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1

Biofilms: Microbial Life on Surfaces  

PubMed Central

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.

2002-01-01

2

Biofilms: Microbial Life on Surfaces  

Microsoft Academic Search

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 pro- cess regulated by diverse characteristics of the growth medium, substratum, and cell surface. An estab- lished biofilm structure comprises

Rodney M. Donlan

2002-01-01

3

Microbial life in sedimentary biofilms the challenge to microbial ecologists  

Microsoft Academic Search

ABSTRACT: Modification and,decomposition,processes of material in sedirnents are dominated,by microorganisms. Through microbial colonization, cells become immobilized at particle surfaces and embedded,in an organic matrix of extracellular polysaccharides. The development,of complex,sedi- mentary,biofilms is the net result of transport and exchange,processes,between,the biofilm and sur- rounding water, and modification and transformation processes of matter within the biofilm. This arti- cle illustrates aspects of

Lutz-Arend Meyer-Reil

1994-01-01

4

Insight into Biofilm-Associated Microbial Life  

Microsoft Academic Search

Microbes cohabit our planet and are engaged in a struggle for survival though on a microscopic scale. This endeavor allows them to develop and devise means for survival and proliferation. One such strategy is the formation of biofilms leading to establishment of a protected community. Such multi-communities may consist of harmful and pathogenic microbes, and they may cause economic problems

V. S. Bhinu

2005-01-01

5

Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats  

Microsoft Academic Search

This article hypothesizes that the origin of the first microbial cell(s) occurred as a series of increasing levels of organization within a prebiotic gel attached to a mineral surface, which made the transition to a biofilm composed of the first cell(s) capable of growth and division. A gel microenvironment attached to a surface for the origin of life, and subsequent

Jack T. Trevors

2011-01-01

6

Biofilms: A microbial home  

PubMed Central

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.

Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

2011-01-01

7

The Biofilm Returns: Microbial Life at the Interface  

Microsoft Academic Search

\\u000a Scientific studies over the past few decades have shown that the vast majority of microbes in the aqueous environment do not\\u000a live as free-floating (i.e., planktonic) forms, but rather prefer to live as attached communities termed biofilms. Biofilm\\u000a formation onto surfaces is usually detrimental to human health and man-made structures; biofilm-related problems range from\\u000a antibiotic-resistant infections in humans and animals

Anand Jain; Enrico Marsili; Narayan B. Bhosle

8

Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats.  

PubMed

This article hypothesizes that the origin of the first microbial cell(s) occurred as a series of increasing levels of organization within a prebiotic gel attached to a mineral surface, which made the transition to a biofilm composed of the first cell(s) capable of growth and division. A gel microenvironment attached to a surface for the origin of life, and subsequent living cells offers numerous advantages. These include acting as a water and nutrient trap on a surface, physical protection as well as protection from UV radiation. The prebiotic gel and the living biofilm contained the necessary water, does not impede diffusion of molecules including gases, provides a structured gel microscopic location for biochemical interactions and polymerisation reactions, where the necessary molecules for life need to be present and not limiting. The composition of the first gel environment may have been an oily-water mixture (or the interface between an oily-water mixture) of microscopic dimensions, but large enough for the organization of the first cell(s). The living biofilm then made the evolutionary transition to a microbial mat. PMID:21513895

Trevors, Jack T

2011-03-25

9

Cooperation and Conflict in Microbial Biofilms  

Microsoft Academic Search

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

Joao B. Xavier; Kevin R. Foster

2007-01-01

10

Spectroelectrochemical analyses of electroactive microbial biofilms.  

PubMed

Understanding the mechanism of ET (electron transfer) through electroactive microbial biofilms is a challenge in the field of fundamental and applied life sciences. To date, electrochemical techniques such as CV (cyclic voltammetry) have been applied successfully to study the ET process in intact microbial biofilms on electrodes, providing important insight into their redox properties. However, CV as such does not provide any structural information about the species involved in the redox process. This shortcoming may limit the understanding of the ET process in microbial biofilms. To overcome this restriction, spectroelectrochemical techniques have been designed consisting of a spectroscopic technique performed in combination with electrochemical methods on the same electrode sample. These analytical approaches allow in vivo measurements of microbial biofilms under physiologically relevant conditions and controlled applied potential. The present review describes these spectroelectrochemical methodologies and critically addresses their impact on the understanding of the ET through biofilms. PMID:23176469

Millo, Diego

2012-12-01

11

Materials Research Society Spring Meeting Symposium KK: Microbial Life on Surfaces: Biofilm-Material Interactions: Life at Interfaces. Held in San Francisco, California on 25-27 April 2011 (Abstracts).  

