks. Because people consume large amounts of seafood, such disease outbreaks are increasing worldwide. Seafood contamination is largely due to the naturally occurring phenomenon of biofilm formation. The common seafood bacterial pathogens that form biofilms are Vibrio spp., Aeromonas hydrophila, Salmonella spp., and Listeria monocytogenes. As these organisms pose a global health threat, recent research has focused on elucidating methods to eliminate these biofilm-forming bacteria from seafood, thereby improving food hygiene. Therefore, we highlight recent advances in our understanding of the underlying molecular mechanisms of biofilm formation, the factors that regulate biofilm development and the role of quorum sensing and biofilm formation in the virulence of foodborne pathogens. Currently, several novel methods have been successfully developed for controlling biofilms present in seafood. In this review, we also discuss the epidemiology of seafood-related diseases and the novel methods that could be used for future control of biofilm formation in seafood. PMID:25846914

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

    PubMed

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

    2013-07-01

    Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean. PMID:23745679

  3. Maintenance of Geobacter-dominated biofilms in microbial fuel cells treating synthetic wastewater.

    PubMed

    Commault, Audrey S; Lear, Gavin; Weld, Richard J

    2015-12-01

    Geobacter-dominated biofilms can be selected under stringent conditions that limit the growth of competing bacteria. However, in many practical applications, such stringent conditions cannot be maintained and the efficacy and stability of these artificial biofilms may be challenged. In this work, biofilms were selected on low-potential anodes (-0.36 V vs Ag/AgCl, i.e. -0.08 V vs SHE) in minimal acetate or ethanol media. Selection conditions were then relaxed by transferring the biofilms to synthetic wastewater supplemented with soil as a source of competing bacteria. We tracked community succession and functional changes in these biofilms. The Geobacter-dominated biofilms showed stability in their community composition and electrochemical properties, with Geobacter sp. being still electrically active after six weeks in synthetic wastewater with power densities of 100±19 mW·m(-2) (against 74±14 mW·m(-2) at week 0) for all treatments. After six weeks, the ethanol-selected biofilms, despite their high taxon richness and their efficiency at removing the chemical oxygen demand (0.8 g·L(-1) removed against the initial 1.3 g·L(-1) injected), were the least stable in terms of community structure. These findings have important implications for environmental microbial fuel cells based on Geobacter-dominated biofilms and suggest that they could be stable in challenging environments. PMID:25935865

  4. 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.

  5. Extracellular polymeric substances, microbial activity and microbial community of biofilm and suspended sludge at different divalent cadmium concentrations.

    PubMed

    Wang, Zichao; Gao, Mengchun; Wei, Junfeng; Ma, Kedong; Zhang, Jing; Yang, Yusuo; Yu, Shuping

    2016-04-01

    The differences between biofilm and suspended sludge (S-sludge) in extracellular polymeric substances (EPS), microbial activity, and microbial community in an anoxic-aerobic sequencing batch biofilm reactor (SBBR) at different concentrations of divalent cadmium (Cd(II)) were investigated. As the increase of Cd(II) concentration from 0 to 50mgL(-1), the specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR) of biofilm decreased from 4.85, 5.22 and 45mgNg(-1) VSSh(-1) to 1.54, 2.38 and 26mgNg(-1)VSSh(-1), respectively, and the SAOR, SNOR and SNRR of S-sludge decreased from 4.80, 5.02 and 34mgNg(-1)VSSh(-1) to 1.46, 2.20 and 17mgNg(-1)VSSh(-1), respectively. Biofilm had higher protein (PN) content in EPS than S-sludge. Contrast to S-sludge, biofilm could provide Nitrobacter vulgaris, beta proteobacterium INBAF015, and Pseudoxanthomonas mexicana with the favorable conditions of growth and reproduction. PMID:26829529

  6. Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina).

    PubMed

    Urbieta, María Sofía; González-Toril, Elena; Bazán, Ángeles Aguilera; Giaveno, María Alejandra; Donati, Edgardo

    2015-03-01

    Copahue is a natural geothermal field (Neuquén province, Argentina) dominated by the Copahue volcano. As a consequence of the sustained volcanic activity, Copahue presents many acidic pools, hot springs and solfataras with different temperature and pH conditions that influence their microbial diversity. The occurrence of microbial biofilms was observed on the surrounding rocks and the borders of the ponds, where water movements and thermal activity are less intense. Microbial biofilms are particular ecological niches within geothermal environments; they present different geochemical conditions from that found in the water of the ponds and hot springs which is reflected in different microbial community structure. The aim of this study is to compare microbial community diversity in the water of ponds and hot springs and in microbial biofilms in the Copahue geothermal field, with particular emphasis on Cyanobacteria and other photosynthetic species that have not been detected before in Copahue. In this study, we report the presence of Cyanobacteria, Chloroflexi and chloroplasts of eukaryotes in the microbial biofilms not detected in the water of the ponds. On the other hand, acidophilic bacteria, the predominant species in the water of moderate temperature ponds, are almost absent in the microbial biofilms in spite of having in some cases similar temperature conditions. Species affiliated with Sulfolobales in the Archaea domain are the predominant microorganism in high temperature ponds and were also detected in the microbial biofilms. PMID:25605537

  7. Ecological roles and biotechnological applications of marine and intertidal microbial biofilms.

    PubMed

    Mitra, Sayani; Sana, Barindra; Mukherjee, Joydeep

    2014-01-01

    This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor. PMID:24817086

  8. Community-based interference against integration of Pseudomonas aeruginosa into human salivary microbial biofilm

    PubMed Central

    He, Xuesong; Hu, Wei; He, Jian; Guo, Lihong; Lux, Renate; Shi, Wenyuan

    2012-01-01

    As part of the human gastrointestinal tract, the oral cavity represents a complex biological system and harbors diverse bacterial species. Unlike the gut microbiota which is often considered a health asset, studies of the oral commensal microbial flora have been largely limited to their implication in oral diseases such as dental caries and periodontal diseases; Little emphasis has been given to their potential beneficial roles, especially the protective effects against oral colonization by foreign/pathogenic bacteria. In this study, we used the salivary microbiota derived from healthy human subjects to investigate protective effects against the colonization and integration of Pseudomonas aeruginosa, an opportunistic bacterial pathogen, into developing and pre-formed salivary biofilms. When co-cultivated in saliva medium, P. aeruginosa persisted in the planktonic phase, but failed to integrate into salivary microbial community during biofilm formation. Furthermore, in the saliva medium supplemented with 0.05% (w/v) sucrose, the oral flora inhibited the growth of P. aeruginosa by producing lactic acid. More interestingly, while pre-formed salivary biofilms were able to prevent P. aeruginosa colonization, the same biofilms recovered from mild chlorhexidine gluconate treatment displayed a shift in microbial composition and showed a drastic reduction in protection. Our study indicates that normal oral communities with balanced microbial compositions could be important in effectively preventing the integration of foreign/pathogenic bacterial species, such as P. aeruginosa. PMID:22053962

  9. Microbial cell surface proteins and secreted metabolites involved in multispecies biofilms.

    PubMed

    Demuyser, Liesbeth; Jabra-Rizk, Mary Ann; Van Dijck, Patrick

    2014-04-01

    A considerable number of infectious diseases involve multiple microbial species coexisting and interacting in a host. Only recently however the impact of these polymicrobial diseases has been appreciated and investigated. Often, the causative microbial species are embedded in an extracellular matrix forming biofilms, a form of existence that offers protection against chemotherapeutic agents and host immune defenses. Therefore, recent efforts have focused on developing novel therapeutic strategies targeting biofilm-associated polymicrobial infections, a task that has proved to be challenging. One promising approach to inhibit the development of such complex infections is to impede the interactions between the microbial species via inhibition of adhesion. To that end, studies have focused on identifying specific cell wall adhesins and receptors involved in the interactions between the various bacterial species and the most pathogenic human fungal species Candida albicans. This review highlights the important findings from these studies and describes the available tools and techniques that have provided insights into the role of secreted molecules orchestrating microbial interactions in biofilms. Specifically, we focus on the interactions that take place in oral biofilms and the implications of these interactions on oral health and therapeutic strategies. PMID:24376219

  10. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms.

    PubMed

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare; Settanni, Luca

    2015-01-01

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese. PMID:26546430

  11. Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy

    PubMed Central

    Macalady, Jennifer L.; Lyon, Ezra H.; Koffman, Bess; Albertson, Lindsey K.; Meyer, Katja; Galdenzi, Sandro; Mariani, Sandro

    2006-01-01

    Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. ?-, ?-, ?-, and ?-proteobacteria in sulfur-cycling clades accounted for ?75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating ?-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous ?-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of ?-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks. PMID:16885314

  12. Influence of Microbial Biofilms on the Preservation of Primary Soft Tissue in Fossil and Extant Archosaurs

    PubMed Central

    Peterson, Joseph E.; Lenczewski, Melissa E.; Scherer, Reed P.

    2010-01-01

    Background Mineralized and permineralized bone is the most common form of fossilization in the vertebrate record. Preservation of gross soft tissues is extremely rare, but recent studies have suggested that primary soft tissues and biomolecules are more commonly preserved within preserved bones than had been presumed. Some of these claims have been challenged, with presentation of evidence suggesting that some of the structures are microbial artifacts, not primary soft tissues. The identification of biomolecules in fossil vertebrate extracts from a specimen of Brachylophosaurus canadensis has shown the interpretation of preserved organic remains as microbial biofilm to be highly unlikely. These discussions also propose a variety of potential mechanisms that would permit the preservation of soft-tissues in vertebrate fossils over geologic time. Methodology/Principal Findings This study experimentally examines the role of microbial biofilms in soft-tissue preservation in vertebrate fossils by quantitatively establishing the growth and morphology of biofilms on extant archosaur bone. These results are microscopically and morphologically compared with soft-tissue extracts from vertebrate fossils from the Hell Creek Formation of southeastern Montana (Latest Maastrichtian) in order to investigate the potential role of microbial biofilms on the preservation of fossil bone and bound organic matter in a variety of taphonomic settings. Based on these analyses, we highlight a mechanism whereby this bound organic matter may be preserved. Conclusions/Significance Results of the study indicate that the crystallization of microbial biofilms on decomposing organic matter within vertebrate bone in early taphonomic stages may contribute to the preservation of primary soft tissues deeper in the bone structure. PMID:20967227

  13. Acoustic and electrical property changes due to microbial growth and biofilm formation in porous media

    NASA Astrophysics Data System (ADS)

    Davis, Caroline A.; Pyrak-Nolte, Laura J.; Atekwana, Estella A.; Werkema, Douglas D.; Haugen, Marisa E.

    2010-09-01

    A laboratory study was conducted to investigate the effect of microbial growth and biofilm formation on compressional waves, and complex conductivity during stimulated microbial growth. Over the 29 day duration of the experiment, compressional wave amplitudes and arrival times for the control (nonbiostimulated) sample were observed to be relatively uniform over the scanned 2-D region. However, the biostimulated sample exhibited a high degree of spatial variability in both the amplitude and arrival times, with portions of the sample exhibiting increased attenuation (˜80%) concurrent with an increase in the arrival times, while other portions exhibited decreased attenuation (˜45%) and decreased arrival times. The acoustic amplitude and arrival times changed significantly in the biostimulated column between days 5 and 7 of the experiment, consistent with a peak in the imaginary conductivity (σ″) values. The σ″ response is interpreted as recording the different stages of biofilm development with peak σ″ representing maximum biofilm thickness and decreasing σ″ representing cell death or detachment. Environmental scanning electron microscope imaging confirmed microbial cell attachment to sand surfaces and showed apparent differences in the morphology of attached biomass between regions of increased and decreased attenuation. The heterogeneity in the elastic properties arises from the differences in the morphology and structure of attached biofilms. These results suggest that combining acoustic imaging and complex conductivity techniques can provide a powerful tool for assessing microbial growth or biofilm formation and the associated changes in porous media, such as those that occur during bioremediation and microbial enhanced oil recovery.

  14. Microbial Extremophiles in Aspect of Limits of Life

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Tang, Jane

    2007-01-01

    During Earth's evolution accompanied by geophysical and climatic changes a number of ecosystems have been formed. These ecosystems differ by the broad variety of physicochemical and biological factors composing our environment. Traditionally, pH and salinity are considered as geochemical extremes, as opposed to the temperature, pressure and radiation that are referred to as physical extremes (Van den Burg, 2003). Life inhabits all possible places on Earth interacting with the environment and within itself (cross species relations). In nature it is very rare when an ecotope is inhabited by a single species. As a rule, most ecosystems contain the functionally related and evolutionarily adjusted communities (consortia and populations). In contrast to the multicellular structure of eukaryotes (tissues, organs, systems of organs, whole organism), the highest organized form of prokaryotic life in nature is the benthic colonization in biofilms and microbial mats. In these complex structures all microbial cells of different species are distributed in space and time according to their functions and to physicochemical gradients that allow more effective system support, self-protection, and energy distribution. In vitro, of course, the most primitive organized structure for bacterial and archaeal cultures is the colony, the size, shape, color, consistency, and other characteristics of which could carry varies specifics on species or subspecies levels. In table 1 all known types of microbial communities are shown (Pikuta et a]., 2005). In deep underground (lithospheric) and deep-sea ecosystems an additional factor - pressure, and irradiation - could also be included in the list of microbial communities. Currently the beststudied ecosystems are: human body (due to the medical importance), and fresh water and marine ecosystems (due to the reason of an environmental safety). For a long time, extremophiles were terra incognita, since the environments with aggressive parameters (compared to the human body temperature, pH, mineralization, and pressure) were considered a priori as a dead zone.

  15. Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    PubMed Central

    Sun, Jing; Hu, Shihu; Sharma, Keshab Raj; Ni, Bing-Jie

    2014-01-01

    Simultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescence in situ hybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera, Desulfobulbus, Desulfomicrobium, Desulfovibrio, Desulfatiferula, and Desulforegula, while about 90% of the MA population belonged to the genus Methanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates. PMID:25192994

  16. Shifts in microbial community structure and function in light- and dark-grown biofilms driven by warming.

    PubMed

    Roman, Anna M; Borrego, Carles M; Daz-Villanueva, Vernica; Freixa, Anna; Gich, Frederic; Ylla, Irene

    2014-08-01

    Biofilms are dynamic players in biogeochemical cycling in running waters and are subjected to environmental stressors like those provoked by climate change. We investigated whether a 2C increase in flowing water would affect prokaryotic community composition and heterotrophic metabolic activities of biofilms grown under light or dark conditions. Neither light nor temperature treatments were relevant for selecting a specific bacterial community at initial phases (7-day-old biofilms), but both variables affected the composition and function of mature biofilms (28-day-old). In dark-grown biofilms, changes in the prokaryotic community composition due to warming were mainly related to rotifer grazing, but no significant changes were observed in functional fingerprints. In light-grown biofilms, warming also affected protozoan densities, but its effect on prokaryotic density and composition was less evident. In contrast, heterotrophic metabolic activities in light-grown biofilms under warming showed a decrease in the functional diversity towards a specialized use of several carbohydrates. Results suggest that prokaryotes are functionally redundant in dark biofilms but functionally plastic in light biofilms. The more complex and self-serving light-grown biofilm determines a more buffered response to temperature than dark-grown biofilms. Despite the moderate increase in temperature of only 2C, warming conditions drive significant changes in freshwater biofilms, which responded by finely tuning a complex network of interactions among microbial populations within the biofilm matrix. PMID:24552130

  17. Microbial life in the phyllosphere.

    PubMed

    Vorholt, Julia A

    2012-12-01

    Our knowledge of the microbiology of the phyllosphere, or the aerial parts of plants, has historically lagged behind our knowledge of the microbiology of the rhizosphere, or the below-ground habitat of plants, particularly with respect to fundamental questions such as which microorganisms are present and what they do there. In recent years, however, this has begun to change. Cultivation-independent studies have revealed that a few bacterial phyla predominate in the phyllosphere of different plants and that plant factors are involved in shaping these phyllosphere communities, which feature specific adaptations and exhibit multipartite relationships both with host plants and among community members. Insights into the underlying structural principles of indigenous microbial phyllosphere populations will help us to develop a deeper understanding of the phyllosphere microbiota and will have applications in the promotion of plant growth and plant protection. PMID:23154261

  18. Effective Prevention of Microbial Biofilm Formation on Medical Devices by Low-Energy Surface Acoustic Waves▿

    PubMed Central

    Hazan, Zadik; Zumeris, Jona; Jacob, Harold; Raskin, Hanan; Kratysh, Gera; Vishnia, Moshe; Dror, Naama; Barliya, Tilda; Mandel, Mathilda; Lavie, Gad

    2006-01-01

    Low-energy surface acoustic waves generated from electrically activated piezo elements are shown to effectively prevent microbial biofilm formation on indwelling medical devices. The development of biofilms by four different bacteria and Candida species is prevented when such elastic waves with amplitudes in the nanometer range are applied. Acoustic-wave-activated Foley catheters have all their surfaces vibrating with longitudinal and transversal dispersion vectors homogeneously surrounding the catheter surfaces. The acoustic waves at the surface are repulsive to bacteria and interfere with the docking and attachment of planktonic microorganisms to solid surfaces that constitute the initial phases of microbial biofilm development. FimH-mediated adhesion of uropathogenic Escherichia coli to guinea pig erythrocytes was prevented at power densities below thresholds that activate bacterial force sensor mechanisms. Elevated power densities dramatically enhanced red blood cell aggregation. We inserted Foley urinary catheters attached with elastic-wave-generating actuators into the urinary tracts of male rabbits. The treatment with the elastic acoustic waves maintained urine sterility for up to 9 days compared to 2 days in control catheterized animals. Scanning electron microscopy and bioburden analyses revealed diminished biofilm development on these catheters. The ability to prevent biofilm formation on indwelling devices and catheters can benefit the implanted medical device industry. PMID:16940055

  19. Effective prevention of microbial biofilm formation on medical devices by low-energy surface acoustic waves.

    PubMed

    Hazan, Zadik; Zumeris, Jona; Jacob, Harold; Raskin, Hanan; Kratysh, Gera; Vishnia, Moshe; Dror, Naama; Barliya, Tilda; Mandel, Mathilda; Lavie, Gad

    2006-12-01

    Low-energy surface acoustic waves generated from electrically activated piezo elements are shown to effectively prevent microbial biofilm formation on indwelling medical devices. The development of biofilms by four different bacteria and Candida species is prevented when such elastic waves with amplitudes in the nanometer range are applied. Acoustic-wave-activated Foley catheters have all their surfaces vibrating with longitudinal and transversal dispersion vectors homogeneously surrounding the catheter surfaces. The acoustic waves at the surface are repulsive to bacteria and interfere with the docking and attachment of planktonic microorganisms to solid surfaces that constitute the initial phases of microbial biofilm development. FimH-mediated adhesion of uropathogenic Escherichia coli to guinea pig erythrocytes was prevented at power densities below thresholds that activate bacterial force sensor mechanisms. Elevated power densities dramatically enhanced red blood cell aggregation. We inserted Foley urinary catheters attached with elastic-wave-generating actuators into the urinary tracts of male rabbits. The treatment with the elastic acoustic waves maintained urine sterility for up to 9 days compared to 2 days in control catheterized animals. Scanning electron microscopy and bioburden analyses revealed diminished biofilm development on these catheters. The ability to prevent biofilm formation on indwelling devices and catheters can benefit the implanted medical device industry. PMID:16940055

  20. Mini Review of Phytochemicals and Plant Taxa with Activity as Microbial Biofilm and Quorum Sensing Inhibitors.

    PubMed

    Ta, Chieu Anh Kim; Arnason, John Thor

    2015-01-01

    Microbial biofilms readily form on many surfaces in nature including plant surfaces. In order to coordinate the formation of these biofilms, microorganisms use a cell-to-cell communication system called quorum sensing (QS). As formation of biofilms on vascular plants may not be advantageous to the hosts, plants have developed inhibitors to interfere with these processes. In this mini review, research papers published on plant-derived molecules that have microbial biofilm or quorum sensing inhibition are reviewed with the objectives of determining the biosynthetic classes of active compounds, their biological activity in assays, and their families of occurrence and range. The main findings are the identification of plant phenolics, including benzoates, phenyl propanoids, stilbenes, flavonoids, gallotannins, proanthocyanidins and coumarins as important inhibitors with both activities. Some terpenes including monoterpenes, sesquiterpenes, diterpenes and triterpenes also have anti-QS and anti-biofilm activities. Relatively few alkaloids were reported. Quinones and organosulfur compounds, especially from garlic, were also active. A common feature is the polar nature of these compounds. Phytochemicals with these activities are widespread in Angiosperms in temperate and tropical regions, but gymnosperms, bryophytes and pteridophytes were not represented. PMID:26712734

  1. The spatial organization and microbial community structure of an epilithic biofilm.

    PubMed

    Cutler, Nick A; Chaput, Dominique L; Oliver, Anna E; Viles, Heather A

    2015-03-01

    Microbial biofilms are common on lithic surfaces, including stone buildings. However, the ecology of these communities is poorly understood. Few studies have focused on the spatial characteristics of lithobiontic biofilms, despite the fact that spatial structure has been demonstrated to influence ecosystem function (and hence biodegradation) and community diversity. Furthermore, relatively few studies have utilized molecular techniques to characterize these communities, even though molecular methods have revealed unexpected microbial diversity in other habitats. This study investigated (1) the spatial structure and (2) the taxonomic composition of an epilithic biofilm using molecular techniques, namely amplicon pyrosequencing and terminal restriction fragment length polymorphism. Dispersion indices and Mantel correlograms were used to test for the presence of spatial structure in the biofilm. Diversity metrics and rank-abundance distributions (RADs) were also generated. The study revealed spatial structure on a centimetre scale in eukaryotic microbes (fungi and algae), but not the bacteria. Fungal and bacterial communities were highly diverse; algal communities much less so. The RADs were characterized by a distinctive 'hollow' (concave up) profile and long tails of rare taxa. These findings have implications for understanding the ecology of epilithic biofilms and the spatial heterogeneity of stone biodeterioration. PMID:25764559

  2. Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

    NASA Astrophysics Data System (ADS)

    Patil, Rajendra; Gholap, Haribhau; Warule, Sambhaji; Banpurkar, Arun; Kulkarni, Gauri; Gade, Wasudeo

    2015-01-01

    The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet-visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications.

  3. 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.

  4. Microbial Community Composition and Dynamics of Moving Bed Biofilm Reactor Systems Treating Municipal Sewage

    PubMed Central

    Turner, Susan J.

    2012-01-01

    Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems. PMID:22138984

  5. 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; Pastn, 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. PMID:24355512

  6. Growth dynamic of Naegleria fowleri in a microbial freshwater biofilm.

    PubMed

    Goudot, Sbastien; Herbelin, Pascaline; Mathieu, Laurence; Soreau, Sylvie; Banas, Sandrine; Jorand, Frdric

    2012-09-01

    The presence of pathogenic free-living amoebae (FLA) such as Naegleria fowleri in freshwater environments is a potential public health risk. Although its occurrence in various water sources has been well reported, its presence and associated factors in biofilm remain unknown. In this study, the density of N. fowleri in biofilms spontaneously growing on glass slides fed by raw freshwater were followed at 32 C and 42 C for 45 days. The biofilms were collected with their substrata and characterized for their structure, numbered for their bacterial density, thermophilic free-living amoebae, and pathogenic N. fowleri. The cell density of N. fowleri within the biofilms was significantly affected both by the temperature and the nutrient level (bacteria/amoeba ratio). At 32 C, the density remained constantly low (1-10 N. fowleri/cm(2)) indicating that the amoebae were in a survival state, whereas at 42 C the density reached 30-900 N. fowleri/cm(2) indicating an active growth phase. The nutrient level, as well, strongly affected the apparent specific growth rate (?) of N. fowleri in the range of 0.03-0.23 h(-1). At 42 C a hyperbolic relationship was found between ? and the bacteria/amoeba ratio. A ratio of 10(6) to 10(7) bacteria/amoeba was needed to approach the apparent ?(max) value (0.23 h(-1)). Data analysis also showed that a threshold for the nutrient level of close to 10(4) bacteria/amoeba is needed to detect the growth of N. fowleri in freshwater biofilm. This study emphasizes the important role of the temperature and bacteria as prey to promote not only the growth of N. fowleri, but also its survival. PMID:22695355

  7. Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm.

    PubMed

    Nocker, Andreas; Lepo, Joe E; Snyder, Richard A

    2004-11-01

    We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the gamma- and delta-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries. PMID:15528551

  8. Influence of an Oyster Reef on Development of the Microbial Heterotrophic Community of an Estuarine Biofilm

    PubMed Central

    Nocker, Andreas; Lepo, Joe E.; Snyder, Richard A.

    2004-01-01

    We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the ?- and ?-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries. PMID:15528551

  9. Biofilms and biofilm reactors. (Latest citations from the Life Sciences Collection database). Published Search

    SciTech Connect

    Not Available

    1993-05-01

    The bibliography contains citations concerning the formation and characterization of biofilms. Biofilms occur in fermentation, wastewater treatment, packed-bed reactors, fluidized-bed reactors, medical prostheses, fouling, biomass reactors, waste supply systems, and other aquatic systems. Topics include microorganism makeup of biofilms, controlling biofilm formation, biological and chemical properties, model studies, kinetic studies, and biofilm identification and detection. (Contains a minimum of 209 citations and includes a subject term index and title list.)

  10. Detection of microbial biofilms on food processing surfaces: hyperspectral fluorescence imaging study

    NASA Astrophysics Data System (ADS)

    Jun, Won; Kim, Moon S.; Chao, Kaunglin; Lefcourt, Alan M.; Roberts, Michael S.; McNaughton, James L.

    2009-05-01

    We used a portable hyperspectral fluorescence imaging system to evaluate biofilm formations on four types of food processing surface materials including stainless steel, polypropylene used for cutting boards, and household counter top materials such as formica and granite. The objective of this investigation was to determine a minimal number of spectral bands suitable to differentiate microbial biofilm formation from the four background materials typically used during food processing. Ultimately, the resultant spectral information will be used in development of handheld portable imaging devices that can be used as visual aid tools for sanitation and safety inspection (microbial contamination) of the food processing surfaces. Pathogenic E. coli O157:H7 and Salmonella cells were grown in low strength M9 minimal medium on various surfaces at 22 +/- 2 °C for 2 days for biofilm formation. Biofilm autofluorescence under UV excitation (320 to 400 nm) obtained by hyperspectral fluorescence imaging system showed broad emissions in the blue-green regions of the spectrum with emission maxima at approximately 480 nm for both E. coli O157:H7 and Salmonella biofilms. Fluorescence images at 480 nm revealed that for background materials with near-uniform fluorescence responses such as stainless steel and formica cutting board, regardless of the background intensity, biofilm formation can be distinguished. This suggested that a broad spectral band in the blue-green regions can be used for handheld imaging devices for sanitation inspection of stainless, cutting board, and formica surfaces. The non-uniform fluorescence responses of granite make distinctions between biofilm and background difficult. To further investigate potential detection of the biofilm formations on granite surfaces with multispectral approaches, principal component analysis (PCA) was performed using the hyperspectral fluorescence image data. The resultant PCA score images revealed distinct contrast between biofilms and granite surfaces. This investigation demonstrated that biofilm formations on food processing surfaces, even for background materials with heterogeneous fluorescence responses, can be detected. Furthermore, a multispectral approach in developing handheld inspection devices may be needed to inspect surface materials that exhibit non-uniform fluorescence.

  11. Comparing the temporal colonization and microbial diversity of showerhead biofilms in Hawai'i and Colorado.

    PubMed

    Abe, Jonathan; Alop-Mabuti, Aleena; Burger, Peyton; Button, Jackson; Ellsberry, Madeline; Hitzeman, Jaycinth; Morgenstern, David; Nunies, Kasey; Strother, Mara; Darling-Munson, Jared; Chan, Yvonne L; Cassady, Robert; Vasconcellos, Sarah Maile K; Iseman, Michael D; Chan, Edward D; Honda, Jennifer R

    2016-02-01

    The household is a potential source of opportunistic pathogens to humans, a particularly critical issue for immunodeficient individuals. An important human-microbe interface is the biofilm that develops on showerhead surfaces. Once microbe-laden biofilms become aerosolized, they can potentially be inhaled into the lungs. Understanding how quickly a new showerhead becomes colonized would provide useful information to minimize exposure to potentially pathogenic environmental microbes. High school scientists sampled the inner surfaces of pre-existing and newly fitted showerheads monthly over a nine-month period and applied standard microbiologic culture techniques to qualitatively assess microbial growth. Water chemistry was also monitored using commercial test strips. Sampling was performed in households on Oahu, Hawai'i and Denver, Colorado, representing warm/humid and cold/arid environments, respectively. Pre-existing showerheads in Hawai'i showed more diverse microbial growth and significantly greater microbial numbers than a comparable showerhead from Colorado. New, chrome-plated or plastic showerheads in Hawai'i showed diverse and abundant growth one month after installment compared to new showerheads from Colorado. The pH, total chlorine and water hardness levels varied significantly between the Hawai'i and Colorado samples. Enthusiastic student and teacher participation allowed us to answer long-standing questions regarding the temporal colonization of microbial biofilms on pre-existing and new showerhead surfaces. PMID:26764424

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

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

    PubMed

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

    2004-02-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. PMID:14994179

  14. Power limits for microbial life.

    PubMed

    LaRowe, Douglas E; Amend, Jan P

    2015-01-01

    To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm(-3)) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ?10(-12) and 10(-16) W cm(-3). The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm(-3) can be well-captured using a maintenance power, 190 zW cell(-1), two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50-3500 zW cell(-1), with most values under ?300 zW cell(-1). Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell(-1). PMID:26236299

  15. Power limits for microbial life

    PubMed Central

    LaRowe, Douglas E.; Amend, Jan P.

    2015-01-01

    To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm-3) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10-12 and 10-16 W cm-3. The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm-3 can be well-captured using a maintenance power, 190 zW cell-1, two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50–3500 zW cell-1, with most values under ∼300 zW cell-1. Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell-1. PMID:26236299

  16. Metabolic profiling of biofilm bacteria known to cause microbial influenced corrosion.

    PubMed

    Beale, D J; Morrison, P D; Key, C; Palombo, E A

    2014-01-01

    This study builds upon previous research that demonstrated the simplicity of obtaining metabolite profiles of bacteria in urban water networks, by using the metabolic profile of bacteria extracted from a reticulation pipe biofilm, which is known to cause microbial influenced corrosion (MIC). The extracellular metabolites of the isolated bacteria, and those bacteria in consortium, were analysed in isolation, and after exposure to low levels of copper. Applying chemometric analytical methodologies to the metabolomic data, we were able to better understand the profile of the isolated biofilm bacteria, which were differentiated according to their activity and copper exposure. It was found that the metabolic activity of the isolated bacteria and the bacteria in consortium varied according to the bacterium's ability to metabolise copper. This demonstrates the power of metabolomic techniques for the discrimination of water reticulation biofilms comprising similar bacteria in consortium, but undergoing different physico-chemical activities, such as corrosion and corrosion inhibition. PMID:24434961

  17. Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

    PubMed Central

    2012-01-01

    Background Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. Results Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems. Conclusions The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms. PMID:22727216

  18. Successional change in microbial communities of benthic Phormidium-dominated biofilms.

    PubMed

    Brasell, Katie A; Heath, Mark W; Ryan, Ken G; Wood, Susanna A

    2015-02-01

    Benthic cyanobacterial blooms are increasing worldwide and can be harmful to human and animal health if they contain toxin-producing species. Microbial interactions are important in the formation of benthic biofilms and can lead to increased dominance and/or toxin production of one or few taxa. This study investigated how microbial interactions contribute to proliferation of benthic blooms dominated by the neurotoxin-producing Phormidium autumnale. Following a rainfall event that cleared the substrate, biofilm succession was characterised at a site on the Hutt River (New Zealand) by sampling every 2-3 days over 32 days. A combination of morphological and molecular community analyses (automated ribosomal intergenic spacer analysis and Illumina MiSeq sequencing) identified three distinct phases of succession in both the micro-algal and bacterial communities within P. autumnale-dominated biofilms. Bacterial composition shifted between the phases, and these changes occurred several days before those of the micro-algal community. Alphaproteobacteria and Betaproteobacteria dominate in the early phase; Alphaproteobacteria, Betaproteobacteria, Sphingobacteria and Flavobacteria in the mid-phase; and Sphingobacteria and Flavobacteria in the late phase. Collectively, the results suggest that succession is driven by bacteria in the early stages but becomes dependent on micro-algae in the mid- and late stages of biofilm formation. PMID:25467742

  19. Photosynthetic solar cell using nanostructured proton exchange membrane for microbial biofilm prevention.

    PubMed

    Lee, Dong Hyun; Oh, Hwa Jin; Bai, Seoung Jae; Song, Young Seok

    2014-06-24

    Unwanted biofilm formation has a detrimental effect on bioelectrical energy harvesting in microbial cells. This issue still needs to be solved for higher power and longer durability and could be resolved with the help of nanoengineering in designing and manufacturing. Here, we demonstrate a photosynthetic solar cell (PSC) that contains a nanostructure to prevent the formation of biofilm by micro-organisms. Nanostructures were fabricated using nanoimprint lithography, where a film heater array system was introduced to precisely control the local wall temperature. To understand the heat and mass transfer phenomena behind the manufacturing and energy harvesting processes of PSC, we carried out a numerical simulation and experimental measurements. It revealed that the nanostructures developed on the proton exchange membrane enable PSC to produce enhanced output power due to the retarded microbial attachment on the Nafion membrane. We anticipate that this strategy can provide a pathway where PSC can ensure more renewable, sustainable, and efficient energy harvesting performance. PMID:24840499

  20. Microbial fuel cell biofilm characterization with thermogravimetric analysis on bare and polyethyleneimine surface modified carbon foam anodes

    NASA Astrophysics Data System (ADS)

    Kramer, Jessica; Soukiazian, Souren; Mahoney, Sky; Hicks-Garner, Jocelyn

    2012-07-01

    Thermogravimetric analysis (TGA) of microbial biofilms on bare and polyethyleneimine (PEI) surface modified carbon foam is described. PEI-modified carbon foam was incorporated into a microbial fuel cell (MFC) as the anode, inoculated with electrogenic bacteria, and the voltage and power outputs were monitored over five weeks. The results were compared to MFCs containing unmodified carbon foam anodes. Biofilm formation was investigated by scanning electron microscopy and TGA. TGA is presented as a new method to assess the relative amounts of biofilm on an electrode surface.

  1. Molecular techniques revealed highly diverse microbial communities in natural marine biofilms on polystyrene dishes for invertebrate larval settlement.

    PubMed

    Lee, On On; Chung, Hong Chun; Yang, Jiangke; Wang, Yong; Dash, Swagatika; Wang, Hao; Qian, Pei-Yuan

    2014-07-01

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. PMID:24402362

  2. Biofilm formation and electricity generation of a microbial fuel cell started up under different external resistances

    NASA Astrophysics Data System (ADS)

    Zhang, Liang; Zhu, Xun; Li, Jun; Liao, Qiang; Ye, Dingding

    2011-08-01

    To investigate the effects of external resistance on the biofilm formation and electricity generation of microbial fuel cells (MFCs), active biomass, the content of extracellular polymeric substances (EPS) and the morphology and structure of the biofilms developed at 10, 50, 250 and 1000 Ω are characterized. It is demonstrated that the structure of biofilm plays a crucial role in the maximum power density and sustainable current generation of MFCs. The results show that the maximum power density of the MFCs increases from 0.93 ± 0.02 W m-2 to 2.61 ± 0.18 W m-2 when the external resistance decreases from 1000 to 50 Ω. However, on further decreasing the external resistance to 10 Ω, the maximum power density decreased to 1.25 ± 0.01 W m-2 because of a less active biomass and higher EPS content in the biofilm. Additionally, the 10 Ω MFC shows a highest maximum sustainable current of 8.49 ± 0.19 A m-2. This result can be attributed to the existence of void spaces beneficial for proton and buffer transport within the anode biofilm, which maintains a suitable microenvironment for electrochemically active microorganisms.

  3. The phylogenetic structure of microbial biofilms and free-living bacteria in a small stream.

    PubMed

    Brablcov, Lenka; Burinkov, Iva; Badurov, Pavlna; Rulk, Martin

    2013-05-01

    The phylogenetic composition, bacterial biomass, and biovolume of both planktonic and biofilm communities were studied in a low-order Byst?ice stream near Olomouc City, in the Czech Republic. The aim of the study was to compare the microbial communities colonizing different biofilm substrata (stream aggregates, stream sediment, underwater tree roots, stream stones, and aquatic macrophytes) to those of free-living bacteria. The phylogenetic composition was analyzed using fluorescence in situ hybridization for main phylogenetic groups. All phylogenetic groups studied were detected in all sample types. The stream stone was the substratum where nearly all phylogenetic groups were the most abundant, while the lowest proportion to the DAPI-stained cells was found for free-living bacteria. The probe specific for the domain Bacteria detected 20.6 to 45.8% of DAPI-stained cells while the probe specific for the domain Archaea detected 4.3 to 17.9%. The most abundant group of Proteobacteria was Alphaproteobacteria with a mean of 14.2%, and the least abundant was Betaproteobacteria with a mean of 11.4%. The average value of the Cytophaga-Flavobacteria group was 10.5%. Total cell numbers and bacterial biomass were highest in sediment and root biofilm. The value of cell biovolume was highest in stone biofilm and lowest in sediment. Overall, this study revealed relevant differences in phylogenetic composition, bacterial biomass, and biovolume between different stream biofilms and free-living bacteria. PMID:23129136

  4. Imaging Microbial Biofilms in Opaque Three-dimensional Porous Media: Opportunities and Limitations (Invited)

    NASA Astrophysics Data System (ADS)

    Wildenschild, D.; Iltis, G.

    2013-12-01

    Microbial biofilms are observed in both natural and engineered subsurface environments and can dramatically alter the physical properties of porous media. Current understanding of biofilm formation and the associated impacts to structural and hydrodynamic properties of porous media are limited by our ability to observe changes to pore morphology non-destructively. Imaging biofilm within opaque porous media has historically presented a significant challenge. X-ray computed microtomography has traditionally been used for non-destructive imaging of a variety of processes and phenomena in porous media, yet, the conventional contrast agents used in tomography research tend to diffuse quite readily into both the aqueous phase as well as the porous media-associated biofilm, thereby preventing delineation of the two phases. A couple of new methods for imaging biofilm within opaque porous media using x-ray microtomography have been developed in recent years, and this presentation will discuss advantages and limitations to using polychromatic vs. monochromatic (synchrotron) radiation, as well as different types, and various concentrations of, contrast agents.

  5. Implications of in situ calcification for photosynthesis in a ~ 3.3 Ga-old microbial biofilm from the Barberton greenstone belt, South Africa

    NASA Astrophysics Data System (ADS)

    Westall, Frances; Cavalazzi, Barbara; Lemelle, Laurence; Marrocchi, Yves; Rouzaud, Jean-Nol; Simionovici, Alexandre; Salom, Murielle; Mostefaoui, Smail; Andreazza, Caroline; Foucher, Frdric; Toporski, Jan; Jauss, Andrea; Thiel, Volker; Southam, Gordon; MacLean, Lachlan; Wirick, Susan; Hofmann, Axel; Meibom, Anders; Robert, Franois; Dfarge, Christian

    2011-10-01

    Timing the appearance of photosynthetic microorganisms is crucial to understanding the evolution of life on Earth. The ability of the biosphere to use sunlight as a source of energy (photoautotrophy) would have been essential for increasing biomass and for increasing the biogeochemical capacity of all prokaryotes across the range of redox reactions that support life. Typical proxies for photosynthesis in the rock record include features, such as a mat-like, laminated morphology (stratiform, domical, conical) often associated with bulk geochemical signatures, such as calcification, and a fractionated carbon isotope signature. However, to date, in situ, calcification related to photosynthesis has not been demonstrated in the oldest known microbial mats. We here use in situ nanometre-scale techniques to investigate the structural and compositional architecture in a 3.3 billion-year (Ga) old microbial biofilm from the Barberton greenstone belt, thus documenting in situ calcification that was most likely related to anoxygenic photosynthesis. The Josefsdal Chert Microbial Biofilm (JCMB) formed in a littoral (photic) environment. It is characterised by a distinct vertical structural and compositional organisation. The lower part is calcified in situ by aragonite, progressing upwards into uncalcified kerogen characterised by up to 1% sulphur, followed by an upper layer that contains intact filaments at the surface. Crystallites of pseudomorphed pyrite are also associated with the biofilm suggesting calcification related to the activity of heterotrophic sulphur reducing bacteria. In this anoxygenic, nutrient-limited environment, the carbon required by the sulphur reducing bacteria could only have been produced by photoautotrophy. We conclude that the Josfsdal Chert Microbial Biofilm was formed by a consortium of anoxygenic microorganisms, including photosynthesisers and sulphur reducing bacteria.

  6. Role of Cyanobacterial Exopolysaccharides in Phototrophic Biofilms and in Complex Microbial Mats

    PubMed Central

    Rossi, Federico; De Philippis, Roberto

    2015-01-01

    Exopolysaccharides (EPSs) are an important class of biopolymers with great ecological importance. In natural environments, they are a common feature of microbial biofilms, where they play key protective and structural roles. As the primary colonizers of constrained environments, such as desert soils and lithic and exposed substrates, cyanobacteria are the first contributors to the synthesis of the EPSs constituting the extracellular polymeric matrix that favors the formation of microbial associations with varying levels of complexity called biofilms. Cyanobacterial colonization represents the first step for the formation of biofilms with different levels of complexity. In all of the possible systems in which cyanobacteria are involved, the synthesis of EPSs contributes a structurally-stable and hydrated microenvironment, as well as chemical/physical protection against biotic and abiotic stress factors. Notwithstanding the important roles of cyanobacterial EPSs, many aspects related to their roles and the relative elicited biotic and abiotic factors have still to be clarified. The aim of this survey is to outline the state-of-the-art of the importance of the cyanobacterial EPS excretion, both for the producing cells and for the microbial associations in which cyanobacteria are a key component. PMID:25837843

  7. Role of cyanobacterial exopolysaccharides in phototrophic biofilms and in complex microbial mats.

    PubMed

    Rossi, Federico; De Philippis, Roberto

    2015-01-01

    Exopolysaccharides (EPSs) are an important class of biopolymers with great ecological importance. In natural environments, they are a common feature of microbial biofilms, where they play key protective and structural roles. As the primary colonizers of constrained environments, such as desert soils and lithic and exposed substrates, cyanobacteria are the first contributors to the synthesis of the EPSs constituting the extracellular polymeric matrix that favors the formation of microbial associations with varying levels of complexity called biofilms. Cyanobacterial colonization represents the first step for the formation of biofilms with different levels of complexity. In all of the possible systems in which cyanobacteria are involved, the synthesis of EPSs contributes a structurally-stable and hydrated microenvironment, as well as chemical/physical protection against biotic and abiotic stress factors. Notwithstanding the important roles of cyanobacterial EPSs, many aspects related to their roles and the relative elicited biotic and abiotic factors have still to be clarified. The aim of this survey is to outline the state-of-the-art of the importance of the cyanobacterial EPS excretion, both for the producing cells and for the microbial associations in which cyanobacteria are a key component. PMID:25837843

  8. Biofilm dispersion in Pseudomonas aeruginosa.

    PubMed

    Kim, Soo-Kyoung; Lee, Joon-Hee

    2016-02-01

    In recent decades, many researchers have written numerous articles about microbial biofilms. Biofilm is a complex community of microorganisms and an example of bacterial group behavior. Biofilm is usually considered a sessile mode of life derived from the attached growth of microbes to surfaces, and most biofilms are embedded in self-produced extracellular matrix composed of extracellular polymeric substances (EPSs), such as polysaccharides, extracellular DNAs (eDNA), and proteins. Dispersal, a mode of biofilm detachment indicates active mechanisms that cause individual cells to separate from the biofilm and return to planktonic life. Since biofilm cells are cemented and surrounded by EPSs, dispersal is not simple to do and many researchers are now paying more attention to this active detachment process. Unlike other modes of biofilm detachment such as erosion or sloughing, which are generally considered passive processes, dispersal occurs as a result of complex spatial differentiation and molecular events in biofilm cells in response to various environmental cues, and there are many biological reasons that force bacterial cells to disperse from the biofilms. In this review, we mainly focus on the spatial differentiation of biofilm that is a prerequisite for dispersal, as well as environmental cues and molecular events related to the biofilm dispersal. More specifically, we discuss the dispersal-related phenomena and mechanisms observed in Pseudomonas aeruginosa, an important opportunistic human pathogen and representative model organism for biofilm study. PMID:26832663

  9. Effect of biofilm formation on the performance of microbial fuel cell for the treatment of palm oil mill effluent.

    PubMed

    Baranitharan, E; Khan, Maksudur R; Prasad, D M R; Teo, Wee Fei Aaron; Tan, Geok Yuan Annie; Jose, Rajan

    2015-01-01

    Anode biofilm is a crucial component in microbial fuel cells (MFCs) for electrogenesis. Better knowledge about the biofilm development process on electrode surface is believed to improve MFC performance. In this study, double-chamber microbial fuel cell was operated with diluted POME (initial COD = 1,000 mg L(-1)) and polyacrylonitrile carbon felt was used as electrode. The maximum power density, COD removal efficiency and Coulombic efficiency were found as 22 mW m(-2), 70 and 24 %, respectively. FTIR and TGA analysis confirmed the formation of biofilm on the electrode surface during MFC operation. The impact of anode biofilm on anodic polarization resistance was investigated using electrochemical impedance spectroscopy (EIS) and microbial community changes during MFC operation using denaturing gradient gel electrophoresis (DGGE). The EIS-simulated results showed the reduction of charge transfer resistance (R ct) by 16.9 % after 14 days of operation of the cell, which confirms that the development of the microbial biofilm on the anode decreases the R ct and therefore improves power generation. DGGE analysis showed the variation in the biofilm composition during the biofilm growth until it forms an initial stable microbial community, thereafter the change in the diversity would be less. The power density showed was directly dependent on the biofilm development and increased significantly during the initial biofilm development period. Furthermore, DGGE patterns obtained from 7th and 14th day suggest the presence of less diversity and probable functional redundancy within the anodic communities possibly responsible for the stable MFC performance in changing environmental conditions. PMID:24981021

  10. Characteristics of microbial biofilm on wooden vats ('gerles') in PDO Salers cheese.

    PubMed

    Didienne, Robert; Defargues, Catherine; Callon, Ccile; Meylheuc, Thierry; Hulin, Sophie; Montel, Marie-Christine

    2012-05-15

    The purpose of this study was to characterize microbial biofilms from 'gerles' (wooden vats for making PDO Salers cheese) and identify their role in milk inoculation and in preventing pathogen development. Gerles from ten farms producing PDO Salers cheese were subjected to microbial analysis during at least 4 periods spread over two years. They were distinguished by their levels of Lactobacillus (between 4.50 and 6.01 log CFU/cm(2)), Gram negative bacteria (between 1.45 and 4.56 log CFU/cm(2)), yeasts (between 2.91 and 5.57 log CFU/cm(2)), and moulds (between 1.72 and 4.52 log CFU/cm(2)). They were then classed into 4 groups according their microbial characteristics. These 4 groups were characterized by different milk inoculations (with either sour whey or starter culture, daily or not), and different washing procedures (with water or whey from cheese making). The farm gerles were not contaminated by Salmonella, Listeria monocytogenes or Staphylococcus aureus. Only one slight, punctual contamination was found on one gerle among the ten studied. Even when the milk was deliberately contaminated with L. monocytogenes and S. aureus in the 40 L experimental gerles, these pathogens were found neither on the gerle surfaces nor in the cheeses. Using 40 L experimental gerles it was shown that the microbial biofilms on the gerle surfaces formed in less than one week and then remained stable. They were mainly composed of a great diversity of lactic acid bacteria (Leuconostoc pseudomesenteroides, Lactococcus lactis, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus hilgardii,), Gram positive catalase positive bacteria (Curtobacterium flaccumfaciens, Curtobacterium oceanosedimentum Citrococcus spp., Brachybacterium rhamnosum, Kocuria rhizophila, Arthrobacter spp.) and yeast (Kluyveromyces lactis, Kluyveromyces marxianus). In less than 1 min, even in a 500 L farm gerle, the gerle's microbial biofilm can inoculate pasteurized milk with micro-organisms at levels superior to those in raw milk. PMID:22483401

  11. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities.

    PubMed

    Aliaga Goltsman, Daniela S; Comolli, Luis R; Thomas, Brian C; Banfield, Jillian F

    2015-04-01

    A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ? 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time. PMID:25361394

  12. Microbial Diversity in the Early In Vivo-Formed Dental Biofilm.

    PubMed

    Heller, D; Helmerhorst, E J; Gower, A C; Siqueira, W L; Paster, B J; Oppenheim, F G

    2016-01-01

    Although the mature dental biofilm composition is well studied, there is very little information on the earliest phase of in vivo tooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made with Haemophilus parainfluenzae, Gemella haemolysans, Slackia exigua, and Rothia species. Abundance changes over time were noted for Streptococcus anginosus and Streptococcus intermedius (P = 0.02), Streptococcus mitis bv. 2 (P = 0.0002), Streptococcus oralis (P = 0.0002), Streptococcus cluster I (P = 0.003), G. haemolysans (P = 0.0005), and Stenotrophomonas maltophilia (P = 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease. PMID:26746720

  13. Microbial Biofilm Voltammetry: Direct Electrochemical Characterization of Catalytic Electrode-Attached Biofilms?

    PubMed Central

    Marsili, Enrico; Rollefson, Janet B.; Baron, Daniel B.; Hozalski, Raymond M.; Bond, Daniel R.

    2008-01-01

    While electrochemical characterization of enzymes immobilized on electrodes has become common, there is still a need for reliable quantitative methods for study of electron transfer between living cells and conductive surfaces. This work describes growth of thin (<20 ?m) Geobacter sulfurreducens biofilms on polished glassy carbon electrodes, using stirred three-electrode anaerobic bioreactors controlled by potentiostats and nondestructive voltammetry techniques for characterization of viable biofilms. Routine in vivo analysis of electron transfer between bacterial cells and electrodes was performed, providing insight into the main redox-active species participating in electron transfer to electrodes. At low scan rates, cyclic voltammetry revealed catalytic electron transfer between cells and the electrode, similar to what has been observed for pure enzymes attached to electrodes under continuous turnover conditions. Differential pulse voltammetry and electrochemical impedance spectroscopy also revealed features that were consistent with electron transfer being mediated by an adsorbed catalyst. Multiple redox-active species were detected, revealing complexity at the outer surfaces of this bacterium. These techniques provide the basis for cataloging quantifiable, defined electron transfer phenotypes as a function of potential, electrode material, growth phase, and culture conditions and provide a framework for comparisons with other species or communities. PMID:18849456

  14. Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms.

    PubMed

    Ragon, Marie; Fontaine, Michal C; Moreira, David; Lpez-Garca, Purificacin

    2012-08-01

    Microbial biogeography studies expend much effort in determining whether environmental selection or stochastic processes related to dispersal are more important in shaping community composition. While both types of factors are possibly influential, it is tacitly assumed that protists, or microbial eukaryotes in general, behave biogeographically as prokaryotes because of their small physical size. However, direct evidence for this in exactly the same environment and at the same phylogenetic depth is lacking. In this study, we compared the structure of both prokaryotic and eukaryotic components of microbial communities forming biofilms on mineral substrates in different geographic locations at the level of small-subunit (SSU) rRNA-based operational taxonomic units (OTUs). These microbial communities are subjected to strong environmental selection and contain significant proportions of extremophilic microorganisms adapted to desiccation and UV radiation. We find that the nature of the substrate as well as climatic variables and geography influences microbial community structure. However, constrained correspondence analyses and distance-decay curves showed that, whereas the substrate type was the most significant factor structuring bacterial communities, geographic location was the most influential factor for microbial eukaryote communities. Biological explanations implying a higher dispersal success for bacteria combined with more mobile lifestyles for predatory protists may underlie these different prokaryote versus microbial eukaryote biogeographic patterns. PMID:22686398

  15. Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations.

    PubMed

    Nocker, Andreas; Lepo, Joe Eugene; Martin, Linda Lin; Snyder, Richard Allan

    2007-10-01

    The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time. PMID:17351811

  16. Waste Water Derived Electroactive Microbial Biofilms: Growth, Maintenance, and Basic Characterization

    PubMed Central

    Gimkiewicz, Carla; Harnisch, Falk

    2013-01-01

    The growth of anodic electroactive microbial biofilms from waste water inocula in a fed-batch reactor is demonstrated using a three-electrode setup controlled by a potentiostat. Thereby the use of potentiostats allows an exact adjustment of the electrode potential and ensures reproducible microbial culturing conditions. During growth the current production is monitored using chronoamperometry (CA). Based on these data the maximum current density (jmax) and the coulombic efficiency (CE) are discussed as measures for characterization of the bioelectrocatalytic performance. Cyclic voltammetry (CV), a nondestructive, i.e. noninvasive, method, is used to study the extracellular electron transfer (EET) of electroactive bacteria. CV measurements are performed on anodic biofilm electrodes in the presence of the microbial substrate, i.e. turnover conditions, and in the absence of the substrate, i.e. nonturnover conditions, using different scan rates. Subsequently, data analysis is exemplified and fundamental thermodynamic parameters of the microbial EET are derived and explained: peak potential (Ep), peak current density (jp), formal potential (Ef) and peak separation (?Ep). Additionally the limits of the method and the state-of the art data analysis are addressed. Thereby this video-article shall provide a guide for the basic experimental steps and the fundamental data analysis. PMID:24430581

  17. daime, a novel image analysis program for microbial ecology and biofilm research.

    PubMed

    Daims, Holger; Lcker, Sebastian; Wagner, Michael

    2006-02-01

    Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms. PMID:16423009

  18. Impact of flow conditions on ammonium uptake and microbial community structure in benthic biofilms

    NASA Astrophysics Data System (ADS)

    Arnon, Shai; Yanuka, Keren; Nejidat, Ali

    2010-05-01

    Excess nitrogen in surface waters is widely recognized to be a major global problem that adversely affects ecosystems, human health, and the economy. Today, most efforts to understand and model nutrient dynamics at large scales relies on macro-scale parameterization, such as mean channel geometry and velocity with uniform flow assumptions, as well as gross averages of in-situ nutrient transformation rates. However, there is increasing evidence that nutrient transformations in hyporheic zone are regulated by coupling between physical, chemical, and microbiological processes. Ignoring this greatly hinders the estimation of average biochemical transformation rates under the variable flow conditions found in aquatic systems. We used a combination of macro- and micro-scale observations in laboratory flumes to show that interplay between hydrodynamic transport, redox gradients, and microbial metabolism controls ammonium utilization by hyporheic microbial communities. Biofilm structural characteristics were quantified using denaturing gradient gel electrophoresis (DGGE) and real time PCR, while redox and pH gradients were measured using microelectrodes. We found that overlying velocities had profound effect on ammonium uptake due to mass transfer of ammonium from the bulk water to the benthic biofilms, but also due to the delivery of oxygen into the sediment bed. Under laminar flow conditions we didn't observe any change of ammonium uptake as a response to increase in overlying velocity. However, under non-laminar conditions we observe monotonic increase in ammonium uptake, with the greatest uptake under the fastest flow condition. We will discuss ammonium uptake rates results in the context of the different microbial communities and the micro-scale observations that were obtained using the microelectrodes. We anticipate that combined knowledge of the response of the microbial community and bulk nitrogen utilization rates to flow conditions will support the development of improved strategies that rely on biofilm growth to enhance nitrogen removal in natural and engineered systems.

  19. Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches.

    PubMed

    Vandecandelaere, Ilse; Matthijs, Nele; Van Nieuwerburgh, Filip; Deforce, Dieter; Vosters, Peter; De Bus, Liesbet; Nelis, Hans J; Depuydt, Pieter; Coenye, Tom

    2012-01-01

    Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm. PMID:22693635

  20. Optically Transparent Porous Medium for Nondestructive Studies of Microbial Biofilm Architecture and Transport Dynamics

    PubMed Central

    Leis, Andrew P.; Schlicher, Sven; Franke, Hilmar; Strathmann, Martin

    2005-01-01

    We describe a novel and noninvasive, microscopy-based method for visualizing the structure and dynamics of microbial biofilms, individual fluorescent microbial cells, and inorganic colloids within a model porous medium. Biofilms growing in flow cells packed with granules of an amorphous fluoropolymer could be visualized as a consequence of refractive index matching between the solid fluoropolymer grains and the aqueous immersion medium. In conjunction with the capabilities of confocal microscopy for nondestructive optical sectioning, the use of amorphous fluoropolymers as a solid matrix permits observation of organisms and dynamic processes to a depth of 2 to 3 mm, whereas sediment biofilms growing in sand-filled flow cells can only be visualized in the region adjacent to the flow cell wall. This method differs fundamentally from other refractive index-matching applications in that optical transparency was achieved by matching a solid phase to water (and not vice versa), thereby permitting real-time microscopic studies of particulate-containing, low-refractive-index media such as biological and chromatographic systems. PMID:16085878

  1. Assessment of Microbial Diversity in Biofilms Recovered from Endotracheal Tubes Using Culture Dependent and Independent Approaches

    PubMed Central

    Vandecandelaere, Ilse; Matthijs, Nele; Van Nieuwerburgh, Filip; Deforce, Dieter; Vosters, Peter; De Bus, Liesbet; Nelis, Hans J.; Depuydt, Pieter; Coenye, Tom

    2012-01-01

    Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm. PMID:22693635

  2. Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics.

    PubMed

    Pellicer-Ncher, Carles; Franck, Stphanie; Glay, Arda; Ruscalleda, Mal; Terada, Akihiko; Al-Soud, Waleed Abu; Hansen, Martin Asser; Srensen, Sren J; Smets, Barth F

    2014-01-01

    Membrane-aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration can bring the rapid and long-term suppression of NOB and the onset of the activity of anaerobic ammonium oxidizing bacteria (AnAOB). Real-time quantitative polymerase chain reaction analyses confirmed that such shift in performance was mirrored by a change in population densities, with a very drastic reduction of the NOB?Nitrospira and Nitrobacter and a 10-fold increase in AnAOB numbers. The study of biofilm sections with relevant 16S rRNA fluorescent probes revealed strongly stratified biofilm structures fostering aerobic ammonium oxidizing bacteria (AOB) in biofilm areas close to the membrane surface (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r-strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal. PMID:24112350

  3. Analysis of Structural and Physiological Profiles To Assess the Effects of Cu on Biofilm Microbial Communities

    PubMed Central

    Massieux, B.; Boivin, M. E. Y.; van den Ende, F. P.; Langenskild, J.; Marvan, P.; Barranguet, C.; Admiraal, W.; Laanbroek, H. J.; Zwart, G.

    2004-01-01

    We investigated the effects of copper on the structure and physiology of freshwater biofilm microbial communities. For this purpose, biofilms that were grown during 4 weeks in a shallow, slightly polluted ditch were exposed, in aquaria in our laboratory, to a range of copper concentrations (0, 1, 3, and 10 ?M). Denaturing gradient gel electrophoresis (DGGE) revealed changes in the bacterial community in all aquaria. The extent of change was related to the concentration of copper applied, indicating that copper directly or indirectly caused the effects. Concomitantly with these changes in structure, changes in the metabolic potential of the heterotrophic bacterial community were apparent from changes in substrate use profiles as assessed on Biolog plates. The structure of the phototrophic community also changed during the experiment, as observed by microscopic analysis in combination with DGGE analysis of eukaryotic microorganisms and cyanobacteria. However, the extent of community change, as observed by DGGE, was not significantly greater in the copper treatments than in the control. Yet microscopic analysis showed a development toward a greater proportion of cyanobacteria in the treatments with the highest copper concentrations. Furthermore, copper did affect the physiology of the phototrophic community, as evidenced by the fact that a decrease in photosynthetic capacity was detected in the treatment with the highest copper concentration. Therefore, we conclude that copper affected the physiology of the biofilm and had an effect on the structure of the communities composing this biofilm. PMID:15294780

  4. Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces.

    PubMed

    Lenhart, Tiffany R; Duncan, Kathleen E; Beech, Iwona B; Sunner, Jan A; Smith, Whitney; Bonifay, Vincent; Biri, Bernadette; Suflita, Joseph M

    2014-01-01

    Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed 'cookies,' revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted. PMID:25115517

  5. Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics

    PubMed Central

    Pellicer-Nàcher, Carles; Franck, Stéphanie; Gülay, Arda; Ruscalleda, Maël; Terada, Akihiko; Al-Soud, Waleed Abu; Hansen, Martin Asser; Sørensen, Søren J; Smets, Barth F

    2014-01-01

    Membrane-aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration can bring the rapid and long-term suppression of NOB and the onset of the activity of anaerobic ammonium oxidizing bacteria (AnAOB). Real-time quantitative polymerase chain reaction analyses confirmed that such shift in performance was mirrored by a change in population densities, with a very drastic reduction of the NOB Nitrospira and Nitrobacter and a 10-fold increase in AnAOB numbers. The study of biofilm sections with relevant 16S rRNA fluorescent probes revealed strongly stratified biofilm structures fostering aerobic ammonium oxidizing bacteria (AOB) in biofilm areas close to the membrane surface (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r-strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal. PMID:24112350

  6. Microbial biofilms for the removal of Cu? from CMP wastewater.

    PubMed

    Mosier, Aaron P; Behnke, Jason; Jin, Eileen T; Cady, Nathaniel C

    2015-09-01

    The modern semiconductor industry relies heavily on a process known as chemical mechanical planarization, which uses physical and chemical processes to remove excess material from the surface of silicon wafers during microchip fabrication. This process results in large volumes of wastewater containing dissolved metals including copper (Cu(2+)), which must then be filtered and treated before release into municipal waste systems. We have investigated the potential use of bacterial and fungal biomass as an alternative to the currently used ion-exchange resins for the adsorption of dissolved Cu(2+) from high-throughput industrial waste streams. A library of candidate microorganisms, including Lactobacillus casei and Pichia pastoris, was screened for ability to bind Cu(2+) from solution and to form static biofilm communities within packed-bed adsorption columns. The binding efficiency of these biomass-based adsorption columns was assessed under various flow conditions and compared to that of industrially used ion-exchange resins. We demonstrated the potential to regenerate the biomass within the adsorption columns through the use of a hydrochloric acid wash, and subsequently reuse the columns for additional copper binding. While the binding efficiency and capacity of the developed L. casei/P. pastoris biomass filters was inferior to ion-exchange resin, the potential for repeated reuse of these filters, coupled with the advantages of a more sustainable "green" adsorption process, make this technique an attractive candidate for use in industrial-scale CMP wastewater treatment. PMID:26093466

  7. Wiring microbial biofilms to the electrode by osmium redox polymer for the performance enhancement of microbial fuel cells.

    PubMed

    Yuan, Yong; Shin, Hyosul; Kang, Chan; Kim, Sunghyun

    2016-04-01

    An osmium redox polymer, PAA-PVI-[Os(4,4'-dimethyl-2,2'-bipyridine)2Cl](+/2+) that has been used in enzymatic fuel cells and microbial sensors, was applied for the first time to the anode of single-chamber microbial fuel cells with the mixed culture inoculum aiming at enhancing performance. Functioning as a molecular wire connecting the biofilm to the anode, power density increased from 1479mWm(-2) without modification to 2355mWm(-2) after modification of the anode. Evidence from cyclic voltammetry showed that the catalytic activity of an anodic biofilm was greatly enhanced in the presence of an osmium redox polymer, indicating that electrons were more efficiently transferred to the anode via co-immobilized osmium complex tethered to wiring polymer chains at the potential range of -0.3V-+0.1V (vs. SCE). The optimum amount of the redox polymer was determined to be 0.163mgcm(-2). PMID:26599210

  8. Microbial biofilms control economic metal mobility in an acid-sulfate hydrothermal system

    NASA Astrophysics Data System (ADS)

    Phillips-Lander, C. M.; Roberts, J. A.; Hernandez, W.; Mora, M.; Fowle, D. A.

    2012-12-01

    Trace metal cycling in hydrothermal systems has been the subject of a variety of geochemical and economical geology studies. Typically in these settings these elements are sequestered in sulfide and oxide mineral fractions, however in near-surface low-temperature environments organic matter and microorganisms (typically in mats) have been implicated in their mobility through sorption. Here we specifically examine the role of microbial biofilms on metal partitioning in an acid-sulfate hydrothermal system. We studied the influence of microorganisms and microbial biofilms on trace metal adsorption in Pailas de Aguas I, an acid-sulfate hot spring on the southwest flank of Rincon de la Vieja, a composite stratovolcano in the Guanacaste Province, Costa Rica. Spring waters contain high suspended loads, and are characterized by high T (79.6-89.3oC), low pH (2.6-4), and high ionic strengths (I= 0.5-0.8). Waters contain high concentrations of the biogeochemically active elements Fe (4-6 mmol/l) and SO42- (38 mmol/l), but PO43- are below detection limits (bdl). Silver, Ni, and Mo concentrations are bdl; however other trace metals are present in solution in concentrations of 0.1-0.2 mg/l Cd, 0.2-0.4 mg/l Cr and V, 0.04-1 mg/l Cu,. Preliminary 16S rRNA analyses of microorganisms in sediments reveal several species of algae, including Galderia sp., Cyanidium sp, ?-proteobacteria, Acidithiobacillus caldus, Euryarcheota, and methanogens. To evaluate microbial biofilms' impact on trace metal mobility we analyzed a combination of suspended, bulk and biofilm associated sediment samples via X-ray diffraction (XRD) and trace element sequential extractions (SE). XRD analysis indicated all samples were primarily composed of Fe/Al clay minerals (nontronite, kaolinite), 2- and 6-line ferrihydrite, goethite, and hematite, quartz, and opal-?. SE showed the highest concentrations of Cu, Mo, and V were found in the suspended load. Molybdenum was found primarily in the residual and organic fractions of suspended sediments. Copper is distributed in all but the carbonate fraction of suspended sediments. Vanadium was bound primarily to the oxide and residual fractions with Si, which is probably found as opal-?. In contrast, biofilm sediments had the highest concentrations of Fe, Si, Cd, Al, Zn, Ag, and Ni. Trace metals were sequestered mainly in the organic fraction in decreasing concentrations of: Cu biofilm sediments, which may be the result of sulfur oxidizing organisms generating elemental sulfur. Because trace metals are primarily bound in the organic fraction we posit that this may be a strategy by microorganisms to reduce metal toxicity in an acid environment through sequestration, making these metals relatively immobile until geochemical conditions dramatically changed. Similar patterns of trace metal partitioning into microbial biofilms have been observed in other acid systems, including acid mine drainage at Rio Tinto, Spain. Therefore, microbial sequestration of toxic metals may be a common coping mechanism in acid sulfate systems.

  9. Identification of Biofilm Matrix-Associated Proteins from an Acid Mine Drainage Microbial Community

    SciTech Connect

    Jiao, Yongqin; D'Haeseleer, Patrik M; Dill, Brian; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.; Thelen, Michael P.

    2011-01-01

    In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbial physiology. To investigate this in biofilms from an extremely acidic environment, we used shotgun proteomics analyses to identify proteins associated with EPS in biofilms at two developmental stages, designated DS1 and DS2. The proteome composition of the EPS was significantly different from that of the cell fraction, with more than 80% of the cellular proteins underrepresented or undetectable in EPS. In contrast, predicted periplasmic, outer membrane, and extracellular proteins were overrepresented by 3- to 7-fold in EPS. Also, EPS proteins were more basic by 2 pH units on average and about half the length. When categorized by predicted function, proteins involved in motility, defense, cell envelope, and unknown functions were enriched in EPS. Chaperones, such as histone-like DNA binding protein and cold shock protein, were overrepresented in EPS. Enzymes, such as protein peptidases, disulfide-isomerases, and those associated with cell wall and polysaccharide metabolism, were also detected. Two of these enzymes, identified as -N-acetylhexosaminidase and cellulase, were confirmed in the EPS fraction by enzymatic activity assays. Compared to the differences between EPS and cellular fractions, the relative differences in the EPS proteomes between DS1 and DS2 were smaller and consistent with expected physiological changes during biofilm development.

  10. Microbial biofilm formation and contamination of dental-unit water systems in general dental practice.

    PubMed

    Walker, J T; Bradshaw, D J; Bennett, A M; Fulford, M R; Martin, M V; Marsh, P D

    2000-08-01

    Dental-unit water systems (DUWS) harbor bacterial biofilms, which may serve as a haven for pathogens. The aim of this study was to investigate the microbial load of water from DUWS in general dental practices and the biofouling of DUWS tubing. Water and tube samples were taken from 55 dental surgeries in southwestern England. Contamination was determined by viable counts on environmentally selective, clinically selective, and pathogen-selective media, and biofouling was determined by using microscopic and image analysis techniques. Microbial loading ranged from 500 to 10(5) CFU. ml(-1); in 95% of DUWS water samples, it exceeded European Union drinking water guidelines and in 83% it exceeded American Dental Association DUWS standards. Among visible bacteria, 68% were viable by BacLight staining, but only 5% of this "viable by BacLight" fraction produced colonies on agar plates. Legionella pneumophila, Mycobacterium spp., Candida spp., and Pseudomonas spp. were detected in one, five, two, and nine different surgeries, respectively. Presumptive oral streptococci and Fusobacterium spp. were detected in four and one surgeries, respectively, suggesting back siphonage and failure of antiretraction devices. Hepatitis B virus was never detected. Decontamination strategies (5 of 55 surgeries) significantly reduced biofilm coverage but significantly increased microbial numbers in the water phase (in both cases, P < 0.05). Microbial loads were not significantly different in DUWS fed with soft, hard, deionized, or distilled water or in different DUWS (main, tank, or bottle fed). Microbiologically, no DUWS can be considered "cleaner" than others. DUWS deliver water to patients with microbial levels exceeding those considered safe for drinking water. PMID:10919792

  11. Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell

    PubMed Central

    Ishii, Shun'ichi; Shimoyama, Takefumi; Hotta, Yasuaki; Watanabe, Kazuya

    2008-01-01

    Background Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood. Results A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population. Conclusion Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community. PMID:18186940

  12. Exoelectrogenic bacterium phylogenetically related to Citrobacter freundii, isolated from anodic biofilm of a microbial fuel cell.

    PubMed

    Huang, Jianjian; Zhu, Nengwu; Cao, Yanlan; Peng, Yue; Wu, Pingxiao; Dong, Wenhao

    2015-02-01

    An electrogenic bacterium, named Citrobacter freundii Z7, was isolated from the anodic biofilm of microbial fuel cell (MFC) inoculated with aerobic sewage sludge. Cyclic voltammetry (CV) analysis exhibited that the strain Z7 had relatively high electrochemical activity. When the strain Z7 was inoculated into MFC, the maximum power density can reach 204.5 mW/m(2) using citrate as electron donor. Series of substrates including glucose, glycerol, lactose, sucrose, and rhammose could be utilized to generate power. CV tests and the addition of anode solution as well as AQDS experiments indicated that the strain Z7 might transfer electrons indirectly via secreted mediators. PMID:25427595

  13. Fate of organo-mineral particles in streams: Microbial degradation by streamwater & biofilm assemblages

    NASA Astrophysics Data System (ADS)

    Hunter, W. R.; Raich, M.; Wanek, W.; Battin, T. J.

    2013-12-01

    Inland waters are of global biogeochemical importance. They receive carbon inputs of ~ 4.8 Pg C/ y of which, 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One aspect of this is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. their use as carbon (C) and nitrogen (N) sources within aquatic systems. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We experimentally tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of 13C:15N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of 13C:15N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and water sampled from the Oberer Seebach stream (Austria). Each incubation experienced a 16:8 light:dark regime, with metabolism monitored via changes in oxygen concentrations between photoperiods. The relative fate of the organo-mineral particles was quantified by tracing the mineralization of the 13C and 15N labels and their incorporation into microbial biomass. Here we present the initial results of 13C-label mineralization, incorporation and retention within dissolved organic carbon pool. The results indicate that 514 (× 219) μmol/ mmol of the 13:15N labeled free amino acids were mineralized over the 7-day incubations. By contrast, 186 (× 97) μmol/ mmol of the mineral-sorbed amino acids were mineralized over a similar period. Thus, organo-mineral complexation reduced amino acid mineralization by ~ 60 %, with no differences observed between the streamwater and biofilm assemblages. Throughout the incubations, biofilms were observed to leach dissolved organic carbon (DOC). However, within the streamwater assemblage the presence of both organo-mineral particles and kaolin particles was associated with significant DOC removal (-1.7 % and -7.5 % respectively). Consequently, the study demonstrates that mineral and organo-mineral particles can limit the availability of DOC in aquatic systems, providing nucleation sites for flocculation and fresh mineral surfaces, which facilitate OM-sorption. The formation of these organo-mineral particles subsequently restricts microbial OM degradation, potentially altering the transport and facilitating the burial of OM within streams.

  14. Microbial biofilm development on neonatal enteral feeding tubes.

    PubMed

    Juma, Noha A; Forsythe, Stephen J

    2015-01-01

    Neonates in intensive care units often require supporting medical devices and antibiotic treatment. The intensive care treatment combined with their immature immune system, the increased permeability of mucosa, and the undeveloped microflora of the gut may render the neonates highly vulnerable to colonisation and subsequent infections when exposed to opportunistic pathogens. These infections may not only be local gastrointestinal infections, but also systematic following translocation from the gastrointestinal system. This could be particularly alarming considering that common antibiotics may not be effective if the causative strain is multi-drug resistant.This chapter reviews our information on the microbial colonization of neonatal feeding tubes. The range of organisms which have been recovered are wide, and while primarily bacterial, fungi such as Candida have also been found. The bacteria are principally Staphylococcus spp. and Enterobacteriaceae. The Enterobacteriaceae isolates are predominantly Enterobacter cancerogenus, Serratia marcescens, Enterobacter hormaechei, Escherichia coli and Klebsiella pneumoniae. Many of these isolates encode for antibiotic resistance; E. hormaechei (ceftazidine and cefotaxime) and S. marcescens strains (amoxicillin and co-amoxiclav). PMID:25366224

  15. Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach

    PubMed Central

    Ishii, Shun’ichi; Suzuki, Shino; Tenney, Aaron; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Bretschger, Orianna

    2015-01-01

    Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli. PMID:26443302

  16. Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Tenney, Aaron; Norden-Krichmar, Trina M; Nealson, Kenneth H; Bretschger, Orianna

    2015-01-01

    Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli. PMID:26443302

  17. The Biofilm Life-Cycle and Virulence of Pseudomonas aeruginosa are Dependent on a Filamentous Prophage

    PubMed Central

    Rice, Scott A.; Tan, Chuan Hao; Mikkelsen, Per Jensen; Kung, Vanderlene; Woo, Jerry; Tay, Martin; Hauser, Alan; McDougald, Diane; Webb, Jeremy S.; Kjelleberg, Staffan

    2009-01-01

    Mature Pseudomonas aeruginosa biofilms undergo specific developmental events. Using a bacteriophage mutant, generated by deletion of the entire filamentous Pf4 prophage, we show that the phage is essential for several stages of the biofilm life-cycle and that it significantly contributes to the virulence of P. aeruginosa in vivo. Here, we show for the first time that biofilms of the Pf4 phage deficient mutant did not develop hollow centres or undergo cell death, typical of the differentiation process of wild-type P. aeruginosa PAO1 biofilms. Furthermore, microcolonies of the Pf4 mutant were significantly smaller in size and less stable compared to the wild-type biofilm. Small colony variants (SCVs) were detectable in the dispersal population of the wild-type biofilm at the time of dispersal and cell death, whilst no SCVs were detected in the effluent of the Pf4 biofilm. This study shows that at the time when cell death occurs in biofilms of the wild-type, the Pf4 phage converts into a superinfective form, which correlates with the appearance of variants in the dispersal population. Unexpectedly, mice infected with the Pf4 mutant survived significantly longer than those infected with its isogenic wild-type strain, demonstrating that Pf4 contributes to the virulence of P. aeruginosa. Hence, a filamentous prophage is a major contributor to the life cycle and adaptive behaviour of P. aeruginosa and offers an explanation for the prevalence of phage in this organism. PMID:19005496

  18. Biodiversity, community structure and function of biofilms in stream ecosystems.

    PubMed

    Besemer, Katharina

    2015-12-01

    Multi-species, surface-attached biofilms often dominate microbial life in streams and rivers, where they contribute substantially to biogeochemical processes. The microbial diversity of natural biofilms is huge, and may have important implications for the functioning of aquatic environments and the ecosystem services they provide. Yet the causes and consequences of biofilm biodiversity remain insufficiently understood. This review aims to give an overview of current knowledge on the distribution of stream biofilm biodiversity, the mechanisms generating biodiversity patterns and the relationship between biofilm biodiversity and ecosystem functioning. PMID:26027773

  19. Enhanced phosphorus recovery and biofilm microbial community changes in an alternating anaerobic/aerobic biofilter.

    PubMed

    Tian, Qing; Ong, Say Kee; Xie, Xuehui; Li, Fang; Zhu, Yanbin; Wang, Feng Rui; Yang, Bo

    2016-02-01

    The operation of an alternating anaerobic/aerobic biofilter (AABF), treating synthetic wastewater, was modified to enhance recovery of phosphorus (P). The AABF was periodically fed with an additional carbon source during the anaerobic phase to force the release of biofilm-sequestered P which was then harvested and recovered. A maximum of 48% of the total influent P was found to be released in the solution for recovery. Upon implementation of periodic P bio-sequestering and P harvesting, the predominant bacterial communities changed from β-Proteobacteria to γ-Proteobacteria groups. The genus Pseudomonas of γ-Proteobacteria was found to enrich greatly with 98% dominance. Dense intracellular poly-P granules were found within the cells of the biofilm, confirming the presence of P accumulating organisms (PAOs). Periodic addition of a carbon source to the AABF coupled with intracellular P reduction during the anaerobic phase most probably exerted environmental stress in the selection of Pseudomonas PAOs over PAOs of other phylogenic types. Results of the study provided operational information on the selection of certain microbial communities for P removal and recovery. This information can be used to further advance P recovery in biofilm systems such as the AABFs. PMID:26524149

  20. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems

    PubMed Central

    Liu, Yang; Zhang, Wei; Sileika, Tadas; Warta, Richard; Cianciotto, Nicholas P.; Packman, Aaron

    2009-01-01

    The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems. PMID:19177226

  1. The ecology and biogeochemistry of stream biofilms.

    PubMed

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

    2016-03-14

    Streams and rivers form dense networks, shape the Earth's surface and, in their sediments, provide an immensely large surface area for microbial growth. Biofilms dominate microbial life in streams and rivers, drive crucial ecosystem processes and contribute substantially to global biogeochemical fluxes. In turn, water flow and related deliveries of nutrients and organic matter to biofilms constitute major constraints on microbial life. In this Review, we describe the ecology and biogeochemistry of stream biofilms and highlight the influence of physical and ecological processes on their structure and function. Recent advances in the study of biofilm ecology may pave the way towards a mechanistic understanding of the effects of climate and environmental change on stream biofilms and the biogeochemistry of stream ecosystems. PMID:26972916

  2. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    NASA Astrophysics Data System (ADS)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  3. Sulfur as a Matrix for the Development of Microbial Biofilm Communities

    NASA Astrophysics Data System (ADS)

    Parker, C.; Bell, E.; Johnson, J. E.; Ma, X.; Stamps, B. W.; Rideout, J.; Johnson, H. A.; Vuono, D.; Spear, J. R.; Hanselmann, K.

    2013-12-01

    The high temperature, low oxygen, and high sulfide concentration of many hot springs select for a low diversity of organisms. The stringent requirements for growth and survival limit the types of interactions, which allow the microbial sulfur metabolism to be examined in depth. We combined geochemical, microbial and molecular data to understand mat development in the warm, oxygen-poor sulfidic Stinking Spring, Utah, USA. The upper flow zone of this spring has a variety of observable microbial biofilm structures that are linked to the activities of both sulfide-oxidizing and oxygenic bacteria. The diverse architecture of the microbial assemblages consist of bulbous ridge structures on the bottom of the streambed, floating mats that cover a large portion of the water surface area, and two morphologically different streamers; green long filaments and white shorter filaments, which both contain large amounts of elemental sulfur. We performed structural analysis using phase contrast and epifluorescence microscopy, and SEM coupled with EDS mapping. Amplicon sequenced 16S rRNA genes analyzed by QIIME and ARB indicated that the predominant organisms present were the cyanobacterial genus Leptolyngbya, and an ɛ-Proteobacteria closely related to the sulfur oxidizing genus Sulfurovum. Metagenomic analysis was conducted on six libraries from three locations using MG-RAST to analyze for genes associated with sulfur metabolism, specifically sulfur oxidation (sox) genes. The presence of sox genes and the microbial sulfur deposition strategy changes downstream as the sulfide concentration decreases. When sulfide is low, the streamers themselves become white and shorter with elemental sulfur deposited intracellularly, and diatoms seem to dominate over cyanobacteria, but do not form associations with the streamer structures. We propose that the microbial biofilms and green streamers present in the sulfide-rich section of the stream are formed in a multi-step process. Initial growth of cyanobacteria on bottom sulfur mats form green bulbous ridges that rise from the streambed by gas produced inside the mat. The bulbous features then break off and form floating mats. This is followed by colonization of remnant filaments by the proposed Sulfurovum. A repeating cycle ensues, in which the Sulfurovum produce a crust of elemental sulfur that the cyanobacteria must migrate past. This slowly builds up a core of elemental sulfur strings sheathed in cyanobacteria. Together, the co-habitation and interactions between sulfide-oxidizing bacteria and photosynthetic cyanobacteria construct visible physical structures that can potentially be preserved in the rock record.

  4. Electrical stimulation on biodegradation of phenol and responses of microbial communities in conductive carriers supported biofilms of the bioelectrochemical reactor.

    PubMed

    Ailijiang, Nuerla; Chang, Jiali; Liang, Peng; Li, Peng; Wu, Qing; Zhang, Xiaoyuan; Huang, Xia

    2016-02-01

    Conductive carbon felts (Cf) were used as biofilm carriers in bioelectrochemical reactors to enhance the electrical stimulation on treatment of phenol-containing synthetic wastewater. In batch test, phenol biodegradation was accelerated under an optimum direct current (DC), which was 2mA for Cf biofilm carriers, lower than that for non-conductive white foam carriers. The stimulation effect was consistent with Adenosine Triphosphate contents in biofilms. The long-term operation further demonstrated that a high and stable phenol removal efficiency could be achieved with applied DC of 2mA, and intermittent DC application was better than continuous one, with phenol removal efficiency of over 97%. Although the quantities of whole microbial communities kept at a high level under all conditions, special microorganisms related with genera of Zoogloea and Desulfovibrio were distinctively enriched under intermittent applied DC pattern. This study shows that the electrical stimulation is potentially effective for biofilm reactors treating phenol-containing wastewater. PMID:26615496

  5. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    SciTech Connect

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  6. Structural, physicochemical and microbial properties of flocs and biofilms in integrated fixed-film activated sludge (IFFAS) systems.

    PubMed

    Mahendran, Basuvaraj; Lishman, Lori; Liss, Steven N

    2012-10-15

    Integrated fixed-film activated sludge systems (IFFAS) may achieve year-round nitrification or gain additional treatment capacity due to the presence of both flocs and biofilms, and the potential for multiple redox states and long solids retention time. Flocs and biofilms are distinctive microbial structures and characterization of the physicochemical and structural properties of these may provide insight into their respective roles in wastewater treatment and contaminant removal in IFFAS. Flocs and biofilms were examined from five different pilot media systems being evaluated for potential full scale implementation at a large municipal wastewater treatment plant. Flocs and biofilms within the same system possessed different surface characteristics; flocs were found to have a higher negative surface charge (-0.35 to -0.65 meq./g VSS) and are more hydrophobic (60%-75%) than biofilms (-0.05 to -0.07 meq/g VSS; 19-34%). The EPS content of flocs was significantly higher (range of 2.1-4.5 folds) than that of biofilms. In floc-derived extracellular polymeric substances (EPS), protein (PN) was clearly dominant; whereas in biofilm-derived EPS, PN and polysaccharide (PS) were present in approximately equal proportions. Biofilm EPS had a higher proportion of DNA when compared to flocs. Biofilm growth was preferential on the protected internal surfaces of the media. Colonization of the external surfaces of the media was evident by the presence of small microcolonies. The structural heterogeneity of the biofilms examined was supported by observed differences in biomass content, thickness and roughness of biofilm surface. The biofilm on the interior surface of media was found to be patchy with clusters of cells connected by an irregular arrangement of interconnecting EPS projections. Biofilm thickness ranged between 139 ?m and 253 ?m. The pattern of oxygen penetration is expected to be complex. Nitrifiers and denitrifiers were predominantly associated with the biofilms, and the latter were found to be dispersed throughout the film and arranged in micro-clusters, suggesting partial oxygen penetration. PMID:22832219

  7. The effect of inorganic carbon on microbial interactions in a biofilm nitritation-anammox process.

    PubMed

    Ma, Yiwei; Sundar, Suneethi; Park, Hongkeun; Chandran, Kartik

    2015-03-01

    The overarching goal of this study was to determine the role of inorganic carbon (IC) in influencing the microbial ecology, performance and nitrogen turnover by individual microbial communities of a biofilm based combined nitritation-anammox process. IC limitation was transiently imposed by reducing the IC input from 350% to 40% of the stoichiometric requirement for 40 days. The principal impact observed during IC limitation was the overgrowth of nitrite oxidizing bacteria (NOB) at the expense of anaerobic ammonia oxidizing bacteria (AMX). On the other hand, the concentrations of ammonia oxidizing bacteria (AOB) were relatively stable during the imposition of and recovery from IC limitation. The resulting dominance of NOB, in terms of their concentration and contribution to nitrite consumption over AMX, resulted, in turn, in a decrease in overall nitrogen removal from 78 ± 2.0% before IC limitation to 46 ± 2.9% during IC limitation. Upon recovery back to non-limiting IC input, it took an inordinately long time (about 57*HRT) for the N-removal to recover back to pre-limitation conditions. Even after recovery, NOB were still persistent in the biofilm and could not be washed out to pre-limitation concentrations. The emission of nitrous oxide (N₂O) and nitric oxide (NO), likely from AOB, transiently increased in concert with transient increases in ammonia and hydroxylamine concentrations during the period of IC limitation. Therefore, an unintended consequence of IC limitation in nitritation-anammox systems can be an increase in their greenhouse gas footprint, in addition to compromised process performance. Most emphasis to date on nitritation and anammox studies has been on the nitrogen cycle. The results of this study demonstrate that the differing strategies used by AOB, NOB and AMX to compete for their preferred assimilative carbon source can also significantly influence the microbial ecology, performance and carbon footprint of such processes. PMID:25540838

  8. Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella

    PubMed Central

    Behrendt, Lars; Larkum, Anthony W D; Trampe, Erik; Norman, Anders; Sørensen, Søren J; Kühl, Michael

    2012-01-01

    We assessed the microbial diversity and microenvironmental niche characteristics in the didemnid ascidian Lissoclinum patella using 16S rRNA gene sequencing, microsensor and imaging techniques. L. patella harbors three distinct microbial communities spatially separated by few millimeters of tunic tissue: (i) a biofilm on its upper surface exposed to high irradiance and O2 levels, (ii) a cloacal cavity dominated by the prochlorophyte Prochloron spp. characterized by strong depletion of visible light and a dynamic chemical microenvironment ranging from hyperoxia in light to anoxia in darkness and (iii) a biofilm covering the underside of the animal, where light is depleted of visible wavelengths and enriched in near-infrared radiation (NIR). Variable chlorophyll fluorescence imaging demonstrated photosynthetic activity, and hyperspectral imaging revealed a diversity of photopigments in all microhabitats. Amplicon sequencing revealed the dominance of cyanobacteria in all three layers. Sequences representing the chlorophyll d containing cyanobacterium Acaryochloris marina and anoxygenic phototrophs were abundant on the underside of the ascidian in shallow waters but declined in deeper waters. This depth dependency was supported by a negative correlation between A. marina abundance and collection depth, explained by the increased attenuation of NIR as a function of water depth. The combination of microenvironmental analysis and fine-scale sampling techniques used in this investigation gives valuable first insights into the distribution, abundance and diversity of bacterial communities associated with tropical ascidians. In particular, we show that microenvironments and microbial diversity can vary significantly over scales of a few millimeters in such habitats; which is information easily lost by bulk sampling. PMID:22134643

  9. Microbial life beneath a high arctic glacier.

    PubMed

    Skidmore, M L; Foght, J M; Sharp, M J

    2000-08-01

    The debris-rich basal ice layers of a high Arctic glacier were shown to contain metabolically diverse microbes that could be cultured oligotrophically at low temperatures (0.3 to 4 degrees C). These organisms included aerobic chemoheterotrophs and anaerobic nitrate reducers, sulfate reducers, and methanogens. Colonies purified from subglacial samples at 4 degrees C appeared to be predominantly psychrophilic. Aerobic chemoheterotrophs were metabolically active in unfrozen basal sediments when they were cultured at 0.3 degrees C in the dark (to simulate nearly in situ conditions), producing (14)CO(2) from radiolabeled sodium acetate with minimal organic amendment (> or =38 microM C). In contrast, no activity was observed when samples were cultured at subfreezing temperatures (< or =-1.8 degrees C) for 66 days. Electron microscopy of thawed basal ice samples revealed various cell morphologies, including dividing cells. This suggests that the subglacial environment beneath a polythermal glacier provides a viable habitat for life and that microbes may be widespread where the basal ice is temperate and water is present at the base of the glacier and where organic carbon from glacially overridden soils is present. Our observations raise the possibility that in situ microbial production of CO(2) and CH(4) beneath ice masses (e.g., the Northern Hemisphere ice sheets) is an important factor in carbon cycling during glacial periods. Moreover, this terrestrial environment may provide a model for viable habitats for life on Mars, since similar conditions may exist or may have existed in the basal sediments beneath the Martian north polar ice cap. PMID:10919772

  10. Microbial Life beneath a High Arctic Glacier

    PubMed Central

    Skidmore, Mark L.; Foght, Julia M.; Sharp, Martin J.

    2000-01-01

    The debris-rich basal ice layers of a high Arctic glacier were shown to contain metabolically diverse microbes that could be cultured oligotrophically at low temperatures (0.3 to 4C). These organisms included aerobic chemoheterotrophs and anaerobic nitrate reducers, sulfate reducers, and methanogens. Colonies purified from subglacial samples at 4C appeared to be predominantly psychrophilic. Aerobic chemoheterotrophs were metabolically active in unfrozen basal sediments when they were cultured at 0.3C in the dark (to simulate nearly in situ conditions), producing 14CO2 from radiolabeled sodium acetate with minimal organic amendment (?38 ?M C). In contrast, no activity was observed when samples were cultured at subfreezing temperatures (??1.8C) for 66 days. Electron microscopy of thawed basal ice samples revealed various cell morphologies, including dividing cells. This suggests that the subglacial environment beneath a polythermal glacier provides a viable habitat for life and that microbes may be widespread where the basal ice is temperate and water is present at the base of the glacier and where organic carbon from glacially overridden soils is present. Our observations raise the possibility that in situ microbial production of CO2 and CH4 beneath ice masses (e.g., the Northern Hemisphere ice sheets) is an important factor in carbon cycling during glacial periods. Moreover, this terrestrial environment may provide a model for viable habitats for life on Mars, since similar conditions may exist or may have existed in the basal sediments beneath the Martian north polar ice cap. PMID:10919772

  11. Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

    PubMed

    Douterelo, Isabel; Jackson, M; Solomon, C; Boxall, J

    2016-04-01

    Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality. PMID:26637423

  12. Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers

    NASA Astrophysics Data System (ADS)

    Passarelli, Claire; Meziane, Tarik; Thiney, Najet; Boeuf, Dominique; Jesus, Bruno; Ruivo, Mickael; Jeanthon, Christian; Hubas, Cédric

    2015-02-01

    Biofilms, or microbial mats, are common associations of microorganisms in tidal flats; they generally consist of a large diversity of organisms embedded in a matrix of Extracellular Polymeric Substances (EPS). These molecules are mainly composed of carbohydrates and proteins, but their detailed monomer compositions and seasonal variations are currently unknown. Yet this composition determines the numerous roles of biofilms in these systems. This study investigated the changes in composition of carbohydrates in intertidal microbial mats over a year to decipher seasonal variations in biofilms and in varying hydrodynamic conditions. This work also aimed to assess how these compositions are related to microbial assemblages. In this context, natural biofilms whose development was influenced or not by artificial structures mimicking polychaete tubes were sampled monthly for over a year in intertidal flats of the Chausey archipelago. Biofilms were compared through the analysis of their fatty acid and pigment contents, and the monosaccharide composition of their EPS carbohydrates. Carbohydrates from both colloidal and bound EPS contained mainly glucose and, to a lower extent, galactose and mannose but they showed significant differences in their detailed monosaccharide compositions. These two fractions displayed different seasonal evolution, even if glucose accumulated in both fractions in summer; bound EPS only were affected by artificial biogenic structures. Sediment composition in fatty acids and pigments showed that microbial communities were dominated by diatoms and heterotrophic bacteria. Their relative proportions, as well as those of other groups like cryptophytes, changed between times and treatments. The changes in EPS composition were not fully explained by modifications of microbial assemblages but also depended on the processes taking place in sediments and on environmental conditions. These variations of EPS compositions are likely to alter different ecosystem processes such as biostabilisation or pollutants trapping.

  13. Microbial community development of biofilm in Amaranth decolourization technology analysed by FISH

    PubMed Central

    Belouhova, Mihaela; Schneider, Irina; Chakarov, Stoyan; Ivanova, Iliana; Topalova, Yana

    2014-01-01

    The aim of this study was to elucidate the role, the space distribution and the relationships of the bacteria from the genus Pseudomonas in a biofilm community during semi-continuous Amaranth decolourization process in model sand biofilters. The examined parameters of the process were as follows: technological parameters; key enzyme activities (azoreductase, succinate dehydrogenase, catechol-1,2-dioxygenase, catechol-2,3-dioxygenase); the number of azo-degrading bacteria and the bacteria from genus Pseudomonas (plate count technique); the amount and the location of Pseudomonas sp. using fluorescent in situ hybridization (FISH). The results showed that the increase of the Amaranth removal rate with 120% was accompanied with increase of the enzyme activities of the biofilm (azoreductase activity – with 25.90% and succinate dehydrogenase – with 10.61%). The enzyme assays showed absence of activity for сatechol-1,2-dioxygenase and catechol-2,3-dioxygenase at the early phase and high activities of the same oxygenases at the late phase (2.76 and 1.74 μmol/min mg protein, respectively). In the beginning of the process (0–191 h), the number of the culturable microorganisms from genus Pseudomonas was increased with 48.76% but at the late phase (191–455 h) they were decreased with 15.25% while the quantity of the non-culturable bacteria from this genus with synergetic relationships was increased with 23.26%. The dominant microbial factors were identified in the structure of the biofilm during the azo-degradation process by using FISH analysis. Furthermore, the inner mechanisms for increase of the rate and the range of the detoxification were revealed during the complex wastewater treatment processes. PMID:26019551

  14. [Analysis of structure changes of microbial community in medium biofilm by ERIC-PCR fingerprinting].