National Technical Information Service (NTIS)

Bacterial communities living on surfaces are called biofilms. Microbial life on a surface has specific consequences for both the microbes (in terms of their physiology, metabolism, and gene expression), and for the substrate, as evidenced by the fouling a...

W. Goodson

2012-01-01

12

Manipulatiaon of Biofilm Microbial Ecology  

SciTech Connect

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.

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

1998-08-09

13

Manipulation of Biofilm Microbial Ecology  

SciTech Connect

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.

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

14

Biofilm formation and microbial corrosion  

SciTech Connect

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.

Goldstein, R.; Porcella, D.

1992-07-01

15

Optical sectioning of microbial biofilms.  

PubMed Central

Scanning confocal laser microscopy (SCLM) was used to visualize fully hydrated microbial biofilms. The improved rejection of out-of-focus haze and the increased resolution of SCLM made it preferable to conventional phase microscopy for the analysis of living biofilms. The extent of image improvement was dependent on the characteristics of individual biofilms and was most apparent when films were dispersed in three dimensions, when they were thick, and when they contained a high number of cells. SCLM optical sections were amenable to quantitative computer-enhanced microscopy analyses, with minimal interference originating from overlying or underlying cell material. By using SCLM in conjunction with viable negative fluorescence staining techniques, horizontal (xy) and sagittal (xz) sections of intact biofilms of Pseudomonas aeruginosa, Pseudomonas fluorescens, and Vibrio parahaemolyticus were obtained. These optical sections were then analyzed by image-processing techniques to assess the distribution of cellular and noncellular areas within the biofilm matrices. The Pseudomonas biofilms were most cell dense at their attachment surfaces and became increasingly diffuse near their outer regions, whereas the Vibrio biofilms exhibited the opposite trend. Biofilms consisting of different species exhibited distinctive arrangements of the major biofilm structural components (cellular and extracellular materials and space). In general, biofilms were found to be highly hydrated, open structures composed of 73 to 98% extracellular materials and space. The use of xz sectioning revealed more detail of biofilm structure, including the presence of large void spaces within the Vibrio biofilms. In addition, three-dimensional reconstructions of biofilms were constructed and were displayed as stereo pairs. Application of the concepts of architectural analysis to mixed- or pure-species biofilms will allow detailed examination of the relationships among biofilm structure, adaptation, and response to stress. Images FIG. 1 FIG. 2a FIG. 2b FIG. 3a FIG. 3b FIG. 5 FIG. 6

Lawrence, J R; Korber, D R; Hoyle, B D; Costerton, J W; Caldwell, D E

1991-01-01

16

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

SciTech Connect

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.

Singer, Steven [Lawrence Livermore National Laboratory (LLNL); Erickson, Brian K [ORNL; Verberkmoes, Nathan C [ORNL; Hwang, Mona [Lawrence Livermore National Laboratory (LLNL); Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley; Thelen, Michael P. [University of California, Berkeley

2010-01-01

17

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

Microsoft Academic Search

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)

Steven W Singer; Brian K Erickson; Nathan C VerBerkmoes; Mona Hwang; Manesh B Shah; Robert L Hettich; Jillian F. Banfield; Michael P. Thelen

2010-01-01

18

Community Proteomics of a Natural Microbial Biofilm  

Microsoft Academic Search

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

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

2005-01-01

19

Microbial landscapes: new paths to biofilm research.  

PubMed

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms. PMID:17170748

Battin, Tom J; Sloan, William T; Kjelleberg, Staffan; Daims, Holger; Head, Ian M; Curtis, Tom P; Eberl, Leo

2007-01-01

20

Microbial Biofilms: from Ecology to Molecular Genetics  

PubMed Central

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.