    PubMed

    Li, Hua-zhi; Li, Xiu-yan; Zhao, Ya-ping; Huang, Min-sheng; Yu, Xue-zhen; Jin, Cheng-xiang; Xu, Ya-tong

    2006-12-01

    A new technique, with medium biofilms and hydrophytes as main components, with microbes, plankton, hydrophytes and aquatic animals as basic ecological elements, was adopted to deal with eutrophication water in Shanghai. A pilot-scale test was carried on, with influent as 6 m(3)/d, 7 ponds parallelly connected, and with continuous influent and effluent. Water qualities were analyzed and ERIC-PCR fingerprinting method was used to study the natures of biofilm microbes. The results show that, the device has obvious affection on eutrophication water pollution removal, COD, TN, NH4+-N and TP removal efficiencies are respectively 20.7% - 48.5%, 20.1% - 49.7%, 39.8% - 66.2 % and 60.0% - 73.9% higher than those of control experiment. Water plants contribute for N and P absorption and removal, the three ponds with plants have higher TN and TP removal efficiency than the tree ones without hydrophytes, the enhanced TN removal efficiencies are 30.1%, 24.9% and 17.6% respectively. ERIC-PCR fingerprinting indicate that the three ponds with water plants have more similar microbial community structure to each other than no hydrophyte ponds, and that mean pairwise similarity coefficient value are 71.8% , 86.9% and 91.0% respectively on 2nd, 15th and 30th day, and at the same time the population diversity indexes rang from 1.89 to 2.22, 2.17 to 2.43 and 2.28 to 2.68, respectively. The above discussions conclude that the systemic population diversity indexes and structure similarity increase, biofilm microbes have gradually abundant population and stable structure, which are in accord with pollution removal efficiencies. PMID:17304855

  15. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms.

    PubMed

    Terefework, Zewdu; Pham, Chi L; Prosperi, Anja C; Entius, Mark M; Errami, Abdellatif; van Spanning, Rob J M; Zaura, Egija; Ten Cate, Jacob M; Crielaard, Wim

    2008-12-01

    A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts. PMID:18824042

  16. Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities

    PubMed Central

    Dopheide, Andrew; Lear, Gavin; He, Zhili; Zhou, Jizhong; Lewis, Gillian D.

    2015-01-01

    We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition. PMID:25849814

  17. [Microbial ecology analysis of the biofilm from two biological contact oxidation processes with different performance].

    PubMed

    Qian, Yin; Quan, Xiang-Chun; Pei, Yuan-Sheng; Ma, Jing-Yun; Tao, Kun

    2012-03-01

    This study investigated the performance of one-step aerobic biological oxidation process and anoxic/aerobic two-step biological oxidation process treating modeled river water containing low carbon and rich ammonia. Biofilm microbial ecology was analyzed with multiple molecular technologies including PCR-DGGE, FISH/CLSM and FISH/FCM to investigate the succession of bacteria community and space distribution along with abundance of the main functional bacteria, and to research the micro-influential factors and the mechanism of different biological contact oxidation processes for their performance. Results showed that two-step contact oxidation process achieved higher removal percentage than that of the one-step process, with COD and NH4(+) -N removal enhanced about 10% and 32%-59%, respectively. A much thicker biofilm was obtained by the one-step process compared to the two-step process, and nitrobacterium was mainly distributed in the depth of 180-200 microm and 105-125 microm, respectively. PCR-DGGE results found that the two-step process demonstrated less microbial diversity than that of the one-step process, FISH/FCM results showed that ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) abundance increased in the two-step process with the increase of operation time, while that of the one-step process declined. Experiment results demonstrate that functional partitioning of the anoxic-aerobic two-step biological contact oxidation process could be in favor for harvesting nitrobacteria and other special bacteria in different reactor spaces, which can improve removal efficiency for organics and ammonia finally. PMID:22624389

  18. Metabolic modeling of spatial heterogeneity of biofilms in microbial fuel cells reveals substrate limitations in electrical current generation.

    PubMed

    Jayasinghe, Nadeera; Franks, Ashley; Nevin, Kelly P; Mahadevan, Radhakrishnan

    2014-10-01

    Microbial fuel cells (MFCs) have been proposed as an alternative energy resource for the conversion of organic compounds to electricity. In an MFC, microorganisms such as Geobacter sulfurreducens form an anode-associated biofilm that can completely oxidize organic matter (electron donor) to carbon dioxide with direct electron transfer to the anode (electron acceptor). Mathematical models are useful in analyzing biofilm processes; however, existing models rely on Nernst-Monod type expressions, and evaluate extracellular processes separated from the intracellular metabolism of the microorganism. Thus, models that combine both extracellular and intracellular components, while addressing spatial heterogeneity, are essential for improved representation of biofilm processes. The goal of this work is to develop a model that integrates genome-scale metabolic models with the model of biofilm environment. This integrated model shows the variations of electrical current production and biofilm thickness under the presence/absence of NH4 in the bulk solution, and under varying maintenance energy demands. Further, sensitivity analysis suggested that conductivity is not limiting electrical current generation and that increasing cell density can lead to enhanced current generation. In addition, the modeling results also highlight instances such as the transformation into respiring cells, where the mechanism of electrical current generation during biofilm development is not yet clearly understood. PMID:25113946

  19. Microbial biofilms associated with fluid chemistry and megafaunal colonization at post-eruptive deep-sea hydrothermal vents

    NASA Astrophysics Data System (ADS)

    O'Brien, Charles E.; Giovannelli, Donato; Govenar, Breea; Luther, George W.; Lutz, Richard A.; Shank, Timothy M.; Vetriani, Costantino

    2015-11-01

    At deep-sea hydrothermal vents, reduced, super-heated hydrothermal fluids mix with cold, oxygenated seawater. This creates temperature and chemical gradients that support chemosynthetic primary production and a biomass-rich community of invertebrates. In late 2005/early 2006 an eruption occurred on the East Pacific Rise at 9°50‧N, 104°17‧W. Direct observations of the post-eruptive diffuse-flow vents indicated that the earliest colonizers were microbial biofilms. Two cruises in 2006 and 2007 allowed us to monitor and sample the early steps of ecosystem recovery. The main objective of this work was to characterize the composition of microbial biofilms in relation to the temperature and chemistry of the hydrothermal fluids and the observed patterns of megafaunal colonization. The area selected for this study had local seafloor habitats of active diffuse flow (in-flow) interrupted by adjacent habitats with no apparent expulsion of hydrothermal fluids (no-flow). The in-flow habitats were characterized by higher temperatures (1.6-25.2 °C) and H2S concentrations (up to 67.3 μM) than the no-flow habitats, and the microbial biofilms were dominated by chemosynthetic Epsilonproteobacteria. The no-flow habitats had much lower temperatures (1.2-5.2 °C) and H2S concentrations (0.3-2.9 μM), and Gammaproteobacteria dominated the biofilms. Siboglinid tubeworms colonized only in-flow habitats, while they were absent at the no-flow areas, suggesting a correlation between siboglinid tubeworm colonization, active hydrothermal flow, and the composition of chemosynthetic microbial biofilms.

  20. Eukaryotic life in biofilms formed in a uranium mine.

    PubMed

    Zirnstein, Isabel; Arnold, Thuro; Krawczyk-Brsch, Evelyn; Jenk, Ulf; Bernhard, Gert; Rske, Isolde

    2012-06-01

    The underground uranium mine Knigstein (Saxony, Germany), currently in the process of remediation, represents an underground acid mine drainage (AMD) environment, that is, low pH conditions and high concentrations of heavy metals including uranium, in which eye-catching biofilm formations were observed. During active uranium mining from 1984 to 1990, technical leaching with sulphuric acid was applied underground on-site resulting in a change of the underground mine environment and initiated the formation of AMD and also the growth of AMD-related copious biofilms. Biofilms grow underground in the mine galleries in a depth of 250 m (50 m above sea level) either as stalactite-like slime communities or as acid streamers in the drainage channels. The eukaryotic diversity of these biofilms was analyzed by microscopic investigations and by molecular methods, that is, 18S rDNA PCR, cloning, and sequencing. The biofilm communities of the Knigstein environment showed a low eukaryotic biodiversity and consisted of a variety of groups belonging to nine major taxa: ciliates, flagellates, amoebae, heterolobosea, fungi, apicomplexa, stramenopiles, rotifers and arthropoda, and a large number of uncultured eukaryotes, denoted as acidotolerant eukaryotic cluster (AEC). In Knigstein, the flagellates Bodo saltans, the stramenopiles Diplophrys archeri, and the phylum of rotifers, class Bdelloidea, were detected for the first time in an AMD environment characterized by high concentrations of uranium. This study shows that not only bacteria and archaea may live in radioactive contaminated environments, but also species of eukaryotes, clearly indicating their potential influence on carbon cycling and metal immobilization within AMD-affected environment. PMID:22950016

  1. Eukaryotic life in biofilms formed in a uranium mine

    PubMed Central

    Zirnstein, Isabel; Arnold, Thuro; Krawczyk-Bärsch, Evelyn; Jenk, Ulf; Bernhard, Gert; Röske, Isolde

    2012-01-01

    The underground uranium mine Königstein (Saxony, Germany), currently in the process of remediation, represents an underground acid mine drainage (AMD) environment, that is, low pH conditions and high concentrations of heavy metals including uranium, in which eye-catching biofilm formations were observed. During active uranium mining from 1984 to 1990, technical leaching with sulphuric acid was applied underground on-site resulting in a change of the underground mine environment and initiated the formation of AMD and also the growth of AMD-related copious biofilms. Biofilms grow underground in the mine galleries in a depth of 250 m (50 m above sea level) either as stalactite-like slime communities or as acid streamers in the drainage channels. The eukaryotic diversity of these biofilms was analyzed by microscopic investigations and by molecular methods, that is, 18S rDNA PCR, cloning, and sequencing. The biofilm communities of the Königstein environment showed a low eukaryotic biodiversity and consisted of a variety of groups belonging to nine major taxa: ciliates, flagellates, amoebae, heterolobosea, fungi, apicomplexa, stramenopiles, rotifers and arthropoda, and a large number of uncultured eukaryotes, denoted as acidotolerant eukaryotic cluster (AEC). In Königstein, the flagellates Bodo saltans, the stramenopiles Diplophrys archeri, and the phylum of rotifers, class Bdelloidea, were detected for the first time in an AMD environment characterized by high concentrations of uranium. This study shows that not only bacteria and archaea may live in radioactive contaminated environments, but also species of eukaryotes, clearly indicating their potential influence on carbon cycling and metal immobilization within AMD-affected environment. PMID:22950016

  2. Enrichment of anodic biofilm inoculated with anaerobic or aerobic sludge in single chambered air-cathode microbial fuel cells.

    PubMed

    Gao, Chongyang; Wang, Aijie; Wu, Wei-Min; Yin, Yalin; Zhao, Yang-Guo

    2014-09-01

    Aerobic sludge after anaerobic pretreatment and anaerobic sludge were separately used as inoculum to start up air-cathode single-chamber MFCs. Aerobic sludge-inoculated MFCs arrived at 0.27 V with a maximum power density of 5.79 W m(-3), while anaerobic sludge-inoculated MFCs reached 0.21 V with 3.66 W m(-3). Microbial analysis with DGGE profiling and high-throughput sequencing indicated that aerobic sludge contained more diverse bacterial populations than anaerobic sludge. Nitrospira species dominated in aerobic sludge, while anaerobic sludge was dominated by Desulfurella and Acidithiobacillus species. Microbial community structure and composition in anodic biofilms enriched, respectively from aerobic and anaerobic sludges tended gradually to be similar. Potentially exoelectrogenic Geobacter and Anaeromusa species, biofilm-forming Zoogloea and Acinetobacter species were abundant in both anodic biofilms. This study indicated that aerobic sludge performed better for MFCs startup, and the enrichment of anodic microbial consortium with different inocula but same substrate resulted in uniformity of functional microbial communities. PMID:24973773

  3. Monitoring of biofilm formation on different material surfaces of medical devices using hyperspectral imaging method

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Contamination of the inner surface of indwelling (implanted) medical devices by microbial biofilm is a serious problem. Some microbial bacteria such as Escherichia coli form biofilms that lead to potentially life-threatening infections. Other types of medical devices such as bronchoscopes and duod...

  4. Characterisation of microbial flocs formed from raw textile wastewater in aerobic biofilm reactor (ABR).

    PubMed

    Ibrahim, Zaharah; Amin, Mohamad Faiz Mohd; Yahya, Adibah; Aris, Azmi; Umor, Noor Azrimi; Muda, Khalida; Sofian, Nur Shalena

    2009-01-01

    Microbial flocs formed from raw textile wastewater in a prototype Aerobic Biofilm Reactor (ABR) system were characterised and studied for their potential use in the treatment of textile wastewater. After 90-100 days of operation, microbial flocs of loose irregular structures were obtained from the reactor with good settling velocity of 33 m/h and sludge volume index (SVI) of 48.2 mL/g. Molecular analysis of the flocs using PCR-amplified 16S rDNA sequence showed 98% homology to those of Bacillus sp, Paenibacillus sp and Acromobacter sp. Detection of Ca(2+)(131 mg/g) and Fe(2+)(131 mg/g) using atomic absorption spectrometer might be implicated with the flocs formation. In addition, presence of Co(2+) and Ni(2+) were indicative of the flocs ability to accumulate at least a fraction of the metals' present in the wastewater. When the flocs were used for the treatment of raw textile wastewater, they showed good removal of COD and colour about 55% and 70% respectively, indicating their potential application. PMID:19657163

  5. Enhanced biofilm distribution and cell performance of microfluidic microbial fuel cells with multiple anolyte inlets.

    PubMed

    Yang, Yang; Ye, Dingding; Liao, Qiang; Zhang, Pengqing; Zhu, Xun; Li, Jun; Fu, Qian

    2016-05-15

    A laminar-flow controlled microfluidic microbial fuel cell (MMFC) is considered as a promising approach to be a bio-electrochemical system (BES). But poor bacterial colonization and low power generation are two severe bottlenecks to restrict its development. In this study, we reported a MMFC with multiple anolyte inlets (MMFC-MI) to enhance the biofilm formation and promote the power density of MMFCs. Voltage profiles during the inoculation process demonstrated MMFC-MI had a faster start-up process than the conventional microfluidic microbial fuel cell with one inlet (MMFC-OI). Meanwhile, benefited from the periodical replenishment of boundary layer near the electrode, a more densely-packed bacterial aggregation was observed along the flow direction and also the substantially low internal resistance for MMFC-MI. Most importantly, the output power density of MMFC-MI was the highest value among the reported µl-scale MFCs to our best knowledge. The presented MMFC-MI appears promising for bio-chip technology and extends the scope of microfluidic energy. PMID:26735875

  6. Microbial Life in a Liquid Asphalt Desert

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

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

  7. Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water

    PubMed Central

    Islam, M. Shahinoor; Zhang, Yanyan; McPhedran, Kerry N.

    2015-01-01

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>109 gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

  8. Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water.

    PubMed

    Islam, M Shahinoor; Zhang, Yanyan; McPhedran, Kerry N; Liu, Yang; Gamal El-Din, Mohamed

    2015-06-15

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

  9. Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

    NASA Technical Reports Server (NTRS)

    Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

    1985-01-01

    Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

  10. Microbial Life Under Extreme Energy Limitation

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Jorgensen, Bo Barker

    2013-01-01

    A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

  11. Nitrogen removal in a single-chamber microbial fuel cell with nitrifying biofilm enriched at the air cathode.

    PubMed

    Yan, Hengjing; Saito, Tomonori; Regan, John M

    2012-05-01

    Nitrogen removal is needed in microbial fuel cells (MFCs) for the treatment of most waste streams. Current designs couple biological denitrification with side-stream or combined nitrification sustained by upstream or direct aeration, which negates some of the energy-saving benefits of MFC technology. To achieve simultaneous nitrification and denitrification, without extra energy input for aeration, the air cathode of a single-chamber MFC was pre-enriched with a nitrifying biofilm. Diethylamine-functionalized polymer (DEA) was used as the Pt catalyst binder on the cathode to improve the differential nitrifying biofilm establishment. With pre-enriched nitrifying biofilm, MFCs with the DEA binder had an ammonia removal efficiency of up to 96.8% and a maximum power density of 900 25 mW/m(2), compared to 90.7% and 945 42 mW/m(2) with a Nafion binder. A control with Nafion that lacked nitrifier pre-enrichment removed less ammonia and had lower power production (54.5% initially, 750 mW/m(2)). The nitrifying biofilm MFCs had lower Coulombic efficiencies (up to 27%) than the control reactor (up to 36%). The maximum total nitrogen removal efficiency reached 93.9% for MFCs with the DEA binder. The DEA binder accelerated nitrifier biofilm enrichment on the cathode, and enhanced system stability. These results demonstrated that with proper cathode pre-enrichment it is possible to simultaneously remove organics and ammonia in a single-chamber MFC without supplemental aeration. PMID:22386083

  12. Structure and microbial diversity of biofilms on different pipe materials of a model drinking water distribution systems.

    PubMed

    Rożej, Agnieszka; Cydzik-Kwiatkowska, Agnieszka; Kowalska, Beata; Kowalski, Dariusz

    2015-01-01

    The experiment was conducted in three model drinking water distribution systems (DWDSs) made of unplasticized polyvinyl chloride (PVC), silane cross-linked polyethylene (PEX) and high density polyethylene (HDPE) pipes to which tap water was introduced. After 2 years of system operation, microbial communities in the DWDSs were characterized with scanning electron microscopy, heterotrophic plate count, and denaturing gradient gel electrophoresis. The most extensive biofilms were found in HDPE pipes where bacteria were either attached to mineral deposits or immersed in exopolymers. On PEX surfaces, bacteria did not form large aggregates; however, they were present in the highest number (1.24 × 10(7) cells cm(-2)). PVC biofilm did not contain mineral deposits but was made of single cells with a high abundance of Pseudomonas aeruginosa, which can be harmful to human health. The members of Proteobacteria and Bacteroidetes were found in all biofilms and the water phase. Sphingomonadales and Methylophilaceae bacteria were found only in PEX samples, whereas Geothrix fermentans, which can reduce Fe(III), were identified only in PEX biofilm. The DNA sequences closely related to the members of Alphaproteobacteria were the most characteristic and intense amplicons detected in the HDPE biofilm. PMID:25342310

  13. Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure.

    PubMed

    Stevenson, Bradley S; Drilling, Heather S; Lawson, Paul A; Duncan, Kathleen E; Parisi, Victoria A; Suflita, Joseph M

    2011-04-01

    The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies. PMID:21261797

  14. Microbial life in a liquid asphalt desert.

    PubMed

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

    2011-04-01

    Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan. PMID:21480792

  15. Molecular characterization of microbial communities and quantification of Mycobacterium immunogenum in metal removal fluids and their associated biofilms.

    PubMed

    Wu, Jianfeng; Franzblau, Alfred; Xi, Chuanwu

    2016-03-01

    A number of human health effects have been associated with exposure to metal removal fluids (MRFs). Multiple lines of research suggest that a newly identified organism, Mycobacterium immunogenum (MI), appears to have an etiologic role in hypersensitivity pneumonitis (HP) in case of MRFs exposed workers. However, our knowledge of this organism, other possible causative agents (e.g., Pseudomonads), and the microbial ecology of MRFs in general, is limited. In this study, culture-based methods and small subunit ribosomal RNA gene clone library approach were used to characterize microbial communities in MRF bulk fluid and associated biofilm samples collected from fluid systems in an automobile engine plant. PCR amplification data using universal primers indicate that all samples had bacterial and fungal contaminated. Five among 15 samples formed colonies on the Mycobacteria agar 7H9 suggesting the likely presence of Mycobacteria in these five samples. This observation was confirmed with PCR amplification of 16S rRNA gene fragment using Mycobacteria specific primers. Two additional samples, Biofilm-1 and Biofilm-3, were positive in PCR amplification for Mycobacteria, yet no colonies formed on the 7H9 cultivation agar plates. Real-time PCR was used to quantify the abundance of M. immunogenum in these samples, and the data showed that the copies of M. immunogenum 16S rRNA gene in the samples ranges from 4.33 × 10(4) copy/ml to 4.61 × 10(7) copy/ml. Clone library analysis revealed that Paecilomyces sp. and Acremonium sp. and Acremonium-like were dominant fungi in MRF samples. Various bacterial species from the major phylum of proteobacteria were found and Pseudomonas is the dominant bacterial genus in these samples. Mycobacteria (more specifically MI) were found in all biofilm samples, including biofilms collected from inside the MRF systems and from adjacent environmental surfaces, suggesting that biofilms may play an important role in microbial ecology in MRFs. Biofilms may provide a shield or sheltered microenvironment for the growth and/or colonization of Mycobacteria in MRFs. PMID:25874435

  16. Microbial geomorphology: A neglected link between life and landscape

    NASA Astrophysics Data System (ADS)

    Viles, Heather A.

    2012-07-01

    Whilst recognition is increasing that life and landscapes are intimately related, as evidenced by growing research into ecosystem engineering, biogeomorphology and allied topics, the microbial contribution to such interactions has been relatively neglected. A revolution in environmental microbiology, based on molecular techniques, is now driving a reconsideration of the role of microbial processes in geomorphology at all scales. Recent research illustrates the hitherto unknown microbial diversity present in many extreme geomorphic environments, such as hyperarid deserts, subglacial lakes, hot springs, and much richer microbial life than previously suspected within the soils and sediments that blanket most other landscapes. Such microbial communities have been found to play important geomorphic roles across a wide range of environments, notably in weathering, precipitation of minerals and protecting surfaces from erosion. These geomorphic roles can also be conceptualised as examples of ecosystem engineering, and can pave the way for further plant-geomorphology and zoogeomorphology processes. Three key aspects which emerge from a review of microbial influences on Earth surface processes are a) that microbes play roles on a continuum from full control to passive involvement, b) that complex and widespread communities of microorganisms are involved and c) that microbial activity usually affects several Earth surface processes at once. Examples of the contribution of microbial life to geomorphology over long, medium and short timescales suggest that microorganisms play key geomorphological roles in two major situations; on the cusp between stable states, and in extreme environments where higher plant and animal life is limited and many abiotic processes are also constrained. The dominant link between microbial life and geomorphology appears to take on different forms depending on the timescale under consideration, with a stabilising microbial role apparent over short timescales being replaced by a denudational role over longer timescales. Further research involving microbiologists and geomorphologists is now needed to address three main questions, i.e. under what conditions are microbial and geomorphological processes most closely linked?, what scale issues surround links between microbes and geomorphology? And how do microbiological processes underpin broader biogeomorphological interactions?

  17. Microbial life in the deep terrestrial subsurface

    SciTech Connect

    Fliermans, C.B.; Balkwill, D.L.; Beeman, R.E.

    1988-12-31

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

  18. Wide boundaries of microbial life as due to anabiosis

    NASA Astrophysics Data System (ADS)

    Abyzov, S. A.; Mulyukin, A. L.; Mitskevich, I. N.; Ivanov, M. V.

    Gaining more insights to the boundaries in which microbial life can exist came from comprehensive studies of various especially extreme terrestrial environments They differ in their origin age temperature salinity energy flux and many other factors that are of paramount importance for life sustenance Microbiological studies of ancient Antarctic glaciers gave experimentally substantiated information on time and the lowest boundary of temperature in which viable pro- and eukaryotic microbial cells survived Noticeably the total number of viable microorganisms that are present in Antarctic ice horizons with temperature varying from -50 oC to -2 4 oC and the age range from 0 2 to 500 thousands of years The existence of microbial cells in so widely ranging temperature and age is regarded as due to super-long anabiosis Theoretically there is no difference between microorganisms that existed in the anabiotic state for tens of hundreds to millennia of years if they faced to low temperatures Hence wide boundaries of microbial life are associated to the state of anabiosis and this is true not only for deep cold environments such as Antarctic glaciers Indeed sensational findings of viable microorganisms in a variety of terrestrial ancient objects extend our knowledge of life boundaries Revelations of ancient microbial cells especially in those habitats where the number of microorganisms is very low unavoidably concerns the problem of authentication Therefore it is great importance to develop and use the methods that exclude contamination of studied samples by

  19. Medical Biofilms

    PubMed Central

    2009-01-01

    For more than two decades, Biotechnology and Bioengineering has documented research focused on natural and engineered microbial biofilms within aquatic and subterranean ecosystems, wastewater and waste-gas treatment systems, marine vessels and structures, and industrial bioprocesses. Compared to suspended culture systems, intentionally engineered biofilms are heterogeneous reaction systems that can increase reactor productivity, system stability, and provide inherent cell: product separation. Unwanted biofilms can create enormous increases in fluid frictional resistances, unacceptable reductions in heat transfer efficiency, product contamination, enhanced material deterioration, and accelerated corrosion. Missing from B&B has been an equivalent research dialogue regarding the basic molecular microbiology, immunology, and biotechnological aspects of medical biofilms. Presented here are the current problems related to medical biofilms; current concepts of biofilm formation, persistence, and interactions with the host immune system; and emerging technologies for controlling medical biofilms. PMID:18366134

  20. Microbial adhesion and biofilm formation on microfiltration membranes: a detailed characterization using model organisms with increasing complexity.

    PubMed

    Vanysacker, L; Denis, C; Declerck, P; Piasecka, A; Vankelecom, I F J

    2013-01-01

    Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development. PMID:23986906

  1. Modeling the Effects of Hydrodynamic Regimes on Microbial Communities within Fluvial Biofilms: Combining Deterministic and Stochastic Processes.

    PubMed

    Li, Yi; Wang, Chao; Zhang, Wenlong; Wang, Peifang; Niu, Lihua; Hou, Jun; Wang, Jing; Wang, Linqiong

    2015-11-01

    To fully understand the effects of hydrodynamics on a microbial community, the roles of niche-based and neutral processes must be considered in a mathematical model. To this end, a two-dimensional model combining mechanisms of immigration, dispersal, and niche differentiation was first established to describe the effects of hydrodynamics on bacterial communities within fluvial biofilms. Deterministic factors of the model were identified via the calculation of Spearman's rank correlation coefficients between parameters of hydrodynamics and the bacterial community. It was found that turbulent kinetic energy and turbulent intensity were considered as a set of reasonable predictors of community composition, whereas flow velocity and turbulent intensity can be combined together to predict biofilm bacterial biomass. According to the modeling result, the bacterial community could get its favorable assembly condition with a flow velocity ranging from 0.041 to 0.061 m/s. However, the driving force for biofilm community assembly changed with the local hydrodynamics. Individuals reproduction within the biofilm was the main driving force with flow velocity less than 0.05 m/s, while cell migration played a much more important role with velocity larger than 0.05 m/s. The developed model could be considered as a useful tool for improving the technologies of water environment protection and remediation. PMID:26437120

  2. A protective coat of microorganisms on macroalgae: inhibitory effects of bacterial biofilms and epibiotic microbial assemblages on barnacle attachment.

    PubMed

    Nasrolahi, Ali; Stratil, Stephanie B; Jacob, Katharina J; Wahl, Martin

    2012-09-01

    Effects of epibiotic bacteria associated with macroalgae on barnacle larval attachment were investigated. Eight bacterial isolates obtained from samples of three macroalga species were cultured as monospecies bacterial films and tested for their activity against barnacle (Amphibalanus improvisus) attachment in field experiments (Western Baltic Sea). Furthermore, natural biofilm communities associated with the surface of the local brown alga, Fucus vesiculosus, which were exposed to different temperatures (5, 15 and 20C), were harvested and subsequently tested. Generally, monospecies bacterial biofilms, as well as natural microbial assemblages, inhibited barnacle attachment by 20-67%. denaturing gradient gel electrophoresis fingerprints showed that temperature treatment shifted the bacterial community composition and weakened the repellent effects at 20C. Repellent effects were absent when settlement pressure of cyprids was high. Nonviable bacteria tended to repel cyprids when compared to the unfilmed surfaces. We conclude that biofilms can have a repellent effect benefiting the host by preventing heavy fouling on its surface. However, severe settlement pressure, as well as stressful temperature, may reduce the protective effects of the alga's biofilm. Our results add to the notion that the performance of F.vesiculosus may be reduced by multiple stressors in the course of global warming. PMID:22486721

  3. Atmospheres and evolution. [of microbial life on earth

    NASA Technical Reports Server (NTRS)

    Margulis, L.; Lovelock, J. E.

    1981-01-01

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

  4. Slow Microbial Life in the Seabed.

    PubMed

    Jørgensen, Bo Barker; Marshall, Ian P G

    2016-01-01

    Global microbial cell numbers in the seabed exceed those in the overlying water column, yet these organisms receive less than 1% of the energy fixed as organic matter in the ocean. The microorganisms of this marine deep biosphere subsist as stable and diverse communities with extremely low energy availability. Growth is exceedingly slow, possibly regulated by virus-induced mortality, and the mean generation times are tens to thousands of years. Intermediate substrates such as acetate are maintained at low micromolar concentrations, yet their turnover time may be several hundred years. Owing to slow growth, a cell community may go through only 10,000 generations from the time it is buried beneath the mixed surface layer until it reaches a depth of tens of meters several million years later. We discuss the efficiency of the energy-conserving machinery of subsurface microorganisms and how they may minimize energy consumption through necessary maintenance, repair, and growth. PMID:26209150

  5. Slow Microbial Life in the Seabed

    NASA Astrophysics Data System (ADS)

    Jørgensen, Bo Barker; Marshall, Ian P. G.

    2016-01-01

    Global microbial cell numbers in the seabed exceed those in the overlying water column, yet these organisms receive less than 1% of the energy fixed as organic matter in the ocean. The microorganisms of this marine deep biosphere subsist as stable and diverse communities with extremely low energy availability. Growth is exceedingly slow, possibly regulated by virus-induced mortality, and the mean generation times are tens to thousands of years. Intermediate substrates such as acetate are maintained at low micromolar concentrations, yet their turnover time may be several hundred years. Owing to slow growth, a cell community may go through only 10,000 generations from the time it is buried beneath the mixed surface layer until it reaches a depth of tens of meters several million years later. We discuss the efficiency of the energy-conserving machinery of subsurface microorganisms and how they may minimize energy consumption through necessary maintenance, repair, and growth.

  6. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  7. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  8. Microbial life detection with minimal assumptions

    NASA Astrophysics Data System (ADS)

    Kounaves, Samuel P.; Noll, Rebecca A.; Buehler, Martin G.; Hecht, Michael H.; Lankford, Kurt; West, Steven J.

    2002-02-01

    To produce definitive and unambiguous results, any life detection experiment must make minimal assumptions about the nature of extraterrestrial life. The only criteria that fits this definition is the ability to reproduce and in the process create a disequilibrium in the chemical and redox environment. The Life Detection Array (LIDA), an instrument proposed for the 2007 NASA Mars Scout Mission, and in the future for the Jovian moons, enables such an experiment. LIDA responds to minute biogenic chemical and physical changes in two identical 'growth' chambers. The sensitivity is provided by two differentially monitored electrochemical sensor arrays. Growth in one of the chambers alters the chemistry and ionic properties and results in a signal. This life detection system makes minimal assumptions; that after addition of water the microorganism replicates and in the process will produce small changes in its immediate surroundings by consuming, metabolizing, and excreting a number of molecules and/or ionic species. The experiment begins by placing an homogenized split-sample of soil or water into each chamber, adding water if soil, sterilizing via high temperature, and equilibrating. In the absence of any microorganism in either chamber, no signal will be detected. The inoculation of one chamber with even a few microorganisms which reproduce, will create a sufficient disequilibrium in the system (compared to the control) to be detectable. Replication of the experiment and positive results would lead to a definitive conclusion of biologically induced changes. The split sample and the nanogram inoculation eliminates chemistry as a causal agent.

  9. Microbial community structures and in situ sulfate-reducing and sulfur-oxidizing activities in biofilms developed on mortar specimens in a corroded sewer system.

    PubMed

    Satoh, Hisashi; Odagiri, Mitsunori; Ito, Tsukasa; Okabe, Satoshi

    2009-10-01

    Microbially induced concrete corrosion (MICC) caused by sulfuric acid attack in sewer systems has been a serious problem for a long time. A better understanding of microbial community structures of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their in situ activities is essential for the efficient control of MICC. In this study, the microbial community structures and the in situ hydrogen sulfide production and consumption rates within biofilms and corroded materials developed on mortar specimens placed in a corroded manhole was investigated by culture-independent 16S rRNA gene-based molecular techniques and microsensors for hydrogen sulfide, oxygen, pH and the oxidation-reduction potential. The dark-gray gel-like biofilm was developed in the bottom (from the bottom to 4 cm) and the middle (4-20 cm from the bottom of the manhole) parts of the mortar specimens. White filamentous biofilms covered the gel-like biofilm in the middle part. The mortar specimens placed in the upper part (30 cm above the bottom of the manhole) were corroded. The 16S rRNA gene-cloning analysis revealed that one clone retrieved from the bottom biofilm sample was related to an SRB, 12 clones and 6 clones retrieved from the middle biofilm and the corroded material samples, respectively, were related to SOB. In situ hybridization results showed that the SRB were detected throughout the bottom biofilm and filamentous SOB cells were mainly detected in the upper oxic layer of the middle biofilm. Microsensor measurements demonstrated that hydrogen sulfide was produced in and diffused out of the bottom biofilms. In contrast, in the middle biofilm the hydrogen sulfide produced in the deeper parts of the biofilm was oxidized in the upper filamentous biofilm. pH was around 3 in the corroded materials developed in the upper part of the mortar specimens. Therefore, it can be concluded that hydrogen sulfide provided from the bottom biofilms and the sludge settling tank was emitted to the sewer atmosphere, then oxidized to corrosive compounds in the upper and middle parts of the manhole, and only the upper part of the mortar specimens were corroded, because in the middle part of the manhole the generated corrosive compounds (e.g., sulfuric acid) was reduced in the deeper parts of the biofilm. PMID:19709714

  10. Microbial diversity in paleolithic caves: a study case on the phototrophic biofilms of the Cave of Bats (Zuheros, Spain).

    PubMed

    Urz, Clara; De Leo, Filomena; Bruno, Laura; Albertano, Patrizia

    2010-07-01

    The biological colonization of rocks in the Cave of Bats (Cueva de Los Murcilagos, Zuheros, Spain) was studied in order to reveal the diversity of microorganisms involved in the biofilm formation. The culturable, metabolically active fraction of biodeteriogens present on surfaces was investigated focusing on morphological, ultrastructural, and genetic features, and their presence related to the peculiar environmental conditions of the underground site. PCR-ITS analysis and 16S rDNA sequences were used to clusterize and characterize the isolated strains. The presence of bacterial taxa associated to the photosynthetic microflora and fungi within the biofilm contributed to clarify the relationships inside the microbial community and to explain the alteration observed at the different sites. These results will contribute to the application of more successful strategies for the preventive conservation of subterranean archaeological sites. PMID:20607532

  11. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.

    PubMed

    Cole, Jessica K; Hutchison, Janine R; Renslow, Ryan S; Kim, Young-Mo; Chrisler, William B; Engelmann, Heather E; Dohnalkova, Alice C; Hu, Dehong; Metz, Thomas O; Fredrickson, Jim K; Lindemann, Stephen R

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

  12. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    PubMed Central

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice C.; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

  13. Toxic metal resistance in biofilms: diversity of microbial responses and their evolution.

    PubMed

    Koechler, Sandrine; Farasin, Julien; Cleiss-Arnold, Jessica; Arsène-Ploetze, Florence

    2015-12-01

    Since biofilms are an important issue in the fields of medicine and health, several recent microbiological studies have focused on their formation and their contribution to toxic compound resistance mechanisms. In this review, we describe how metals impact biofilm formation and resistance, and how biofilms can help cells resist toxic metals. First, the organic matrix acts as a barrier isolating the cells from many environmental stresses. Secondly, the metabolism of the cells changes, and a slowly-growing or non-growing sub-population of cells known as persisters emerges. Thirdly, in the case of multispecies biofilms, metabolic interactions are developed, allowing cells to be more persistent or to have greater capacity to survive than a single species biofilm. Finally, we discuss how the high density of the cells may promote horizontal gene transfer processes, resulting in the acquisition of new features. All these crucial mechanisms enable microorganisms to survive and colonize toxic environments, and probably accelerate ongoing evolutionary processes. PMID:25869223

  14. Microbial dynamics during conversion from supragingival to subgingival biofilms in an in vitro model.

    PubMed

    Thurnheer, T; Bostanci, N; Belibasakis, G N

    2016-04-01

    The development of dental caries and periodontal diseases result from distinct shifts in the microbiota of the tooth-associated biofilm. This in vitro study aimed to investigate changes in biofilm composition and structure, during the shift from a 'supragingival' aerobic profile to a 'subgingival' anaerobic profile. Biofilms consisting of Actinomyces oris, Candida albicans, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus mutans and Veillonella dispar were aerobically grown in saliva-containing medium on hydroxyapatite disks. After 64 h, Campylobacter rectus, Prevotella intermedia and Streptococcus anginosus were further added along with human serum, while culture conditions were shifted to microaerophilic. After 96 h, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were finally added and the biofilm was grown anaerobically for another 64 h. At the end of each phase, biofilms were harvested for species-specific quantification and localization. Apart from C. albicans, all other species gradually increased during aerobic and microaerophilic conditions, but remained steady during anaerobic conditions. Biofilm thickness was doubled during the microaerophilic phase, but remained steady throughout the anaerobic phase. Extracellular polysaccharide presence was gradually reduced throughout the growth period. Biofilm viability was reduced during the microaerophilic conversion, but was recovered during the anaerobic phase. This in vitro study has characterized the dynamic structural shifts occurring in an oral biofilm model during the switch from aerobic to anaerobic conditions, potentially modeling the conversion of supragingival to subgingival biofilms. Within the limitations of this experimental model, the findings may provide novel insights into the ecology of oral biofilms. PMID:26033167

  15. Microbial programming of health and disease starts during fetal life.

    PubMed

    Koleva, Petya T; Kim, Ji-Sun; Scott, James A; Kozyrskyj, Anita L

    2015-12-01

    The pioneer microbiota of the neonatal gut are essential for gut maturation, and metabolic and immunologic programming. Recent research has shown that early bacterial colonization may impact the occurrence of disease later in life (microbial programming). Despite early conflicting evidence, it has long been considered that the womb is a sterile environment and human microbial colonization begins at birth. In the last few years, several findings have reiterated the presence of microbes in infant first stool (meconium) and pointed to the existence of in utero microbial colonization of the infant gut. The dominant bacterial taxa detected in meconium specimens belong to the Enterobacteriaceae family (Escherichia genus) and lactic acid bacteria (notably members of the genera Leuconostoc, Enterococcus, and Lactococcus). Maternal atopy promotes dominance of Enterobacteriaceae in newborn meconium, which in turn may lead to respiratory problems in the infant. This microbial interaction with the host immune system may in fact, originate during fetal life. Our review evaluates the evidence for an intrauterine origin of meconium microbiota, their composition and influences, and potential clinical implications on infant health. Birth Defects Research (Part C) 105:265-277, 2015. © 2015 Wiley Periodicals, Inc. PMID:26663884

  16. Hydraulic continuity and biological effects of low strength very low frequency electromagnetic waves: Case of microbial biofilm growth in water treatment.

    PubMed

    Grard, Merlin; Noamen, Omri; Evelyne, Gonze; Eric, Valette; Gilles, Cauffet; Marc, Henry

    2015-10-15

    This study aims to elucidate the interactions between water, subjected to electromagnetic waves of very low frequency (VLF) (kHz) with low strength electromagnetic fields (3.5mT inside the coils), and the development of microbial biofilms in this exposed water. Experimental results demonstrate that in water exposed to VLF electromagnetic waves, the biomass of biofilm is limited if hydraulic continuity is achieved between the electromagnetic generator and the biofilm media. The measured amount of the biofilm's biomass is approximately a factor two lower for exposed biofilm than the non-exposed biofilm. Measurements of electromagnetic fields in the air and simulations exhibit very low intensities of fields (<10nT and 2V/m) in the biofilm-exposed region at a distance of 1m from the electromagnetic generator. Exposure to electric and magnetic fields of the quoted intensities cannot explain thermal and ionizing effects on the biofilm. A variable electrical potential with a magnitude close to 20mV was detected in the tank in hydraulic continuity with the electromagnetic generator. The application of quantum field theory may help to explain the observed effects in this case. PMID:26150067

  17. The universe: a cryogenic habitat for microbial life.

    PubMed

    Wickramasinghe, Chandra

    2004-04-01

    Panspermia, an ancient idea, posits that microbial life is ubiquitous in the Universe. After several decades of almost irrational rejection, panspermia is at last coming to be regarded as a serious contender for the beginnings of life on our planet. Astronomical data is shown to be consistent with the widespread distribution of complex organic molecules and dust particles that may have a biological provenance. A minuscule (10(-21)) survival rate of freeze-dried bacteria in space is all that is needed to ensure the continual re-cycling of cosmic microbial life in the galaxy. Evidence that terrestrial life may have come from elsewhere in the solar system has accumulated over the past decade. Mars is seen by some as a possible source of terrestrial life, but some hundreds of billions of comets that enveloped the entire solar system, are a far more likely primordial reservoir of life. Comets would then have seeded Earth, Mars, and indeed all other habitable planetary bodies in the inner regions of the solar system. The implications of this point of view, which was developed in conjunction with the late Sir Fred Hoyle since the 1970s, are now becoming amenable to direct empirical test by studies of pristine organic material in the stratosphere. The ancient theory of panspermia may be on the verge of vindication, in which case the entire universe would be a grand crucible of cryomicrobiology. PMID:15094088

  18. Characterisation of the physical composition and microbial community structure of biofilms within a model full-scale drinking water distribution system.

    PubMed

    Fish, Katherine E; Collins, Richard; Green, Nicola H; Sharpe, Rebecca L; Douterelo, Isabel; Osborn, A Mark; Boxall, Joby B

    2015-01-01

    Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS. PMID:25706303

  19. Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

    PubMed Central

    Fish, Katherine E.; Collins, Richard; Green, Nicola H.; Sharpe, Rebecca L.; Douterelo, Isabel; Osborn, A. Mark; Boxall, Joby B.

    2015-01-01

    Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS. PMID:25706303

  20. Innovative biofilm inhibition and anti-microbial behavior of molybdenum sulfide nanostructures generated by microwave-assisted solvothermal route

    NASA Astrophysics Data System (ADS)

    Qureshi, Nilam; Patil, Rajendra; Shinde, Manish; Umarji, Govind; Causin, Valerio; Gade, Wasudev; Mulik, Uttam; Bhalerao, Anand; Amalnerkar, Dinesh P.

    2015-03-01

    The incessant use of antibiotics against infectious diseases has translated into a vicious circle of developing new antibiotic drug and its resistant strains in short period of time due to inherent nature of micro-organisms to alter their genes. Many researchers have been trying to formulate inorganic nanoparticles-based antiseptics that may be linked to broad-spectrum activity and far lower propensity to induce microbial resistance than antibiotics. The way-out approaches in this direction are nanomaterials based (1) bactericidal and (2) bacteriostatic activities. We, herein, present hitherto unreported observations on microbial abatement using non-cytotoxic molybdenum disulfide nanostructures (MSNs) which are synthesized using microwave assisted solvothermal route. Inhibition of biofilm formation using MSNs is a unique feature of our study. Furthermore, this study evinces antimicrobial mechanism of MSNs by reactive oxygen species (ROS) dependent generation of superoxide anion radical via disruption of cellular functions.

  1. Role of Fusobacterium nucleatum and Coaggregation in Anaerobe Survival in Planktonic and Biofilm Oral Microbial Communities during Aeration

    PubMed Central

    Bradshaw, David J.; Marsh, Philip D.; Watson, G. Keith; Allison, Clive

    1998-01-01

    Coaggregation is a well-characterized phenomenon by which specific pairs of oral bacteria interact physically. The aim of this study was to examine the patterns of coaggregation between obligately anaerobic and oxygen-tolerant species that coexist in a model oral microbial community. Obligate anaerobes other than Fusobacterium nucleatum coaggregated only poorly with oxygen-tolerant species. In contrast, F. nucleatum was able to coaggregate not only with both oxygen-tolerant and other obligately anaerobic species but also with otherwise-noncoaggregating obligate anaerobeoxygen-tolerant species pairs. The effects of the presence or absence of F. nucleatum on anaerobe survival in both the biofilm and planktonic phases of a complex community of oral bacteria grown in an aerated (gas phase, 200 ml of 5% CO2 in air min?1) chemostat system were then investigated. In the presence of F. nucleatum, anaerobes persisted in high numbers (>107 ml?1 in the planktonic phase and >107 cm?2 in 4-day biofilms). In an equivalent culture in the absence of F. nucleatum, the numbers of black-pigmented anaerobes (Porphyromonas gingivalis and Prevotella nigrescens) were significantly reduced (P ? 0.001) in both the planktonic phase and in 4-day biofilms, while the numbers of facultatively anaerobic bacteria increased in these communities. Coaggregation-mediated interactions between F. nucleatum and other species facilitated the survival of obligate anaerobes in aerated environments. PMID:9746571

  2. 3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface

    SciTech Connect

    Thomas, Mathew; Marshall, Matthew J.; Miller, Erin A.; Kuprat, Andrew P.; Kleese van Dam, Kerstin; Carson, James P.

    2014-08-26

    Understanding the interactions of structured communities known as biofilms and other complex matrixes is possible through the X-ray micro tomography imaging of the biofilms. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilms and bacteria in the datasets. The datasets are very large and often require manual interventions due to low contrast between objects and high noise levels. Thus new software is required for the effectual interpretation and analysis of the data. This work specifies the evolution and application of the ability to analyze and visualize high resolution X-ray micro tomography datasets.

  3. The involvement of rhamnolipids in microbial cell adhesion and biofilm development - an approach for control?

    PubMed

    Nickzad, A; Déziel, E

    2014-05-01

    Biofilms are omnipresent in clinical and industrial settings and most of the times cause detrimental side effects. Finding efficient strategies to control surface-growing communities of micro-organisms remains a significant challenge. Rhamnolipids are extracellular secondary metabolites with surface-active properties mainly produced by Pseudomonas aeruginosa. There is growing evidence for the implication of this biosurfactant in different stages of biofilm development of this bacterium. Furthermore, rhamnolipids display a significant potential as anti-adhesive and disrupting agents against established biofilms formed by several bacterial and fungal species. Their low toxicity, biodegradability, efficiency and specificity, compared to synthetic surfactants typically used in biofilm control, might compensate for the economic hurdle still linked to their superior production costs and make them promising antifouling agents. PMID:24372465

  4. Microbial biofilm detection on food contact surfaces by macro-scale fluorescence imaging

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral fluorescence imaging methods were utilized to evaluate the potential of multispectral fluorescence methods for detection of pathogenic biofilm formations on four types of food contact surface materials: stainless steel, high density polyethylene (HDPE) commonly used for cutting boards,...

  5. Inhibitory effects of Lactobacillus fermentum on microbial growth and biofilm formation.

    PubMed

    Rybalchenko, Oxana V; Bondarenko, Viktor M; Orlova, Olga G; Markov, Alexander G; Amasheh, S

    2015-10-01

    Beneficial effects of Lactobacilli have been reported, and lactic bacteria are employed for conservation of foods. Therefore, the effects of a Lactobacillus fermentum strain were analyzed regarding inhibitory effects on staphylococci, Candida albicans and enterotoxigenic enterobacteria by transmission electron microscopy (TEM). TEM of bacterial biofilms was performed using cocultures of bacteriocin-producing L. fermentum 97 with different enterotoxigenic strains: Staphylococcus epidermidis expressing the ica gene responsible for biofilm formation, Staphylococcus aureus producing enterotoxin type A, Citrobacter freundii, Enterobacter cloaceae, Klebsiella oxytoca, Proteus mirabilis producing thermolabile and thermostable enterotoxins determined by elt or est genes, and Candida albicans. L. fermentum 97 changed morphological features and suppressed biofilm formation of staphylococci, enterotoxigenic enterobacteria and Candida albicans; a marked transition to resting states, a degradation of the cell walls and cytoplasm, and a disruption of mature bacterial biofilms were observed, the latter indicating efficiency even in the phase of higher cell density. PMID:26267163

  6. Bidirectional microbial electron transfer: Switching an acetate oxidizing biofilm to nitrate reducing conditions.

    PubMed

    Pous, Narcs; Carmona-Martnez, Alessandro A; Vilajeliu-Pons, Anna; Fiset, Erika; Baeras, Lluis; Trably, Eric; Balaguer, M Dolors; Colprim, Jess; Bernet, Nicolas; Puig, Sebasti

    2016-01-15

    Up to date a few electroactive bacteria embedded in biofilms are described to catalyze both anodic and cathodic reactions in bioelectrochemical systems (i.e. bidirectional electron transfer). How these bacteria transfer electrons to or from the electrode is still uncertain. In this study the extracellular electron transfer mechanism of bacteria within an electroactive biofilm was investigated by using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). First, a mature anodic electroactive biofilm was developed from an activated sludge sample (inoculum), acetate as electron donor and a poised electrode (+397mV vs. SHE). Later, this biofilm was "switched" to biocathodic conditions by feeding it with a medium containing nitrates and poising the electrode at -303mV vs. SHE. The electrochemical characterization indicated that both, acetate oxidation and nitrate reduction took place at a similar formal potential of -17505 and -17534mV vs. SHE, respectively. The biofilm was predominantly composed by Geobacter sp. at both experimental conditions. Taken together, the results indicated that both processes could be catalyzed by using the same electron conduit, and most likely by the same bacterial consortium. Hence, this study suggests that electroactive bacteria within biofilms could use the same electron transfer conduit for catalyzing anodic and cathodic reactions. PMID:26339932

  7. Uranium removal and microbial community in a H2-based membrane biofilm reactor.

    PubMed

    Zhou, Chen; Ontiveros-Valencia, Aura; Cornette de Saint Cyr, Louis; Zevin, Alexander S; Carey, Sara E; Krajmalnik-Brown, Rosa; Rittmann, Bruce E

    2014-11-01

    We evaluated a hydrogen-based membrane biofilm reactor (MBfR) for its capacity to reduce and remove hexavalent uranium [U(VI)] from water. After a startup period that allowed slow-growing U(VI) reducers to form biofilms, the MBfR successfully achieved and maintained 94-95% U(VI) removal over 8 months when the U surface loading was 6-11e(-) mEq/m(2)-day. The MBfR biofilm was capable of self-recovery after a disturbance due to oxygen exposure. Nanocrystalline UO2 aggregates and amorphous U precipitates were associated with vegetative cells and apparently mature spores that accumulated in the biofilm matrix. Despite inoculation with a concentrated suspension of Desulfovibrio vulgaris, this bacterium was not present in the U(VI)-reducing biofilm. Instead, the most abundant group in the biofilm community contained U(VI) reducers in the Rhodocyclaceae family when U(VI) was the only electron acceptor. When sulfate was present, the community dramatically shifted to the Clostridiaceae family, which included spores that were potentially involved in U(VI) reduction. PMID:25073000

  8. 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.