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

2000-01-01

21

Microbial Biofilms: How Effective in Rhizobium –Legume Symbiosis?  

Microsoft Academic Search

\\u000a Diverse genera of bacteria live as microbial communities called biofilms on biotic or abiotic surfaces, or interfaces. They\\u000a exhibit elevated microbial action, as a result of symbiosis in biofilm structure and physiological adaptation. The formation\\u000a of fungal–bacterial biofilms by bacterial colonization on biotic fungal surfaces gives the biofilms enhanced microbial effectiveness\\u000a compared to monocultures. When the bacteria include rhizobia, they

G. Seneviratne; M. L. M. A. W. Weerasekara; J. S. Zavahir

22

Computational modeling of synthetic microbial biofilms.  

PubMed

Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency and their resistance to changes in their local environment. These properties make biofilms an attractive target for engineering, particularly for the production of chemicals such as pharmaceutical ingredients or biofuels, with the potential to significantly improve yields and lower maintenance costs. Biofilms are also a major cause of persistent infection, and a better understanding of their organization could lead to new strategies for their disruption. Despite this potential, the design of synthetic biofilms remains a major challenge, due to the complex interplay between transcriptional regulation, intercellular signaling, and cell biophysics. Computational modeling could help to address this challenge by predicting the behavior of synthetic biofilms prior to their construction; however, multiscale modeling has so far not been achieved for realistic cell numbers. This paper presents a computational method for modeling synthetic microbial biofilms, which combines three-dimensional biophysical models of individual cells with models of genetic regulation and intercellular signaling. The method is implemented as a software tool (CellModeller), which uses parallel Graphics Processing Unit architectures to scale to more than 30,000 cells, typical of a 100 ?m diameter colony, in 30 min of computation time. PMID:23651288

Rudge, Timothy J; Steiner, Paul J; Phillips, Andrew; Haseloff, Jim

2012-08-10

23

Combating biofilms.  

PubMed

Biofilms are complex microbial communities consisting of microcolonies embedded in a matrix of self-produced polymer substances. Biofilm cells show much greater resistance to environmental challenges including antimicrobial agents than their free-living counterparts. The biofilm mode of life is believed to significantly contribute to successful microbial survival in hostile environments. Conventional treatment, disinfection and cleaning strategies do not proficiently deal with biofilm-related problems, such as persistent infections and contamination of food production facilities. In this review, strategies to control biofilms are discussed, including those of inhibition of microbial attachment, interference of biofilm structure development and differentiation, killing of biofilm cells and induction of biofilm dispersion. PMID:22066868

Yang, Liang; Liu, Yang; Wu, Hong; Song, Zhijun; Høiby, Niels; Molin, Søren; Givskov, Michael

2012-07-01

24

The Effects of Eutrophication on the Structure and Function of Microbial Biofilms  

Microsoft Academic Search

Biofilms are the dominate form of microbial life in aquatic ecosystems and are responsible for performing a wide variety of ecosystem services including nutrient and organic matter processing and retention. Understanding how eutrophication impacts these communities is essential for ecosystem managers as many aquatic ecosystems are being enriched by anthropogenic activities. This study investigated the effects of eutrophication on biofilm

David J. Van Horn; Cliff N. Dahm

25

Biofilm and dental implant: The microbial link  

PubMed Central

Mouth provides a congenial environment for the growth of the microorganisms as compared to any other part of the human body by exhibiting an ideal nonshedding surface. Dental plaque happens to be a diverse community of the microorganisms found on the tooth surface. Periodontal disease and the peri-implant disease are specific infections that are originating from these resident microbial species when the balance between the host and the microbial pathogenicity gets disrupted. This review discusses the biofilms in relation to the peri-implant region, factors affecting its presence, and the associated treatment to manage this complex microbial colony. Search Methodology: Electronic search of the medline was done with the search words: Implants and biofilms/dental biofilm formation/microbiology at implant abutment interface/surface free energy/roughness and implant, periimplantitis/local drug delivery and dental implant. Hand search across the journals – clinical oral implant research, implant dentistry, journal of dental research, international journal of oral implantology, journal of prosthetic dentistry, perioodntology 2000, journal of periodontology were performed. The articles included in the review comprised of in vivo studies, in vivo (animal and human) studies, abstracts, review articles.

Dhir, Sangeeta

2013-01-01

26

Microbial diversity and interactions in subgingival biofilm communities.  

PubMed

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

Diaz, Patricia I

2011-11-11

27

Evaluation of some halogen biocides using a microbial biofilm system  

Microsoft Academic Search

A simple method for the formation of microbial biofilms of three species, Pseudomonas fluorescens, Pseudomonas aeruginosa, and Klebsiella pneumoniae, on a small glass slide was established, and its suitability for evaluation of disinfectant efficacy was examined. The biofilms formed were observed in situ by confocal laser scanning microscopy (CLSM). Using the biofilms established, biocidal efficacy of several halogen biocides, such

Mariko Tachikawa; Masakatsu Tezuka; Masahiro Morita; Katsuhisa Isogai; Shoji Okada

2005-01-01

28

High-throughput metal susceptibility testing of microbial biofilms  

Microsoft Academic Search

BACKGROUND: Microbial biofilms exist all over the natural world, a distribution that is paralleled by metal cations and oxyanions. Despite this reality, very few studies have examined how biofilms withstand exposure to these toxic compounds. This article describes a batch culture technique for biofilm and planktonic cell metal susceptibility testing using the MBEC assay. This device is compatible with standard

Joe J Harrison; Raymond J Turner; Howard Ceri

2005-01-01

29

Proteogenomic studies of natural microbial biofilms  

NASA Astrophysics Data System (ADS)

Acid mine drainage (AMD) forms when rocks rich in pyrite, FeS2, are oxidized upon exposure to air and water. Iron-oxidizing microorganisms accelerate pyrite dissolution by generating ferric iron, an especially effective sulfide oxidant. We have used cultivation-independent methods to study the gene (Tyson et al., 2004) and protein (Ram et al., in review) complements of microbial biofilms from an AMD environment in Richmond, CA. The genomes of the biofilm organisms indicated potential proteins and other small molecules that each organism type can produce. We then used this genome data in combination with 2D LC-MS/MS mass spectrometry to identify proteins within extracellular/periplasmic, soluble, and membrane fractions of the biofilm. This method enabled us to infer the most abundant proteins in each fraction and their general location. In particular, it led us to identify an extracellular/periplasmic cytochrome central to iron oxidation and acid mine drainage, as well as to analyze hypothetical proteins (proteins predicted from the genome with no significant homology to known proteins), some of which are likely to be adaptations by the biofilm organisms for thriving in this unique metal-rich acidic environment.

Ram, R. J.; Verberkmoes, N. C.; Thelen, M. P.; Tyson, G. W.; Baker, B. J.; Shah, M.; Blake, R. C.; Hettich, R. L.; Banfield, J. F.

2005-05-01

30

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...

31

OpinionMicrobial landscapes: new paths to biofilm research  

Microsoft Academic Search

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept

William T. Sloan; Staffan Kjelleberg; Holger Daims; Ian M. Head; Tom P. Curtis; Leo Eberl; Tom J. Battin

2007-01-01

32

Hypersaline Microbial Systems of Sabkhas: Examples of Life's Survival in  

Microsoft Academic Search

Life and living systems need several important factors to establish themselves and to have a continued tradition. In this article the nature of the borderline situation for microbial life under heavy salt stress is analyzed and discussed using the example of biofilms and microbial mats of sabkha systems of the Red Sea. Important factors ruling such environments are described, and

Wolfgang Elisabeth Krumbein; Anna A. Gorbushina; Elisabeth Holtkamp-Tacken

2004-01-01

33

Microbial biofilm communities in the gastrointestinal tract.  