  9. Microbial Community Structure and Physiological Status of Different Types of Biofilms in an Acid Mine Drainage Site Determined by Phospholipid Analysis

    NASA Astrophysics Data System (ADS)

    Fang, J.

    2009-12-01

    A unique aspect of the acid mine drainage (AMD) system at the Green Valley coal mine site (GVS) in western Indiana is the abundance of biofims and biolaminates - stromatolites. Three major types of biofilms have been observed from the AMD site: bright green biofilm dominated by the acidophilic, oxygenic photosynthetic protozoan Euglena mutabilis, olive green biofilm of photosynthetic diatom belonging to the genus Nitzschia, and an olive-green to brownish-green filamentous algae-dominated community. These biofilms are either attached to hard substrata of the effluent channel, or floating at the surface of the effluent with abundant oxygen bubbles, with or without encrusted Fe precipitates. We analyzed lipids (hydrocarbons, wax esters, phospholipids, glycolipids, and neutral lipids) to determine the microbial biomass, community structure and physiological status of biofims collected from the GVS site. Distinctive lipid compositions were observed. The attached, red-crusted biofilms were characterized by abundant wax esters, monounsaturated fatty acids, whereas the floating biofilms by phytadienes, phytanol, polyunsaturated n-alkenes, polyunsaturated fatty acids. The accumulation of abundant wax esters probably reflects the readily available carbon and limitation of nutrients to the biofilm. Alternatively, the wax esters may be the biochemical relics of the anaerobic past of the Earth and the detection of these compounds has important implications for the evolution of eukaryotes and the paleo-environmental conditions on early Earth. This type of biochemical machine may have allowed early eukaryotes to survive recurrent anoxic conditions on early Earth.

  10. Microsensor determination of multiple microbial processes in an oxygen-based membrane aerated biofilm.

    PubMed

    Tan, Shuying; Yu, Tong; Shi, Han-chang

    2014-01-01

    Microsensor techniques were used to investigate in situ the simultaneous occurrence of sulfate reduction and nitrogen removal in a membrane aerated biofilm reactor. H2S, O2, pH, ORP, NH4(+) and NO3(-) microsensors were fabricated and used to measure the profiles inside the membrane aerated biofilm. Production and consumption rates of H2S, O2, NH4(+) and NO3(-) were estimated using corresponding concentration profiles. The results showed that in anoxic zone, located from the interface between biofilm and bulk liquid to about 550 ?m below the interface, both sulfate reduction and denitrification occurred. Highest H2S production rates (around 0.27 mg L(-1)s(-1)) were found about 400 to 450 ?m below the interface. Below the anoxic zone, an aerobic zone was present. High H2S oxidation activity occurred at around 550-700 ?m below the interface. High oxygen consumption rates (0.34 mg L(-1)s(-1)) occurred at around 750-900 ?m below the interface. Nitrification activity occurred at about 500-650 ?m below the interface. Along the entire biofilm depth, pH changed slightly (within 0.2 unit). Near the interface of the aerobic and anoxic zone, there was a drastic redox potential change. These results demonstrated simultaneous sulfate reduction and nitrogen removal in a piece of membrane aerated biofilm. PMID:24622536

  11. Focus on the physics of biofilms

    NASA Astrophysics Data System (ADS)

    Lecuyer, Sigolene; Stocker, Roman; Rusconi, Roberto

    2015-03-01

    Bacteria are the smallest and most abundant form of life. They have traditionally been considered as primarily planktonic organisms, swimming or floating in a liquid medium, and this view has shaped many of the approaches to microbial processes, including for example the design of most antibiotics. However, over the last few decades it has become clear that many bacteria often adopt a sessile, surface-associated lifestyle, forming complex multicellular communities called biofilms. Bacterial biofilms are found in a vast range of environments and have major consequences on human health and industrial processes, from biofouling of surfaces to the spread of diseases. Although the study of biofilms has been biologists’ territory for a long time, a multitude of phenomena in the formation and development of biofilms hinges on physical processes. We are pleased to present a collection of research papers that discuss some of the latest developments in many of the areas to which physicists can contribute a deeper understanding of biofilms, both experimentally and theoretically. The topics covered range from the influence of physical environmental parameters on cell attachment and subsequent biofilm growth, to the use of local probes and imaging techniques to investigate biofilm structure, to the development of biofilms in complex environments and the modeling of colony morphogenesis. The results presented contribute to addressing some of the major challenges in microbiology today, including the prevention of surface contamination, the optimization of biofilm disruption methods and the effectiveness of antibiotic treatments.

  12. Method for recovery of intact DNA for community analysis of marine intertidal microbial biofilms.

    PubMed

    Narvez-Zapata, Jos A; Rodrguez-Avila, Norma; Ortega-Morales, Benjamn O

    2005-05-01

    A protocol is described for rapid DNA isolation from marine biofilm microorganisms embedded in large amounts of exopolysaccharides. The method is a modification of the hot phenol protocol used for plants tissues, where nonexpensive and easily available enzymes were used. The method is based on the incubation of biofilm biomass samples in an extraction buffer mixed with phenol preheated at 65 degrees C. The procedure can be completed in 2 h and up to 20 samples can be processed simultaneously with ease and DNA of excellent quality, as shown by successfully amplification of polymerase chain reaction (PCR) products. DNA was recovered from a range of intertidal marine biofilms with varying amounts of exopolysaccharides. PMID:15805576

  13. Biofilm-based central line-associated bloodstream infections.

    PubMed

    Yousif, Ammar; Jamal, Mohamed A; Raad, Issam

    2015-01-01

    Different types of central venous catheters (CVCs) have been used in clinical practice to improve the quality of life of chronically and critically ill patients. Unfortunately, indwelling devices are usually associated with microbial biofilms and eventually lead to catheter-related bloodstream infections (CLABSIs).An estimated 250,000-400,000 CLABSIs occur every year in the United States, at a rate of 1.5 per 1,000 CVC days and a mortality rate of 12-25 %. The annual cost of caring for patients with CLABSIs ranges from 296 million to 2.3 billion dollars.Biofilm formation occurs on biotic and abiotic surfaces in the clinical setting. Extensive studies have been conducted to understand biofilm formation, including different biofilm developmental stages, biofilm matrix compositions, quorum-sensing regulated biofilm formation, biofilm dispersal (and its clinical implications), and multi-species biofilms that are relevant to polymicrobial infections.When microbes form a matured biofilm within human hosts through medical devices such as CVCs, the infection becomes resistant to antibiotic treatment and can develop into a chronic condition. For that reason, many techniques have been used to prevent the formation of biofilm by targeting different stages of biofilm maturation. Other methods have been used to diagnose and treat established cases of CLABSI.Catheter removal is the conventional management of catheter associated bacteremia; however, the procedure itself carries a relatively high risk of mechanical complications. Salvaging the catheter can help to minimize these complications.In this article, we provide an overview of microbial biofilm formation; describe the involvement of various genetic determinants, adhesion proteins, organelles, mechanism(s) of biofilm formation, polymicrobial infections, and biofilm-associated infections on indwelling intravascular catheters; and describe the diagnosis, management, and prevention of catheter-related bloodstream infections. PMID:25366227

  14. How do changes in dissolved oxygen concentration influence microbially-controlled phosphorus cycling in stream biofilms?

    NASA Astrophysics Data System (ADS)

    Saia, S. M.; Locke, N. A.; Regan, J. M.; Carrick, H. J.; Buda, A. R.; Walter, M. T.

    2014-12-01

    Advances in molecular microbiology techniques (e.g. epi-fluorescent microscopy and PCR) are making it easier to study the influence of specific microorganisms on nutrient transport. Polyphosphate accumulating organisms (PAOs) are commonly used in wastewater treatment plants to remove excess phosphorus (P) from effluent water. PAOs have also been identified in natural settings but their ecological function is not well known. In this study, we tested the hypothesis that PAOs in natural environments would release and accumulate P during anaerobic and aerobic conditions, respectively. We placed stream biofilms in sealed, covered tubs and subjected them to alternating air (aerobic conditions) and N2 gas (anaerobic condition) bubbling for 12 hours each. Four treatments investigated the influence of changing dissolved oxygen on micribially-controlled P cycling: (1) biofilms bubbled continuously with air, (2) biofilms bubbled alternatively with air and N2, (3) biocide treated biofilms bubbled continuously with air, and (4) biocide treated biofilms bubbled alternatively with air and N2. Treatments 3 and 4 serve as abiotic controls to treatments 1 and 2. We analyzed samples every 12 hours for soluble reactive P (SRP), temperature, dissolved oxygen, and pH. We also used fluorescent microscopy (i.e. DAPI staining) and PCR to verify the presence of PAOs in the stream biofilms. SRP results over the course of the experiment support our hypothesis that anaerobic and aerobic stream conditions may impact PAO mediated P release and uptake, respectively in natural environments. The results of these experiments draw attention to the importance of microbiological controls on P mobility in freshwater ecosystems.

  15. ADAPTATION OF SUBSURFACE MICROBIAL BIOFILM COMMUNITIES IN RESPONSE TO CHEMICAL STRESSORS

    EPA Science Inventory

    The impact of this work will help improve our understanding of how subsurface biofilm communities respond to chemical stressors that are likely to be present at hazardous waste sites. Ultimately, these results can be used to determine more effective ways to insure proper envir...

  16. Microsensor Measurements of Sulfate Reduction and Sulfide Oxidation in Compact Microbial Communities of Aerobic Biofilms

    PubMed Central

    Kühl, Michael; Jørgensen, Bo Barker

    1992-01-01

    The microzonation of O2 respiration, H2S oxidation, and SO42- reduction in aerobic trickling-filter biofilms was studied by measuring concentration profiles at high spatial resolution (25 to 100 μm) with microsensors for O2, S2-, and pH. Specific reaction rates were calculated from measured concentration profiles by using a simple one-dimensional diffusion reaction model. The importance of electron acceptor and electron donor availability for the microzonation of respiratory processes and their reaction rates was investigated. Oxygen respiration was found in the upper 0.2 to 0.4 mm of the biofilm, whereas sulfate reduction occurred in deeper, anoxic parts of the biofilm. Sulfate reduction accounted for up to 50% of the total mineralization of organic carbon in the biofilms. All H2S produced from sulfate reduction was reoxidized by O2 in a narrow reaction zone, and no H2S escaped to the overlying water. Turnover times of H2S and O2 in the reaction zone were only a few seconds owing to rapid bacterial H2S oxidation. Anaerobic H2S oxidation with NO3- could be induced by addition of nitrate to the medium. Total sulfate reduction rates increased when the availability of SO42- or organic substrate increased as a result of deepening of the sulfate reduction zone or an increase in the sulfate reduction intensity, respectively. PMID:16348687

  17. Bovine mastitis disease/pathogenicity: evidence of the potential role of microbial biofilms.

    PubMed

    Gomes, Fernanda; Saavedra, Maria José; Henriques, Mariana

    2016-04-01

    Bovine mastitis (BM) is a disease with high incidence worldwide and one of the most relevant bovine pathologies and the most costly to the dairy industry. BM is an inflammation of the udder and represents one of the most difficult veterinary diseases to control. Biofilm formation is considered a selective advantage for pathogens causing mastitis, facilitating bacterial persistence in the udder. In fact, recently some authors drew attention to the biofilm formation ability presented by several mastitis causing pathogens and to its possible relation with recurrent mastitis infections and with the increased resistance to antimicrobial agents and host immune defence system. Actually, up to now, several researchers reported the potential role of cells in this mode of growth in the previous facts mentioned. As a consequence of the presence of biofilms, the infection here focused is more difficult to treat and eradicate, making this problem a more relevant pressing issue. Thus, we believe that a deeper knowledge of these structures in mastitis can help to determine the best control strategy to be used in veterinary practice in order to reduce losses in the dairy industry and to ensure milk safety and quality. The aim of this paper was to review the existing research and consequently to provide an overview of the role of biofilms in BM infections. PMID:26772653

  18. Stabilization of Plutonium in Subsursface Environments via Microbial Reduction and Biofilm Formation

    SciTech Connect

    Holden, Patricia

    2006-06-01

    Our work is towards mechanistically understanding interactions of unsaturated bacterial biofilms and their extracellular polymeric substances (EPS) with actinide metals and metal surrogates under vadose zone conditions. Because metal contaminants in the vadose zone co-occur with organic pollutants, some of our work has included experiments with organic pollutants.

  19. Stabilization of Plutonium in Subsursface Environments via Microbial Reduction and Biofilm Formation

    SciTech Connect

    Holden, Patricia; Neu, Mary P.

    2005-06-01

    Our work is towards mechanistically understanding interactions of unsaturated bacterial biofilms and their extracellular polymeric substances (EPS) with actinide metals and metal surrogates under vadose zone conditions. Because metal contaminants in the vadose zone co-occur with organic pollutants, some of our work has included experiments with organic pollutants.

  20. Detection of microbial biofilms on food processing surfaces: Hyperspectral fluorescence imaging study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We used a portable hyperspectral fluorescence imaging system to evaluate biofilm formations on four types of food processing surface materials including stainless steel, polypropylene used for cutting boards, and household counter top materials such as formica and granite. The objective of this inve...

  1. Effect of different disinfection protocols on microbial and biofilm contamination of dental unit waterlines in community dental practices.

    PubMed

    Dallolio, Laura; Scuderi, Amalia; Rini, Maria S; Valente, Sabrina; Farruggia, Patrizia; Sabattini, Maria A Bucci; Pasquinelli, Gianandrea; Acacci, Anna; Roncarati, Greta; Leoni, Erica

    2014-02-01

    Output water from dental unit waterlines (DUWLs) may be a potential source of infection for both dental healthcare staff and patients. This study compared the efficacy of different disinfection methods with regard to the water quality and the presence of biofilm in DUWLs. Five dental units operating in a public dental health care setting were selected. The control dental unit had no disinfection system; two were disinfected intermittently with peracetic acid/hydrogen peroxide 0.26% and two underwent continuous disinfection with hydrogen peroxide/silver ions (0.02%) and stabilized chlorine dioxide (0.22%), respectively. After three months of applying the disinfection protocols, continuous disinfection systems were more effective than intermittent systems in reducing the microbial contamination of the water, allowing compliance with the CDC guidelines and the European Council regulatory thresholds for drinking water. P. aeruginosa, Legionella spp, sulphite-reducing Clostridium spores, S. aureus and β-haemolytic streptococci were also absent from units treated with continuous disinfection. The biofilm covering the DUWLs was more extensive, thicker and more friable in the intermittent disinfection dental units than in those with continuous disinfection. Overall, the findings showed that the products used for continuous disinfection of dental unit waterlines showed statistically better results than the intermittent treatment products under the study conditions. PMID:24552789

  2. Effect of Different Disinfection Protocols on Microbial and Biofilm Contamination of Dental Unit Waterlines in Community Dental Practices

    PubMed Central

    Dallolio, Laura; Scuderi, Amalia; Rini, Maria S.; Valente, Sabrina; Farruggia, Patrizia; Bucci Sabattini, Maria A.; Pasquinelli, Gianandrea; Acacci, Anna; Roncarati, Greta; Leoni, Erica

    2014-01-01

    Output water from dental unit waterlines (DUWLs) may be a potential source of infection for both dental healthcare staff and patients. This study compared the efficacy of different disinfection methods with regard to the water quality and the presence of biofilm in DUWLs. Five dental units operating in a public dental health care setting were selected. The control dental unit had no disinfection system; two were disinfected intermittently with peracetic acid/hydrogen peroxide 0.26% and two underwent continuous disinfection with hydrogen peroxide/silver ions (0.02%) and stabilized chlorine dioxide (0.22%), respectively. After three months of applying the disinfection protocols, continuous disinfection systems were more effective than intermittent systems in reducing the microbial contamination of the water, allowing compliance with the CDC guidelines and the European Council regulatory thresholds for drinking water. P. aeruginosa, Legionella spp, sulphite-reducing Clostridium spores, S. aureus and β-haemolytic streptococci were also absent from units treated with continuous disinfection. The biofilm covering the DUWLs was more extensive, thicker and more friable in the intermittent disinfection dental units than in those with continuous disinfection. Overall, the findings showed that the products used for continuous disinfection of dental unit waterlines showed statistically better results than the intermittent treatment products under the study conditions. PMID:24552789

  3. Electrochemical response of a biofilm community to changes in electron-acceptor redox potential elucidated using microbial fuel cells

    NASA Astrophysics Data System (ADS)

    Arbour, T.; Wrighton, K. C.; Mullin, S. W.; Luef, B.; Gilbert, B.; Banfield, J. F.

    2012-12-01

    Currently, we have limited insight into how mineral properties affect dissimilatory metal-reducing bacteria (DMRB) or the microbial communities that contain them. Advances in our understanding of DMRB metabolism have been achieved using microbial fuel cells (MFCs), which exploit the ability of these organisms to transfer electrons extracellularly. By replacing the mineral electron acceptor with a conductive electrode under potentiostat control, the activity of microorganisms capable of interfacial electron transfer can be quantified by the current flowing through the electrode and related to the thermodynamics of respiration. We seek to understand how communities and their individual members respond to changes in mineralogy, and expect mineral redox potential to be a primary control. The ability to precisely control the redox potential of the electron-accepting anodic electrode is our primary motivation for using MFCs. We inoculated duplicate MFCs containing 10 mM acetate in phosphate buffered media with a slurry of subsurface sediment and groundwater obtained from the Integrated Field-Scale Research Challenge Site at Rifle, CO. Electroactive biofilms were established on graphite anodes poised at a favorable potential (0.0 V vs. SHE) before poising at -0.2 V—a potential representative of natural iron reduction. The current was stable across both anodes over more than 100 days of operation, and the percentage of the electrons in acetate recovered as current ("Coulombic efficiency") was typically 70 to >90%. Current density reached 0.4 A/m2 at -0.2 V, to a max of over 1.0 A/m2 at or above ~0.0 V (based on geometric electrode surface area). Media exchanges and biofilm cyclic voltammetry (CV) experiments indicate that electrode-attached microbial communities were responsible for primary electron transfer. Cryo-electron and confocal fluorescence microscopies of the biofilm reveal numerous morphologies of viable microorganisms that are currently being characterized using 16S rRNA gene clone library analysis. We studied how the microbial activity changed when the anode potential was varied. Altering the anode potential caused reversible changes in the mid-point potential(s), Em, measured using CV. Qualitatively, the average Em always shifted toward the set anode potential. A maximum shift in the peak of the derivative CV spectra of ~100 mV defines the approximate upper and lower Em values for the proteins contributing to this feature. The change in the electrochemical response was complete ~30 minutes after a 400 mV anode-potential step. We attribute these observations to either a switch in the principle electron-transport pathway (different enzymes) that individual species use to deliver electrons to the anode or changes in the relative contributions of different community members, or both. However, some impact of changes in pH within the biofilm could contribute to the change in Em. Ongoing investigations attempt to resolve these possibilities.

  4. Under the sea: microbial life in volcanic oceanic crust.

    PubMed

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

    2011-10-01

    Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust. PMID:21894169

  5. Determination of the van der Waals, electron donor and electron acceptor surface tension components of static Gram-positive microbial biofilms.

    PubMed

    Briandet, R; Herry, J -M.; Bellon-Fontaine, M -N.

    2001-08-01

    A large number of studies have shown the influence of the physico-chemical properties of a surface on microbial adhesion phenomenon. In this study, we considered that the presence of a bacterial biofilm may be regarded as a "conditioning film" that may modify the physico-chemical characteristics of the support, and thus the adhesion capability of planktonic micro-organisms coming into contact with this substratum. In this context, we adapted a protocol for biofilm formation that allows, under our experimental conditions, contact angle measurements, the reference method to determine the energetic surface properties of a substratum. This made it possible to determine the van der Waals, electron acceptor and electron donor properties of static biofilms grown at 25 degrees C on stainless-steel slides with six Gram-positive bacteria isolated in dairy plants. A variance analysis indicated significant effects (P<0.05) of the bacterial strains and of the physiological state of the micro-organisms (planktonic or sessile) on the contact angles. To link the energetic properties of the six biofilms with direct adhesion experiments, we measured the affinity of fluorescent carboxylate-modified polystyrene beads for the different biofilm surfaces. The results correlated best with the electron-acceptor components of the biofilm surface energies, stressing the importance of Lewis acid-base interactions in adhesion mechanisms. PMID:11397632

  6. Microbial diversities (16S and 18S rDNA gene pyrosequencing) and environmental pathogens within drinking water biofilms grown on the common premise plumbing materials unplasticized polyvinylchloride and copper

    EPA Science Inventory

    Drinking water (DW) biofilm communities influence the survival of opportunistic pathogens, e.g. Legionella pneumophila, via parasitization of free-living amoebae such as Acanthamoebae. Yet knowledge about the microbial composition of DW biofilms developed on common in-premise pl...

  7. Psychrophiles and astrobiology: microbial life of frozen worlds

    NASA Astrophysics Data System (ADS)

    Pikuta, Elena V.; Hoover, Richard B.

    2003-01-01

    Most bodies of our Solar System are "Frozen Worlds" where the prevailing surface temperature remains at or below freezing. On Earth there are vast permanently frozen regions of permafrost, polar ice sheets, and glaciers and the deep oceans and deep-sea marine sediments have remained at 2 - 4°C for eons. Psychrophilic and psychrotrophic microbiota that inhabit these regimes provide analogs for microbial life that might inhabit ice sheets and permafrost of Mars, comets, or the ice/water interfaces or sediments deep beneath the icy crusts of Europa, Callisto, or Ganymede. Cryopreserved micro-organisms can remain viable (in a deep anabiotic state) for millions of years frozen in permafrost and ice. Psychrophilic and psychrotrophic (cold-loving) microbes can carry out metabolic processes in water films and brine, acidic, or alkaline chanels in permafrost or ice at temperatures far below 0°C. These microbes of the cryosphere help define the thermal and temporal limits of life on Earth and may provide clues to where and how to search for evidence of life elsewhere in the Cosmos. Astrobiologists at the NASA Marshall Space Flight Center have collected microbial extremophiles from the Pleistocene ice wedges and frozen thermokarst ponds from the Fox Permafrost Tunnel of Alaska. Microbes have also been isolated from samples of Magellanic Penguin guano from Patagonia; deep-sea marine muds near hydrothermal vents; snow and permafrost from Siberia, and deep ice cores, ice-bubble and cryoconite rocks of the Central Antarctic Ice Sheet. These samples have yielded microbial extremophiles representing a wide variety of anaerobic bacteria and archaea. These microbes have been isolated, cultured, characterized and analyzed by phylogenetic and genomic methods. Images were obtained by Phase Contrast, Environmental, Field Emission Scanning and Transmission Electron Microscopes to study the ultra-microstructure and elemental distribution in the composition of these micro-organisms. We consider the Astrobiological significance of the Fox Tunnel with its rich assemblage of frozen microbes as proxy for developing techniques that may help optimize the search for evidence of life in the permafrost of Mars. We provide images of a novel anaerobic, heterotrophic, psychrotrophic bacterium (str.FTR1) isolated in pure culture from the Fox Tunnel. We also describe novel psychrotrophs isolated from guano of the Magellanic penguin (Spheniscus magellanicus) from the southern tip of Patagonia. These strains PmagG1 and PPP2) represent new species and genera of anaerobic microbes that grow at very low temperatures. The lowest limit for growth without morphological changes of str.PmagG1 is -4°C.

  8. The pulsed light inactivation of veterinary relevant microbial biofilms and the use of a RTPCR assay to detect parasite species within biofilm structures.

    PubMed

    Garvey, M; Coughlan, G; Murphy, N; Rowan, N

    2016-01-01

    The presence of pathogenic organisms namely parasite species and bacteria in biofilms in veterinary settings, is a public health concern in relation to human and animal exposure. Veterinary clinics represent a significant risk factor for the transfer of pathogens from housed animals to humans, especially in cases of wound infection and the shedding of faecal matter. This study aims to provide a means of detecting veterinary relevant parasite species in bacterial biofilms, and to provide a means of disinfecting these biofilms. A real time PCR assay was utilized to detect parasite DNA in Bacillus cereus biofilms on stainless steel and PVC surfaces. Results show that both Cryptosporidium and Giardia attach to biofilms in large numbers (100-1000 oo/cysts) in as little as 72 hours. Pulsed light successfully inactivated all test species (Listeria, Salmonella, Bacillus, Escherichia) in planktonic and biofilm form with an increase in inactivation for every increase in UV dose. PMID:26862516

  9. The pulsed light inactivation of veterinary relevant microbial biofilms and the use of a RTPCR assay to detect parasite species within biofilm structures

    PubMed Central

    Garvey, M.; Coughlan, G.; Murphy, N.; Rowan, N.

    2016-01-01

    The presence of pathogenic organisms namely parasite species and bacteria in biofilms in veterinary settings, is a public health concern in relation to human and animal exposure. Veterinary clinics represent a significant risk factor for the transfer of pathogens from housed animals to humans, especially in cases of wound infection and the shedding of faecal matter. This study aims to provide a means of detecting veterinary relevant parasite species in bacterial biofilms, and to provide a means of disinfecting these biofilms. A real time PCR assay was utilized to detect parasite DNA in Bacillus cereus biofilms on stainless steel and PVC surfaces. Results show that both Cryptosporidium and Giardia attach to biofilms in large numbers (100-1000 oo/cysts) in as little as 72 hours. Pulsed light successfully inactivated all test species (Listeria, Salmonella, Bacillus, Escherichia) in planktonic and biofilm form with an increase in inactivation for every increase in UV dose. PMID:26862516

  10. Composition of Microbial Oral Biofilms during Maturation in Young Healthy Adults

    PubMed Central

    Langfeldt, Daniela; Neulinger, Sven C.; Heuer, Wieland; Staufenbiel, Ingmar; Künzel, Sven; Baines, John F.; Eberhard, Jörg; Schmitz, Ruth A.

    2014-01-01

    In the present study we aimed to analyze the bacterial community structure of oral biofilms at different maturation stages in young healthy adults. Oral biofilms established on membrane filters were collected from 32 human subjects after 5 different maturation intervals (1, 3, 5, 9 and 14 days) and the respective phylogenetic diversity was analyzed by 16S rDNA amplicon sequencing. Our analyses revealed highly diverse entire colonization profiles, spread into 8 phyla/candidate divisions and in 15 different bacterial classes. A large inter-individual difference in the subjects’ microbiota was observed, comprising 35% of the total variance, but lacking conspicuous general temporal trends in both alpha and beta diversity. We further obtained strong evidence that subjects can be categorized into three clusters based on three differently occurring and mutually exclusive species clusters. PMID:24503584

  11. Early microbial succession in re-developing dental biofilms in periodontal health and disease

    PubMed Central

    TELES, F.R.; TELES, R.P.; UZEL, N.G.; SONG, X.Q.; TORRESYAP, G.; SOCRANSKY, S.S.; HAFFAJEE, A.D.

    2011-01-01

    Objective To determine the order of bacterial species succession in re-developing supra and subgingival biofilms. Methods Supra and subgingival plaque samples were taken separately from 28 teeth in 38 healthy and 17 periodontitis subjects immediately after professional cleaning. Samples were taken again from 7 teeth in randomly selected quadrants after 1, 2, 4 and 7 days of no oral hygiene and analyzed using checkerboard DNA-DNA hybridization. % DNA probe counts were averaged within subjects at each time point. Ecological succession was determined using a modified moving window analysis. Results Succession in supragingival biofilms from periodontitis and health was similar. At 1 day, Streptococcus mitis and Neisseria mucosa showed increased proportions, followed by Capnocytophaga gingivalis, Eikenella corrodens, Veillonella parvula and Streptococcus oralis at 14 days. At 47 days, Campylobacter rectus, Campylobacter showae, Prevotella melaninogenica and Prevotella nigrescens became elevated. Subgingival plaque redevelopment was slower and very different from supragingival. Increased proportions were first observed for S. mitis, followed by V. parvula and C. gingivalis and, at 7 days by Capnocytophaga sputigena and P. nigrescens. No significant increase in proportions of periodontal pathogens was observed in any of the clinical groups or locations. Conclusions There is a defined order in bacterial species succession in early supra and subgingival biofilm re-development after professional cleaning. PMID:21895662

  12. Biophysics of Biofilm Infection

    PubMed Central

    Stewart, Philip S.

    2014-01-01

    This article examines a likely basis of the tenacity of biofilm infections that has received relatively little attention: the resistance of biofilms to mechanical clearance. One way that a biofilm infection persists is by withstanding the flow of fluid or other mechanical forces that work to wash or sweep microorganisms out of the body. The fundamental criterion for mechanical persistence is that the biofilm failure strength exceeds the external applied stress. Mechanical failure of the biofilm and release of planktonic microbial cells is also important in vivo because it can result in dissemination of infection. The fundamental criterion for detachment and dissemination is that the applied stress exceeds the biofilm failure strength. The apparent contradiction for a biofilm to both persist and disseminate is resolved by recognizing that biofilm material properties are inherently heterogeneous. There are also mechanical aspects to the ways that infectious biofilms evade leukocyte phagocytosis. The possibility of alternative therapies for treating biofilm infections that work by reducing biofilm cohesion could: 1) allow prevailing hydrodynamic shear to remove biofilm, 2) increase the efficacy of designed interventions for removing biofilms, 3) enable phagocytic engulfment of softened biofilm aggregates, and 4) improve phagocyte mobility and access to biofilm. PMID:24376149

  13. Effects of packing rates of cubic-shaped polyurethane foam carriers on the microbial community and the removal of organics and nitrogen in moving bed biofilm reactors.

    PubMed

    Feng, Quan; Wang, Yuxiao; Wang, Tianmin; Zheng, Hao; Chu, Libing; Zhang, Chong; Chen, Hongzhang; Kong, Xiuqin; Xing, Xin-Hui

    2012-08-01

    The effects of packing rates (20%, 30%, and 40%) of polyurethane foam (PUF) to the removal of organics and nitrogen were investigated by continuously feeding artificial sewage in three aerobic moving bed biofilm reactors. The results indicated that the packing rate of the PUF carriers had little influence on the COD removal efficiency (81% on average). However, ammonium removal was affected by the packing rates, which was presumably due to the different relative abundances of nitrifying bacteria. A high ammonium removal efficiency of 96.3% at a hydraulic retention time of 5h was achieved in 40% packing rate reactor, compared with 37.4% in 20% packing rate. Microprofiles of dissolved oxygen and nitrate revealed that dense biofilm limits the DO transfer distance and nitrate diffusion. Pyrosequencing analysis of the biofilm showed that Proteobacteria, Bacteroidetes and Verrucomicrobia were the three most abundant phyla, but the proportions of the microbial community varied with the packing rate of the PUF carriers. PMID:22621807

  14. Biogeochemical signals from deep microbial life in terrestrial crust.

    PubMed

    Suzuki, Yohey; Konno, Uta; Fukuda, Akari; Komatsu, Daisuke D; Hirota, Akinari; Watanabe, Katsuaki; Togo, Yoko; Morikawa, Noritoshi; Hagiwara, Hiroki; Aosai, Daisuke; Iwatsuki, Teruki; Tsunogai, Urumu; Nagao, Seiya; Ito, Kazumasa; Mizuno, Takashi

    2014-01-01

    In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20-60 diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30) is not indicative of methanogenesis. Except for 2011, the concentrations of H2 ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived 3He relative to radiogenic 4He in groundwater and the flux of H2 along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 M), H2 from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes. PMID:25517230

  15. Biogeochemical Signals from Deep Microbial Life in Terrestrial Crust

    PubMed Central

    Fukuda, Akari; Komatsu, Daisuke D.; Hirota, Akinari; Watanabe, Katsuaki; Togo, Yoko; Morikawa, Noritoshi; Hagiwara, Hiroki; Aosai, Daisuke; Iwatsuki, Teruki; Tsunogai, Urumu; Nagao, Seiya; Ito, Kazumasa; Mizuno, Takashi

    2014-01-01

    In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20–60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30‰) is not indicative of methanogenesis. Except for 2011, the concentrations of H2 ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived 3He relative to radiogenic 4He in groundwater and the flux of H2 along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 µM), H2 from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes. PMID:25517230

  16. Exploration of deep intraterrestrial microbial life: current perspectives.

    PubMed

    Pedersen, K

    2000-04-01

    Intraterrestrial life has been found at depths of several thousand metres in deep sub-sea floor sediments and in the basement crust beneath the sediments. It has also been found at up to 2800-m depth in continental sedimentary rocks, 5300-m depth in igneous rock aquifers and in fluid inclusions in ancient salt deposits from salt mines. The biomass of these intraterrestrial organisms may be equal to the total weight of all marine and terrestrial plants. The intraterrestrial microbes generally seem to be active at very low but significant rates and several investigations indicate chemolithoautotrophs to form a chemosynthetic base. Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of our planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems. Several prospective research areas are foreseen to focus on the importance of microbial communities for metabolic processes such as anaerobic utilisation of hydrocarbons and anaerobic methane oxidation. PMID:10731600

  17. Microbial mats and the early evolution of life

    NASA Technical Reports Server (NTRS)

    Des Marais, D. J.

    1990-01-01

    Microbial mats have descended from perhaps the oldest and most widespread biological communities known. Mats harbor microbes that are crucial for studies of bacterial phylogeny and physiology. They illustrate how several oxygen-sensitive biochemical processes have adapted to oxygen, and they show how life adapted to dry land long before the rise of plants. The search for the earliest grazing protists and metazoa in stromatolites is aided by observations of mats: in them, organic compounds characteristic of ancient photosynthetic protists can be identified. Recent mat studies suggest that the 13C/12C increase observed over geological time in stromatolitic organic matter was driven at least in part by a long-term decline in atmospheric carbon dioxide levels.

  18. Reproducible analyses of microbial food for advanced life support systems.

    PubMed

    Petersen, G R

    1988-10-01

    The use of yeasts in Controlled Ecological Life Support Systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely applicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed. PMID:11541295

  19. Reproducible analyses of microbial food for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Petersen, Gene R.

    1988-01-01

    The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

  20. Three-dimensional X-ray microcomputed tomography of carbonates and biofilm on operated cathode in single chamber microbial fuel cell.

    PubMed

    Santini, Maurizio; Guilizzoni, Manfredo; Lorenzi, Massimo; Atanassov, Plamen; Marsili, Enrico; Fest-Santini, Stephanie; Cristiani, Pierangela; Santoro, Carlo

    2015-01-01

    Power output limitation is one of the main concerns that need to be addressed for full-scale applications of the microbial fuel cell technology. Fouling and biofilm growth on the cathode of single chamber microbial fuel cells (SCMFC) affects their performance in long-term operation with wastewater. In this study, the authors report the power output and cathode polarization curves of a membraneless SCMFC, fed with raw primary wastewater and sodium acetate for over 6 months. At the end of the experiment, the whole cathode surface is analyzed through X-ray microcomputed tomography (microCT), scanning electron microscopy, and energy-dispersive X-ray spectroscopy (EDX) to characterize the fouling layer and the biofilm. EDX shows the distribution of Ca, Na, K, P, S, and other elements on the two faces of the cathode. Na-carbonates and Ca-carbonates are predominant on the air (outer) side and the water (inner) side, respectively. The three-dimensional reconstruction by X-ray microCT shows biofilm spots unevenly distributed above the Ca-carbonate layer on the inner (water) side of the cathode. These results indicate that carbonates layer, rather than biofilm, might lower the oxygen reduction reaction rate at the cathode during long-term SCMFC operation. PMID:26357848

  1. Microbial Life in an Underground Gas Storage Reservoir

    NASA Astrophysics Data System (ADS)

    Bombach, Petra; van Almsick, Tobias; Richnow, Hans H.; Zenner, Matthias; Krüger, Martin

    2015-04-01

    While underground gas storage is technically well established for decades, the presence and activity of microorganisms in underground gas reservoirs have still hardly been explored today. Microbial life in underground gas reservoirs is controlled by moderate to high temperatures, elevated pressures, the availability of essential inorganic nutrients, and the availability of appropriate chemical energy sources. Microbial activity may affect the geochemical conditions and the gas composition in an underground reservoir by selective removal of anorganic and organic components from the stored gas and the formation water as well as by generation of metabolic products. From an economic point of view, microbial activities can lead to a loss of stored gas accompanied by a pressure decline in the reservoir, damage of technical equipment by biocorrosion, clogging processes through precipitates and biomass accumulation, and reservoir souring due to a deterioration of the gas quality. We present here results from molecular and cultivation-based methods to characterize microbial communities inhabiting a porous rock gas storage reservoir located in Southern Germany. Four reservoir water samples were obtained from three different geological horizons characterized by an ambient reservoir temperature of about 45 °C and an ambient reservoir pressure of about 92 bar at the time of sampling. A complementary water sample was taken at a water production well completed in a respective horizon but located outside the gas storage reservoir. Microbial community analysis by Illumina Sequencing of bacterial and archaeal 16S rRNA genes indicated the presence of phylogenetically diverse microbial communities of high compositional heterogeneity. In three out of four samples originating from the reservoir, the majority of bacterial sequences affiliated with members of the genera Eubacterium, Acetobacterium and Sporobacterium within Clostridiales, known for their fermenting capabilities. In contrast, bacteria belonging to Enterobacteriaceae were the most frequently encountered species in the sample from the water production well. Furthermore, bacterial sequences belonging to thermophiles within the family Thermotogaceae were found in all samples investigated. Archaeal community analysis revealed the dominance of methanogens clustering with members of Methanosarcinaceae, Methanomicrobiaceae and Methanobacteriaceae in three reservoir samples and the sample from the water production well. Cultivations of water samples under an atmosphere of storage gas blended by hydrogen as electron source at in situ-like conditions (45°C, 92 bar, p(H2) = 6 bar) revealed that hydrogen was quickly consumed in all laboratory microcosms with reservoir samples. Quantitative PCR analysis of the gene encoding for methyl-coenzyme M reductase (mcrA) along with reaction educt and product analyses suggested that methanogenesis was primarily responsible for hydrogen consumption during the experiments. While it is currently in question whether or not the laboratory data can be upscaled to actual reservoir conditions, they may allude to fermenting and thermophilic bacteria playing an important role for the investigated reservoir microbiology and also indicate potential stimulation of hydrogenotrophic methanogens if hydrogen would be introduced into the reservoir.

  2. Quantification and characterization of microbial biofilm community attached on the surface of fermentation vessels used in green table olive processing.

    PubMed

    Grounta, Athena; Doulgeraki, Agapi I; Panagou, Efstathios Z

    2015-06-16

    The aim of the present study was the quantification of biofilm formed on the surface of plastic vessels used in Spanish-style green olive fermentation and the characterization of the biofilm community by means of molecular fingerprinting. Fermentation vessels previously used in green olive processing were subjected to sampling at three different locations, two on the side and one on the bottom of the vessel. Prior to sampling, two cleaning treatments were applied to the containers, including (a) washing with hot tap water (60 °C) and household detergent (treatment A) and (b) washing with hot tap water, household detergent and bleach (treatment B). Population (expressed as log CFU/cm(2)) of total viable counts (TVC), lactic acid bacteria (LAB) and yeasts were enumerated by standard plating. Bulk cells (whole colonies) from agar plates were isolated for further characterization by PCR-DGGE. Results showed that regardless of the cleaning treatment no significant differences were observed between the different sampling locations in the vessel. The initial microbial population before cleaning ranged between 3.0-4.5 log CFU/cm(2) for LAB and 4.0-4.6 log CFU/cm(2) for yeasts. Cleaning treatments exhibited the highest effect on LAB that were recovered at 1.5 log CFU/cm(2) after treatment A and 0.2 log CFU/cm(2) after treatment B, whereas yeasts were recovered at approximately 1.9 log CFU/cm(2) even after treatment B. High diversity of yeasts was observed between the different treatments and sampling spots. The most abundant species recovered belonged to Candida genus, while Wickerhamomyces anomalus, Debaryomyces hansenii and Pichia guilliermondii were frequently detected. Among LAB, Lactobacillus pentosus was the most abundant species present on the abiotic surface of the vessels. PMID:25770432

  3. 1,5-Anhydro-D-fructose: A natural antibiotic that inhibits the growth of gram-positive bacteria and microbial biofilm formation to prevent nosocomial infection

    PubMed Central

    MENG, XIAOJIE; KAWAHARA, KO-ICHI; MIYANOHARA, HIROAKI; YOSHIMOTO, YASUSHI; YOSHINAGA, KAZUHIRO; NOMA, SATOSHI; KIKUCHI, KIYOSHI; MORIMOTO, YOKO; ITO, TAKASHI; OYAMA, YOKO; YOSHINAGA, NARIMASA; SHRESTHA, BINITA; CHANDAN, BINITA; MERA, KENTARO; TADA, KO-ICHI; MIURA, NAOKI; ONO, YOSHIKO; TAKENOUCHI, KAZUNORI; MAENOSONO, RYUICHI; NAGASATO, TOMOKA; HASHIGUCHI, TERUTO; MARUYAMA, IKURO

    2011-01-01

    Nosocomial infections caused by microbial opportunistic infections or microbial biofilms may occur during hospitalization and increase patient morbidity, mortality and health care costs. Artificial antibiotic agents were initially used to prevent infection; however, the high prevalence of nosocomial infections has resulted in their excessive use, which has led to microbial resistance to these agents. The increase in microbial resistance to antibiotics and the development of antibiotic agents may be the cause of the production of other microbial resistance. Thus, natural compounds that have no adverse side effects would be a preferred treatment modality. Recently, the monosaccharide 1,5-anhydro-D-fructose (1,5-AF), a natural plant compound derived from starch, has been found to have multifunctional properties, including antioxidant, antiplatelet aggregation by thrombin and anti-inflammatory activities. The results of the present study demonstrate that 1,5-AF suppressed the growth of coagulase-negative staphylococci on the hands as well as the growth of Staphylococcus epidermidis, which is a cause of opportunistic infections. Furthermore, 1,5-AF suppressed biofilm formation by the methicillin-resistant Staphylococcus aureus. In conclusion, 1,5-AF is a natural compound that may be effective in preventing nosocomial infections, without causing adverse side effects. PMID:22977551

  4. High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.

    PubMed

    Rosewarne, Carly P; Pope, Phillip B; Denman, Stuart E; McSweeney, Christopher S; O'Cuiv, Paraic; Morrison, Mark

    2011-02-01

    Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions. PMID:20838785

  5. Effects of nitrate treatment on a mixed species, oil field microbial biofilm.

    PubMed

    Dunsmore, Braden; Youldon, James; Thrasher, David R; Vance, Ian

    2006-06-01

    Biofilms of bacteria, indigenous to oil field produced water, were grown in square section, glass capillary flow cells at 45 degrees C. Initially, in situ image analysis microscopy revealed predominantly coccoid bacteria (length-to-width ratio measurements (l (c):w (c)) of bacterial cells gave a mean value of 1.1), while chemical measurements confirmed sulphate reduction and sulphide production. After nitrate ion addition at 100 and 80 mg/l, in the two repeat experiments respectively, the dominance of rod-shaped bacteria (mean l (c):w (c) = 2.8) was observed. This coincided with the occurrence of nitrate reduction in the treated flow cells. Beneficially, no significant increase in biofilm cover was observed after the addition of nitrate. The dominant culturable nitrate-reducing bacterium was Marinobacter aquaeolei. The l (c):w (c) ratio measured here concurs with previously reported cell dimensions for this organism. Several Marinobacter strains were also isolated from different oil fields in the North Sea where nitrate treatment has been applied to successfully treat reservoir souring, implying that this genus may play an important role in nitrate treatment. PMID:16491355

  6. Comparison of microbial community assays for the assessment of stream biofilm ecology.

    PubMed

    Vinten, A J A; Artz, R R E; Thomas, N; Potts, J M; Avery, L; Langan, S J; Watson, H; Cook, Y; Taylor, C; Abel, C; Reid, E; Singh, B K

    2011-06-01

    We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6?g/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577?g/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a "high impact" control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4weeks deployment in a low flow period of early summer 2006. The chlorophyll a content of biofilms after 4weeks was 2.00.29mg/m(2) (meanse). Dry matter content was 16.013.1g/m(2). The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP() assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20min, PLFA 40min, TDI 90min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP() showed significant differences between sites, but none of the assays showed a significant effect of either initial stream trophic status (as classified by the EU Water Framework Directive using chemical standards for soluble P), or of the diffusing solute treatment. Multiple Procrustes analysis on the ordination results showed that the diatom and M-TRFLP data sets hold distinct, though as yet unexplored, information about the ecological factors affecting stream biofilms. The diatom data were subjected to principal components analysis, to identify which taxa were more strongly influenced by site variables, trophic status or treatment effects. These were Acnanthes lanceolata, A. minutissimma, Nitzchia spp., Coccineis spp. and Navicula spp. Further experimentation and data analysis on a larger number of sites, to identify specific M-TRFLP bands that could be used as indicators linked to specific taxa, are desirable. Results highlight the need for a multifactorial approach to understanding controls on stream ecology. PMID:21414363

  7. Influence of Disinfectant Residual on Biofilm Development, Microbial Ecology, and Pathogen Fate and Transport in Drinking Water Infrastructure

    EPA Science Inventory

    This project focuses on providing basic data to bound risk estimates resulting from pathogens associated with pipe biofilms. Researchers will compare biofilm pathogen effects under two different disinfection scenarios (free chlorine or chloramines) for a conventionally treated s...

  8. Photoautotrophic-heterotrophic biofilm communities: a laboratory incubator designed for growing axenic diatoms and bacteria in defined mixed-species biofilms.