PubMed

The human gastrointestinal tract is colonized throughout its length by complex luminal and mucosal microbiotas. Owing to sampling restrictions, most of the studies done to date have concentrated on luminal material. Recently, however, there has been an upsurge in interest in the role of microbial communities that occur in biofilms on surfaces in the gut. In the human biota, biofilms have been shown to exist on artificial surfaces and devices implanted in the host, on particulate materials in the gut lumen, and on the colonic mucosa. Owing to their proximity to host tissues, mucosal bacteria interact more readily with the gut epithelium and immune system than their luminal counterparts, and recent research indicates that they play an important role in health and disease processes. Because bacteria growing in biofilms are more resistant to antibiotics than their luminal counterparts, there is increased interest in the use of alternative therapeutic strategies to target potential pathogens on the mucosal surface, especially with respect to applications involving probiotics, prebiotics, and synbiotics. PMID:18806707

Macfarlane, Sandra

2008-09-01

34

Microbial community structures in a closed raw water distribution system biofilm as revealed by 454-pyrosequencing analysis and the effect of microbial biofilm communities on raw water quality.  

PubMed

This is the first report on the characterization of the microbial biofilm community structure and water quality change along a closed and stable raw water distribution system. 454-pyrosequencing was employed to investigate the microbial communities in four biofilm samples. 25,426 optimized sequences were obtained. Results showed Proteobacteria was the dominant phylum in each biofilm sample. The abundance of Nitrospiraes in M6 biofilm, Firmicutes in M8 biofilm, Actinobacteria in M9 biofilm were higher by comparing with other three biofilm samples. The M6 microbial biofilm community structure was similar to that of M7, dissimilar to that of M9. Dissolved oxygen and nitrogen was probably major factors to influence the microbial biofilm communities. Nitrospiraes in M6 biofilm and Firmicutes in M8 biofilm were crucial to remove ammonia nitrogen and nitrate in raw water. How to enrich functional microbes in biofilm to pretreat raw water is an important area of future research. PMID:24055963

Luo, Jianghan; Liang, Heng; Yan, Lijun; Ma, Jun; Yang, Yanling; Li, Guibai

2013-08-31

35

The Biofilm Mode of Life  

Microsoft Academic Search

Recent advances in studies of biofilm systems have generated a wealth of novel informa- tion on multicellular prokaryotic biology and have established models for the formation of biofilms and the biology of their lifecycles. As a prelude to the subsequent chapters in this volume, this introductory article is aimed at identifying the contextual scientific and experimental framework for contemporary biofilm

Staffan Kjelleberg; Michael Givskov

36

Single-species microbial biofilm screening for industrial applications  

Microsoft Academic Search

While natural microbial biofilms often consist of multiple species, single-species biofilms are of great interest to biotechnology.\\u000a The current study evaluates biofilm formation for common industrial and laboratory microorganisms. A total of 68 species of\\u000a biosafety level one bacteria and yeasts from over 40 different genera and five phyla were screened by growing them in microtiter\\u000a plates and estimating attached

Xuan Zhong Li; Bernhard Hauer; Bettina Rosche

2007-01-01

37

An inexpensive chemostat apparatus for the study of microbial biofilms  

Microsoft Academic Search

Continuous culture is a powerful technique for studying microbial biofilms because it allows for the control of growth rate through nutrient limitation. These conditions offer a realistic view of how microorganisms interact in natural ecosystems. The vast majority of biofilm research is performed with batch cultures, due to the high cost of commercially produced chemostats. We describe a chemostat that

Marvin Whiteley; Erin Brown; Robert J. C. McLean

1997-01-01

38

Early microbial biofilm formation on marine plastic debris  

Microsoft Academic Search

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 3weeks in order to study early stage processes. Microbial biofilms developed rapidly on the plastic and coincided with

Delphine Lobelle; Michael Cunliffe

2011-01-01

39

Peppermint ( Mentha piperita) inhibits microbial biofilms in vitro  

Microsoft Academic Search

Microbial biofilms have become increasingly problematic in the food processing and medical industries where they cause food and surface contamination. Biofilms have also been implicated as the cause of serious infections in humans as their occurrence makes it difficult to treat common infections and the likelihood of recurrent infections is high. Due to emerging resistance, conventional control methods are fast

M. Sandasi; C. M. Leonard; S. F. Van Vuuren; A. M. Viljoen

2011-01-01

40

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...

41

The biofilm ecology of microbial biofouling, biocide resistance and corrosion  

SciTech Connect

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.

White, D.C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Oak Ridge National Lab., TN (United States). Environmental Science Div.; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Arrage, A.A. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Microbial Insights, Inc., Rockford, TN (United States)

1997-06-01

42

Method for Studying Microbial Biofilms in Flowing-Water Systems  

PubMed Central

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?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?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 (?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.