    PubMed

    Buhmann, Matthias; Kroth, Peter G; Schleheck, David

    2012-02-01

    Biofilm communities in the euphotic zone of aquatic habitats comprise photoautotrophic microorganisms, such as diatoms, green algae and cyanobacteria, which produce the organic carbon that fuels the life of a heterotrophic contingent of microorganisms, mostly bacteria. Such photoautotrophic-heterotrophic mixed-species biofilms have received little attention in biofilm research due to a lack of suitable pure-culture laboratory model systems. However, they offer important insight into microbial population dynamics and community interactions during a biofilm-developmental process that shapes highly structured, extremely well-adapted microbial landscapes. Here, we report on the development of a sterile incubation chamber for growing and monitoring axenic phototrophic biofilms, i.e. a sterilizable, illuminated, continuous-flow system for a routine work with pure cultures. The system has been designed to simulate the growth conditions in the shallow, littoral zone of aquatic habitats (horizontal surface, submerged in water, illuminated, aerated). Additional features of the concept include automated photometrical monitoring of biofilm density (as biofilm turbidity), analysis via confocal microscopy, direct harvesting of cells, and options to control illumination, flow velocity, and composition of culture fluid. The application of the system was demonstrated in growth experiments using axenic diatom biofilms, or axenic diatom biofilms co-cultivated with different bacterial strains isolated from epilithic biofilms of an oligotrophic freshwater lake. PMID:23757240

  9. Metagenome Analyses of Corroded Concrete Wastewater Pipe Biofilms Reveals a Complex Microbial System

    EPA Science Inventory

    Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. Taxonomic and functio...

  10. Effect of biofilm in irrigation pipes on the microbial quality of irrigation water

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aim: To test the hypothesis that microbial quality of irrigation water can be substantially altered by the association of E. coli with pipe lining in irrigation systems. Methods and Results: The sprinkler irrigation system was outfitted with coupons that were extracted before four 2-hour long irri...

  11. Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients.

    PubMed

    Zhang, L; Gowardman, J; Morrison, M; Runnegar, N; Rickard, C M

    2016-02-01

    Catheter-related bloodstream infection (CRBSI) is one of the most serious complications in hospitalised patients, leading to increased hospitalisation, intensive care admissions, extensive antibiotic treatment and mortality. A greater understanding of these bacterial infections is needed to improve the prevention and the management of CRBSIs. We describe here the systematic culture-independent evaluation of intravascular catheter (IVC) bacteriology. Twelve IVCs (6 central venous catheters and 6 arterial catheters) were collected from 6 patients. By using traditional culture methods, 3 patients were diagnosed with catheter colonisation including 1 patient who also had CRBSI, and 3 had no colonisation. From a total of 839,539 high-quality sequence reads from high-throughput sequencing, 8 microbial phyla and 76 diverse microbial genera were detected. All IVCs examined in this study were colonised with complex microbial communities including "non-colonised IVCs," as defined using traditional culture methods. Two main community types were observed: Enterobacteriaceae spp., dominant in patients without colonisation or CRBSI; and Staphylococcus spp., dominant in patients with colonisation and CRBSI. More diverse pathogens and a higher microbial diversity were present in patients with IVC colonisation and CRBSI. Community composition did not appear to be affected by patients' antibiotic treatment or IVC type. Characterisation of these communities is the first step in elucidating roles of these pathogens in disease progression, and to ultimately facilitate the improved prevention, refined diagnosis and management of CRBSI. PMID:26610337

  12. CMEIAS JFrad: a digital computing tool to discriminate the fractal geometry of landscape architectures and spatial patterns of individual cells in microbial biofilms.

    PubMed

    Ji, Zhou; Card, Kyle J; Dazzo, Frank B

    2015-04-01

    Image analysis of fractal geometry can be used to gain deeper insights into complex ecophysiological patterns and processes occurring within natural microbial biofilm landscapes, including the scale-dependent heterogeneities of their spatial architecture, biomass, and cell-cell interactions, all driven by the colonization behavior of optimal spatial positioning of organisms to maximize their efficiency in utilization of allocated nutrient resources. Here, we introduce CMEIAS JFrad, a new computing technology that analyzes the fractal geometry of complex biofilm architectures in digital landscape images. The software uniquely features a data-mining opportunity based on a comprehensive collection of 11 different mathematical methods to compute fractal dimension that are implemented into a wizard design to maximize ease-of-use for semi-automatic analysis of single images or fully automatic analysis of multiple images in a batch process. As examples of application, quantitative analyses of fractal dimension were used to optimize the important variable settings of brightness threshold and minimum object size in order to discriminate the complex architecture of freshwater microbial biofilms at multiple spatial scales, and also to differentiate the spatial patterns of individual bacterial cells that influence their cooperative interactions, resource use, and apportionment in situ. Version 1.0 of JFrad is implemented into a software package containing the program files, user manual, and tutorial images that will be freely available at http://cme.msu.edu/cmeias/. This improvement in computational image informatics will strengthen microscopy-based approaches to analyze the dynamic landscape ecology of microbial biofilm populations and communities in situ at spatial resolutions that range from single cells to microcolonies. PMID:25256301

  13. Characterization of microbial community structure in a hybrid biofilm-activated sludge reactor for simultaneous nitrogen and phosphorus removal.

    PubMed

    Feng, Cui-Jie; Zhang, Zhao-Ji; Wang, Shu-Mei; Fang, Fang; Ye, Zhi-Long; Chen, Shao-Hua

    2013-04-01

    The microbial communities in a hybrid biofilm-activated sludge reactor (HY) for nitrogen and phosphorus removal were characterized by 16S rRNA-based clone libraries and phylogenetic analysis. The hybrid reactor removed over 90% of COD, 92% of total nitrogen (TN) and 95% of total phosphorus (TP) from the municipal wastewater, respectively. The mean removal rates of COD, TN, and TP in the conventional suspended activated sludge reactor were above 80%, 80% and 94%, respectively. Community structures were determined by phylogenetic analyses of six clone libraries (each nearly 100 clones). The dominant bacterial group with which clones were affiliated to the beta subclass of the Proteobacteria (31% to approximately 77%), following the Bacteroidetes group (10% to approximately 34%). In addition, several clone groups affiliated with unknown bacterial assemblages were identified in the clone libraries. Acinetobacter sp., which was thought to had played an important role in phosphate removal systems, was scarcely represented by clone sequences in both libraries. Differences in community structure were observed between the hybrid reactor and activated sludge reactors. Such differences may account for the differing wastewater treating capabilities of the two different systems. PMID:24620622

  14. The characteristics of extracellular polymeric substances and soluble microbial products in moving bed biofilm reactor-membrane bioreactor.

    PubMed

    Duan, Liang; Jiang, Wei; Song, Yonghui; Xia, Siqing; Hermanowicz, Slawomir W

    2013-11-01

    The characteristics of extracellular polymeric substances (EPS) and soluble microbial products (SMP) in conventional membrane bioreactor (MBR) and in moving bed biofilm reactor-membrane bioreactors (MBBR-MBR) were investigated in long-term (170 days) experiments. The results showed that all reactors had high removal efficiency of ammonium and COD, despite very different fouling conditions. The MBBR-MBR with media fill ratio of 26.7% had much lower total membrane resistance and no obvious fouling were detected during the whole operation. In contrast, MBR and MBBR-MBR with lower and higher media fill experienced more significant fouling. Low fouling at optimum fill ratio may be due to the higher percentage of small molecular size (<1 kDa) and lower percentage of large molecular size (>100 kDa) of EPS and SMP in the reactor. The composition of EPS and SMP affected fouling due to different O-H bonds in hydroxyl functional groups, and less polysaccharides and lipids. PMID:24077152

  15. Antifungal therapy with an emphasis on biofilms.

    PubMed

    Pierce, Christopher G; Srinivasan, Anand; Uppuluri, Priya; Ramasubramanian, Anand K; López-Ribot, José L

    2013-10-01

    Fungal infections are on the rise as advances in modern medicine prolong the lives of severely ill patients. Fungi are eukaryotic organisms and there are a limited number of targets for antifungal drug development; as a result the antifungal arsenal is exceedingly limited. Azoles, polyenes and echinocandins constitute the mainstay of antifungal therapy for patients with life-threatening mycoses. One of the main factors complicating antifungal therapy is the formation of fungal biofilms, microbial communities displaying resistance to most antifungal agents. A better understanding of fungal biofilms provides for new opportunities for the development of urgently needed novel antifungal agents and strategies. PMID:24011516

  16. Antifungal therapy with an emphasis on biofilms

    PubMed Central

    Pierce, Christopher G.; Srinivasan, Anand; Uppuluri, Priya; Ramasubramanian, Anand K.; López-Ribot, José Luis

    2013-01-01

    Fungal infections are on the rise as advances in modern medicine prolong the lives of severely ill patients. Fungi are eukaryotic organisms and there are a limited number of targets for antifungal drug development; as a result the antifungal arsenal is exceedingly limited. Azoles, polyenes and echinocandins, constitute the mainstay of antifungal therapy for patients with life-threatening mycoses. One of the main factors complicating antifungal therapy is the formation of fungal biofilms, microbial communities displaying resistance to most antifungal agents. A better understanding of fungal biofilms provides for new opportunities for the development of urgently needed novel antifungal agents and strategies. PMID:24011516

  17. Distribution and Rate of Microbial Processes in an Ammonia-Loaded Air Filter Biofilm?

    PubMed Central

    Juhler, Susanne; Revsbech, Niels Peter; Schramm, Andreas; Herrmann, Martina; Ottosen, Lars D. M.; Nielsen, Lars Peter

    2009-01-01

    The in situ activity and distribution of heterotrophic and nitrifying bacteria and their potential interactions were investigated in a full-scale, two-section, trickling filter designed for biological degradation of volatile organics and NH3 in ventilation air from pig farms. The filter biofilm was investigated by microsensor analysis, fluorescence in situ hybridization, quantitative PCR, and batch incubation activity measurements. In situ aerobic activity showed a significant decrease through the filter, while the distribution of ammonia-oxidizing bacteria (AOB) was highly skewed toward the filter outlet. Nitrite oxidation was not detected during most of the experimental period, and the AOB activity therefore resulted in NO2?, accumulation, with concentrations often exceeding 100 mM at the filter inlet. The restriction of AOB to the outlet section of the filter was explained by both competition with heterotrophic bacteria for O2 and inhibition by the protonated form of NO2?, HNO2. Product inhibition of AOB growth could explain why this type of filter tends to emit air with a rather constant NH3 concentration irrespective of variations in inlet concentration and airflow. PMID:19363071

  18. Electrical spiking in bacterial biofilms.

    PubMed

    Masi, Elisa; Ciszak, Marzena; Santopolo, Luisa; Frascella, Arcangela; Giovannetti, Luciana; Marchi, Emmanuela; Viti, Carlo; Mancuso, Stefano

    2015-01-01

    In nature, biofilms are the most common form of bacterial growth. In biofilms, bacteria display coordinated behaviour to perform specific functions. Here, we investigated electrical signalling as a possible driver in biofilm sociobiology. Using a multi-electrode array system that enables high spatio-temporal resolution, we studied the electrical activity in two biofilm-forming strains and one non-biofilm-forming strain. The action potential rates monitored during biofilm-forming bacterial growth exhibited a one-peak maximum with a long tail, corresponding to the highest biofilm development. This peak was not observed for the non-biofilm-forming strain, demonstrating that the intensity of the electrical activity was not linearly related to the bacterial density, but was instead correlated with biofilm formation. Results obtained indicate that the analysis of the spatio-temporal electrical activity of bacteria during biofilm formation can open a new frontier in the study of the emergence of collective microbial behaviour. PMID:25392401

  19. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life?

    PubMed Central

    Gautier, Céline; Renault, Pierre; Briandet, Romain; Guédon, Eric

    2015-01-01

    Microorganisms have a long history of use in food production and preservation. Their adaptation to food environments has profoundly modified their features, mainly through genomic flux. Streptococcus thermophilus, one of the most frequent starter culture organisms consumed daily by humans emerged recently from a commensal ancestor. As such, it is a useful model for genomic studies of bacterial domestication processes. Many streptococcal species form biofilms, a key feature of the major lifestyle of these bacteria in nature. However, few descriptions of S. thermophilus biofilms have been reported. An analysis of the ability of a representative collection of natural isolates to form biofilms revealed that S. thermophilus was a poor biofilm producer and that this characteristic was associated with an inability to attach firmly to surfaces. The identification of three biofilm-associated genes in the strain producing the most biofilms shed light on the reasons for the rarity of this trait in this species. These genes encode proteins involved in crucial stages of biofilm formation and are heterogeneously distributed between strains. One of the biofilm genes appears to have been acquired by horizontal transfer. The other two are located in loci presenting features of reductive evolution, and are absent from most of the strains analyzed. Their orthologs in commensal bacteria are involved in adhesion to host cells, suggesting that they are remnants of ancestral functions. The biofilm phenotype appears to be a commensal trait that has been lost during the genetic domestication of S. thermophilus, consistent with its adaptation to the milk environment and the selection of starter strains for dairy fermentations. PMID:26035177

  20. Microbial Biofilms on Needleless Connectors for Central Venous Catheters: Comparison of Standard and Silver-Coated Devices Collected from Patients in an Acute Care Hospital

    PubMed Central

    Perez, Elizabeth; Williams, Margaret; Jacob, Jesse T.; Reyes, Mary Dent; Chernetsky Tejedor, Sheri; Steinberg, James P.; Rowe, Lori; Ganakammal, Satishkumar Ranganathan; Changayil, Shankar; Weil, M. Ryan

    2014-01-01

    Microorganisms may colonize needleless connectors (NCs) on intravascular catheters, forming biofilms and predisposing patients to catheter-associated infection (CAI). Standard and silver-coated NCs were collected from catheterized intensive care unit patients to characterize biofilm formation using culture-dependent and culture-independent methods and to investigate the associations between NC usage and biofilm characteristics. Viable microorganisms were detected by plate counts from 46% of standard NCs and 59% of silver-coated NCs (P = 0.11). There were no significant associations (P > 0.05, chi-square test) between catheter type, side of catheter placement, number of catheter lumens, site of catheter placement, or NC placement duration and positive NC findings. There was an association (P = 0.04, chi-square test) between infusion type and positive findings for standard NCs. Viable microorganisms exhibiting intracellular esterase activity were detected on >90% of both NC types (P = 0.751), suggesting that a large percentage of organisms were not culturable using the conditions provided in this study. Amplification of the 16S rRNA gene from selected NCs provided a substantially larger number of operational taxonomic units per NC than did plate counts (26 to 43 versus 1 to 4 operational taxonomic units/NC, respectively), suggesting that culture-dependent methods may substantially underestimate microbial diversity on NCs. NC bacterial communities were clustered by patient and venous access type and may reflect the composition of the patient's local microbiome but also may contain organisms from the health care environment. NCs provide a portal of entry for a wide diversity of opportunistic pathogens to colonize the catheter lumen, forming a biofilm and increasing the potential for CAI, highlighting the importance of catheter maintenance practices to reduce microbial contamination. PMID:24371233

  1. Development of Electroactive and Anaerobic Ammonium-Oxidizing (Anammox) Biofilms from Digestate in Microbial Fuel Cells.

    PubMed

    Di Domenico, Enea Gino; Petroni, Gianluca; Mancini, Daniele; Geri, Alberto; Di Palma, Luca; Ascenzioni, Fiorentina

    2015-01-01

    Microbial Fuel cells (MFCs) have been proposed for nutrient removal and energy recovery from different wastes. In this study the anaerobic digestate was used to feed H-type MFC reactors, one with a graphite anode preconditioned with Geobacter sulfurreducens and the other with an unconditioned graphite anode. The data demonstrate that the digestate acts as a carbon source, and even in the absence of anode preconditioning, electroactive bacteria colonise the anodic chamber, producing a maximum power density of 172.2 mW/m(2). The carbon content was also reduced by up to 60%, while anaerobic ammonium oxidation (anammox) bacteria, which were found in the anodic compartment of the reactors, contributed to nitrogen removal from the digestate. Overall, these results demonstrate that MFCs can be used to recover anammox bacteria from natural sources, and it may represent a promising bioremediation unit in anaerobic digestor plants for the simultaneous nitrogen removal and electricity generation using digestate as substrate. PMID:26273609

  2. Development of Electroactive and Anaerobic Ammonium-Oxidizing (Anammox) Biofilms from Digestate in Microbial Fuel Cells

    PubMed Central

    Di Domenico, Enea Gino; Petroni, Gianluca; Mancini, Daniele; Geri, Alberto; Palma, Luca Di; Ascenzioni, Fiorentina

    2015-01-01

    Microbial Fuel cells (MFCs) have been proposed for nutrient removal and energy recovery from different wastes. In this study the anaerobic digestate was used to feed H-type MFC reactors, one with a graphite anode preconditioned with Geobacter sulfurreducens and the other with an unconditioned graphite anode. The data demonstrate that the digestate acts as a carbon source, and even in the absence of anode preconditioning, electroactive bacteria colonise the anodic chamber, producing a maximum power density of 172.2 mW/m2. The carbon content was also reduced by up to 60%, while anaerobic ammonium oxidation (anammox) bacteria, which were found in the anodic compartment of the reactors, contributed to nitrogen removal from the digestate. Overall, these results demonstrate that MFCs can be used to recover anammox bacteria from natural sources, and it may represent a promising bioremediation unit in anaerobic digestor plants for the simultaneous nitrogen removal and electricity generation using digestate as substrate. PMID:26273609

  3. Molecular and ecological analyses of microbial community structures in biofilms of a full-scale Aerated Up-Flow Biobead process.

    PubMed

    Ju, Dong-Hun; Choi, Min-Kyung; Ahn, Jae-Hyung; Kim, Mi-Hwa; Cho, Jae-Chang; Kim, Taesung; Kim, Taesan; Seong, Chi Nam; Ka, Jong-Ok

    2007-02-01

    Molecular and cultivation techniques were used to characterize the bacterial communities of biobead reactor biofilms in a sewage treatment plant to which an Aerated Up-Flow Biobead process was applied. With this biobead process, the monthly average values of various chemical parameters in the effluent were generally kept under the regulation limits of the effluent quality of the sewage treatment plant during the operation period. Most probable number (MPN) analysis revealed that the population of denitrifying bacteria was abundant in the biobead #1 reactor, denitrifying and nitrifying bacteria coexisted in the biobead #2 reactor, and nitrifying bacteria prevailed over denitrifying bacteria in the biobead #3 reactor. The results of the MPN test suggested that the biobead #2 reactor was a transition zone leading to acclimated nitrifying biofilms in the biobead #3 reactor. Phylogenetic analysis of 16S rDNA sequences cloned from biofilms showed that the biobead #1 reactor, which received a high organic loading rate, had much diverse microorganisms, whereas the biobead #2 and #3 reactors were dominated by the members of Proteobacteria. DGGE analysis with the ammonia monooxygenase (amoA) gene supported the observation from the MPN test that the biofilms of September were fully developed and specialized for nitrification in the biobead reactor #3. All of the DNA sequences of the amoA DGGE bands were very similar to the sequence of the amoA gene of Nitrosomonas species, the presence of which is typical in the biological aerated filters. The results of this study showed that organic and inorganic nutrients were efficiently removed by both denitrifying microbial populations in the anaerobic tank and heterotrophic and nitrifying bacterial biofilms well-formed in the three functional biobead reactors in the Aerated Up-Flow Biobead process. PMID:18051756

  4. Biofilm-associated persistence of food-borne pathogens.

    PubMed

    Bridier, A; Sanchez-Vizuete, P; Guilbaud, M; Piard, J-C; Natali, M; Briandet, R

    2015-02-01

    Microbial life abounds on surfaces in both natural and industrial environments, one of which is the food industry. A solid substrate, water and some nutrients are sufficient to allow the construction of a microbial fortress, a so-called biofilm. Survival strategies developed by these surface-associated ecosystems are beginning to be deciphered in the context of rudimentary laboratory biofilms. Gelatinous organic matrices consisting of complex mixtures of self-produced biopolymers ensure the cohesion of these biological structures and contribute to their resistance and persistence. Moreover, far from being just simple three-dimensional assemblies of identical cells, biofilms are composed of heterogeneous sub-populations with distinctive behaviours that contribute to their global ecological success. In the clinical field, biofilm-associated infections (BAI) are known to trigger chronic infections that require dedicated therapies. A similar belief emerging in the food industry, where biofilm tolerance to environmental stresses, including cleaning and disinfection/sanitation, can result in the persistence of bacterial pathogens and the recurrent cross-contamination of food products. The present review focuses on the principal mechanisms involved in the formation of biofilms of food-borne pathogens, where biofilm behaviour is driven by its three-dimensional heterogeneity and by species interactions within these biostructures, and we look at some emergent control strategies. PMID:25500382

  5. Bifunctional Ag/Fe/N/C Catalysts for Enhancing Oxygen Reduction via Cathodic Biofilm Inhibition in Microbial Fuel Cells.

    PubMed

    Dai, Ying; Chan, Yingzi; Jiang, Baojiang; Wang, Lei; Zou, Jinlong; Pan, Kai; Fu, Honggang

    2016-03-23

    Limitation of the oxygen reduction reaction (ORR) in single-chamber microbial fuel cells (SC-MFCs) is considered an important hurdle in achieving their practical application. The cathodic catalysts faced with a liquid phase are easily primed with the electrolyte, which provides more surface area for bacterial overgrowth, resulting in the difficulty in transporting protons to active sites. Ag/Fe/N/C composites prepared from Ag and Fe-chelated melamine are used as antibacterial ORR catalysts for SC-MFCs. The structure-activity correlations for Ag/Fe/N/C are investigated by tuning the carbonization temperature (600-900 °C) to clarify how the active-constituents of Ag/Fe and N-species influence the antibacterial and ORR activities. A maximum power density of 1791 mW m(-2) is obtained by Ag/Fe/N/C (630 °C), which is far higher than that of Pt/C (1192 mW m(-2)), only having a decline of 16.14% after 90 days of running. The Fe-bonded N and the cooperation of pyridinic N and pyrrolic N in Ag/Fe/N/C contribute equally to the highly catalytic activity toward ORR. The ·OH or O2(-) species originating from the catalysis of O2 can suppress the biofilm growth on Ag/Fe/N/C cathodes. The synergistic effects between the Ag/Fe heterojunction and N-species substantially contribute to the high power output and Coulombic efficiency of Ag/Fe/N/C catalysts. These new antibacterial ORR catalysts show promise for application in MFCs. PMID:26938657

  6. Microbial life in volcanic/geothermal areas: how soil geochemistry shapes microbial communities

    NASA Astrophysics Data System (ADS)

    Gagliano, Antonina Lisa; D'Alessandro, Walter; Franzetti, Andrea; Parello, Francesco; Tagliavia, Marcello; Quatrini, Paola

    2015-04-01

    Extreme environments, such as volcanic/geothermal areas, are sites of complex interactions between geosphere and biosphere. Although biotic and abiotic components are strictly related, they were separately studied for long time. Nowadays, innovative and interdisciplinary approaches are available to explore microbial life thriving in these environments. Pantelleria island (Italy) hosts a high enthalpy geothermal system characterized by high CH4 and low H2S fluxes. Two selected sites, FAV1 and FAV2, located at Favara Grande, the main exhalative area of the island, show similar physical conditions with a surface temperature close to 60° C and a soil gas composition enriched in CH4, H2 and CO2. FAV1 soil is characterized by harsher conditions (pH 3.4 and 12% of H2O content); conversely, milder conditions were recorded at site FAV2 (pH 5.8 and 4% of H2O content). High methanotrophic activity (59.2 nmol g-1 h-1) and wide diversity of methanotrophic bacteria were preliminary detected at FAV2, while no activity was detected at FAV1(1). Our aim was to investigate how the soil microbial communities of these two close geothermal sites at Pantelleria island respond to different geochemical conditions. Bacterial and Archaeal communities of the sites were investigated by MiSeq Illumina sequencing of hypervariable regions of the 16S rRNA gene. More than 33,000 reads were obtained for Bacteria and Archaea from soil samples of the two sites. At FAV1 99% of the bacterial sequences were assigned to four main phyla (Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi). FAV2 sequences were distributed in the same phyla with the exception of Chloroflexi that was represented below 1%. Results indicate a high abundance of thermo-acidophilic chemolithotrophs in site FAV1 dominated by Acidithiobacillus ferrooxidans (25%), Nitrosococcus halophilus (10%), Alicyclobacillus spp. (7%) and the rare species Ktedonobacter racemifer (11%). The bacterial community at FAV2 soil is dominated by the methanotrophs (~40% of the reads) Methylocaldum gracile, Beijerinckia sp. and Methylobacterium sp.. The Archaea assemblages are similar in both sites and dominated by the moderately thermophilic chemolithotrophic ammonia-oxidating candidate species Nitrososphaera gargensis, in the phylum Thaumarchaeota. Volcanic/geothermal activities represent a complex phenomenon, this shaping different and peculiar microbial niches even at adjacent sites. Lower pH, higher water, NH4+ and H2content are probably the discriminating factors that prevent methanotrophy at FAV1 and favor chemolithotrophy. Site FAV2 hosts an extraordinary diversity of methanotrophs due to large supply of CH4, scarce presence of inhibitors of methanotrophy (H2S and NH3) and slightly acidic soil pH. This study integrates geochemical and biological information to move a step ahead in the still scarce knowledge on the complex ecology of microbes living in geothermal sites and their interactions with the geosphere. (1)Gagliano et al., 2014 Biogeosciences, 11, 5865-5875

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  8. Dissolved carbon dioxide and oxygen concentrations in purge of vacuum-packaged pork chops and the relationship to shelf life and models for estimating microbial populations.

    PubMed

    Adams, K R; Niebuhr, S E; Dickson, J S

    2015-12-01

    The objectives of this study were to determine the dissolved CO2 and O2 concentrations in the purge of vacuum-packaged pork chops over a 60 day storage period, and to elucidate the relationship of dissolved CO2 and O2 to the microbial populations and shelf life. As the populations of spoilage bacteria increased, the dissolved CO2 increased and the dissolved O2 decreased in the purge. Lactic acid bacteria dominated the spoilage microflora, followed by Enterobacteriaceae and Brochothrix thermosphacta. The surface pH decreased to 5.4 due to carbonic acid and lactic acid production before rising to 5.7 due to ammonia production. A mathematical model was developed which estimated microbial populations based on dissolved CO2 concentrations. Scanning electron microscope images were also taken of the packaging film to observe the biofilm development. The SEM images revealed a two-layer biofilm on the packaging film that was the result of the tri-phase growth environment. PMID:26143235

  9. Energy, ecology and the distribution of microbial life

    PubMed Central

    Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

    2013-01-01

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

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

    PubMed Central

    Kim, Minsu; Or, Dani

    2016-01-01

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

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

    PubMed

    Kim, Minsu; Or, Dani

    2016-01-01

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

  12. A miniature microbial fuel cell with conducting nanofibers-based 3D porous biofilm

    NASA Astrophysics Data System (ADS)

    Jiang, Huawei; Halverson, Larry J.; Dong, Liang

    2015-12-01

    Miniature microbial fuel cell (MFC) technology has received growing interest due to its potential applications in high-throughput screening of bacteria and mutants to elucidate mechanisms of electricity generation. This paper reports a novel miniature MFC with an improved output power density and short startup time, utilizing electrospun conducting poly(3,4-ethylenedioxythiophene) (PEDOT) nanofibers as a 3D porous anode within a 12 μl anolyte chamber. This device results in 423 μW cm‑3 power density based on the volume of the anolyte chamber, using Shewanella oneidensis MR-1 as a model biocatalyst without any optimization of bacterial culture. The device also excels in a startup time of only 1hr. The high conductivity of the electrospun nanofibers makes them suitable for efficient electron transfer. The mean pore size of the conducting nanofibers is several micrometers, which is favorable for bacterial penetration and colonization of surfaces of the nanofibers. We demonstrate that S. oneidensis can fully colonize the interior region of this nanofibers-based porous anode. This work represents a new attempt to explore the use of electrospun PEDOT nanofibers as a 3D anode material for MFCs. The presented miniature MFC potentially will provide a high-sensitivity, high-throughput tool to screen suitable bacterial species and mutant strains for use in large-size MFCs.

  13. Assessing microbial competition in a hydrogen-based membrane biofilm reactor (MBfR) using multidimensional modeling.

    PubMed

    Martin, Kelly J; Picioreanu, Cristian; Nerenberg, Robert

    2015-09-01

    The membrane biofilm reactor (MBfR) is a novel technology that safely delivers hydrogen to the base of a denitrifying biofilm via gas-supplying membranes. While hydrogen is an effective electron donor for denitrifying bacteria (DNB), it also supports sulfate-reducing bacteria (SRB) and methanogens (MET), which consume hydrogen and create undesirable by-products. SRB and MET are only competitive for hydrogen when local nitrate concentrations are low, therefore SRB and MET primarily grow near the base of the biofilm. In an MBfR, hydrogen concentrations are greatest at the base of the biofilm, making SRB and MET more likely to proliferate in an MBfR system than a conventional biofilm reactor. Modeling results showed that because of this, control of the hydrogen concentration via the intramembrane pressure was a key tool for limiting SRB and MET development. Another means is biofilm management, which supported both sloughing and erosive detachment. For the conditions simulated, maintaining thinner biofilms promoted higher denitrification fluxes and limited the presence of SRB and MET. The 2-d modeling showed that periodic biofilm sloughing helped control slow-growing SRB and MET. Moreover, the rough (non-flat) membrane assembly in the 2-d model provided a special niche for SRB and MET that was not represented in the 1-d model. This study compared 1-d and 2-d biofilm model applicability for simulating competition in counter-diffusional biofilms. Although more computationally expensive, the 2-d model captured important mechanisms unseen in the 1-d model. PMID:25854894

  14. Bacterial cellulose may provide the microbial-life biosignature in the rock records

    NASA Astrophysics Data System (ADS)

    Zaets, I.; Podolich, O.; Kukharenko, O.; Reshetnyak, G.; Shpylova, S.; Sosnin, M.; Khirunenko, L.; Kozyrovska, N.; de Vera, J.-P.

    2014-03-01

    Bacterial cellulose (BC) is a matrix for a biofilm formation, which is critical for survival and persistence of microbes in harsh environments. BC could play a significant role in the formation of microbial mats in pristine ecosystems on Earth. The prime objective of this study was to measure to what extent spectral and other characteristics of BC were changed under the performance of BC interaction with the earthly rock - anorthosite - via microorganisms. The spectral analyses (Fourier Transform Infrared FT-IR, spectroscopy, and atomic absorption spectroscopy) showed unprecedented accumulation of chemical elements in the BC-based biofilm. The absorption capacity of IR by BC was shielded a little by mineral crust formed by microorganisms on the BC-based biofilm surface, especially clearly seen in the range of 1200-900 cm-1 in FT-IR spectra. Confocal scanning laser microscopy analysis revealed that elements bioleached from anorthosite created surface coats on the BC nanofibril web. At the same time, the vibrational spectra bands showed the presence of the characteristic region of anomeric carbons (960-730 cm-1), wherein a band at 897 cm-1 confirmed the presence of ?-1, 4-linkages, which may serve as the cellulose fingerprint region. Results show that BC may be a biosignature for search signs of living organisms in rock records.

  15. A prospective study on evaluation of pathogenesis, biofilm formation, antibiotic susceptibility of microbial community in urinary catheter

    NASA Astrophysics Data System (ADS)

    Younis, Khansa Mohammed; Usup, Gires; Ahmad, Asmat

    2015-09-01

    This study is aimed to isolate, detect biofilm formation ability and antibiotic susceptibility of urinary catheter adherent microorganisms from elderly hospitalized patient at the Universiti Kebangsaan Malaysia Medical Center. Microorganisms were isolated from three samples of urinary catheters (UC) surface; one of the acute vascular rejection patient (UCB) and two from benign prostate hyperplasia patients (UCC and UCD). A total of 100 isolates was isolated with 35 from UCB, 38 (UCC) and 28 (UCD). Ninety six were identified as Gram-negative bacilli, one Gram-positive bacilli and three yeasts. Results of biofilm forming on sterile foley catheter showed that all the isolates can form biofilm at different degrees; strong biofilm forming: 32% from the 35 isolates (UCB), 25% out of 38 isolates (UCC), 26% out of 28 isolates (UCD). As for moderate biofilm forming; 3% from UCB, 10% from UCC and 2% from UCD. Weak biofilm forming in UCC (3%). The antibiotic susceptibility for (UCB) isolates showed highly resistant to ampicillin, novobiocin and penicillin 100 (%), kanamycin (97%), tetracycline (94%), chloramphenicol (91%), streptomycin (77%) and showed low level of resistance to gentamycin (17%), while all the isolates from (UCC-D) showed high resistant towards ampicillin and penicillin, novobiocin (94%), tetracycline (61%), streptomycin (53%), gentamycin (50%) and low level of resistance to kanamycin (48%), chloramphenicol (47%). The findings indicate that these isolates can spread within the community on urinary catheters surface and produce strong biofilm, therefore, monitoring antibiotic susceptibility of bacteria isolated in the aggregation is recommended.

  16. Stabilization of Plutonium in Subsurface Environments via Microbial Reduction and Biofilm Formation

    SciTech Connect

    Hakim Boukhalfa; Gary A. Icopini; Sean D. Reilly; Mary P. Neu

    2007-04-19

    Plutonium has a long half-life (2.4 x 104 years) and is of concern because of its chemical and radiological toxicity, high-energy alpha radioactive decay. A full understanding of its speciation and interactions with environmental processes is required in order to predict, contain, or remediate contaminated sites. Under aerobic conditions Pu is sparingly soluble, existing primarily in its tetravalent oxidation state. To the extent that pentavalent and hexavalent complexes and small colloidal species form they will increase the solubility and resultant mobility from contamination sources. There is evidence that in both marine environments and brines substantial fractions of the plutonium in solution is present as hexavalent plutonyl, PuO2 2+.

  17. Influences of metal ions on microcystin-LR degradation capacity and dynamics in microbial distribution of biofilm collected from water treatment plant nearby Kasumigaura Lake.

    PubMed

    Wang, Xin; Utsumi, Motoo; Gao, Yu; Li, Qintong; Tian, Xiaowei; Shimizu, Kazuya; Sugiura, Norio

    2016-03-01

    Microcystins-LR (MC-LR) which is a kind of potent hepatotoxin for humans and wildlife can be biodegraded by microbial community. In this study, the capacity of biofilm in degrading MC-LR was investigated with and without additional metal ions (Mn(2+), Zn(2+) and Cu(2+)) at the concentration of 1 mg L(-1). The results indicated that the degradation rate of MC-LR by biofilm was inhibited by introduced Mn(2+) and Cu(2+) during the whole culture period. MC-LR cannot be degraded until a period of culture time passed both in the cases with Zn(2+) and Cu(2+) (2 and 8 days for Zn(2+) and Cu(2+), respectively). The results of mlrA gene analysis showed that the abundance of MC-LR degradation bacteria (MCLDB) in the microbial community under Mn(2+) condition was generally lower than that under no additional metal ion condition. Meanwhile, a two days lag phase for the proliferation of MCLDB occurred after introducing Zn(2+). And a dynamic change of MCLDB from Cu(2+) inhibited species to Cu(2+) promoted species was observed under Cu(2+) condition. The maximum ratio of MCLDB to overall bacteria under various conditions during culture process was found to follow the tendency as: Cu(2+) > Zn(2+) ≈ no additional metal ion (Control) > Mn(2+), suggesting the adverse effect of Mn(2+), no obvious effect of Zn(2+) and positive effect of Cu(2+) on the distribution ratio of MCLDB over the biofilm. PMID:26766360

  18. 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.

  19. IMPACTS OF BIOFILM FORMATION ON CELLULOSE FERMENTATION

    SciTech Connect

    Leschine, Susan

    2009-10-31

    This project addressed four major areas of investigation: i) characterization of formation of Cellulomonas uda biofilms on cellulose; ii) characterization of Clostridium phytofermentans biofilm development; colonization of cellulose and its regulation; iii) characterization of Thermobifida fusca biofilm development; colonization of cellulose and its regulation; and iii) description of the architecture of mature C. uda, C. phytofermentans, and T. fusca biofilms. This research is aimed at advancing understanding of biofilm formation and other complex processes involved in the degradation of the abundant cellulosic biomass, and the biology of the microbes involved. Information obtained from these studies is invaluable in the development of practical applications, such as the single-step bioconversion of cellulose-containing residues to fuels and other bioproducts. Our results have clearly shown that cellulose-decomposing microbes rapidly colonize cellulose and form complex structures typical of biofilms. Furthermore, our observations suggest that, as cells multiply on nutritive surfaces during biofilms formation, dramatic cell morphological changes occur. We speculated that morphological changes, which involve a transition from rod-shaped cells to more rounded forms, might be more apparent in a filamentous microbe. In order to test this hypothesis, we included in our research a study of biofilm formation by T. fusca, a thermophilic cellulolytic actinomycete commonly found in compost. The cellulase system of T. fusca has been extensively detailed through the work of David Wilson and colleagues at Cornell, and also, genome sequence of a T. fusca strain has been determine by the DOE Joint Genome Institute. Thus, T. fusca is an excellent subject for studies of biofilm development and its potential impacts on cellulose degradation. We also completed a study of the chitinase system of C. uda. This work provided essential background information for understanding how C. uda colonizes and degrades insoluble substrates. Major accomplishments of the project include: • Development of media containing dialysis tubing (described by the manufacturer as “regenerated cellulose”) as sole carbon and energy source and a nutritive surface for the growth of cellulolytic bacteria, and development of various microscopic methods to image biofilms on dialysis tubing. • Demonstration that cultures of C. phytofermentans, an obligate anaerobe, C. uda, a facultative aerobe, and T. fusca, a filamentous aerobe, formed microbial communities on the surface of dialysis tubing, which possessed architectural features and functional characteristics typical of biofilms. • Demonstration that biofilm formation on the nutritive surface, cellulose, involves a complex developmental processes, including colonization of dialysis tubing, formation of cell clusters attached to the nutritive surface, cell morphological changes, formation of complex structures embedded in extracellular polymeric matrices, and dispersal of biofilm communities as the nutritive surface is degraded. • Determination of surface specificity and regulatory aspects of biofilm formation by C. phytofermentans, C. uda, and T. fusca. • Demonstration that biofilm formation by T. fusca forms an integral part of the life cycle of this filamentous cellulolytic bacterium, including studies on the role of mycelial pellet formation in the T. fusca life cycle and a comparison of mycelial pellets to surface-attached T. fusca biofilms. • Characterization of T. fusca biofilm EPS, including demonstration of a functional role for EPS constituents. • Correlation of T. fusca developmental life cycle and cellulase gene expression.

  20. Functional Tomographic Fluorescence Imaging of pH Microenvironments in Microbial Biofilms by Use of Silica Nanoparticle Sensors▿ †

    PubMed Central

    Hidalgo, Gabriela; Burns, Andrew; Herz, Erik; Hay, Anthony G.; Houston, Paul L.; Wiesner, Ulrich; Lion, Leonard W.

    2009-01-01

    Attached bacterial communities can generate three-dimensional (3D) physicochemical gradients that create microenvironments where local conditions are substantially different from those in the surrounding solution. Given their ubiquity in nature and their impacts on issues ranging from water quality to human health, better tools for understanding biofilms and the gradients they create are needed. Here we demonstrate the use of functional tomographic imaging via confocal fluorescence microscopy of ratiometric core-shell silica nanoparticle sensors (C dot sensors) to study the morphology and temporal evolution of pH microenvironments in axenic Escherichia coli PHL628 and mixed-culture wastewater biofilms. Testing of 70-, 30-, and 10-nm-diameter sensor particles reveals a critical size for homogeneous biofilm staining, with only the 10-nm-diameter particles capable of successfully generating high-resolution maps of biofilm pH and distinct local heterogeneities. Our measurements revealed pH values that ranged from 5 to >7, confirming the heterogeneity of the pH profiles within these biofilms. pH was also analyzed following glucose addition to both suspended and attached cultures. In both cases, the pH became more acidic, likely due to glucose metabolism causing the release of tricarboxylic acid cycle acids and CO2. These studies demonstrate that the combination of 3D functional fluorescence imaging with well-designed nanoparticle sensors provides a powerful tool for in situ characterization of chemical microenvironments in complex biofilms. PMID:19801466

  1. Calibration of Biosignatures in Microbial Ca:Mg Carbonates: Fossilized Evidence for Ancient Life

    NASA Astrophysics Data System (ADS)

    McKenzie, J. A.; Bontognali, T. R.; Vasconcelos, C.

    2008-12-01

    Ca carbonate minerals, such as calcite or aragonite, are known to precipitate by both abiologically and biologically produced processes. The abundant sedimentary mineral dolomite (CaMgCO3), however, precipitates exclusively as a microbial induced product under Earth surface conditions. Thus, the study of microbial dolomite precipitation in natural environments and laboratory culture experiments provides the potential to calibrate and evaluate the range of microbial biosignatures that may become fossilized in the carbonate rock record. Structural biosignatures associated with microbial dolomite, which are microscopically observable, include characteristic shapes, such as dumbbell, spheroid or cruciform structures, and pervasive exopolymeric substance (EPS) matrices within which the mineral nucleates. The occurrence of these biostructures fossilized in geologic dolomite samples provides unambiguous evidence for the past presence of microorganisms. Identification of comparable biostructures associated with other more ambiguous biominerals may be significant physical evidence for the activity of microorganisms in a variety of terrestrial and planetary environments. Furthermore, the study of microbial dolomite precipitation provides valuable information on relevant environmental conditions that can be extrapolated to interpret paleoenvironments. In particular, microbial dolomite forms under hypersaline conditions often associated with a range of anaerobic microbial processes, such as bacterial sulfate reduction and/or anaerobic methane oxidation. The interactions of these complex microbial communities lead to the incorporation of characteristic carbon-isotope signatures reflecting the various metabolisms involved in the biomineralization. Additionally, the specific organic functional groups of metabolically produced organic molecules, which are included in modern and ancient biominerals, can be quantitatively compared using Electron Energy Loss Spectroscopy (EELS). Finally, combining these recently calibrated microbial biosignatures with the ultimate classic macroscopic evidence for microbial life, i.e. stromatolites, provides a powerful approach to corroborate the biogenicity of this earliest life form.

  2. Mini-review: Biofilm responses to oxidative stress.

    PubMed

    Gambino, Michela; Cappitelli, Francesca

    2016-02-01

    Biofilms constitute the predominant microbial style of life in natural and engineered ecosystems. Facing harsh environmental conditions, microorganisms accumulate reactive oxygen species (ROS), potentially encountering a dangerous condition called oxidative stress. While high levels of oxidative stress are toxic, low levels act as a cue, triggering bacteria to activate effective scavenging mechanisms or to shift metabolic pathways. Although a complex and fragmentary picture results from current knowledge of the pathways activated in response to oxidative stress, three main responses are shown to be central: the existence of common regulators, the production of extracellular polymeric substances, and biofilm heterogeneity. An investigation into the mechanisms activated by biofilms in response to different oxidative stress levels could have important consequences from ecological and economic points of view, and could be exploited to propose alternative strategies to control microbial virulence and deterioration. PMID:26901587

  3. Antimicrobial Tolerance in Biofilms

    PubMed Central

    Stewart, Philip S.

    2015-01-01

    The tolerance of microorganisms in biofilms to antimicrobial agents is examined through a meta-analysis of literature data. A numerical tolerance factor comparing the rates of killing in the planktonic and biofilm states is defined to provide a quantitative basis for the analysis. Tolerance factors for biocides and antibiotics range over three orders of magnitude. This variation is not explained by taking into account the molecular weight of the agent, the chemistry of the agent, the substratum material, or the speciation of the microorganisms. Tolerance factors do depend on the areal cell density of the biofilm at the time of treatment and on the age of the biofilm as grown in a particular experimental system. This suggests that there is something that happens during biofilm maturation, either physical or physiological, that is essential for full biofilm tolerance. Experimental measurements of antimicrobial penetration times in biofilms range over orders of magnitude, with slower penetration (>12 min) observed for reactive oxidants and cationic molecules. These agents are retarded through the interaction of reaction, sorption, and diffusion. The specific physiological status of microbial cells in a biofilm contributes to antimicrobial tolerance. A conceptual framework for categorizing physiological cell states is discussed in the context of antimicrobial susceptibility. It is likely that biofilms harbor cells in multiple states simultaneously (e.g., growing, stress-adapted, dormant, inactive) and that this physiological heterogeneity is an important factor in the tolerance of the biofilm state. PMID:26185072

  4. Planetary protection and Life detection: a single (but complex) question for microbial ecologists

    NASA Astrophysics Data System (ADS)

    Prieur, Daniel

    Life on Earth is (almost) everywhere, often non visible, with millions of microbes for every cubic centimeter of water, soil or air. For these reasons, to build and launch a sterile spacecraft is totally impossible. As a consequence, some microbial contamination of a spacecraft landing site cannot be rulled out. On the targeted planet, where no big size living forms have been observed, the only possibility for extinct or extant life is microbial-like entities. Finally, on the landing/sampling site, scientists will have to face the following problem: how to detect non viable extraterrestrial life forms (or signatures) among non visible terrestrial forms (or remains) that might have accompanied the spacecraft. This is a typical series of questions for microbial ecologists: Who is there? How many are there? What are they doing? An additionnal difficulty is that both components are almost certainly in a very low density, and in unknown proportions. Such a situation requires to considerably decrease the presently available levels of detections for microbial entities, and stong methodology efforts should be untertaken, with this respect. However, one term of this biological equation can be fixed: the microbial charge of the spacecraft before, and after the flight. A coordinated (through space agencies) efforts should be carried out to study microbial communities associated with spacecrafts in various places and conditions (phylogenetic diversity, physiology, distribution, abundance, etc. Such studies should be carried out at different steps of sterilization procedures, and followed by experiments dedicated to determine the responses of selected organisms to flight conditions. All these studies would feed a data base of spacecraft associated organisms and their post- flight signatures, to serve as a control for in situ life detection experiments, and a guideline for planetary protection policies. Planetary protection studies, Life detection methods are usually run in separate meetings and workshops, although they are dependent on similar concepts and technologies of Microbial Ecology.

  5. Life under flow: A novel microfluidic device for the assessment of anti-biofilm technologies

    PubMed Central

    Salta, Maria; Capretto, Lorenzo; Carugo, Dario; Wharton, Julian A.; Stokes, Keith R.

    2013-01-01

    In the current study, we have developed and fabricated a novel lab-on-a-chip device for the investigation of biofilm responses, such as attachment kinetics and initial biofilm formation, to different hydrodynamic conditions. The microfluidic flow channels are designed using computational fluid dynamic simulations so as to have a pre-defined, homogeneous wall shear stress in the channels, ranging from 0.03 to 4.30?Pa, which are relevant to in-service conditions on a ship hull, as well as other man-made marine platforms. Temporal variations of biofilm formation in the microfluidic device were assessed using time-lapse microscopy, nucleic acid staining, and confocal laser scanning microscopy (CLSM). Differences in attachment kinetics were observed with increasing shear stress, i.e., with increasing shear stress there appeared to be a delay in bacterial attachment, i.e., at 55, 120, 150, and 155?min for 0.03, 0.60, 2.15, and 4.30?Pa, respectively. CLSM confirmed marked variations in colony architecture, i.e.,: (i) lower shear stresses resulted in biofilms with distinctive morphologies mainly characterised by mushroom-like structures, interstitial channels, and internal voids, and (ii) for the higher shear stresses compact clusters with large interspaces between them were formed. The key advantage of the developed microfluidic device is the combination of three architectural features in one device, i.e., an open-system design, channel replication, and multiple fully developed shear stresses. PMID:24454610

  6. Microbial Life in a Fjord: Metagenomic Analysis of a Microbial Mat in Chilean Patagonia

    PubMed Central

    Ugalde, Juan A.; Gallardo, Maria J.; Belmar, Camila; Muñoz, Práxedes; Ruiz-Tagle, Nathaly; Ferrada-Fuentes, Sandra; Espinoza, Carola; Allen, Eric E.; Gallardo, Victor A.

    2013-01-01

    The current study describes the taxonomic and functional composition of metagenomic sequences obtained from a filamentous microbial mat isolated from the Comau fjord, located in the northernmost part of the Chilean Patagonia. The taxonomic composition of the microbial community showed a high proportion of members of the Gammaproteobacteria, including a high number of sequences that were recruited to the genomes of Moritella marina MP-1 and Colwelliapsycherythraea 34H, suggesting the presence of populations related to these two psychrophilic bacterial species. Functional analysis of the community indicated a high proportion of genes coding for the transport and metabolism of amino acids, as well as in energy production. Among the energy production functions, we found protein-coding genes for sulfate and nitrate reduction, both processes associated with Gammaproteobacteria-related sequences. This report provides the first examination of the taxonomic composition and genetic diversity associated with these conspicuous microbial mat communities and provides a framework for future microbial studies in the Comau fjord. PMID:24015199

  7. Understanding Biofilms in Chronic Sinusitis.

    PubMed

    Tajudeen, Bobby A; Schwartz, Joseph S; Palmer, James N

    2016-01-01

    Chronic sinusitis is a burdensome disease that has substantial individual and societal impact. Although great advances in medical and surgical therapies have been made, some patients continue to have recalcitrant infections. Microbial biofilms have been implicated as a cause of recalcitrant chronic sinusitis, and recent studies have tried to better understand the pathogenesis of chronic sinusitis as it relates to microbial biofilms. Here, we provide an overview of biofilms in chronic sinusitis with emphasis on pathogenesis, treatment, and future directions. In addition, recent evidence is presented, elucidating the role of bitter taste receptors as a possible key factor leading to biofilm formation. PMID:26758863

  8. Limestone Corrosion and Sulfur Cycling by Biofilms in the Frasassi Caves, Italy

    NASA Astrophysics Data System (ADS)

    Jones, D. S.; Macalady, J. L.; Druschel, G. K.; Eastman, D. D.; Albertson, L. K.

    2006-12-01

    In the Frasassi cave system, central Italy, a microbial-based ecosystem thrives on chemolithoautotrophic energy derived from hydrogen sulfide oxidation. Microbial life is prolific near the watertable, and biofilms cover nearly all subaerial and subaqueous surfaces. Subaerial biofilms are dominated by acidophilic members of the archaeal lineage Thermoplasmales and bacterial genus Acidithiobacillus. Subaqueous biofilms are diverse and are dominated by sulfide oxidizing, sulfate reducing, and sulfur disproportionating Proteobacteria. The morphology, abundance, and distribution of biofilms is controlled by physical and chemical factors such as seasonal changes in the cave hydrologic regime. In situ microelectrode voltammetry has revealed that stream biofilms speciate sulfur in diverse ways, with implications for acid production and limestone dissolution rates. Hydrogen sulfide loss from the streams cannot be accounted for solely by volatilization. Based on degassing measurements and abiotic sulfide oxidation rate calculations, stream biofilms are responsible for the majority of sulfide disappearance in streams. Rates of limestone corrosion are comparable in subaerial and subaqueous cave regions, indicating that subaerial microbial communities also have an important role in speleogenesis. Metagenomic studies targeting subaerial biofilms have confirmed that they have extremely low diversity, and offer glimpses into the physiology and biogeochemistry of extreme acidophiles in sulfidic cave communities.

  9. Effects of ocean acidification on microbial community composition of, and oxygen fluxes through, biofilms from the Great Barrier Reef.

    PubMed

    Witt, Verena; Wild, Christian; Anthony, Kenneth R N; Diaz-Pulido, Guillermo; Uthicke, Sven

    2011-11-01

    Rising anthropogenic CO(2) emissions acidify the oceans, and cause changes to seawater carbon chemistry. Bacterial biofilm communities reflect environmental disturbances and may rapidly respond to ocean acidification. This study investigates community composition and activity responses to experimental ocean acidification in biofilms from the Australian Great Barrier Reef. Natural biofilms grown on glass slides were exposed for 11 d to four controlled pCO(2) concentrations representing the following scenarios: A) pre-industrial (?300 ppm), B) present-day (?400 ppm), C) mid century (?560 ppm) and D) late century (?1140 ppm). Terminal restriction fragment length polymorphism and clone library analyses of 16S rRNA genes revealed CO(2) -correlated bacterial community shifts between treatments A, B and D. Observed bacterial community shifts were driven by decreases in the relative abundance of Alphaproteobacteria and increases of Flavobacteriales (Bacteroidetes) at increased CO(2) concentrations, indicating pH sensitivity of specific bacterial groups. Elevated pCO(2) (C + D) shifted biofilm algal communities and significantly increased C and N contents, yet O(2) fluxes, measured using in light and dark incubations, remained unchanged. Our findings suggest that bacterial biofilm communities rapidly adapt and reorganize in response to high pCO(2) to maintain activity such as oxygen production. PMID:21906222

  10. Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane.

    PubMed

    Shin, Hyun Chul; Ju, Dong-Hun; Jeon, Byoung Seung; Choi, Okkyoung; Kim, Hyun Wook; Um, Youngsoon; Lee, Dong-Hoon; Sang, Byoung-In

    2015-01-01

    Hydrogenotrophic methanogens can use gaseous substrates, such as H2 and CO2, in CH4 production. H2 gas is used to reduce CO2. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH4 production from CO2 and H2. CO2 and H2 were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5-5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH4 production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp., restricted the development of acetoclastic methanogens in the acidic CH4 production process. The results show that acidic operation of a CH4 production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens. PMID:26694756

  11. The effect of recycling flux on the performance and microbial community composition of a biofilm hydrolytic-aerobic recycling process treating anthraquinone reactive dyes.

    PubMed

    Wang, Yuanpeng; Zhu, Kang; Zheng, Yanmei; Wang, Haitao; Dong, Guowen; He, Ning; Li, Qingbiao

    2011-01-01

    Synthetic dyes are extensively used and rarely degraded. Microbial decomposition is a cost-effective alternative to chemical and physical degradation processes. In this study, the decomposition of simulated anthraquinone reactive dye (Reactive Blue 19; RB19) at a concentration of 400-mg/L in wastewater by a biofilm hydrolytic-aerobic recycling system was investigated over a range of recycling fluxes. The 16S rDNA-based fingerprint technique was also used to investigate the microbial community composition. Results indicated that the recycling flux was a key factor that influenced RB19 degradation. The RB19 and COD removal efficiency could reach values as high as 82.1% and 95.4%, respectively, with a recycling flux of 10 mL/min. Molecular analysis indicated that some strains were similar to Aeromonadales, Tolumonas, and some uncultured clones were assumed to be potential decolorization bacteria. However, the microbial community composition in the reactors remained relatively stable at different recycling fluxes. This study provided insights on the decolorization capability and the population dynamics during the decolorization process of anthraquinone dye wastewater. PMID:22117173

  12. Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane

    PubMed Central

    Jeon, Byoung Seung; Choi, Okkyoung; Kim, Hyun Wook; Um, Youngsoon; Lee, Dong-Hoon; Sang, Byoung-In

    2015-01-01

    Hydrogenotrophic methanogens can use gaseous substrates, such as H2 and CO2, in CH4 production. H2 gas is used to reduce CO2. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH4 production from CO2 and H2. CO2 and H2 were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5–5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH4 production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp., restricted the development of acetoclastic methanogens in the acidic CH4 production process. The results show that acidic operation of a CH4 production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens. PMID:26694756

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

    NASA Technical Reports Server (NTRS)

    Des Marais, David J.

    2011-01-01

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

  14. Endolithic microbial life in hot and cold deserts

    NASA Technical Reports Server (NTRS)

    Friedmann, E. I.

    1980-01-01

    Endolithic microorganisms (those living inside rocks) occur in hot and cold deserts and exist under extreme environmental conditions. These conditions are discussed on a comparative basis. Quantitative estimates of biomass are comparable in hot and cold deserts. Despite the obvious differences between the hot and cold desert environment, survival strategies show some common features. These endolithic organisms are able to 'switch' rapidly their metabolic activities on and off in response to changes in the environment. Conditions in hot deserts impose a more severe environmental stress on the organisms than in the cold Antarctic desert. This is reflected in the composition of the microbial flora which in hot desert rocks consist entirely of prokaryotic microorganisms, while under cold desert conditions eukaryotes predominate.

  15. Searching for microbial life remotely: Satellite-to-rover habitat mapping in the Atacama Desert, Chile

    NASA Astrophysics Data System (ADS)

    Warren-Rhodes, K.; Weinstein, S.; Dohm, J.; Piatek, J.; Minkley, E.; Hock, A.; Cockell, C.; Pane, D.; Ernst, L. A.; Fisher, G.; Emani, S.; Waggoner, A. S.; Cabrol, N. A.; Wettergreen, D. S.; Apostolopoulos, D.; Coppin, P.; Grin, E.; Diaz, Chong; Moersch, J.; Oril, G. G.; Smith, T.; Stubbs, K.; Thomas, G.; Wagner, M.; Wyatt, M.

    2007-12-01

    The Atacama Desert, one of the most arid landscapes on Earth, serves as an analog for the dry conditions on Mars and as a test bed in the search for life on other planets. During the Life in the Atacama (LITA) 2004 field experiment, satellite imagery and ground-based rover data were used in concert with a `follow-the-water' exploration strategy to target regions of biological interest in two (1 coastal, 1 inland) desert study sites. Within these regions, environments were located, studied and mapped with spectroscopic and fluorescence imaging (FI) for habitats and microbial life. Habitats included aqueous sedimentary deposits (e.g., evaporites), igneous materials (e.g., basalt, ash deposits), rock outcrops, drainage channels and basins, and alluvial fans. Positive biological signatures (chlorophyll, DNA, protein) were detected at 81% of the 21 locales surveyed with the FI during the long-range, autonomous traverses totaling 30 km. FI sensitivity in detecting microbial life in extreme deserts explains the high percentage of positives despite the low actual abundance of heterotrophic soil bacteria in coastal (<1-104 CFU/g-soil) and interior (<1-102 CFU/g-soil) desert soils. Remote habitat, microbial and climate observations agreed well with ground-truth, indicating a drier and less microbially rich interior compared to the relatively wetter and abundant biology of the coastal site where rover sensors detected the presence of fog and abundant surface lichens. LITA project results underscore the importance of an explicit focus by all engineering and science disciplines on microbially relevant scales (mm to nm), and highlight the success of satellite-based and `follow-the-water' strategies for locating diverse habitats of biological promise and detecting the microbial hotspots within them.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  17. Membrane Vesicle Release in Bacteria, Eukaryotes, and Archaea: a Conserved yet Underappreciated Aspect of Microbial Life

    PubMed Central

    Deatherage, Brooke L.

    2012-01-01

    Interaction of microbes with their environment depends on features of the dynamic microbial surface throughout cell growth and division. Surface modifications, whether used to acquire nutrients, defend against other microbes, or resist the pressures of a host immune system, facilitate adaptation to unique surroundings. The release of bioactive membrane vesicles (MVs) from the cell surface is conserved across microbial life, in bacteria, archaea, fungi, and parasites. MV production occurs not only in vitro but also in vivo during infection, underscoring the influence of these surface organelles in microbial physiology and pathogenesis through delivery of enzymes, toxins, communication signals, and antigens recognized by the innate and adaptive immune systems. Derived from a variety of organisms that span kingdoms of life and called by several names (membrane vesicles, outer membrane vesicles [OMVs], exosomes, shedding microvesicles, etc.), the conserved functions and mechanistic strategies of MV release are similar, including the use of ESCRT proteins and ESCRT protein homologues to facilitate these processes in archaea and eukaryotic microbes. Although forms of MV release by different organisms share similar visual, mechanistic, and functional features, there has been little comparison across microbial life. This underappreciated conservation of vesicle release, and the resulting functional impact throughout the tree of life, explored in this review, stresses the importance of vesicle-mediated processes throughout biology. PMID:22409932

  18. Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life.

    PubMed

    Deatherage, Brooke L; Cookson, Brad T

    2012-06-01

    Interaction of microbes with their environment depends on features of the dynamic microbial surface throughout cell growth and division. Surface modifications, whether used to acquire nutrients, defend against other microbes, or resist the pressures of a host immune system, facilitate adaptation to unique surroundings. The release of bioactive membrane vesicles (MVs) from the cell surface is conserved across microbial life, in bacteria, archaea, fungi, and parasites. MV production occurs not only in vitro but also in vivo during infection, underscoring the influence of these surface organelles in microbial physiology and pathogenesis through delivery of enzymes, toxins, communication signals, and antigens recognized by the innate and adaptive immune systems. Derived from a variety of organisms that span kingdoms of life and called by several names (membrane vesicles, outer membrane vesicles [OMVs], exosomes, shedding microvesicles, etc.), the conserved functions and mechanistic strategies of MV release are similar, including the use of ESCRT proteins and ESCRT protein homologues to facilitate these processes in archaea and eukaryotic microbes. Although forms of MV release by different organisms share similar visual, mechanistic, and functional features, there has been little comparison across microbial life. This underappreciated conservation of vesicle release, and the resulting functional impact throughout the tree of life, explored in this review, stresses the importance of vesicle-mediated processes throughout biology. PMID:22409932

  19. Hexacyanoferrate-adapted biofilm enables the development of a microbial fuel cell biosensor to detect trace levels of assimilable organic carbon (AOC) in oxygenated seawater.

    PubMed

    Cheng, Liang; Quek, Soon Bee; Cord-Ruwisch, Ralf

    2014-12-01

    A marine microbial fuel cell (MFC) type biosensor was developed for the detection of assimilable organic carbon (AOC) in ocean water for the purpose of online water quality monitoring for seawater desalination plants prone to biofouling of reverse osmosis (RO) membranes. The anodophilic biofilm that developed on the graphite tissue anode could detect acetate as the model AOC to concentrations as low as 5?M (120?g/L of AOC), which is sufficiently sensitive as an online biofouling risk sensor. Although the sensor was operated at a higher (+200??10?mV) than the usual (-300?mV) anodic potential, the presence of oxygen completely suppressed the electrical signal. In order to overcome this outcompeting effect of oxygen over the anode as electron acceptor by the bacteria, hexacyanoferrate (HCF(III)) was found to enable the development of an adapted biofilm that transferred electrons to HCF(III) rather than oxygen. As the resultant of the reduced HCF(II) could readily transfer electrons to the anode while being re-oxidised to HCF(III), the marine MFC biosensor developed could be demonstrated to work in the presence of oxygen unlike traditional MFC. The possibility of operating the marine MFC in batch or continuous (in-line) mode has been explored by using coulombic or potentiometric interpretation of the signal. PMID:24942462

  20. A 3.8 b.y. History of Bacterial Biofilms and Their Significance in the Search for Extraterrestrial Life

    NASA Technical Reports Server (NTRS)

    Westall, Frances; Steele, Andrew; Toporski, Jan; Walsh, Maud; Allen, Carlton; Guidry, Sean; McKay, David; Gibson, Everett; Chafetz, Henry

    2000-01-01

    Bacterial biofilms are almost ubiquitous in terrestrial environments, many similar to past or present Martian environments. Together with ToF-SIMS analysis of the in situ organics, fossil biofilms constitute reliable biomarkers.

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

    PubMed Central

    Baquero, Fernando; Moya, Andrés

    2012-01-01

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

  2. Microbial life in cold, hydrologically active oceanic crustal fluids

    NASA Astrophysics Data System (ADS)

    Meyer, J. L.; Jaekel, U.; Girguis, P. R.; Glazer, B. T.; Huber, J. A.

    2012-12-01

    It is estimated that at least half of Earth's microbial biomass is found in the deep subsurface, yet very little is known about the diversity and functional roles of these microbial communities due to the limited accessibility of subseafloor samples. Ocean crustal fluids, which may have a profound impact on global nutrient cycles given the large volumes of water moving through the crustal aquifer, are particularly difficult to sample. Access to uncontaminated ocean crustal fluids is possible with CORK (Circulation Obviation Retrofit Kit) observatories, installed through the Integrated Ocean Drilling Program (IODP). Here we present the first microbiological characterization of the formation fluids from cold, oxygenated igneous crust at North Pond on the western flank of the Mid Atlantic Ridge. Fluids were collected from two CORKs installed at IODP boreholes 1382A and 1383C and include fluids from three different depth horizons within oceanic crust. Collection of borehole fluids was monitored in situ using an oxygen optode and solid-state voltammetric electrodes. In addition, discrete samples were analyzed on deck using a comparable lab-based system as well as a membrane-inlet mass spectrometer to quantify all dissolved volatiles up to 200 daltons. The instruments were operated in parallel and both in situ and shipboard geochemical measurements point to a highly oxidized fluid, revealing an apparent slight depletion of oxygen in subsurface fluids (~215?M) relative to bottom seawater (~245?M). We were unable to detect reduced hydrocarbons, e.g. methane. Cell counts indicated the presence of roughly 2 x 10^4 cells per ml in all fluid samples, and DNA was extracted and amplified for the identification of both bacterial and archaeal community members. The utilization of ammonia, nitrate, dissolved inorganic carbon, and acetate was measured using stable isotopes, and oxygen consumption was monitored to provide an estimate of the rate of respiration per cell per day. These results provide the first dataset describing the diversity of microbes present in cold, oxygenated ocean crustal fluids and the biogeochemical processes they mediate in the subseafloor.

  3. Spatial patterns of carbonate biomineralization in biofilms.

    PubMed

    Li, Xiaobao; Chopp, David L; Russin, William A; Brannon, Paul T; Parsek, Matthew R; Packman, Aaron I

    2015-11-01

    Microbially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method for in situ, real-time imaging of biomineralization in biofilms and use it to show that Pseudomonas aeruginosa biofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization produced in situ were substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties. PMID:26276112

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

    PubMed

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

    2009-05-01

    Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology. PMID:19212428

  5. In situ biofilm coupon device

    DOEpatents

    Peyton, Brent M.; Truex, Michael J.

    1997-01-01

    An apparatus for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements.

  6. In situ biofilm coupon device

    DOEpatents

    Peyton, B.M.; Truex, M.J.

    1997-06-24

    An apparatus is disclosed for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements. 3 figs.

  7. Life on the rocks.

    PubMed

    Gorbushina, Anna A

    2007-07-01

    Biofilms are interface micro-habitats formed by microbes that differ markedly from those of the ambient environment. The term 'subaerial biofilm' (SAB) was coined for microbial communities that develop on solid mineral surfaces exposed to the atmosphere. Subaerial biofilms are ubiquitous, self-sufficient, miniature microbial ecosystems that are found on buildings, bare rocks in deserts, mountains, and at all latitudes where direct contact with the atmosphere and solar radiation occurs. Subaerial biofilms on exposed terrestrial surfaces are characterized by patchy growth that is dominated by associations of fungi, algae, cyanobacteria and heterotrophic bacteria. Inherent subaerial settlers include specialized actinobacteria (e.g. Geodermatophilus), cyanobacteria and microcolonial fungi. Individuals within SAB communities avoid sexual reproduction, but cooperate extensively with one another especially to avoid loss of energy and nutrients. Subaerial biofilm metabolic activity centres on retention of water, protecting the cells from fluctuating environmental conditions and solar radiation as well as prolonging their vegetative life. Atmospheric aerosols, gases and propagatory particles serve as sources of nutrients and inoculum for these open communities. Subaerial biofilms induce chemical and physical changes to rock materials, and they penetrate the mineral substrate contributing to rock and mineral decay, which manifests itself as bio-weathering of rock surfaces. Given their characteristic slow and sensitive growth, SAB may also serve as bioindicators of atmospheric and/or climate change. PMID:17564597

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

    PubMed

    Cleland, Carol E

    2007-12-01

    The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'. PMID:18053938

  9. Biogenic selenium and tellurium nanoparticles synthesized by environmental microbial isolates efficaciously inhibit bacterial planktonic cultures and biofilms

    PubMed Central

    Zonaro, Emanuele; Lampis, Silvia; Turner, Raymond J.; Qazi, S. Junaid S.; Vallini, Giovanni

    2015-01-01

    The present study deals with Se0- and Te0-based nanoparticles bio-synthesized by two selenite- and tellurite-reducing bacterial strains, namely Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1, isolated from polluted sites. We evidenced that, by regulating culture conditions and exposure time to the selenite and tellurite oxyanions, differently sized zero-valent Se and Te nanoparticles were produced. The results revealed that these Se0 and Te0 nanoparticles possess antimicrobial and biofilm eradication activity against Escherichia coli JM109, Pseudomonas aeruginosa PAO1, and Staphylococcus aureus ATCC 25923. In particular, Se0 nanoparticles exhibited antimicrobial activity at quite low concentrations, below that of selenite. Toxic effects of both Se0 and Te0 nanoparticles can be related to the production of reactive oxygen species upon exposure of the bacterial cultures. Evidence so far achieved suggests that the antimicrobial activity seems to be strictly linked to the dimensions of the nanoparticles: indeed, the highest activity was shown by nanoparticles of smaller sizes. In particular, it is worth noting how the bacteria tested in biofilm mode responded to the treatment by Se0 and Te0 nanoparticles with a susceptibility similar to that observed in planktonic cultures. This suggests a possible exploitation of both Se0 and Te0 nanoparticles as efficacious antimicrobial agents with a remarkable biofilm eradication capacity. PMID:26136728

  10. Discovering Biofilms: Inquiry-Based Activities for the Classroom

    ERIC Educational Resources Information Center

    Redelman, Carly V.; Marrs, Kathleen; Anderson, Gregory G.

    2012-01-01

    In nature, bacteria exist in and adapt to different environments by forming microbial communities called "biofilms." We propose simple, inquiry-based laboratory exercises utilizing a biofilm formation assay, which allows controlled biofilm growth. Students will be able to qualitatively assess biofilm growth via staining. Recently, we developed a

  11. Discovering Biofilms: Inquiry-Based Activities for the Classroom

    ERIC Educational Resources Information Center

    Redelman, Carly V.; Marrs, Kathleen; Anderson, Gregory G.

    2012-01-01

    In nature, bacteria exist in and adapt to different environments by forming microbial communities called "biofilms." We propose simple, inquiry-based laboratory exercises utilizing a biofilm formation assay, which allows controlled biofilm growth. Students will be able to qualitatively assess biofilm growth via staining. Recently, we developed a…

  12. Characterising the flux of carbon between calcium carbonate substrata, aqueous fluids, bacteria and a biofilm matrix

    NASA Astrophysics Data System (ADS)

    Rankin, S. C.; Cooke, D. A.; Handley, P. S.; Merrifield, C. M.; Wogelius, R. A.

    2003-04-01

    Quantification of the flux of elements between minerals, biofilms and aqueous solutions is essential in order to fully elucidate the role of microorganisms in mass transfer processes. Bacteria play a fundamental role in nearly all life and environmental processes and are by far the most abundant organisms on the planet. Their main mode of growth is in the form of biofilms growing on surfaces and although extensive study has been carried out into the problems biofilms cause to humans, the effects of biofilms in the environment are still poorly understood. Much of the published research describing biofilm growth on geological substrata emphasises the species present rather than their effect on the substratum. Although previous studies have shown that the production of organic or mineral acids by microbial biofilms can cause dissolution of mineral substrata, there is little quantitative data on the specific flux of elements between minerals, microbial cells, biofilm matrix and aqueous solutions. With growing evidence that microbial life occurs in abundance in the subsurface, biofilm activity within buried rocks and sediments may have important implications for global geochemical cycling of specific elements. Results will be presented as part of an ongoing laboratory analog experiment which has been designed to quantify the flux of carbon between all matrices in a laboratory substratum-biofilm-aqueous system. Water collected from a limestone cave system (pH 7.5-8; viable count 4.710^3 - 2.010^4 cfu.ml-1{) is used as innoculum and nutrient source for growing mixed consortium biofilms on a natural calcite (CaCO_3) substratum in a flow-through reaction cell (24 days; 25^oC; 1ml.min^{-1). Portions of the biofilm are periodically removed for microbiological analysis and the mineral surface microscopically examined for extent of alteration. A parallel experiment utilises an isotopically labelled synthetic 13C-CaCO_3 substratum. This enables carbon to be traced from the substratum, through the biofilm and into the aqueous and gas phase by analysing 13C/12C isotopic ratios in all system components. Through this mass-balance approach it is possible to quantify, for the first time, the carbon fluxes into the biofilm and the aqueous solution from the carbonate mineral substrate.

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

    PubMed

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

    2015-01-01

    The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities. PMID:26617595

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

    PubMed Central

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

    2015-01-01

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

  15. Anti-Biofilm Activities from Marine Cold Adapted Bacteria Against Staphylococci and Pseudomonas aeruginosa

    PubMed Central

    Papa, Rosanna; Selan, Laura; Parrilli, Ermenegilda; Tilotta, Marco; Sannino, Filomena; Feller, Georges; Tutino, Maria L.; Artini, Marco

    2015-01-01

    Microbial biofilms have great negative impacts on the world’s economy and pose serious problems to industry, public health and medicine. The interest in the development of new approaches for the prevention and treatment of bacterial adhesion and biofilm formation has increased. Since, bacterial pathogens living in biofilm induce persistent chronic infections due to the resistance to antibiotics and host immune system. A viable approach should target adhesive properties without affecting bacterial vitality in order to avoid the appearance of resistant mutants. Many bacteria secrete anti-biofilm molecules that function in regulating biofilm architecture or mediating the release of cells from it during the dispersal stage of biofilm life cycle. Cold-adapted marine bacteria represent an untapped reservoir of biodiversity able to synthesize a broad range of bioactive compounds, including anti-biofilm molecules. The anti-biofilm activity of cell-free supernatants derived from sessile and planktonic cultures of cold-adapted bacteria belonging to Pseudoalteromonas, Psychrobacter, and Psychromonas species were tested against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa strains. Reported results demonstrate that we have selected supernatants, from cold-adapted marine bacteria, containing non-biocidal agents able to destabilize biofilm matrix of all tested pathogens without killing cells. A preliminary physico-chemical characterization of supernatants was also performed, and these analyses highlighted the presence of molecules of different nature that act by inhibiting biofilm formation. Some of them are also able to impair the initial attachment of the bacterial cells to the surface, thus likely containing molecules acting as anti-biofilm surfactant molecules. The described ability of cold-adapted bacteria to produce effective anti-biofilm molecules paves the way to further characterization of the most promising molecules and to test their use in combination with conventional antibiotics. PMID:26696962

  16. Anti-Biofilm Activities from Marine Cold Adapted Bacteria Against Staphylococci and Pseudomonas aeruginosa.

    PubMed

    Papa, Rosanna; Selan, Laura; Parrilli, Ermenegilda; Tilotta, Marco; Sannino, Filomena; Feller, Georges; Tutino, Maria L; Artini, Marco

    2015-01-01

    Microbial biofilms have great negative impacts on the world's economy and pose serious problems to industry, public health and medicine. The interest in the development of new approaches for the prevention and treatment of bacterial adhesion and biofilm formation has increased. Since, bacterial pathogens living in biofilm induce persistent chronic infections due to the resistance to antibiotics and host immune system. A viable approach should target adhesive properties without affecting bacterial vitality in order to avoid the appearance of resistant mutants. Many bacteria secrete anti-biofilm molecules that function in regulating biofilm architecture or mediating the release of cells from it during the dispersal stage of biofilm life cycle. Cold-adapted marine bacteria represent an untapped reservoir of biodiversity able to synthesize a broad range of bioactive compounds, including anti-biofilm molecules. The anti-biofilm activity of cell-free supernatants derived from sessile and planktonic cultures of cold-adapted bacteria belonging to Pseudoalteromonas, Psychrobacter, and Psychromonas species were tested against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa strains. Reported results demonstrate that we have selected supernatants, from cold-adapted marine bacteria, containing non-biocidal agents able to destabilize biofilm matrix of all tested pathogens without killing cells. A preliminary physico-chemical characterization of supernatants was also performed, and these analyses highlighted the presence of molecules of different nature that act by inhibiting biofilm formation. Some of them are also able to impair the initial attachment of the bacterial cells to the surface, thus likely containing molecules acting as anti-biofilm surfactant molecules. The described ability of cold-adapted bacteria to produce effective anti-biofilm molecules paves the way to further characterization of the most promising molecules and to test their use in combination with conventional antibiotics. PMID:26696962

  17. Biogeophysical interactions control the formation of iron oxide microbial biofilms in acidic geothermal outflow channels of Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Beam, J.; Berstein, H. C.; Jay, Z.; Kozubal, M. A.; Jennings, R. D.; Inskeep, W. P.

    2012-12-01

    Amorphous iron oxyhydroxide microbial mats in acidic (pH ~ 3) geothermal outflow channels of Yellowstone National Park (YNP) are habitats for diverse populations of autotrophic and heterotrophic microorganisms from the domains Archaea and Bacteria. These systems have been extensively characterized with regards to geochemical, physical, and microbiological (e.g., metagenomics) analyses; however, there is minimal data describing the formation of these iron oxide microbial mats. A conceptual model of Fe(III)-oxide microbial mat development was created, which includes four distinct stages. Autotrophic archaea (Metallosphaera yellowstonensis) and bacteria (Hydrogenobaculum spp.) are the first colonizers (Stage I) that provide pools of organic carbon for heterotrophic thermophiles (Stage II). M. yellowstonensis is an autotrophic Sulfolobales that is responsible for the oxidation of Fe(II) and can thus be defined as the mat 'architect' creating suitable habitats for microbial niches (e.g., anaerobic microorganisms) (Stage III). The last phase of mat formation (Stage IV) represents a pseudo-steady state mature microbial mat, which has been the subject of all previous microbial surveys of these systems. The conceptual model for Fe(III)-oxide microbial mat development was tested by inserting glass (SiO2) microscope slides into the main flow channels of two acidic geothermal springs in YNP. Slides were removed at various time intervals and analyzed for total iron accretion, microbial community structure (i.e., 16S rRNA gene abundance), and mRNA expression of community members. Routine geochemical and physical (e.g., flow) parameters were also measured to decipher their relative contribution to mat development. Initial and previous results show that autotrophic microorganisms (e.g, M. yellowstonensis) are often the first to colonize the glass slides and their activity was confirmed by mRNA expression of genes related to iron oxidation and carbon fixation. Heterotrophs are rare during the initial stages of Fe (III)-oxide mat formation (< 28 days) and become more abundant after ~28 days, which likely coincides with a higher abundance of organic carbon from autotrophs. Aerobic microorganisms have been detected in greater abundance at the mat/water interface where oxygen microelectrode measurements reveal steep gradients in oxygen consumption (i.e., niche partitioning). A mature microbial mat is typically formed after ~2-4 months and reaches a pseudo-steady state depth of ~7-10 mm. Flow rates had a significant affect on Fe(III)-oxide deposition and community structure. These results suggest that dynamic biological, geochemical, and physical processes control the formation and cycling of Fe(III)-oxide microbial mats in acidic geothermal springs.

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

    PubMed

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

    2012-03-01

    Information on factors limiting the shelf life of extended shelf life (ESL) milk produced by microfiltration and subsequent pasteurization is very limited. In this study, three different batches of ESL milk were analyzed at different stages of the production process and during storage at 4 C, 8 C and 10 C in order to evaluate the changes in bacterial cell counts, microbial diversity and enzymatic quality. Additionally, detailed biodiversity analyses of 250 retail ESL milk packages produced by five manufacturers in Germany, Austria and Switzerland were performed at the end of shelf life. It was observed that microfiltration decreased the microbial loads by 5-6 log?? units to lower than 1 CFU/mL. However, bacterial counts at the end of shelf life were extremely variable and ranged between <1 and 8 log?? CFU/mL. 8% of all samples showed spoilage indicated by cell counts higher than 6 log?? CFU/mL. The main spoilage groups of bacteria were Gram-negative post-process recontaminants (Acinetobacter, Chryseobacterium, Psychrobacter, Sphingomonas) and the spore formers Paenibacillus and Bacillus cereus, while other spore formers and Microbacterium spp. did not reach spoilage levels. Paenibacillus spp. and B. cereus apparently influenced enzymatic spoilage, as indicated by increased free fatty acid production, pH 4.6 soluble peptide fractions and off-flavors. In some cases, enzymatic spoilage was observed although microbial counts were well below 6 log?? CFU/mL. Thirteen B. cereus isolates were characterized for their toxin profiles and psychrotolerance. Hbl, nhe, and cytK toxin genes were detected in ten, thirteen, and four isolates, respectively, whereas the ces gene was always absent. Interestingly, only three of the thirteen isolates could be allocated to psychrotolerant genotypes, as indicated by the major cold shock cspA gene signature. Generally, large discrepancies in microbial loads and biodiversity were observed at the end of shelf life, even among packages of the same production batch. We suggest that such unexpected differences may be due to very low cell counts after ESL treatment, causing stochastic variations of initial species distributions in individual packages. This would result in the development of significantly different bacterial populations during cold storage, including the occasional development of high numbers of pathogenic species such as B. cereus or Acinetobacter. PMID:22240060

  19. Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis.

    PubMed

    Loureno, Talita Gomes Bata; Heller, Dbora; do Souto, Renata Martins; Silva-Senem, Mayra Xavier E; Varela, Victor Macedo; Torres, Maria Cynesia Barros; Feres-Filho, Eduardo Jorge; Colombo, Ana Paula Vieira

    2015-06-01

    This study evaluates the antimicrobial susceptibility and composition of subgingival biofilms in generalized aggressive periodontitis (GAP) patients treated using mechanical/antimicrobial therapies, including chlorhexidine (CHX), amoxicillin (AMX) and metronidazole (MET). GAP patients allocated to the placebo (C, n = 15) or test group (T, n = 16) received full-mouth disinfection with CHX, scaling and root planning, and systemic AMX (500 mg)/MET (250 mg) or placebos. Subgingival plaque samples were obtained at baseline, 3, 6, 9 and 12 months post-therapy from 3-4 periodontal pockets, and the samples were pooled and cultivated under anaerobic conditions. The minimum inhibitory concentrations (MICs) of AMX, MET and CHX were assessed using the microdilution method. Bacterial species present in the cultivated biofilm were identified by checkerboard DNA-DNA hybridization. At baseline, no differences in the MICs between groups were observed for the 3 antimicrobials. In the T group, significant increases in the MICs of CHX (p < 0.05) and AMX (p < 0.01) were detected during the first 3 months; however, the MIC of MET decreased at 12 months (p < 0.05). For several species, the MICs significantly changed over time in both groups, i.e., Streptococci MICs tended to increase, while for several periodontal pathogens, the MICs diminished. A transitory increase in the MIC of the subgingival biofilm to AMX and CHX was observed in GAP patients treated using enhanced mechanical therapy with topical CHX and systemic AMX/MET. Both protocols presented limited effects on the cultivable subgingival microbiota. PMID:26273264

  20. Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis

    PubMed Central

    Lourenço, Talita Gomes Baêta; Heller, Débora; do Souto, Renata Martins; Silva-Senem, Mayra Xavier e; Varela, Victor Macedo; Torres, Maria Cynesia Barros; Feres-Filho, Eduardo Jorge; Colombo, Ana Paula Vieira

    2015-01-01

    This study evaluates the antimicrobial susceptibility and composition of subgingival biofilms in generalized aggressive periodontitis (GAP) patients treated using mechanical/antimicrobial therapies, including chlorhexidine (CHX), amoxicillin (AMX) and metronidazole (MET). GAP patients allocated to the placebo (C, n = 15) or test group (T, n = 16) received full-mouth disinfection with CHX, scaling and root planning, and systemic AMX (500 mg)/MET (250 mg) or placebos. Subgingival plaque samples were obtained at baseline, 3, 6, 9 and 12 months post-therapy from 3–4 periodontal pockets, and the samples were pooled and cultivated under anaerobic conditions. The minimum inhibitory concentrations (MICs) of AMX, MET and CHX were assessed using the microdilution method. Bacterial species present in the cultivated biofilm were identified by checkerboard DNA-DNA hybridization. At baseline, no differences in the MICs between groups were observed for the 3 antimicrobials. In the T group, significant increases in the MICs of CHX (p < 0.05) and AMX (p < 0.01) were detected during the first 3 months; however, the MIC of MET decreased at 12 months (p < 0.05). For several species, the MICs significantly changed over time in both groups, i.e., Streptococci MICs tended to increase, while for several periodontal pathogens, the MICs diminished. A transitory increase in the MIC of the subgingival biofilm to AMX and CHX was observed in GAP patients treated using enhanced mechanical therapy with topical CHX and systemic AMX/MET. Both protocols presented limited effects on the cultivable subgingival microbiota. PMID:26273264

  1. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    SciTech Connect

    University of Illinois at Chicago; Montana State University; Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-04-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups two ?pure? groups and a mixed region. Furthermore, the ?pure? regions of the E. coli cocultures showed greater variance by PCA when analyzed by 7.87 eV photon energies than by 10.5 eV radiation. Comparison of the 7.87 and 10.5 eV data is consistent with the expectation that the lower photon energy selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

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

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  3. "Primers" on Research Techniques Used in Geomicrobiology for Students and Novices from Microbial Life Educational Resources

    NASA Astrophysics Data System (ADS)

    Bruckner, M. Z.; Rice, G.; Mogk, D. W.

    2007-12-01

    Microbial Life Educational Resources (MLER) provides web-based resources and services that support learning about the diversity, ecology and evolution of the (geo)microbial world for students, K-12 teachers, university faculty, as well as for the general public. One of the main goals of MLER is to facilitate integration of modern research techniques and results and effective instructional practices. Two new collections of on-line resources include 1) TechniqueSheets which are 'primers' on analytical techniques commonly used in field and laboratory studies, and 2) focused case studies that demonstrate the use of these techniques in research projects supported by NSF's Microbial Observatory program. TechniqueSheets provide educators and students with essential information about common field and laboratory techniques with image-rich contemporary examples of the employment of these methods in the biogeosciences and microbial life realms. A wide variety of techniques are described including environmental sampling, biogeochemical methods, genomic methods, and microscopy. Every technique includes a general description of what the technique is and how it works, background theory, instrumentation, typical applications and limitations, sampling and sample preparation protocols, data collection, reduction, and representation; interpretations, links to the scientific literature, and collections of related teaching activities. Web-based profiles of the Microbial Observatory projects provide students with case-based learning environments that a) define the "big scientific questions," b) introduce the research teams, c) demonstrate modern research strategies and methodologies, and d) present the key scientific findings. These case studies span a variety of locations from microbial life in the extreme environments of Yellowstone National Park to the diversity of marine sponges in Florida to microbial diversity in Antarctic lakes. The goal of these websites is to help students and other novice-learners to be "critical consumers" of scientific data, to understand how the data were obtained and interpreted, to be able to ask the next important question, to be able to communicate with colleagues in related disciplines, to be able to attend a departmental seminar or read a journal article and be able to comprehend the evidence and interpretations, and ultimately, to provide the foundations that will allow students to design and implement their own research projects employing these techniques. This project was supported by NSF grants 0333402 and 0333363.

  4. Microbial life at high salt concentrations: phylogenetic and metabolic diversity

    PubMed Central

    Oren, Aharon

    2008-01-01

    Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine, ectoine and other amino acid derivatives, sugars and sugar alcohols. The 'high-salt-in strategy' is not limited to the Halobacteriaceae. The Halanaerobiales (Firmicutes) also accumulate salt rather than organic solutes. A third, phylogenetically unrelated organism accumulates KCl: the red extremely halophilic Salinibacter (Bacteroidetes), recently isolated from saltern crystallizer brines. Analysis of its genome showed many points of resemblance with the Halobacteriaceae, probably resulting from extensive horizontal gene transfer. The case of Salinibacter shows that more unusual types of halophiles may be waiting to be discovered. PMID:18412960

  5. Microbial interaction between a CTXM-15 -producing Escherichia coli and a susceptible Pseudomonas aeruginosa isolated from bronchoalveolar lavage: influence of cefotaxime in the dual-species biofilm formation.

    PubMed

    Bessa, Lucinda J; Mendes, Ângelo; Gomes, Rita; Curvelo, Sara; Cravo, Sara; Sousa, Emília; Vasconcelos, Vitor; Martins da Costa, Paulo

    2015-06-01

    Two isolates, Escherichia coli ella00 and Pseudomonas aeruginosa ella01, obtained from bronchoalveolar lavage, were found to be closely associated in clusters in agar medium. Escherichia coli ella00 was multidrug resistant and CTXM-15 extended-spectrum β-lactamase producer, while P. aeruginosa ella01 was susceptible to all antimicrobials tested. These observations impelled for further studies aimed to understand their microbial interaction. The P. aeruginosa ella01 biofilm-forming capacity was reduced and not affected when it was co-cultured with E. coli ella00 and E. coli ATCC 25922 respectively. Interestingly, the co-culture of ella isolates in the presence of high concentrations, such as 160 μg ml(-1) , of cefotaxime allowed the formation of more biofilm than in the absence of the antibiotic. As revealed by fluorescence in situ hybridization, in co-culture, P. aeruginosa ella01 survived and subsequently flourished when exposed to this third-generation cephalosporin at a concentration 10 × higher than its minimum inhibitory concentration (MIC), and this was mostly due to β-lactamases production by E. coli ella00. In fact, it was demonstrated by high-performance liquid chromatography that cefotaxime was absent for the culture medium 4 h after application. In conclusion, we demonstrate that bacterial species can interact differently depending on the surrounding conditions (favourable or stressing), and that those interactions can switch from unprofitable to beneficial. PMID:25625458

  6. Biofilm in endodontics: A review.

    PubMed

    Jhajharia, Kapil; Parolia, Abhishek; Shetty, K Vikram; Mehta, Lata Kiran

    2015-01-01

    Endodontic disease is a biofilm-mediated infection, and primary aim in the management of endodontic disease is the elimination of bacterial biofilm from the root canal system. The most common endodontic infection is caused by the surface-associated growth of microorganisms. It is important to apply the biofilm concept to endodontic microbiology to understand the pathogenic potential of the root canal microbiota as well as to form the basis for new approaches for disinfection. It is foremost to understand how the biofilm formed by root canal bacteria resists endodontic treatment measures. Bacterial etiology has been confirmed for common oral diseases such as caries and periodontal and endodontic infections. Bacteria causing these diseases are organized in biofilm structures, which are complex microbial communities composed of a great variety of bacteria with different ecological requirements and pathogenic potential. The biofilm community not only gives bacteria effective protection against the host's defense system but also makes them more resistant to a variety of disinfecting agents used as oral hygiene products or in the treatment of infections. Successful treatment of these diseases depends on biofilm removal as well as effective killing of biofilm bacteria. So, the fundamental to maintain oral health and prevent dental caries, gingivitis, and periodontitis is to control the oral biofilms. From these aspects, the formation of biofilms carries particular clinical significance because not only host defense mechanisms but also therapeutic efforts including chemical and mechanical antimicrobial treatment measures have the most difficult task of dealing with organisms that are gathered in a biofilm. The aim of this article was to review the mechanisms of biofilms' formation, their roles in pulpal and periapical pathosis, the different types of biofilms, the factors influencing biofilm formation, the mechanisms of their antimicrobial resistance, techniques to identify biofilms. PMID:25767760

  7. Life in a drop of Ocean: microfluidic insights into microbial ecology

    NASA Astrophysics Data System (ADS)

    Stocker, Roman

    2008-03-01

    Bacteria are the most abundant and successful form of life on Earth. Their physico-chemical interactions with their fluid environment are surprisingly complex and have enormous implications, which we can only hope to grasp if we learn to study microorganisms within realistic microenvironments. Microfluidics for the first time enables us to create microhabitats, including chemical and fluid mechanical landscapes, while visualizing bacterial behavior at a single-cell resolution. Here I focus on the application of microfluidics to gain insight in the life of marine bacteria. In their quest for nturients, marine bacteria often experience the Ocean as a desert, where rare and ephemeral nutrient patches represent transient resource oases. In this patchy seascape, swimming and chemotaxis represent critical assets, but effective patch utilization is constrained by energetic requirements. And then there are predators and viruses... These interactions form the basis of the 'microbial loop', the ensemble of microbial processes known to directly impact the productivity of marine ecosystems and the rates of carbon turnover in the Ocean. I will show how fundamental new insight on selected aspects of microbial life in a drop of Ocean can be achieved by a combination of microfluidic experiments and theoretical modeling.

  8. Metagenomic Analysis of Showerhead Biofilms from a Hospital in Ohio

    EPA Science Inventory

    Background: The National Institute of Health estimated that 80% of human microbial infections are associated with biofilms. Although water supplies and hospital equipments are constantly treated with disinfectants, the presence of biofilms in these areas has been frequently obser...

  9. Pyrosequencing analysis of eukaryotic and bacterial communities in faucet biofilms.

    PubMed

    Liu, Ruyin; Yu, Zhisheng; Guo, Hongguang; Liu, Miaomiao; Zhang, Hongxun; Yang, Min

    2012-10-01

    In order to understand the microbial communities in drinking water biofilms, both eukaryotic and bacterial communities in three faucet biofilms were characterized by 454 pyrosequencing and quantitative PCR approaches. Microbial assemblages of the biofilms were dominated by bacteria, with Sphingomonadales, Rhizobiales, and Burkholderiales comprising the major bacterial populations. Although about 2 years of biofilm development occurred, the microbial community at site WSW still demonstrates the characteristics of a young biofilm community, e.g. low biomass, abundant aggregating bacteria (Blastomonas spp. and Acidovorax spp.) etc. Hartmannella of amoebae was the dominant eukaryotic predator in the biofilms, and correlated closely with biofilm bacterial biomass. Nonetheless, there was no obvious association of pathogens with amoebae in the faucet biofilms. In contrast, residual chlorine seems to be a dominant factor impacting the abundance of Legionella and Mycobacterium, two primary potential opportunistic pathogens detected in all faucet biofilms. PMID:22846772

  10. Viscoelastic Properties of Levan-DNA Mixtures Important in Microbial Biofilm Formation as Determined by Micro- and Macrorheology

    PubMed Central

    Stojković, Biljana; Sretenovic, Simon; Dogsa, Iztok; Poberaj, Igor; Stopar, David

    2015-01-01

    We studied the viscoelastic properties of homogeneous and inhomogeneous levan-DNA mixtures using optical tweezers and a rotational rheometer. Levan and DNA are important components of the extracellular matrix of bacterial biofilms. Their viscoelastic properties influence the mechanical as well as molecular-transport properties of biofilm. Both macro- and microrheology measurements in homogeneous levan-DNA mixtures revealed pseudoplastic behavior. When the concentration of DNA reached a critical value, levan started to aggregate, forming clusters of a few microns in size. Microrheology using optical tweezers enabled us to measure local viscoelastic properties within the clusters as well as in the DNA phase surrounding the levan aggregates. In phase-separated levan-DNA mixtures, the results of macro- and microrheology differed significantly. The local viscosity and elasticity of levan increased, whereas the local viscosity of DNA decreased. On the other hand, the results of bulk viscosity measurements suggest that levan clusters do not interact strongly with DNA. Upon treatment with DNase, levan aggregates dispersed. These results demonstrate the advantages of microrheological measurements compared to bulk viscoelastic measurements when the materials under investigation are complex and inhomogeneous, as is often the case in biological samples. PMID:25650942

  11. Towards a Miniaturized System for Microbial Monitoring of Life Support Applications

    NASA Astrophysics Data System (ADS)

    Abaibou, Hafid; Storrs, Michele; Broyer, Patrick; Drevet, Christophe; Guy, Michel; Mabilat, Claude; Lasseur, Christophe

    Russian astronauts and associated research organisations have demonstrated the risks associ-ated with microbial contamination for long term manned missions. These risks concern both crew health through the contamination of metabolic consumables (water, air) and also degra-dation of hardware. Over the last 10 years, ESA and bioMérieux S.A. (F, I, NL) have been developing an automated instrument for rapid microbial detection for air and surface samples based on molecular detection. Rapid molecular biology techniques are perceived as an attractive alternative to traditional culture-based methods for the detection of microbial contamination allowing fast time to results and permitting fast implementation of appropriate corrective action if needed. To date, there are no commercially-available fully automated systems allowing such tests due to the technical challenges required for test development and the need for full automation. This presentation will first explain the life support requirements for long term manned space missions and then describe the rapid molecular tools which have been developed in collaboration between ESA and bioMérieux. These tools allow the detection of nucleic acids of all bacteria and all fungi (microbial load) in a sample, that is a molecular total count of all microbes present in a sample. We will also describe a prototype instrument which can simultaneously perform nucleic acid extraction from environmental samples (air, surfaces and water) and amplification/detection of their purified nucleic acids, enabling a molecular microbial load count in less than 3 hours. It is currently being adapted to life support context with the help of an European space industry (NTE, Spain). This system was presented at Cospar 2008 from a planetary protection viewpoint. Here we update on the development concentrating on crew health aspects.

  12. The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life

    PubMed Central

    Renwick, Julie; McNally, Paul; John, Bettina; DeSantis, Todd; Linnane, Barry; Murphy, Philip

    2014-01-01

    Background Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF) airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF. Methods Bronchoalveolar lavage (BAL) fluid and paired oropharyngeal swabs from clinically stable children with CF (n?=?13) and BAL from children without CF (n?=?9) were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed. Results A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p?=?0.001; t test) and Principle coordinate analysis (p?=?0.01; Adonis test). Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu. Conclusion The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF. PMID:25526264

  13. Deep microbial life in the Altmark natural gas reservoir: baseline characterization prior CO2 injection

    NASA Astrophysics Data System (ADS)

    Morozova, Daria; Shaheed, Mina; Vieth, Andrea; Krüger, Martin; Kock, Dagmar; Würdemann, Hilke

    2010-05-01

    Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of about 3500m, is characterised by high salinity fluid and temperatures up to 127° C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery) the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism) and DGGE (Denaturing Gradient Gel Electrophoresis). First results of the baseline survey indicate the presence of microorganisms similar to representatives from other saline, hot, anoxic, deep environments. However, due to the hypersaline and hyperthermophilic reservoir conditions, cell numbers are low, so that the quantification of those microorganisms as well as the determination of microbial activity was not yet possible. Microbial monitoring methods have to be further developed to study microbial activities under these extreme conditions to access their influence on the EGR technique and on enhancing the long term safety of the process by fixation of carbon dioxide by precipitation of carbonates. We would like to thank GDF SUEZ for providing the data for the Rotliegend reservoir, sample material and enabling sampling campaigns. The CLEAN project is funded by the German Federal Ministry of Education and Research (BMBF) in the frame of the Geotechnologien Program.

  14. Impact of drinking water conditions and copper materials on downstream biofilm microbial communities and legionella pneumophila colonization

    EPA Science Inventory

    Legionella pneumophila, the medically important species within the genus Legionella, is a concern in engineered water systems. Its ability to amplify within free-living amoebae is well documented, but its interactions/ecology within the microbial community of drinking water biofi...

  15. Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

    PubMed

    Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

    2014-11-01

    Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. PMID:25109340

  16. Biofilm in endodontics: A review

    PubMed Central

    Jhajharia, Kapil; Parolia, Abhishek; Shetty, K Vikram; Mehta, Lata Kiran

    2015-01-01

    Endodontic disease is a biofilm-mediated infection, and primary aim in the management of endodontic disease is the elimination of bacterial biofilm from the root canal system. The most common endodontic infection is caused by the surface-associated growth of microorganisms. It is important to apply the biofilm concept to endodontic microbiology to understand the pathogenic potential of the root canal microbiota as well as to form the basis for new approaches for disinfection. It is foremost to understand how the biofilm formed by root canal bacteria resists endodontic treatment measures. Bacterial etiology has been confirmed for common oral diseases such as caries and periodontal and endodontic infections. Bacteria causing these diseases are organized in biofilm structures, which are complex microbial communities composed of a great variety of bacteria with different ecological requirements and pathogenic potential. The biofilm community not only gives bacteria effective protection against the host's defense system but also makes them more resistant to a variety of disinfecting agents used as oral hygiene products or in the treatment of infections. Successful treatment of these diseases depends on biofilm removal as well as effective killing of biofilm bacteria. So, the fundamental to maintain oral health and prevent dental caries, gingivitis, and periodontitis is to control the oral biofilms. From these aspects, the formation of biofilms carries particular clinical significance because not only host defense mechanisms but also therapeutic efforts including chemical and mechanical antimicrobial treatment measures have the most difficult task of dealing with organisms that are gathered in a biofilm. The aim of this article was to review the mechanisms of biofilms’ formation, their roles in pulpal and periapical pathosis, the different types of biofilms, the factors influencing biofilm formation, the mechanisms of their antimicrobial resistance, techniques to identify biofilms. PMID:25767760

  17. Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

    PubMed Central

    Cahenzli, Julia; Köller, Yasmin; Wyss, Madeleine; Geuking, Markus B.; McCoy, Kathy D.

    2013-01-01

    Summary Microbial exposure following birth profoundly impacts mammalian immune system development. Microbiota alterations are associated with increased incidence of allergic and autoimmune disorders with elevated serum IgE as a hallmark. The previously reported abnormally high serum IgE levels in germ-free mice suggests that immunoregulatory signals from microbiota are required to control basal IgE levels. We report that germ-free mice and those with low-diversity microbiota develop elevated serum IgE levels in early life. B cells in neonatal germ-free mice undergo isotype switching to IgE at mucosal sites in a CD4 T-cell- and IL-4-dependent manner. A critical level of microbial diversity following birth is required in order to inhibit IgE induction. Elevated IgE levels in germ-free mice lead to increased mast-cell-surface-bound IgE and exaggerated oral-induced systemic anaphylaxis. Thus, appropriate intestinal microbial stimuli during early life are critical for inducing an immunoregulatory network that protects from induction of IgE at mucosal sites. PMID:24237701

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

    NASA Technical Reports Server (NTRS)

    Friedmann, E. Imre; Friedmann, Roseli O.

    1989-01-01

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

  19. In Situ Identification and Stratification of Monochloramine Inhibition Effects on Nitrifying Biofilms as Determined by the Use of Microelectrodes

    EPA Science Inventory

    The nitrifying biofilm grown in an annular biofilm reactor and the microbial deactivation achieved after monochloramine treatment were investigated using microelectrodes. The nitrifying biofilm ammonium microprofile was measured and the effect of monochloramine on nitrifying bio...

  20. Bifunctional quaternary ammonium compounds to inhibit biofilm growth and enhance performance for activated carbon air-cathode in microbial fuel cells

    NASA Astrophysics Data System (ADS)

    Li, Nan; Liu, Yinan; An, Jingkun; Feng, Cuijuan; Wang, Xin

    2014-12-01

    The slow diffusion of hydroxyl out of the catalyst layer as well as the biofouling on the surface of cathode are two problems affecting power for membrane-less air-cathode microbial fuel cells (MFCs). In order to solve both of them simultaneously, here we simply modify activated carbon air-cathode using a bifunctional quaternary ammonium compound (QAC) by forced evaporation. The maximum power density reaches 1041 ± 12 mW m-2 in an unbuffered medium (0.5 g L-1 NaCl), which is 17% higher than the control, probably due to the accelerated anion transport in the catalyst layer. After 2 months, the protein content reduced by a factor of 26 and the power density increases by 33%, indicating that the QAC modification can effectively inhibit the growth of cathodic biofilm and improve the stability of performance. The addition of NaOH and QAC epoxy have a negative effect on power production due to the clogging of pores in catalyst layer.

  1. Development and Test of a Probe to Remotely Sense Microbial Life

    NASA Astrophysics Data System (ADS)

    Bramall, N.; Bay, R.; Price, B.

    2003-12-01

    Fluorescence spectroscopy is a powerful and highly sensitive tool useful for remotely searching for sub-surface microbial life. Ubiquitous biomolecules in microorganisms (e.g. tryptophan and NADH) have unique autofluorescence spectra that allow them to be optically detected at low levels even in the presence of a fluorescence background from minerals. Based on this technique, we have developed and tested a first-generation Biospectral Logger (BSL); an instrument suitable for logging boreholes and aquatic environments which uses a 370 nm excitation source and a bank of seven notch-filtered phototubes to record the spectrum of microbial NADH fluorescence. The first generation BSL was constructed and tested in Lake Tahoe, where it recorded chlorophyll fluorescence that peaked at a depth of about 57 m and then decreased with depth. NADH fluorescence was found to peak and fall off with chlorophyll for shallow depths, but then began increasing again at deeper depths, which agrees with the results of independently performed cell counts. In order to optimize the discrimination between microbial life and its environment, we used a laboratory fluorimeter to map out the emission spectra of a diverse collection of microbes and minerals as a function of excitation wavelength, which we varied between 224 nm and 460 nm. Based on these data, we have planned future developments of the BSL technology that make it more selective and able to be used in more extreme environments such as deep mine boreholes, permafrost, deep-ocean settings, and ultimately Martian permafrost, where its greatly-increased sensitivity will be sufficient to detect microbial concentrations down to ~1 cell/cm3 in media with relatively low background

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

    PubMed

    Unluturk, Sevcan; Atilgan, Mehmet R

    2015-08-01

    The effects of UV-C irradiation on the inactivation of Escherichia coli K-12 (ATCC 25253), a surrogate of E. coli O157:H7, and on the shelf life of freshly squeezed turbid white grape juice (FSWGJ) were investigated. FSWGJ samples were processed at 0.90 mL/s for 32 min by circulating 8 times in an annular flow UV system. The UV exposure time was 244 s per cycle. The population of E. coli K-12 was reduced by 5.34 log cycles after exposure to a total UV dosage of 9.92 J/cm(2) (1.24 J/cm(2) per cycle) at 0.90 mL/s flow rate. The microbial shelf life of UV-C treated FSWGJ was extended up to 14 d at 4 C. UV exposure was not found to alter pH, total soluble solid, and titratable acidity of juice. There was a significant effect (P < 0.05) on turbidity, absorbance coefficient, color, and ascorbic acid content. Furthermore, all physicochemical properties were altered during refrigerated storage. The microbial shelf life of FSWGJ was doubled after UV-C treatment, whereas the quality of juice was adversely affected similarly observed in the control samples. PMID:26177986

  3. Candida Biofilms: Development, Architecture, and Resistance

    PubMed Central

    CHANDRA, JYOTSNA; MUKHERJEE, PRANAB K.

    2015-01-01

    Intravascular device–related infections are often associated with biofilms (microbial communities encased within a polysaccharide-rich extracellular matrix) formed by pathogens on the surfaces of these devices. Candida species are the most common fungi isolated from catheter-, denture-, and voice prosthesis–associated infections and also are commonly isolated from contact lens–related infections (e.g., fungal keratitis). These biofilms exhibit decreased susceptibility to most antimicrobial agents, which contributes to the persistence of infection. Recent technological advances have facilitated the development of novel approaches to investigate the formation of biofilms and identify specific markers for biofilms. These studies have provided extensive knowledge of the effect of different variables, including growth time, nutrients, and physiological conditions, on biofilm formation, morphology, and architecture. In this article, we will focus on fungal biofilms (mainly Candida biofilms) and provide an update on the development, architecture, and resistance mechanisms of biofilms. PMID:26350306

  4. Trace gases in the atmosphere of Mars - An indicator of microbial life

    NASA Technical Reports Server (NTRS)

    Levine, Joel S.; Rinsland, Curtis P.; Boston, Penelope J.; Cofer, Wesley R., III; Chameides, William L.

    1989-01-01

    The detection of certain trace gases in the atmosphere of Mars would indicate the presence of microbial life on the surface. Candidate biogenic gases include CH4, NH3, N2O, and several reduced sulfur species. Chemical thermodynamic equilibrium and photochemical calculations preclude the presence of these gases in any measurable concentrations in the atmosphere of Mars in the absence of biogenic production. A search for these gases utilizing either high-resolution (spectral and spatial) spectroscopy from a Mars orbiter, such as the Mars Observer orbiter, and/or in situ measurements from a Mars lander or rover is proposed.

  5. Synthetic networks in microbial communities

    NASA Astrophysics Data System (ADS)

    Suel, Gurol

    2015-03-01

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

  6. Life on the outside: role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli

    PubMed Central

    Vogeleer, Philippe; Tremblay, Yannick D. N.; Mafu, Akier A.; Jacques, Mario; Harel, Josée

    2014-01-01

    Escherichia coli is a heterogeneous species that can be part of the normal flora of humans but also include strains of medical importance. Among pathogenic members, Shiga-toxin producing E. coli (STEC) are some of the more prominent pathogenic E. coli within the public sphere. STEC disease outbreaks are typically associated with contaminated beef, contaminated drinking water, and contaminated fresh produce. These water- and food-borne pathogens usually colonize cattle asymptomatically; cows will shed STEC in their feces and the subsequent fecal contamination of the environment and processing plants is a major concern for food and public safety. This is especially important because STEC can survive for prolonged periods of time outside its host in environments such as water, produce, and farm soil. Biofilms are hypothesized to be important for survival in the environment especially on produce, in rivers, and in processing plants. Several factors involved in biofilm formation such as curli, cellulose, poly-N-acetyl glucosamine, and colanic acid are involved in plant colonization and adherence to different surfaces often found in meat processing plants. In food processing plants, contamination of beef carcasses occurs at different stages of processing and this is often caused by the formation of STEC biofilms on the surface of several pieces of equipment associated with slaughtering and processing. Biofilms protect bacteria against several challenges, including biocides used in industrial processes. STEC biofilms are less sensitive than planktonic cells to several chemical sanitizers such as quaternary ammonium compounds, peroxyacetic acid, and chlorine compounds. Increased resistance to sanitizers by STEC growing in a biofilm is likely to be a source of contamination in the processing plant. This review focuses on the role of biofilm formation by STEC as a means of persistence outside their animal host and factors associated with biofilm formation. PMID:25071733

  7. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation

    NASA Astrophysics Data System (ADS)

    Yakimov, Michail M.; La Cono, Violetta; Slepak, Vladlen Z.; La Spada, Gina; Arcadi, Erika; Messina, Enzo; Borghini, Mireno; Monticelli, Luis S.; Rojo, David; Barbas, Coral; Golyshina, Olga V.; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

    2013-12-01

    Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [14C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life.

  8. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation

    PubMed Central

    Yakimov, Michail M.; La Cono, Violetta; Slepak, Vladlen Z.; La Spada, Gina; Arcadi, Erika; Messina, Enzo; Borghini, Mireno; Monticelli, Luis S.; Rojo, David; Barbas, Coral; Golyshina, Olga V.; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

    2013-01-01

    Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [14C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life. PMID:24352146

  9. An Update on the Management of Endodontic Biofilms Using Root Canal Irrigants and Medicaments

    PubMed Central

    Mohammadi, Zahed; Soltani, Mohammad Karim; Shalavi, Sousan

    2014-01-01

    Microbial biofilm is defined as a sessile multicellular microbial community characterized by cells that are firmly attached to a surface and enmeshed in a self-produced matrix of extracellular polymeric substances. Biofilms play a very important role in pulp and periradicular pathosis. The aim of this article was to review the role of endodontic biofilms and the effects of root canal irrigants, medicaments as well as lasers on biofilms A Medline search was performed on the English articles published from 1982 to 2013 and was limited to papers published in English. The searched keywords were “Biofilms AND endodontics”, “Biofilms AND sodium hypochlorite”, "Biofilms AND chlorhexidine", "Biofilms AND MTAD", "Biofilms AND calcium hydroxide", “Biofilms AND ozone”, “Biofilms AND lasers” and "Biofilms AND nanoparticles". The reference list of each article was manually searched to find other suitable sources of information. PMID:24688576

  10. Bacterial biofilms: from the natural environment to infectious diseases.

    PubMed

    Hall-Stoodley, Luanne; Costerton, J William; Stoodley, Paul

    2004-02-01

    Biofilms--matrix-enclosed microbial accretions that adhere to biological or non-biological surfaces--represent a significant and incompletely understood mode of growth for bacteria. Biofilm formation appears early in the fossil record (approximately 3.25 billion years ago) and is common throughout a diverse range of organisms in both the Archaea and Bacteria lineages, including the 'living fossils' in the most deeply dividing branches of the phylogenetic tree. It is evident that biofilm formation is an ancient and integral component of the prokaryotic life cycle, and is a key factor for survival in diverse environments. Recent advances show that biofilms are structurally complex, dynamic systems with attributes of both primordial multicellular organisms and multifaceted ecosystems. Biofilm formation represents a protected mode of growth that allows cells to survive in hostile environments and also disperse to colonize new niches. The implications of these survival and propagative mechanisms in the context of both the natural environment and infectious diseases are discussed in this review. PMID:15040259

  11. Microbial ecology and host-microbiota interactions during early life stages

    PubMed Central

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

    2012-01-01

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

  12. Biofilms Role in Planktonic Cell Proliferation

    PubMed Central

    Bester, Elanna; Wolfaardt, Gideon M.; Aznaveh, Nahid B.; Greener, Jesse

    2013-01-01

    The detachment of single cells from biofilms is an intrinsic part of this surface-associated mode of bacterial existence. Pseudomonas sp. strain CT07gfp biofilms, cultivated in microfluidic channels under continuous flow conditions, were subjected to a range of liquid shear stresses (9.42 mPa to 320 mPa). The number of detached planktonic cells was quantified from the effluent at 24-h intervals, while average biofilm thickness and biofilm surface area were determined by confocal laser scanning microscopy and image analysis. Biofilm accumulation proceeded at the highest applied shear stress, while similar rates of planktonic cell detachment was maintained for biofilms of the same age subjected to the range of average shear rates. The conventional view of liquid-mediated shear leading to the passive erosion of single cells from the biofilm surface, disregards the active contribution of attached cell metabolism and growth to the observed detachment rates. As a complement to the conventional conceptual biofilm models, the existence of a biofilm surface-associated zone of planktonic cell proliferation is proposed to highlight the need to expand the traditional perception of biofilms as promoting microbial survival, to include the potential of biofilms to contribute to microbial proliferation. PMID:24201127

  13. Terrestrial Biomarkers for Early Life on Earth as Analogs for Possible Martian Life Forms: Examples of Minerally Replaced Bacteria and Biofilms From the 3.5 - 3.3-Ga Barberton Greenstone Belt, South Africa

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K.; deWit, M. J.; Dann, J.; Gerneke, D.; deRonde, C. E. J.

    1998-01-01

    The search for extraterrestrial life and especially martian life hinges on a variety of methods used to identify vestiges of what we could recognize as life, including chemical signatures, morphological fossils, and biogenic precipitates. Although the possibility of extant life on Mars (subsurface) is being considered, most exploration efforts may be directed toward the search for fossil life. Geomorphological evidence points to a warmer and wetter Mars early on in its history, a scenario that encourages comparison with the early Earth. For this reason, study of the early terrestrial life forms and environment in which they lived may provide clues as to how to search for extinct martian life. As a contribution to the early Archean database of terrestrial microfossils, we present new data on morphological fossils from the 3.5-3.3-Ga Barberton greenstone belt (BGB), South Africa. This study underlines the variety of fossil types already present in some of the oldest, best-preserved terrestrial sediments, ranging from minerally replaced bacteria and bacteria molds of vaRious morphologies (coccoid, coccobacillus, bacillus) to minerally replaced biofilm. Biofilm or extracellular polymeric substance (EPS) is produced by bacteria and appears to be more readily fossilisable than bacteria themselves. The BGB fossils occur in shallow water to subaerial sediments interbedded with volcanic lavas, the whole being deposited on oceanic crust. Penecontemporaneous silicification of sediments and volcanics resulted in the chertification of the rocks, which were later subjected to low-grade metamorphism (lower greenschist).

  14. Bacterial interactions in dental biofilm

    PubMed Central

    Huang, Ruijie; Li, Mingyun

    2011-01-01

    Biofilms are masses of microorganisms that bind to and multiply on a solid surface, typically with a fluid bathing the microbes. The microorganisms that are not attached but are free-floating in an aqueous environment are termed planktonic cells. Traditionally, microbiology research has addressed results from planktonic bacterial cells. However, many recent studies have indicated that biofilms are the preferred form of growth of most microbes and particularly those of a pathogenic nature. Biofilms on animal hosts have significantly increased resistance to various antimicrobials compared to planktonic cells. These microbial communities form microcolonies that interact with each other using very sophisticated communication methods (i.e., quorum-sensing). The development of unique microbiological tools to detect and assess the various biofilms around us is a tremendously important focus of research in many laboratories. In the present review, we discuss the major biofilm mechanisms and the interactions among oral bacteria. PMID:21778817

  15. Innovative Strategies to Overcome Biofilm Resistance

    PubMed Central

    Taraszkiewicz, Aleksandra; Fila, Grzegorz; Grinholc, Mariusz; Nakonieczna, Joanna

    2013-01-01

    We review the recent literature concerning the efficiency of antimicrobial photodynamic inactivation toward various microbial species in planktonic and biofilm cultures. The review is mainly focused on biofilm-growing microrganisms because this form of growth poses a threat to chronically infected or immunocompromised patients and is difficult to eradicate from medical devices. We discuss the biofilm formation process and mechanisms of its increased resistance to various antimicrobials. We present, based on data in the literature, strategies for overcoming the problem of biofilm resistance. Factors that have potential for use in increasing the efficiency of the killing of biofilm-forming bacteria include plant extracts, enzymes that disturb the biofilm structure, and other nonenzymatic molecules. We propose combining antimicrobial photodynamic therapy with various antimicrobial and antibiofilm approaches to obtain a synergistic effect to permit efficient microbial growth control at low photosensitizer doses. PMID:23509680

  16. Characterization of the deep microbial life in the Altmark natural gas reservoir

    NASA Astrophysics Data System (ADS)

    Morozova, D.; Alawi, M.; Vieth-Hillebrand, A.; Kock, D.; Krüger, M.; Wuerdemann, H.; Shaheed, M.

    2010-12-01

    Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of approximately 3500 m, is characterised by high salinity (420 g/l) and temperatures up to 127°C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery), the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism), DGGE (Denaturing Gradient Gel Electrophoresis) and 16S rRNA cloning. First results of the baseline survey indicate the presence of microorganisms similar to representatives from other deep environments. The sequence analyses revealed the presence of several H2-oxidising bacteria (Hydrogenophaga sp., Adicdovorax sp., Ralstonia sp., Pseudomonas sp.), thiosulfate-oxidising bacteria (Diaphorobacter sp.) and biocorrosive thermophilic microorganisms, which have not previously been cultivated. Furthermore, several uncultivated microorganisms were found, that were similar to representatives from other saline, hot, anoxic, deep environments. However, due to the hypersaline and hyperthermophilic reservoir conditions, cell numbers are low, so that the quantification of those microorganisms as well as the determination of microbial activity was not yet possible. Microbial monitoring methods have to be further developed to study microbial activities under these extreme conditions to access their influence on the EGR technique and on enhancing the long term safety of the process by fixation of carbon dioxide by precipitation of carbonates. We thank GDF SUEZ for providing the data for the Rotliegend reservoir, sample material and supporting sampling campaigns. The CLEAN project is funded by the German Federal Ministry of Education and Research (BMBF) in the framework of the GEOTECHNOLOGIEN Program.

  17. Permeabilizing biofilms

    DOEpatents

    Soukos, Nikolaos S. (Revere, MA); Lee, Shun (Arlington, VA); Doukas, Apostolos G. (Belmont, MA)

    2008-02-19

    Methods for permeabilizing biofilms using stress waves are described. The methods involve applying one or more stress waves to a biofilm, e.g., on a surface of a device or food item, or on a tissue surface in a patient, and then inducing stress waves to create transient increases in the permeability of the biofilm. The increased permeability facilitates delivery of compounds, such as antimicrobial or therapeutic agents into and through the biofilm.

  18. Evaluation of the Microbial Population in the Multibiological Life Support System Experiments

    NASA Astrophysics Data System (ADS)

    Fu, Yuming; Tong, Ling; Li, Ming; Hu, Enzhu; Hu, Dawei; He, Wenting; Liu, Hong

    In order to develop and evaluate a ground-based bioregenerative life support system satisfying half of one crew member's requirement towards O2 , Multibiological Life Support System Exper-iments (MLSSE) have been conducted. The MLSSE involved humans participating in the gas exchange with the closed equipment simulating the future extraterrestrial life support systems, which included three phases. The Phase I test involved one person participating in the gas exchange with lettuce in plant chamber as the primary means of air revitalization for 3 months. The Phase II test involved one person participating in the gas exchange with lettuce in plant chamber and micoalgae in bioreactor as the means of air revitalization for 1 month. In the Phase III test, silkworm was introduced into animal chamber for 2 months based on Phase II. The microbial dynamics in the closed chambers were evaluated during the whole experiments. The surfaces, water, and air of closed equipment were sampled for microbial content during the whole experiments. In general, the numbers of microbes in the chambers slowly increased with length of occupation. Compared with Phase I, the numbers of microbes of Phase II ob-viously increased, however, the numbers of microbes of Phase III did not increase relative to Phase II. The types of microbes found on the surfaces and in the air in all the experimental phases were similar. The most common bacteria were Bacillus sp., Pseudomonas sp., as well as Sphingomonas sp., with Pencillium sp. and Cladosporium sp. the most common fungi. A few opportunistic pathogens were also determined, but neither phase had levels of microbes that would be considered an occupational health threat.

  19. Detection of in-situ derivatized peptides in microbial biofilms by laser desorption 7.87 eV postionizaton mass spectrometry.

    SciTech Connect

    Edirisinghe, P. D.; Moore, J. F.; Skinner-Nemec, K. A.; Lindberg, C.; Giometti, C. S.; Veryovkin, I. V.; Hunt, J. E.; Pellin, M. J.; Hanley, L.; Biosciences Division; Univ. of Illinois at Chicago; MassThink

    2007-01-01

    A novel analytical method based on laser desorption postionization mass spectrometry (LDPI-MS) was developed to investigate the competence and sporulation factor-a pentapeptide of amino acid sequence ERGMT-within intact Bacillus subtilis biofilms. Derivatization of the neat ERGMT peptide with quinoline- and anthracene-based tags was separately used to lower the peptide ionization potential and permit direct ionization by 7.87-eV vacuum ultraviolet radiation. The techniques of mass shifting and selective ionization of the derivatized peptide were combined here to permit detection of ERGMT peptide within intact biofilms by LDPI-MS, without any prior extraction or chromatographic separation. Finally, imaging MS specific to the derivatized peptide was demonstrated on an intact biofilm using LDPI-MS. The presence of ERGMT in the biofilms was verified by bulk extraction/LC-MS. However, MALDI imaging MS analyses were unable to detect ERGMT within intact biofilms.

  20. Biofilms Reduce Solar Disinfection of Cryptosporidium parvum Oocysts

    PubMed Central

    Hargreaves, B. R.; Jellison, K. L.

    2012-01-01

    Solar radiation reduces Cryptosporidium infectivity. Biofilms grown from stream microbial assemblages inoculated with oocysts were exposed to solar radiation. The infectivity of oocysts attached at the biofilm surface and oocysts suspended in water was about half that of oocysts attached at the base of a 32-μm biofilm. PMID:22467508

  1. Electrical Conductivity in a Mixed-Species Biofilm

    PubMed Central

    Lau, Joanne; Nevin, Kelly P.; Franks, Ashley E.; Tuominen, Mark T.; Lovley, Derek R.

    2012-01-01

    Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed-species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community. PMID:22706052

  2. Dynamic interactions of neutrophils and biofilms

    PubMed Central

    Hirschfeld, Josefine

    2014-01-01

    Background The majority of microbial infections in humans are biofilm-associated and difficult to treat, as biofilms are highly resistant to antimicrobial agents and protect themselves from external threats in various ways. Biofilms are tenaciously attached to surfaces and impede the ability of host defense molecules and cells to penetrate them. On the other hand, some biofilms are beneficial for the host and contain protective microorganisms. Microbes in biofilms express pathogen-associated molecular patterns and epitopes that can be recognized by innate immune cells and opsonins, leading to activation of neutrophils and other leukocytes. Neutrophils are part of the first line of defense and have multiple antimicrobial strategies allowing them to attack pathogenic biofilms. Objective/design In this paper, interaction modes of neutrophils with biofilms are reviewed. Antimicrobial strategies of neutrophils and the counteractions of the biofilm communities, with special attention to oral biofilms, are presented. Moreover, possible adverse effects of neutrophil activity and their biofilm-promoting side effects are discussed. Results/conclusion Biofilms are partially, but not entirely, protected against neutrophil assault, which include the processes of phagocytosis, degranulation, and formation of neutrophil extracellular traps. However, virulence factors of microorganisms, microbial composition, and properties of the extracellular matrix determine whether a biofilm and subsequent microbial spread can be controlled by neutrophils and other host defense factors. Besides, neutrophils may inadvertently contribute to the physical and ecological stability of biofilms by promoting selection of more resistant strains. Moreover, neutrophil enzymes can degrade collagen and other proteins and, as a result, cause harm to the host tissues. These parameters could be crucial factors in the onset of periodontal inflammation and the subsequent tissue breakdown. PMID:25523872

  3. [Urinary catheter biofilm infections].

    PubMed

    Holá, V; Růzicka, F

    2008-04-01

    Urinary tract infections, most of which are biofilm infections in catheterized patients, account for more than 40% of hospital infections. Bacterial colonization of the urinary tract and catheters causes not only infection but also other complications such as catheter blockage by bacterial encrustation, urolithiasis and pyelonephritis. About 50% of long-term catheterized patients face urinary flow obstruction due to catheter encrustation, but no measure is currently available to prevent it. Encrustation has been known either to result from metabolic dysfunction or to be of microbial origin, with urease positive bacterial species implicated most often. Infectious calculi account for about 15-20% of all cases of urolithiasis and are often associated with biofilm colonization of a long-term indwelling urinary catheter or urethral stent. The use of closed catheter systems is helpful in reducing such problems; nevertheless, such a system only delays the inevitable, with infections emerging a little later. Various coatings intended to prevent the bacterial adhesion to the surface of catheters and implants and thus also the emergence of biofilm infections, unfortunately, do not inhibit the microbial adhesion completely and permanently and the only reliable method for biofilm eradication remains the removal of the foreign body from the patient. PMID:18578409

  4. Antibiotic resistance of biofilms.

    PubMed

    Foley, I; Gilbert, P

    1996-01-01

    Microbial biofilms are notably recalcitrant towards treatment with antibiotics, biocides or disinfectants that would adequately control the same organisms growing in planktonic mode. Much of this resistance has been attributed to an organisation of the biofilm cells within exopolymer matrices. Whilst such exopolymers are unlikely to hinder the diffusion and access of antimicrobial agents to the underlying cells, they will chemically quench reactive biocides such as chlorine and peroxygens, and bind highly charged antibiotics, such as tobramycin and gentamycin, thereby providing some protection to the more deep lying cells. Extracellular enzymes, bound within the glycocalyx and able to degrade the treatment agents, will further reduce the access of susceptible compounds. Diffusion limitation however, is unlikely to be the sole moderator of the resistance properties of microbial biofilms. In addition, gradients of oxygen and nutrients established across the biofilm community will cause growth rates to be much reduced at points remoted from the accessible nutrient. Slow growth rates, and the associated induction of stringent responses further contribute towards this resistance. Finally, there have been recent demonstrations that attachment of microorganisms to surfaces promotes the expression of genes that are not normally expressed in planktonic culture. Whether or not the expression of such genes alters the phenotype in a manner which alters the response of the cells to antimicrobial agents remains to be demonstrated. PMID:22115185

  5. BIOFILMS IN DRINKING WATER DISTRIBUTION SYSTEMS

    EPA Science Inventory

    Virtually anywhere a surface comes into contact with the water in a distribution system, one can find biofilms. Biofilms are formed in distribution system pipelines when microbial cells attach to pipe surfaces and multiply to form a film or slime layer on the pipe. Probably withi...

  6. Biofilms in fresh fruit and vegetables

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteria can attach to surfaces and form biofilms, which have a characteristic structure consisting of microcolonies enclosed in a hydrated matrix of microbially-produced proteins and polysaccharides. In this complex biofilm network, the cells act less as individual entities and more as a collectiv...

  7. Biofilm formation by Borrelia burgdorferi sensu lato.

    PubMed

    Timmaraju, Venkata Arun; Theophilus, Priyanka A S; Balasubramanian, Kunthavai; Shakih, Shafiq; Luecke, David F; Sapi, Eva

    2015-08-01

    Bacterial biofilms are microbial communities held together by an extracellular polymeric substance matrix predominantly composed of polysaccharides, proteins and nucleic acids. We had previously shown that Borrelia burgdorferi sensu stricto, the causative organism of Lyme disease in the United States is capable of forming biofilms in vitro. Here, we investigated biofilm formation by B. afzelii and B. garinii, which cause Lyme disease in Europe. Using various histochemistry and microscopy techniques, we show that B. afzelii and B. garinii form biofilms, which resemble biofilms formed by B. burgdorferi sensu stricto. High-resolution atomic force microscopy revealed similarities in the ultrastructural organization of the biofilms form by three Borrelia species. Histochemical experiments revealed a heterogeneous organization of exopolysaccharides among the three Borrelia species. These results suggest that biofilm formation might be a common trait of Borrelia genera physiology. PMID:26208529

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

    PubMed

    Dimkpa, Christian O

    2014-09-01

    Nanotechnology exploits the enhanced reactivity of materials at the atomic scale to improve various applications for humankind. In agriculture, potential nanotechnology applications include crop protection and fertilization. However, such benefits could come with risks for the environment: non-target plants, plant-beneficial soil microbes and other life forms could be impacted if nanoparticles (nanomaterials) contaminate the environment. This review evaluates the impact of the major metallic nanoparticles (Ag, ZnO, CuO, CeO2 , TiO2 , and FeO-based nanoparticles) on soil microbes involved in agricultural processes. The current literature indicate that in addition to population and organismal-scale effects on microbes, other subtle impacts of nanoparticles are seen in the nitrogen cycle, soil enzyme activities, and processes involved in iron metabolism, phytohormone, and antibiotic production. These effects are negative or positive, the outcome being dependent on specific nanoparticles. Collectively, published results suggest that nanotechnology portends considerable, many negative, implications for soil microbes and, thus, agricultural processes that are microbially driven. Nonetheless, the potential of plant and soil microbial processes to mitigate the bioreactivity of nanoparticles also are observed. Whereas the roots of most terrestrial plants are associated with microbes, studies of nanoparticle interactions with plants and microbes are generally conducted separately. The few studies in actual microbe-plant systems found effects of nanoparticles on the functioning of arbuscular mycorrhizal fungi, nitrogen fixation, as well as on the production of microbial siderophores in the plant rhizosphere. It is suggested that a better understanding of the agro-ecological ramifications of nanoparticles would require more in-depth interactive studies in combined plant-microbe-nanoparticle systems. PMID:24913194

  9. Biofilms On Orbit and On Earth: Current Methods, Future Needs

    NASA Technical Reports Server (NTRS)

    Vega, Leticia

    2013-01-01

    Biofilms have played a significant role on the effectiveness of life support hardware on the Space Shuttle and International Space Station (ISS). This presentation will discuss how biofilms impact flight hardware, how on orbit biofilms are analyzed from an engineering and research perspective, and future needs to analyze and utilize biofilms for long duration, deep space missions.

  10. Biofilms and Inflammation in Chronic Wounds

    PubMed Central

    Zhao, Ge; Usui, Marcia L.; Lippman, Soyeon I.; James, Garth A.; Stewart, Philip S.; Fleckman, Philip; Olerud, John E.

    2013-01-01

    Significance The incidence, cost, morbidity, and mortality associated with non-healing of chronic skin wounds are dramatic. With the increasing numbers of people with obesity, chronic medical conditions, and an increasing life expectancy, the healthcare cost of non-healing ulcers has recently been estimated at $25 billion annually in the United States. The role played by bacterial biofilm in chronic wounds has been emphasized in recent years, particularly in the context of the prolongation of the inflammatory phase of repair. Recent Advances Rapid high-throughput genomic approaches have revolutionized the ability to identify and quantify microbial organisms from wounds. Defining bacterial genomes and using genetic approaches to knock out specific bacterial functions, then studying bacterial survival on cutaneous wounds is a promising strategy for understanding which genes are essential for pathogenicity. Critical Issues When an animal sustains a cutaneous wound, understanding mechanisms involved in adaptations by bacteria and adaptations by the host in the struggle for survival is central to development of interventions that favor the host. Future Directions Characterization of microbiomes of clinically well characterized chronic human wounds is now under way. The use of in vivo models of biofilm-infected cutaneous wounds will permit the study of the mechanisms needed for biofilm formation, persistence, and potential synergistic interactions among bacteria. A more complete understanding of bacterial survival mechanisms and how microbes influence host repair mechanisms are likely to provide targets for chronic wound therapy. PMID:24527355

  11. Do inactivated microbial preparations improve life history traits of the copepod Acartia tonsa?

    PubMed

    Drillet, Guillaume; Rabarimanantsoa, Tahina; Froul, Stphane; Lamson, Jacob S; Christensen, Anette M; Kim-Tiam, Sandra; Hansen, Benni W

    2011-10-01

    We have tested a microbial preparation with probiotic effects (PSI; Sorbial A/S DANISCO) on the calanoid copepod Acartia tonsa (Dana) development time and reproduction effectiveness in culture. The hypotheses were that PSI increases the productivity and quality of copepods in culture (increased egg production and hatching success, HS). This was carried out because the use of copepods as live prey in aquaculture could increase the number of fish successfully raised through their entire life cycle. However, the availability of copepods is limited by their difficulty to be effectively raised. Our results show that the addition of PSI to the algal food increased the individual size of the adult females and their egg production. The PSI, together with Rhodomonas salina, also increased the HS of the eggs produced by PSI-treated females. These effects were observed despite that the biochemical analysis of the PSI revealed that it is a nutritionally poor food lacking essential fatty acids, and hence it cannot be used alone to raise copepods but instead as a food additive. This is the first demonstration that the effectiveness of copepod culturing can be improved using microbial preparations as a food additive. PMID:21213117

  12. Highlights in pathogenic fungal biofilms.

    PubMed

    Sardi, Janaina De Cássia Orlandi; Pitangui, Nayla De Souza; Rodríguez-Arellanes, Gabriela; Taylor, Maria Lucia; Fusco-Almeida, Ana Maria; Mendes-Giannini, Maria José Soares

    2014-01-01

    A wide variety of fungi have demonstrated the ability to colonize surfaces and form biofilms. Most studies on fungal biofilms have focused on Candida albicans and more recently, several authors have reported the involvement of other genera of yeasts and Candida species, as well as of filamentous fungi in the formation of biofilms, including: Cryptococcus neoformans, Cryptococcus gattii, Rhodotorula species, Aspergillus fumigatus, Malassezia pachydermatis, Histoplasma capsulatum, Paracoccidioides brasiliensis, Pneumocystis species, Coccidioides immitis, Fusarium species, Saccharomyces cerevisiae, Trichosporon asahii, Mucorales and Blastoschizomyces. There is a current interest in describing the particular characteristics of the biofilm formation by of these fungi. A major concern is the control of biofilms, requiring knowledge of the biofilm mechanisms. However, our knowledge of these microbial communities is limited, due to the complexity of these systems and metabolic interactions that remain unknown. This mini-review aims to highlight recently discovered fungal biofilms and to compare them with the current knowledge on biofilms. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). PMID:24252828

  13. Patterns of Candida biofilm on intrauterine devices.

    PubMed

    Zahran, Kamal M; Agban, Michael N; Ahmed, Shaaban H; Hassan, Ehsan A; Sabet, Marwa A

    2015-04-01

    Biofilms are colonies of microbial cells encased in a self-produced organic polymeric matrix and represent a common mode of microbial growth. Microbes growing as biofilm are highly resistant to commonly used antimicrobial drugs. We aimed to screen and characterize biofilm formation by different isolates of Candida on removed intrauterine devices (IUDs), to perform experimental biofilm formation with isolated strains, and to examine biofilm by the crystal violet and XTT reduction assays and scanning electron microscopy (SEM). A total of 56 IUDs were examined for biofilm formation using Sabouraud's dextrose chloramphenicol agar. Suspected colonies were identified by different methods. Antifungal susceptibility testing with fluconazole (FLU) and amphotericin B for the isolated strains and in vitro experimental biofilm formation was carried out. The biofilm was quantified by crystal violet, XTT reduction assay and SEM. Among the 56 IUDs investigated, 26 were Candida positive (46.4?%). Candida albicans was recovered from 15 isolates. The biofilm MIC of FLU was increased 64 to 1000 times compared to the MIC for planktonic cells. The XTT method results were dependent on the Candida species; biofilm formation was highest in Candida krusei and Candida glabrata strains, followed by C. albicans and Candida tropicalis. SEM of Candida biofilm revealed a heterogeneous thick biofilm with a mixture of micro-organisms. The main conclusion from this study was non-albicans Candida represents more than a half of the Candida biofilm. Better understanding of Candida biofilms may lead to the development of novel therapeutic approaches for the treatment of fungal infections, especially resistant ones among IUD users. PMID:25681320

  14. A novel role for maternal stress and microbial transmission in early life programming and neurodevelopment

    PubMed Central

    Jašarević, Eldin; Rodgers, Ali B.; Bale, Tracy L.

    2014-01-01

    Perturbations in the prenatal and early life environment can contribute to the development of offspring stress dysregulation, a pervasive symptom in neuropsychiatric disease. Interestingly, the vertical transmission of maternal microbes to offspring and the subsequent bacterial colonization of the neonatal gut overlap with a critical period of brain development. Therefore, environmental factors such as maternal stress that are able to alter microbial populations and their transmission can thereby shape offspring neurodevelopment. As the neonatal gastrointestinal tract is primarily inoculated at parturition through the ingestion of maternal vaginal microflora, disruption in the vaginal ecosystem may have important implications for offspring neurodevelopment and disease risk. Here, we discuss alterations that occur in the vaginal microbiome following maternal insult and the subsequent effects on bacterial assembly of the neonate gut, the production of neuromodulatory metabolites, and the developmental course of stress regulation. PMID:25530984

  15. Biofilms: Survival Mechanisms of Clinically Relevant Microorganisms

    PubMed Central

    Donlan, Rodney M.; Costerton, J. William

    2002-01-01

    Though biofilms were first described by Antonie van Leeuwenhoek, the theory describing the biofilm process was not developed until 1978. We now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. Using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstructured, homogeneous deposits of cells and accumulated slime, but complex communities of surface-associated cells enclosed in a polymer matrix containing open water channels. Further studies have shown that the biofilm phenotype can be described in terms of the genes expressed by biofilm-associated cells. Microorganisms growing in a biofilm are highly resistant to antimicrobial agents by one or more mechanisms. Biofilm-associated microorganisms have been shown to be associated with several human diseases, such as native valve endocarditis and cystic fibrosis, and to colonize a wide variety of medical devices. Though epidemiologic evidence points to biofilms as a source of several infectious diseases, the exact mechanisms by which biofilm-associated microorganisms elicit disease are poorly understood. Detachment of cells or cell aggregates, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are all biofilm processes which could initiate the disease process. Effective strategies to prevent or control biofilms on medical devices must take into consideration the unique and tenacious nature of biofilms. Current intervention strategies are designed to prevent initial device colonization, minimize microbial cell attachment to the device, penetrate the biofilm matrix and kill the associated cells, or remove the device from the patient. In the future, treatments may be based on inhibition of genes involved in cell attachment and biofilm formation. PMID:11932229

  16. Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin.

    PubMed

    Merhej, Vicky; Raoult, Didier

    2012-01-01

    Darwin's theory about the evolution of species has been the object of considerable dispute. In this review, we have described seven key principles in Darwin's book The Origin of Species and tried to present how genomics challenge each of these concepts and improve our knowledge about evolution. Darwin believed that species evolution consists on a positive directional selection ensuring the "survival of the fittest." The most developed state of the species is characterized by increasing complexity. Darwin proposed the theory of "descent with modification" according to which all species evolve from a single common ancestor through a gradual process of small modification of their vertical inheritance. Finally, the process of evolution can be depicted in the form of a tree. However, microbial genomics showed that evolution is better described as the "biological changes over time." The mode of change is not unidirectional and does not necessarily favors advantageous mutations to increase fitness it is rather subject to random selection as a result of catastrophic stochastic processes. Complexity is not necessarily the completion of development: several complex organisms have gone extinct and many microbes including bacteria with intracellular lifestyle have streamlined highly effective genomes. Genomes evolve through large events of gene deletions, duplications, insertions, and genomes rearrangements rather than a gradual adaptative process. Genomes are dynamic and chimeric entities with gene repertoires that result from vertical and horizontal acquisitions as well as de novo gene creation. The chimeric character of microbial genomes excludes the possibility of finding a single common ancestor for all the genes recorded currently. Genomes are collections of genes with different evolutionary histories that cannot be represented by a single tree of life (TOL). A forest, a network or a rhizome of life may be more accurate to represent evolutionary relationships among species. PMID:22973559

  17. Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin

    PubMed Central

    Merhej, Vicky; Raoult, Didier

    2012-01-01

    Darwin's theory about the evolution of species has been the object of considerable dispute. In this review, we have described seven key principles in Darwin's book The Origin of Species and tried to present how genomics challenge each of these concepts and improve our knowledge about evolution. Darwin believed that species evolution consists on a positive directional selection ensuring the survival of the fittest. The most developed state of the species is characterized by increasing complexity. Darwin proposed the theory of descent with modification according to which all species evolve from a single common ancestor through a gradual process of small modification of their vertical inheritance. Finally, the process of evolution can be depicted in the form of a tree. However, microbial genomics showed that evolution is better described as the biological changes over time. The mode of change is not unidirectional and does not necessarily favors advantageous mutations to increase fitness it is rather subject to random selection as a result of catastrophic stochastic processes. Complexity is not necessarily the completion of development: several complex organisms have gone extinct and many microbes including bacteria with intracellular lifestyle have streamlined highly effective genomes. Genomes evolve through large events of gene deletions, duplications, insertions, and genomes rearrangements rather than a gradual adaptative process. Genomes are dynamic and chimeric entities with gene repertoires that result from vertical and horizontal acquisitions as well as de novo gene creation. The chimeric character of microbial genomes excludes the possibility of finding a single common ancestor for all the genes recorded currently. Genomes are collections of genes with different evolutionary histories that cannot be represented by a single tree of life (TOL). A forest, a network or a rhizome of life may be more accurate to represent evolutionary relationships among species. PMID:22973559

  18. Spatial Arrangement of Legionella Colonies in Intact Biofilms from a Model Cooling Water System

    PubMed Central

    Taylor, Michael; Ross, Kirstin; Bentham, Richard

    2013-01-01

    There is disagreement among microbiologists about whether Legionella requires a protozoan host in order to replicate. This research sought to determine where in biofilm Legionellae are found and whether all biofilm associated Legionella would be located within protozoan hosts. While it is accepted that Legionella colonizes biofilm, its life cycle and nutritional fastidiousness suggest that Legionella employs multiple survival strategies to persist within microbial systems. Fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) demonstrated an undulating biofilm surface architecture and a roughly homogenous distribution of heterotrophic bacteria with clusters of protozoa. Legionella displayed 3 distinct spatial arrangements either contained within or directly associated with protozoa, or dispersed in loosely associated clusters or in tightly packed aggregations of cells forming dense colonial clusters. The formation of discreet clusters of tightly packed Legionella suggests that colony formation is influenced by specific environmental conditions allowing for limited extracellular replication. This work represents the first time that an environmentally representative, multispecies biofilm containing Legionella has been fluorescently tagged and Legionella colony morphology noted within a complex microbial system. PMID:24826074

  19. Bacteriophages and Biofilms

    PubMed Central

    Harper, David R.; Parracho, Helena M. R. T.; Walker, James; Sharp, Richard; Hughes, Gavin; Werthén, Maria; Lehman, Susan; Morales, Sandra

    2014-01-01

    Biofilms are an extremely common adaptation, allowing bacteria to colonize hostile environments. They present unique problems for antibiotics and biocides, both due to the nature of the extracellular matrix and to the presence within the biofilm of metabolically inactive persister cells. Such chemicals can be highly effective against planktonic bacterial cells, while being essentially ineffective against biofilms. By contrast, bacteriophages seem to have a greater ability to target this common form of bacterial growth. The high numbers of bacteria present within biofilms actually facilitate the action of bacteriophages by allowing rapid and efficient infection of the host and consequent amplification of the bacteriophage. Bacteriophages also have a number of properties that make biofilms susceptible to their action. They are known to produce (or to be able to induce) enzymes that degrade the extracellular matrix. They are also able to infect persister cells, remaining dormant within them, but re-activating when they become metabolically active. Some cultured biofilms also seem better able to support the replication of bacteriophages than comparable planktonic systems. It is perhaps unsurprising that bacteriophages, as the natural predators of bacteria, have the ability to target this common form of bacterial life.

  20. Quantitative analysis of biofilm EPS uronic acid content.

    PubMed

    Mojica, Kristina; Elsey, Danielle; Cooney, Michael J

    2007-10-01

    The uronic acids assay was evaluated for its ability to measure the amount of uronic acids contained within a biofilm exopolysaccharide matrix. Cytophaga lytica, a marine bacterium isolated from a naturally occurring biofilm, was used to form single-species biofilms for the method assessment. The assay was found to be simple, reproducible, and sensitive to 1 microg levels, suggesting its potential for application as a screening technique for compounds that inhibit the production of microbial biofilm exopolysaccharide containing uronic acids. PMID:17822791

  1. Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park.

    PubMed

    Schubotz, F; Meyer-Dombard, D R; Bradley, A S; Fredricks, H F; Hinrichs, K-U; Shock, E L; Summons, R E

    2013-11-01

    Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show a similar variance, with values resembling the DIC or DOC pool or a mixture thereof. This variance cannot be explained by hot spring chemistry or temperature alone, but instead, we argue that intermittent input of exogenous organic carbon can result in metabolic shifts of the chemotrophic communities from autotrophy to heterotrophy and vice versa. PMID:23981055

  2. Photo-catalytic inactivation of an Enterococcus biofilm: the anti-microbial effect of sulphated and europium-doped titanium dioxide nanopowders.

    PubMed

    Dworniczek, Ewa; Plesch, Gustav; Seniuk, Alicja; Adamski, Ryszard; Michal, Róbert; Čaplovičová, Mária

    2016-04-01

    The control and prevention of biofilm-related infections is an important public healthcare issue. Given the increasing antibiotic resistance among bacteria and fungi that cause serious infections in humans, promotion of new strategies combating microorganisms has been essential. One attractive approach to inactivate microorganisms is the use of semiconductor photo-catalysis, which has become the subject of extensive research. In this study, the bactericidal properties of four photo-catalysts, TiO2, TiO2-S, TiO2-Eu and TiO2-Eu-S, were investigated against established 24, 48, 72 and 96 h biofilms ofEnterococcus The exposure of biofilms to the catalysts induced the production of superoxide radical anions. The best photo-catalytic inactivation was achieved with the TiO2-Eu-S and TiO2-S nanopowders and 24 h biofilms. Transmission electron microscopy images showed significant changes in the structure of the biofilm cells following photo-inactivation. The results suggest that doping with europium and modifying the surface with sulphate groups enhanced the bactericidal activity of the TiO2nanoparticles against enterococcal biofilms. PMID:26940291

  3. Influence of temperature and plumbing material selection on biofilm formation and growth of Legionella pneumophila in a model potable water system containing complex microbial flora.

    PubMed Central

    Rogers, J; Dowsett, A B; Dennis, P J; Lee, J V; Keevil, C W

    1994-01-01

    Survival and growth of Legionella pneumophila in both biofilm and planktonic phases were determined with a two-stage model system. The model used filter-sterilized tap water as the sole source of nutrient to culture a naturally occurring mixed population of microorganisms including virulent L. pneumophila. At 20 degrees C, L. pneumophila accounted for a low proportion of biofilm flora on polybutylene and chlorinated polyvinyl chloride, but was absent from copper surfaces. The pathogen was most abundant on biofilms on plastics at 40 degrees C, where it accounted for up to 50% of the total biofilm flora. Copper surfaces were inhibitory to total biofouling and included only low numbers of L. pneumophila organisms. The pathogen was able to survive in biofilms on the surface of the plastic materials at 50 degrees C, but was absent from the copper surfaces at the same temperature. L. pneumophila could not be detected in the model system at 60 degrees C. In the presence of copper surfaces, biofilms forming on adjacent control glass surfaces were found to incorporate copper ions which subsequently inhibited colonization of their surfaces. This work suggests that the use of copper tubing in water systems may help to limit the colonization of water systems by L. pneumophila. Images PMID:8017938

  4. Deliberations on Microbial Life in the Subglacial Lake Vostok, East Antarctica

    NASA Astrophysics Data System (ADS)

    Bulat, S.; Alekhina, I.; Lipenkov, V.; Lukin, V.; Marie, D.; Petit, J.

    2004-12-01

    The objective was to estimate microbial contents of accretion (lake originating) ice from the Lake Vostok buried beneath 4-km thick East Antarctic ice sheet with the ultimate goal to discover microbial life in this extreme icy environment featured by no light, close to freezing point temperature, ultra-low DOC contents, and an excess of oxygen. The PCR based bacterial and archaeal 16S ribosomal RNA gene sequencing constrained by Forensic Biology and Ancient DNA research criteria was used as a main approach. Epifluorescent and confocal microscopies as well as flow cytometry were implemented. DNA study showed that the accretion ice is essentially bacteria- and archaea-free. Up to now, the only accretion ice type 1 featured by mica-clay sediments presence and namely one horizon of four studied (3607m) allowed the recovery a few bacterial phylotypes. This unexpectedly included the chemolithoautotrophic thermophile Hydrogenophilus thermoluteolus and two more unclassified phylotypes all passing numerous contaminant controls. In contrast, the deeper and cleaner accretion ice 2 (three cores) with no sediments presence and near detection limit gas contents gave no reliable signals. The microbes detected in accretion ice 1 are unbelievable to resist an excess of oxygen in the lake water body (700 - 1300 mg O2/l). They are supposed to be thriving in rather warm anoxic sediments in deep faults at the lake bottom and sporadically flushing out along with sediments to the lake veins in a shallow depth bay due to a seismotectonic activity likely operating in the lake environment. A few geophysical and geological evidences support this scenario. In the bay the presence of mica-clay sediments, higher accretion rate due to relief rise and likely oxygen-depleted upper layer of water can provide microbes with a chance to escape the high oxygen tension by the rapid entrapment into accretion ice 1. Sediment-free accretion ice 2, which forms above a deeper part of the lake, shows no evidence for reasonable source for microbe contribution given highly oxygenated lake water environment. Microscopy and flow cytometry trials on strictly decontaminated ice samples gave supporting results. While microscopy failed to reveal cells because the local concentrations were below the detection limit, the flow cytometry succeeded in a preliminary estimate of 9 and 24 cells/ml for accretion 1 (3561m) and control glacial (2054m) ice samples, respectively. However, given the ratio contaminants to indigenous cells is about 10:1 (from PCR results), the genuine microbial contents for both accretion and glacial ice samples is expected to be as low as 1 cell/ml what practically means "sterile" conditions. Thus, the accretion ice from Lake Vostok contains the very low unevenly distributed biomass indicating that the water body (at least upper layer) should also be hosting a highly sparse life, if any. By this, the Lake Vostok for the first time could present the big natural "sterile" water body on Earth providing a unique test area for searching for life on icy moons and planets. The search for life in Lake Vostok is constrained by a high chance of forward-contamination which can be minimized by using of stringent decontamination procedures and comprehensive biological controls.

  5. Biofilm Dispersal

    PubMed Central

    2010-01-01

    Like all sessile organisms, surface-attached communities of bacteria known as biofilms must release and disperse cells into the environment to colonize new sites. For many pathogenic bacteria, biofilm dispersal plays an important role in the transmission of bacteria from environmental reservoirs to human hosts, in horizontal and vertical cross-host transmission, and in the exacerbation and spread of infection within a host. The molecular mechanisms of bacterial biofilm dispersal are only beginning to be elucidated. Biofilm dispersal is a promising area of research that may lead to the development of novel agents that inhibit biofilm formation or promote biofilm cell detachment. Such agents may be useful for the prevention and treatment of biofilms in a variety of industrial and clinical settings. This review describes the current status of research on biofilm dispersal, with an emphasis on studies aimed to characterize dispersal mechanisms, and to identify environmental cues and inter- and intracellular signals that regulate the dispersal process. The clinical implications of biofilm dispersal and the potential therapeutic applications of some of the most recent findings will also be discussed. PMID:20139339

  6. 3.5 billion years of glass bioalteration: Volcanic rocks as a basis for microbial life?

    SciTech Connect

    Staudigel, H.; Furnes, H.; McLoughlin, N.; Banerjee, N.R.; Connell, L.B.; Templeton, A.

    2009-04-07

    Alteration textures in volcanic glass from the seafloor fall into two classes, one suggestive of abiotic/diffusive hydration and chemical exchange, and another likely to be caused by microbial, cavity-forming, congruent dissolution. Glass bioalteration is common in submarine lavas throughout the world's ocean, dominant in the upper 300 m of the oceanic crust, and found in all well-preserved ophiolites and greenstone belts dating back to 3.5 Ga. It may yield a significant fraction of the global biomass and geochemical fluxes and is relevant to the development of the earliest life on Earth. We present a critical review concerning these glass bioalteration textures and present new data on their microchemical environment. We explore arguments for their biogenicity and further develop the prevalent model for their formation by relating corrosion morphology to the mechanism of microbial dissolution. Biological alteration produces conspicuous micron-scale granular and tubular textures. Granular glass alteration is well explained by colonizing microbes that selectively dissolve the glass in their contact area, forming a sponge-like interconnected network of micron-sized cavities along glass surfaces. Tubular alteration meanwhile, is more likely to be caused by filamentous cell extensions in a process similar to fungal tunneling of soil feldspars and marine carbonates. While we see clear functional similarities to fungal dissolution behavior, we do not know whether fungal or prokaryotic organisms are involved. However, this functional constraint may eventually help to identify potential microbes responsible for these features, potentially including eukaryotic or prokaryotic organisms. Yet, we caution that these organisms may be difficult to identify and to study, because they are likely to be sparsely distributed, slow growing, and difficult to cultivate.

  7. Microbial community structure across the tree of life in the extreme Ro Tinto.

    PubMed

    Amaral-Zettler, Linda A; Zettler, Erik R; Theroux, Susanna M; Palacios, Carmen; Aguilera, Angeles; Amils, Ricardo

    2011-01-01

    Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Ro Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT. PMID:20631808

  8. Microbial community structure across the tree of life in the extreme Ro Tinto

    PubMed Central

    Amaral-Zettler, Linda A; Zettler, Erik R; Theroux, Susanna M; Palacios, Carmen; Aguilera, Angeles; Amils, Ricardo

    2011-01-01

    Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Ro Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT. PMID:20631808

  9. Identification of ypqP as a New Bacillus subtilis Biofilm Determinant That Mediates the Protection of Staphylococcus aureus against Antimicrobial Agents in Mixed-Species Communities

    PubMed Central

    Sanchez-Vizuete, Pilar; Le Coq, Dominique; Bridier, Arnaud; Herry, Jean-Marie; Aymerich, Stéphane

    2014-01-01

    In most habitats, microbial life is organized in biofilms, three-dimensional edifices sustained by extracellular polymeric substances that enable bacteria to resist harsh and changing environments. Under multispecies conditions, bacteria can benefit from the polymers produced by other species (“public goods”), thus improving their survival under toxic conditions. A recent study showed that a Bacillus subtilis hospital isolate (NDmed) was able to protect Staphylococcus aureus from biocide action in multispecies biofilms. In this work, we identified ypqP, a gene whose product is required in NDmed for thick-biofilm formation on submerged surfaces and for resistance to two biocides widely used in hospitals. NDmed and S. aureus formed mixed biofilms, and both their spatial arrangement and pathogen protection were mediated by YpqP. Functional ypqP is present in other natural B. subtilis biofilm-forming isolates. However, the gene is disrupted by the SPβ prophage in the weak submerged-biofilm-forming strains NCIB3610 and 168, which are both less resistant than NDmed to the biocides tested. Furthermore, in a 168 laboratory strain cured of the SPβ prophage, the reestablishment of a functional ypqP gene led to increased thickness and resistance to biocides of the associated biofilms. We therefore propose that YpqP is a new and important determinant of B. subtilis surface biofilm architecture, protection against exposure to toxic compounds, and social behavior in bacterial communities. PMID:25326298

  10. Identification of ypqP as a New Bacillus subtilis biofilm determinant that mediates the protection of Staphylococcus aureus against antimicrobial agents in mixed-species communities.

    PubMed

    Sanchez-Vizuete, Pilar; Le Coq, Dominique; Bridier, Arnaud; Herry, Jean-Marie; Aymerich, Stéphane; Briandet, Romain

    2015-01-01

    In most habitats, microbial life is organized in biofilms, three-dimensional edifices sustained by extracellular polymeric substances that enable bacteria to resist harsh and changing environments. Under multispecies conditions, bacteria can benefit from the polymers produced by other species ("public goods"), thus improving their survival under toxic conditions. A recent study showed that a Bacillus subtilis hospital isolate (NDmed) was able to protect Staphylococcus aureus from biocide action in multispecies biofilms. In this work, we identified ypqP, a gene whose product is required in NDmed for thick-biofilm formation on submerged surfaces and for resistance to two biocides widely used in hospitals. NDmed and S. aureus formed mixed biofilms, and both their spatial arrangement and pathogen protection were mediated by YpqP. Functional ypqP is present in other natural B. subtilis biofilm-forming isolates. However, the gene is disrupted by the SPβ prophage in the weak submerged-biofilm-forming strains NCIB3610 and 168, which are both less resistant than NDmed to the biocides tested. Furthermore, in a 168 laboratory strain cured of the SPβ prophage, the reestablishment of a functional ypqP gene led to increased thickness and resistance to biocides of the associated biofilms. We therefore propose that YpqP is a new and important determinant of B. subtilis surface biofilm architecture, protection against exposure to toxic compounds, and social behavior in bacterial communities. PMID:25326298

  11. Lava Cave Microbial Communities Within Mats and Secondary Mineral Deposits: Implications for Life Detection on Other Planets

    PubMed Central

    Melim, L.A.; Spilde, M.N.; Hathaway, J.J.M.; Garcia, M.G.; Moya, M.; Stone, F.D.; Boston, P.J.; Dapkevicius, M.L.N.E.; Riquelme, C.

    2011-01-01

    Abstract Lava caves contain a wealth of yellow, white, pink, tan, and gold-colored microbial mats; but in addition to these clearly biological mats, there are many secondary mineral deposits that are nonbiological in appearance. Secondary mineral deposits examined include an amorphous copper-silicate deposit (Hawai‘i) that is blue-green in color and contains reticulated and fuzzy filament morphologies. In the Azores, lava tubes contain iron-oxide formations, a soft ooze-like coating, and pink hexagons on basaltic glass, while gold-colored deposits are found in lava caves in New Mexico and Hawai‘i. A combination of scanning electron microscopy (SEM) and molecular techniques was used to analyze these communities. Molecular analyses of the microbial mats and secondary mineral deposits revealed a community that contains 14 phyla of bacteria across three locations: the Azores, New Mexico, and Hawai‘i. Similarities exist between bacterial phyla found in microbial mats and secondary minerals, but marked differences also occur, such as the lack of Actinobacteria in two-thirds of the secondary mineral deposits. The discovery that such deposits contain abundant life can help guide our detection of life on extraterrestrial bodies. Key Words: Biosignatures—Astrobiology—Bacteria—Caves—Life detection—Microbial mats. Astrobiology 11, 601–618. PMID:21879833

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

    NASA Astrophysics Data System (ADS)

    Lasseur, Christophe

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

  13. Methods for Characterizing the Co-development of Biofilm and Habitat Heterogeneity

    PubMed Central

    Li, Xiaobao; Song, Jisun L.; Culotti, Alessandro; Zhang, Wei; Chopp, David L.; Lu, Nanxi; Packman, Aaron I.

    2016-01-01

    Biofilms are surface-attached microbial communities that have complex structures and produce significant spatial heterogeneities. Biofilm development is strongly regulated by the surrounding flow and nutritional environment. Biofilm growth also increases the heterogeneity of the local microenvironment by generating complex flow fields and solute transport patterns. To investigate the development of heterogeneity in biofilms and interactions between biofilms and their local micro-habitat, we grew mono-species biofilms of Pseudomonas aeruginosa and dual-species biofilms of P. aeruginosa and Escherichia coli under nutritional gradients in a microfluidic flow cell. We provide detailed protocols for creating nutrient gradients within the flow cell and for growing and visualizing biofilm development under these conditions. We also present protocols for a series of optical methods to quantify spatial patterns in biofilm structure, flow distributions over biofilms, and mass transport around and within biofilm colonies. These methods support comprehensive investigations of the co-development of biofilm and habitat heterogeneity. PMID:25866914

  14. Linking nitrifying biofilm characteristics and nitrification performance in moving-bed biofilm reactors for polluted raw water pretreatment.

    PubMed

    Zhang, Shuangfu; Wang, Yayi; He, Weitao; Xing, Meiyan; Wu, Min; Yang, Jian; Gao, Naiyun; Sheng, Guangyao; Yin, Daqiang; Liu, Shanhu

    2013-10-01

    Biofilm physiology was characterized by four biofilm constituents, i.e., polysaccharides, proteins (PN), humic-like substances and phospholipids (PL), for the first time to explore the relationships between biofilm characteristics and nitrification performance in moving-bed biofilm reactors (MBBRs) designed for pretreatment of polluted raw surface water for potable supply. The biofilm compositions depended highly on the balance of microbial decay and nitrification processes. The increased ammonia loading greatly regulated the community structure, promoting the dominance of nitrifiers and their proportions in the nitrifying biofilm. Nitrification rate and activity correlated linearly with the fractions of volatile solids (VS), PN and PL, which were related to nitrification processes in the biofilm. The specific biofilm activity demonstrated an exponential-asymptotic relationship with ratios of PN/VS and PL/VS. Thus, analyzing biofilm characteristics can be valid for estimating nitrification performance in MBBRs, and may offer engineers with basis to optimize MBBR design and operation. PMID:23954247

  15. Alumina surfaces with nanoscale topography reduce attachment and biofilm formation by Escherichia coli and Listeria spp.

    PubMed

    Feng, Guoping; Cheng, Yifan; Wang, Shu-Yi; Hsu, Lillian C; Feliz, Yazmin; Borca-Tasciuc, Diana A; Worobo, Randy W; Moraru, Carmen I

    2014-01-01

    This work reports on a simple, robust and scientifically sound method to develop surfaces able to reduce microbial attachment and biofilm development, with possible applications in medicine, dentistry, food processing, or water treatment. Anodic surfaces with cylindrical nanopores 15 to 100nm in diameter were manufactured and incubated with Escherichia coli ATCC 25922 and Listeria innocua. Surfaces with 15 and 25nm pore diameters significantly repressed attachment and biofilm formation. Surface-bacteria interaction forces calculated using the extended Derjaguin Landau Verwey-Overbeek (XDLVO) theory indicate that reduction in attachment and biofilm formation is due to a synergy between electrostatic repulsion and surface effective free energy. An attachment study using E. coli K12 strains unable to express appendages also suggests that the small-pore surfaces may inhibit flagella-dependent attachment. These results can have immediate, far-reaching implications and commercial applications, with substantial benefits for human health and life. PMID:25427545

  16. Successional development of biofilms in moving bed biofilm reactor (MBBR) systems treating municipal wastewater.

    PubMed

    Biswas, Kristi; Taylor, Michael W; Turner, Susan J

    2014-02-01

    Biofilm-based technologies, such as moving bed biofilm reactor (MBBR) systems, are widely used to treat wastewater. Biofilm development is important for MBBR systems as much of the microbial biomass is retained within reactors as biofilm on suspended carriers. Little is known about this process of biofilm development and the microorganisms upon which MBBRs rely. We documented successional changes in microbial communities as biofilms established in two full-scale MBBR systems treating municipal wastewater over two seasons. 16S rRNA gene-targeted pyrosequencing and clone libraries were used to describe microbial communities. These data indicate a successional process that commences with the establishment of an aerobic community dominated by Gammaproteobacteria (up to 52 % of sequences). Over time, this community shifts towards dominance by putatively anaerobic organisms including Deltaproteobacteria and Clostridiales. Significant differences were observed between the two wastewater treatment plants (WWTPs), mostly due to a large number of sequences (up to 55 %) representing Epsilonproteobacteria (mostly Arcobacter) at one site. Archaea in young biofilms included several lineages of Euryarchaeota and Crenarchaeota. In contrast, the mature biofilm consisted entirely of Methanosarcinaceae (Euryarchaeota). This study provides new insights into the community structure of developing biofilms at full-scale WWTPs and provides the basis for optimizing MBBR start-up and operational parameters. PMID:23838795

  17. Electrochemical impedance spectroscopy of biofilms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial activity that leads to the formation of biofilms on process equipment can accelerate corrosion, reduce heat transfer rates, and generally decrease process efficiencies. Additional concerns arise in the food and pharma industries where product quality and safety are a high priority. Pharmac...

  18. Biochemical capacitance of Geobacter sulfurreducens biofilms.

    PubMed

    Bueno, Paulo R; Schrott, Germn D; Bonanni, Pablo S; Simison, Silvia N; Busalmen, Juan P

    2015-08-10

    An electrical model able to decouple the electron pathway from microbial cell machinery impedance terms is introduced. In this context, capacitance characteristics of the biofilm are clearly resolved. In other words, the model allows separating, according to the advantage of frequency and spectroscopic response approach, the different terms controlling the performance of the microbial biofilm respiratory process and thus the directly related electricity production process. The model can be accurately fitted to voltammetry measurements obtained under steady-state conditions and also to biofilm discharge amperometric measurements. The implications of biological aspects of the electrochemical or redox capacitance are discussed theoretically in the context of current knowledge with regard to structure and physiological activity of microbial Geobacter biofilms. PMID:26212121

  19. Mechanisms of biofilm resistance to antimicrobial agents.

    PubMed

    Mah, T F; O'Toole, G A

    2001-01-01

    Biofilms are communities of microorganisms attached to a surface. It has become clear that biofilm-grown cells express properties distinct from planktonic cells, one of which is an increased resistance to antimicrobial agents. Recent work has indicated that slow growth and/or induction of an rpoS-mediated stress response could contribute to biocide resistance. The physical and/or chemical structure of exopolysaccharides or other aspects of biofilm architecture could also confer resistance by exclusion of biocides from the bacterial community. Finally, biofilm-grown bacteria might develop a biofilm-specific biocide-resistant phenotype. Owing to the heterogeneous nature of the biofilm, it is likely that there are multiple resistance mechanisms at work within a single community. Recent research has begun to shed light on how and why surface-attached microbial communities develop resistance to antimicrobial agents. PMID:11166241

  20. Pseudomonas aeruginosa biofilm infections: from molecular biofilm biology to new treatment possibilities.

    PubMed

    Tolker-Nielsen, Tim

    2014-12-01

    Bacteria in natural, industrial and clinical settings predominantly live in biofilms, i.e., sessile structured microbial communities encased in self-produced extracellular matrix material. One of the most important characteristics of microbial biofilms is that the resident bacteria display a remarkable increased tolerance toward antimicrobial attack. Biofilms formed by opportunistic pathogenic bacteria are involved in devastating persistent medical device-associated infections, and chronic infections in individuals who are immune-compromised or otherwise impaired in the host defense. Because the use of conventional antimicrobial compounds in many cases cannot eradicate biofilms, there is an urgent need to develop alternative measures to combat biofilm infections. The present review is focussed on the important opportunistic pathogen and biofilm model organism Pseudomonas aeruginosa. Initially, biofilm infections where P. aeruginosa plays an important role are described. Subsequently, current insights into the molecular mechanisms involved in P.aeruginosa biofilm formation and the associated antimicrobial tolerance are reviewed. And finally, based on our knowledge about molecular biofilm biology, a number of therapeutic strategies for combat of P.aeruginosa biofilm infections are presented. PMID:25399808

  1. Protocol for Identifying Fossil Biofilm Microfabrics in Archean and Martian Sedimentary Rocks

    NASA Astrophysics Data System (ADS)

    Bontognali, T. R. R.; McKenzie, J. A.; Vasconcelos, C.

    2014-12-01

    Microbial communities commonly live and grow in aggregates called biofilm. This slimy material is composed of exopolymeric substances (EPS) secreted from the microbial cell to the surrounding environment. Certain biofilms show internal microscopic fabrics, as for example, regularly shaped alveolar structures. These microfabrics are often considered as artifacts due to the dehydration steps required for scanning electron microscopy. However, recent studies have demonstrated that some microfabrics are not artifacts but actual structures, whose architecture is controlled by the microorganisms. These findings, mainly achieved for medical purposes, may have yet unconsidered implications for the search of early life on Earth and on Mars. Indeed, evidence exists that the microfabrics can be mineralized during early diagenesis, preserving fossil imprints of the original biofilm throughout the geological record. Here, we present the results of microscopic investigations of ancient sediments of various age, composition and metamorphic degree that contain microfabrics that we interpret as fossil biofilms. We compile a list of criteria that need to be evaluated before excluding that the putative fossil biofilms may be artifacts due to sample preparation or late stage contamination of the studied rocks. Additionally, we compare these microfabrics to those produced by pure cultures of microorganism grown in the laboratory, as well as microfabrics present in microbial mats that develop in modern evaporitic environments. Finally, we discuss the hypothesis - and the evidence that already exists in its support - that the micrometric size and the morphology of the EPS fabrics is specific to the organism and the genome concerned. By establishing a linkage between specific microbes and the architecture of the mineralized microfabrics, it may be possible to gain precise taxonomic information on early life, as well as to establish a new type of morphological biosignature to be searched for in Martian rocks during the forthcoming rover missions.

  2. Thermal zonation of microbial biogeography in the hydrothermal fields of Guaymas Basin: insights into the limits of life

    NASA Astrophysics Data System (ADS)

    Mckay, L. J.; Klokman, V.; Teske, A.

    2013-12-01

    Hydrothermally active sediments at Guaymas Basin are rich in organic substrates and host a wide range of shallow subsurface temperatures: from 3C to 200C in the upper 45 centimeters. High temperatures and hydrothermal flow cause upward compression of metabolic zones in Guaymas Basin seafloor sediments. Using push core samples collected by the Alvin submersible (Cruises AT15-40 and 56 in 2008 and 2009) we are investigating thermal structure and carbon and sulfur substrate utilization and their influence on microbial biogeography. As a proxy for viable microbial life total RNA is being extracted from seven high temperature cores that approach, and in three of the cores surpass the upper temperature limit for life at 122C (Takai et al., 2008). We are using reverse transcription PCR and subsequent pyrosequencing of the V5-V8 region of 16S rRNA to determine key hyperthermophilic archaeal and bacterial groups as well as the upper thermal limit for microbial life in situ. Porewater concentrations of sulfur species and concentrations and isotopic values of carbon species have been investigated in parallel to our high temperature cores. A combination of pyrosequencing data and porewater geochemistry profiles of carbon and sulfur species will help to elucidate the boundaries of life and provide insight into physiological mechanisms under extreme environmental conditions.

  3. Towards a hybrid anaerobic digester-microbial fuel cell integrated energy recovery system: an overview of the development of an electrogenic biofilm.

    PubMed

    Higgins, Scott R; Lopez, Ryan J; Pagaling, Eulyn; Yan, Tao; Cooney, Michael J

    2013-05-10

    An electrogenic biofilm was developed on a macroporous chitosan-carbon nanotube (CHIT-CNT) electrode under constant poised potential (-0.25V versus Ag/AgCl reference electrode) and flow through conditions utilizing the effluent of an anaerobic digester as both the inoculant and substrate for the electrogenic biofilm. After 125 days of inoculation the bioelectrode demonstrated an open circuit potential of -0.62V and a current density of 9.43?Acm(-3) (at -0.25V). Scanning electron microscopy images indicate thorough surface coverage of the biofilm with a high density of bacterial nanowires physically connecting bacteria to bacteria and bacteria to carbon nanotube (electrode surface) suggesting the nanowires are electrically conductive. DGGE was used to identify the major bacterial and archaeal populations. PMID:23608503

  4. A 'crytic' microbial mat: A new model ecosystem for extant life on Mars

    NASA Technical Reports Server (NTRS)

    Rothschild, L. J.

    1995-01-01

    If life were present on Mars today, it would face potentially lethal environmental conditions such as a lack of water, frigid temperatures, ultraviolet radiation, and soil oxidants. In addition, the Viking missions did not detect near-surface organic carbon available for assimilation. Autotrophic organisms that lived under a protective layer of sand or gravel would be able to circumvent the ultraviolet radiation and lack of fixed carbon. Two terrestrial photosynthetic near-surface microbial communities have been identified, one in the inter- and supertidal of Laguna Ojo de Liebere (Baja California Sur, Mexico) and one in the acidic gravel near several small geysers in Yellowstone National Park (Wyoming, U.S.A.). Both communities have been studied with respect to their ability to fix carbon under different conditions, including elevated levels of inorganic carbon. Although these sand communities have not been exposed to the entire suite of Martian environmental conditions simultaneously, such communities can provide a useful model ecosystem for a potential extant Martian biota.

  5. Effects of gamma irradiation on chemical, microbial quality and shelf life of shrimp

    NASA Astrophysics Data System (ADS)

    Hocao?lu, Asl?; Skr Demirci, Ahmet; Gms, Tuncay; Demirci, Mehmet

    2012-12-01

    In the present study the combined effect of gamma irradiation (1, 3 and 5 kGy) and storage at two temperatures: refrigeration (+4 C) and frozen (-18 C), on the shelf-life extension of fresh shrimp meat was investigated. The study was based on microbiological and physicochemical changes occuring in the shrimp samples. Total volatile base nitrogen values and trimethylamine values for irradiated shrimp samples were significantly lower than non-irradiated samples at both storage temperatures, and the rate of decrease was more pronounced in samples irradiated at the higher dose (p<0.05). Thiobarbituric acid values for irradiated shrimp samples were significantly higher than non-irradiated samples at both storage temperatures (p<0.05). pH values of shrimp samples were affected significantly by both irradiating dose and storage temperatures (p<0.05). Microbial counts for non-irradiated shrimp samples were higher than the respective irradiated samples at both storage temperatures (p<0.05). The results revealed that irradiation at high dose (5 kGy) might enhance lipid oxidation, although the growth of microorganisms and protein oxidation was inhibited.

  6. Early life microbial exposure and fractional exhaled nitric oxide in school-age children: a prospective birth cohort study

    PubMed Central

    2013-01-01

    Background Inflammation is a key factor in the pathogenesis of respiratory diseases. Early life exposure to microbial agents may have an effect on the development of the immune system and on respiratory health later in life. In the present work we aimed to evaluate the associations between early life microbial exposures, and fractional exhaled nitric oxide (FeNO) at school age. Methods Endotoxin, extracellular polysaccharides (EPS) and ?(1,3)-D-glucan were measured in living room dust collected at 23months of age in homes of participants of three prospective European birth cohorts (LISA, n?=?182; PIAMA, n?=?244; and INMA, n?=?355). Home dampness and pet ownership were periodically reported by the parents through questionnaires. FeNO was measured at age 8 for PIAMA and at age 10/11 for LISA and INMA. Cohort-specific associations between the indoor microbial exposures and FeNO were evaluated using multivariable regression analyses. Estimates were combined using random-effects meta-analyses. Results FeNO at school age was lower in children exposed to endotoxin at age 23months (? -0.05, 95% confidence interval (CI) -0.10;-0.01) and in children with reported dog ownership during the first two years of life (GM ratio 0.82, CI 0.70-0.96). FeNO was not significantly associated with early life exposure to EPS, ?(1,3)-D-glucan, indoor dampness and cat ownership. Conclusion Early life exposure to bacterial endotoxin and early life dog ownership are associated with lower FeNO at school age. Further studies are needed to confirm our results and to unravel the underlying mechanisms and possible clinical relevance of this finding. PMID:24295277

  7. Chemical Biology Strategies for Biofilm Control.

    PubMed

    Yang, Liang; Givskov, Michael

    2015-08-01

    Microbes live as densely populated multicellular surface-attached biofilm communities embedded in self-generated, extracellular polymeric substances (EPSs). EPSs serve as a scaffold for cross-linking biofilm cells and support development of biofilm architecture and functions. Biofilms can have a clear negative impact on humans, where biofilms are a common denominator in many chronic diseases in which they prime development of destructive inflammatory conditions and the failure of our immune system to efficiently cope with them. Our current assortment of antimicrobial agents cannot efficiently eradicate biofilms. For industrial applications, the removal of biofilms within production machinery in the paper and hygienic food packaging industry, cooling water circuits, and drinking water manufacturing systems can be critical for the safety and efficacy of those processes. Biofilm formation is a dynamic process that involves microbial cell migration, cell-to-cell signaling and interactions, EPS synthesis, and cell-EPS interactions. Recent progress of fundamental biofilm research has shed light on novel chemical biology strategies for biofilm control. In this article, chemical biology strategies targeting the bacterial intercellular and intracellular signaling pathways will be discussed. PMID:26350311

  8. DIFFUSION IN BIOFILMS RESPIRING ON ELECTRODES

    PubMed Central

    Renslow, RS; Babauta, JT; Majors, PD; Beyenal, H

    2013-01-01

    The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensional De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that 1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; 2) Drs at a given location decreases with G. sulfurreducens biofilm age; 3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and 4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms. PMID:23420623

  9. Diffusion in biofilms respiring on electrodes

    SciTech Connect

    Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.; Beyenal, Haluk

    2012-11-15

    The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed for noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensional De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that (1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; (2) Drs at a given location decreases with G. sulfurreducens biofilm age; (3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and (4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.

  10. Biogeochemistry of Hot Spring Biofilms: Major and Trace Element Behavior

    NASA Astrophysics Data System (ADS)

    Havig, J. R.; Prapaipong, P.; Zolotova, N.; Moore, G.; Shock, E. L.

    2008-12-01

    Hot spring biofilms are of obvious biological origin, but of surprising composition. Organic carbon makes up a minor percentage of the total mass of chemotrophic and phototrophic biofilms. We have found that the majority of biofilm mass is inorganic material, largely silica, with measurable quantities of dozens of other elements, and that the distribution of major elements mimics that of surrounding rock and soil far more closely than the hot spring fluids. Comparisons of biofilms with the compositions of their geochemical surroundings help identify trace elements that are anomalously enriched or depleted. These anomalies provide insight into the processes of active or passive elemental accumulation by biofilms, which could be used to understand microbial processes of element uptake or to identify evidence for life in hydrothermal deposits in the rock record. Five separate hydrothermal systems in Yellowstone National Park were incorporated into this study: 'Bison Pool' and its outflow (siliceous-sinter depositing, temp. = 93.2 to 56.2 C, pH = 7.4 to 8.3), Flatcone Geyser and its outflow (siliceous-sinter depositing, temp. = 94.3 to 44.3 C, pH = 7.9 to 8.8, Boulder Spring and its outflow (siliceous-sinter depositing, temp. = 92.1 to 64.9 C, pH = 8.2 to 8.7), Octopus Spring and its outflow (siliceous-sinter depositing, temp. = 91.4 to 62.8 C, pH = 7.7 to 8.2), and two unnamed locations in the Obsidian Pool area we have dubbed 'Green Cheese' (temp. = 64.5 to 54.9 C, pH = 5.9 to 6.2) and 'Happy Harfer Pool' (temp. = 59.9 to 48.3 C, pH = 5.5 to 6.3). Analysis of water, biofilm, and contextual samples collected from and around these hot springs offer intriguing patterns of elemental behavior, both similar and dissimilar, among the varying systems. Examples of these patterns include elements that behave the same across all hot spring systems (B, C, Ni, Cu, Ge, Sb, and W), elements with behavior that was consistent throughout most (four of five) of the hot spring systems (Li, N, Si, P, K, Fe, Mn, Zn, Ga, Rb, Y, Cd, Sn, Ba, Hf, Ta, and Pb), and elements that varied across all hot spring systems (V, Sr). These results permit multiple hypotheses concerning active microbial uptake or exclusion of individual elements, expedited mineral/glass dissolution, and temperature and fluid composition effects on abiotic ion exchange processes in complex biofilm matrices.

  11. How Biofilms Evade Host Defenses.

    PubMed

    Roilides, Emmanuel; Simitsopoulou, Maria; Katragkou, Aspasia; Walsh, Thomas J

    2015-06-01

    The steps involved during the biofilm growth cycle include attachment to a substrate followed by more permanent adherence of the microorganisms, microcolony arrangement, and cell detachment required for the dissemination of single or clustered cells to other organ systems. Various methods have been developed for biofilm detection and quantitation. Biofilm-producing microorganisms can be detected in tissue culture plates, using silicone tubes and staining methods, and by visual assessment using scanning electron microscopy or confocal scanning laser microscopy. Quantitative measurement of biofilm growth is determined by using methods that include dry cell weight assays, colony-forming-unit counting, DNA quantification, or XTT 2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide reduction assay. Upon infection, innate immune defense strategies are able to establish an immediate response through effector mechanisms mediated by immune cells, receptors, and several humoral factors. We present an overview of the life cycle of biofilms and their diversity, detection methods for biofilm development, and host immune responses to pathogens. We then focus on current concepts in bacterial and fungal biofilm immune evasion mechanisms. This appears to be of particular importance because the use of host immune responses may represent a novel therapeutic approach against biofilms. PMID:26185085

  12. Dynamic behavior of biofilms

    SciTech Connect

    Worden, R.M. ); Donaldson, T.L. )

    1986-01-01

    Biological fixed films, or biofilms, are composed of a dense cluster of cells bound to one another or a support surface by the glycocalyx, a cell-secreted carbohydrate matrix. A key advantage of fixed films over other types of immobilized-cell systems is that the immobilization occurs naturally, and hence does not require the additional materials and labor for cell entrapment within gels or covalent bonding to supports. Applications of microbial film fermenters have included animal-cell culture, bacterial leaching of ores, waste treatment, and the production of vinegar, ethanol, critic acid, and beer. Analysis of the unsteady-state behavior of biofilms can provide insight into basic scientific phenomena such as intracellular metabolic regulation patterns.

  13. Microfluidics Expanding the Frontiers of Microbial Ecology

    PubMed Central

    Rusconi, Roberto; Garren, Melissa; Stocker, Roman

    2014-01-01

    The ability afforded by microfluidics to observe the behaviors of microbes in highly controlled and confined microenvironments, across scales from a single cell to mixed communities, has significantly contributed to expand the frontiers of microbial ecology over the last decade. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. Here we review applications of microfluidics that have resulted in highly insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible, multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control phenomena such as biofilm formation and antibiotic resistance. PMID:24773019

  14. Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces

    PubMed Central

    Lourenço, Anália; Coenye, Tom; Goeres, Darla M.; Donelli, Gianfranco; Azevedo, Andreia S.; Ceri, Howard; Coelho, Filipa L.; Flemming, Hans-Curt; Juhna, Talis; Lopes, Susana P.; Oliveira, Rosário; Oliver, Antonio; Shirtliff, Mark E.; Sousa, Ana M.; Stoodley, Paul; Pereira, Maria Olivia; Azevedo, Nuno F.

    2015-01-01

    The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization. Instead, MIABiE presents guidelines about the data to be recorded and published in order for the procedure and results to be easily and unequivocally interpreted and reproduced. Overall, MIABiE opens up the discussion about a number of particular areas of interest and attempts to achieve a broad consensus about which biofilm data and metadata should be reported in scientific journals in a systematic, rigorous and understandable manner. PMID:24478124

  15. Biofilms: The Stronghold of Legionella pneumophila

    PubMed Central

    Abdel-Nour, Mena; Duncan, Carla; Low, Donald E.; Guyard, Cyril

    2013-01-01

    Legionellosis is mostly caused by Legionella pneumophila and is defined as a severe respiratory illness with a case fatality rate ranging from 5% to 80%. L. pneumophila is ubiquitous in natural and anthropogenic water systems. L. pneumophila is transmitted by inhalation of contaminated aerosols produced by a variety of devices. While L. pneumophila replicates within environmental protozoa, colonization and persistence in its natural environment are also mediated by biofilm formation and colonization within multispecies microbial communities. There is now evidence that some legionellosis outbreaks are correlated with the presence of biofilms. Thus, preventing biofilm formation appears as one of the strategies to reduce water system contamination. However, we lack information about the chemical and biophysical conditions, as well as the molecular mechanisms that allow the production of biofilms by L. pneumophila. Here, we discuss the molecular basis of biofilm formation by L. pneumophila and the roles of other microbial species in L. pneumophila biofilm colonization. In addition, we discuss the protective roles of biofilms against current L. pneumophila sanitation strategies along with the initial data available on the regulation of L. pneumophila biofilm formation. PMID:24185913

  16. Headwaters are critical reservoirs of microbial diversity for fluvial networks

    PubMed Central

    Besemer, Katharina; Singer, Gabriel; Quince, Christopher; Bertuzzo, Enrico; Sloan, William; Battin, Tom J.

    2013-01-01

    Streams and rivers form conspicuous networks on the Earth and are among nature's most effective integrators. Their dendritic structure reaches into the terrestrial landscape and accumulates water and sediment en route from abundant headwater streams to a single river mouth. The prevailing view over the last decades has been that biological diversity also accumulates downstream. Here, we show that this pattern does not hold for fluvial biofilms, which are the dominant mode of microbial life in streams and rivers and which fulfil critical ecosystem functions therein. Using 454 pyrosequencing on benthic biofilms from 114 streams, we found that microbial diversity decreased from headwaters downstream and especially at confluences. We suggest that the local environment and biotic interactions may modify the influence of metacommunity connectivity on local biofilm biodiversity throughout the network. In addition, there was a high degree of variability in species composition among headwater streams that could not be explained by geographical distance between catchments. This suggests that the dendritic nature of fluvial networks constrains the distributional patterns of microbial diversity similar to that of animals. Our observations highlight the contributions that headwaters make in the maintenance of microbial biodiversity in fluvial networks. PMID:24089333

  17. Activity of disinfectants against multispecies biofilms formed by Staphylococcus aureus, Candida albicans and Pseudomonas aeruginosa.

    PubMed

    Kart, Didem; Tavernier, Sarah; Van Acker, Heleen; Nelis, Hans J; Coenye, Tom

    2014-01-01

    Microbial biofilms are a serious threat to human health. Recent studies have indicated that many clinically relevant biofilms are polymicrobial. In the present study, multispecies biofilms were grown in a reproducible manner in a 96-well microtiter plate. The efficacy of nine commercially available disinfectants against Staphylococcus aureus, Candida albicans, and Pseudomonas aeruginosa in multispecies biofilms was determined and compared. The results showed that the direction and the magnitude of the effect in a multispecies biofilm depend on the strain and the disinfectant used and challenge the common belief that organisms in multispecies biofilms are always less susceptible than in monospecies biofilms. PMID:24579656

  18. Emerging interactions between matrix components during biofilm development.

    PubMed

    Payne, David E; Boles, Blaise R

    2016-02-01

    Bacterial cells are most often found in the form of multicellular aggregates commonly referred to as biofilms. Biofilms offer their member cells several benefits, such as resistance to killing by antimicrobials and predation. During biofilm formation there is a production of extracellular substances that, upon assembly, constitute an extracellular matrix. The ability to generate a matrix encasing the microbial cells is a common feature of biofilms, but there is diversity in matrix composition and in interaction between matrix components. The different components of bacterial biofilm extracellular matrixes, known as matrix interactions, and resulting implications are discussed in this review. PMID:26515441

  19. Microbial Diversity in the Columbia River Basalt Group and the Context for Life in Subsurface Basalts

    NASA Astrophysics Data System (ADS)

    Lavalleur, H. J.; Smith, A.; Fisk, M. R.; Colwell, F. S.

    2012-12-01

    Large igneous provinces constitute a sizable volume of porous and fractured materials in the Earth's crust and many of these environments exist within the boundaries of survival for subsurface life. The results of microbiological studies of basalts and other igneous materials in subsurface settings hint at the types of microbes that dwell in these environments. We investigated the microbes in aquifers in the Columbia River Basalt Group (CRBG) and also considered the microbial communities in subsurface basalts more broadly to determine if there are recurrent themes in the types of microbes and the nature of diversity present in these geological systems. Bacteria and Archaea collected from five intervals in the CRBG were examined using high-throughput DNA sequencing directed at the 16S rRNA genes. The highest bacterial biomass and the highest bacterial diversity were observed in the deepest samples (>1018 meters below land surface) whereas the highest archaeal diversity was detected in the shallowest samples (<449 mbls). Microbes classified as Proteobacteria, Firmicutes, and Actinobacteria dominated the aquifers. These findings are generally consistent with earlier cultivation- and clone library-based studies performed on microbes from the CRBG and the Snake River Plain aquifer. Microbes associated with marine basalts are similar to those found in terrestrial settings and include Proteobacteria, Firmicutes, candidate division bacterium OP1, Euryarchaeota, and Crenarchaeota. Based on 16S rRNA sequence similarities to known microbes, both basaltic regions have taxa with representative physiologies likely to include hydrogen oxidation, iron and sulfur metabolism, acetogenesis, and hydrocarbon metabolism. Research on the microbiology of basalt rich provinces on the planet has informed our understanding of biogeochemical cycling where igneous rocks dominate. The knowledge gained in these investigations also promotes our ability to verify the remediation of contaminants and the sequestration of carbon in basalts.

  20. Magnetite Crystal Chains: Most Promising Evidence of Past Microbial Life on Mars, Also Useful on Earth

    NASA Astrophysics Data System (ADS)

    Friedmann, E.; Wierzchos, J.; Ascaso, C.; Giannuzzi, L. A.

    2005-12-01

    It is not easy to identify "biosignatures", suitable targets in the search for traces of microbial life on early Mars: They need to have withstood billions of years of extreme conditions and to provide unambiguous evidence. Organic molecules were probably destroyed by the highly oxidative environment, at least near the surface. Mineral structures offer hardly more than strong indication, not unambiguous evidence, and no direct information about the organisms that may have produced them. The reason is that soft-bodied bacteria do not leave behind good fossil traces. The only known exception seems to be magnetotactic bacteria, widespread on Earth in most aquatic environments, that produce inside their body chains of magnetite crystals. Single crystals showing properties observed in terrestrial bacteria (definite size range, morphology, chemical purity, rarity of crystallographic defects) may indicate biological origin, but provide no absolute evidence: It is impossible to prove that such crystals can not be produced by non-biological processes on Mars. However, magnetite crystal chains of bacteria have properties that are the direct consequence of being produced by organisms. In the living cell, they are surrounded by a biological membrane or organic matrix. Even in terrestrial fossils, crystals of a single chain show high level of uniformity in size and shape (because the matrix functions as a template), gaps between crystals (organic substance between crystals) and remarkable bends (due to the elasticity of the organic matter between crystals, a property absent in the mineral world). Magnetite chains of bacteria are complex structures whose formation requires the interaction of a series of chemical and physical processes and feedback loops, as well as genetically stored information, the ultimate proof of life. Non-biogenous chains produced in the laboratory do not show such characteristics. Bacterial magnetite chains in terrestrial magnetofossils can be observed in situ by backscattered scanning electron microscopy. While this method permits to locate such chains in sediments, it yields rather fuzzy images. Single chains excised by focused ion beam (FIB) milling instrument can be used to produce images by more advanced methods such as HAADF electron tomography. We suggest that fossil lakebeds on Mars (e.g. Gusev Crater) would be promising targets to search for fossil chains of magnetotactic bacteria.

  1. How Cyanobacterial Distributions Reveal Flow and Irradiance Conditions of Photosynthetic Biofilm Formation

    NASA Technical Reports Server (NTRS)

    Prufert-Bebout, Lee; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Microbial life on Earth is enormously abundant at sediment-water interfaces. The fossil record in fact contains abundant evidence of the preservation of life on such surfaces. It is therefore critical to our interpretation of early Earth history, and potentially to history of life on other planets, to be able to recognize life forms at these interfaces. On Earth this life often occurs as organized structures of microbes and their extracellular exudates known as biofilms. When such biofilms occur in areas receiving sunlight photosynthetic biofilms are the dominant form in natural ecosystems due to selective advantage inherent in their ability to utilize solar energy. Cyanobacteria are the dominant phototrophic microbes in most modern and ancient photosynthetic biofilms, microbial mats and stromatolites. Due to their long (3.5 billion year) evolutionary history, this group has extensively diversified resulting in an enormous array of morphologies and physiological abilities. This enormous diversity and specialization results in very specific selection for a particular cyanobacterium in each available photosynthetic niche. Furthermore these organisms can alter their spatial orientation, cell morphology, pigmentation and associations with heterotrophic organisms in order to fine tune their optimization to a given micro-niche. These adaptations can be detected, and if adequate knowledge of the interaction between environmental conditions and organism response is available, the detectable organism response can be used to infer the environmental conditions causing that response. This presentation will detail two specific examples which illustrate this point, Light and water are essential to photosynthesis in cyanobacteria and these organisms have specific detectable behavioural responses to these parameters. We will present cyanobacterial responses to quantified flow and irradiance to demonstrate the interpretative power of distribution and orientation information. This study presents new results, but many such examples are already found in the literature.

  2. Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

    NASA Astrophysics Data System (ADS)

    Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

    2007-12-01

    The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.