Pedersen, Karsten

1982-01-01

43

Method for attentuating virulence of microbial pathogens and for inhibiting microbial biofilm formation  

US Patent & Trademark Office Database

The present invention relates to the use of the cyclic dinucleotide c-di-GMP and cyclic dinucleotide analogues thereof in a method for attenuating virulence of a microbial pathogen or for inhibiting or reducing colonization by a microbial pathogen. This method further inhibits microbial biofilm formation and is capable of treating bacterial infections. The microbial colonization or biofilm formation inhibited or reduced may be on the skin or on nasal or mucosal surface. The microbial colonization or biofilm formation inhibited can also be on the surfaces of medical devices, especially those in close contact with the patient, as well on the surfaces of industrial and construction material where microbial colonization and biofilm formation is of concern.

2013-02-05

44

The biofilm matrix – an immobilized but dynamic microbial environment  

Microsoft Academic Search

The biofilm matrix is a dynamic environment in which the component microbial cells appear to reach homeostasis and are optimally organized to make use of all available nutrients. The major matrix components are microbial cells, polysaccharides and water, together with excreted cellular products. The matrix therefore shows great microheterogeneity, within which numerous microenvironments can exist. Although exopolysaccharides provide the matrix

Ian W Sutherland

2001-01-01

45

Single-species microbial biofilm screening for industrial applications.  

PubMed

While natural microbial biofilms often consist of multiple species, single-species biofilms are of great interest to biotechnology. The current study evaluates biofilm formation for common industrial and laboratory microorganisms. A total of 68 species of biosafety level one bacteria and yeasts from over 40 different genera and five phyla were screened by growing them in microtiter plates and estimating attached biomass by crystal violet staining. Most organisms showed biofilm formation on surfaces of polystyrene within 24 h. By changing a few simple conditions such as substratum characteristics, inoculum and nutrient availability, 66 strains (97%) demonstrated biofilm formation under at least one of the experimental conditions and over half of these strains were classified as strong biofilm formers, potentially suitable as catalysts in biofilm applications. Many non-motile bacteria were also strong biofilm formers. Biofilm morphologies were visualized for selected strains. A model organism, Zymomonas mobilis, easily established itself as a biofilm on various reactor packing materials, including stainless steel. PMID:17653709

Li, Xuan Zhong; Hauer, Bernhard; Rosche, Bettina

2007-07-26

46

Metamorphosis of a Scleractinian Coral in Response to Microbial Biofilms  

PubMed Central

Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium of Bacteroidetes had the largest influence on overall community composition. A low abundance of Archaea was detected in almost all biofilms, providing the first report of Archaea associated with coral reef biofilms. No differences in the relative densities of each subdivision of Proteobacteria were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no difference was detected in banding profiles between biofilms which induced larval metamorphosis and those where no metamorphosis occurred. This investigation demonstrates that complex microbial communities can induce coral metamorphosis in the absence of CCA.

Webster, Nicole S.; Smith, Luke D.; Heyward, Andrew J.; Watts, Joy E. M.; Webb, Richard I.; Blackall, Linda L.; Negri, Andrew P.

2004-01-01

47

Evaluation of some halogen biocides using a microbial biofilm system.  

PubMed

A simple method for the formation of microbial biofilms of three species, Pseudomonas fluorescens, Pseudomonas aeruginosa, and Klebsiella pneumoniae, on a small glass slide was established, and its suitability for evaluation of disinfectant efficacy was examined. The biofilms formed were observed in situ by confocal laser scanning microscopy (CLSM). Using the biofilms established, biocidal efficacy of several halogen biocides, such as hypochlorite (HOCl), bromochlorodimethylhydantoin (Br, Cl-DMH), ammonia monochloramine (NH2Cl), a stabilized hypobromite biocide named STABREX, and a mixed solution of NH4Br and HOCl, was evaluated. The formation of NHBrCl in the mixed solution was indicated by UV spectra analysis. Biofilm cells were more resistant to these biocides than planktonic cells and the extent of resistance varied with the biocide tested. Among the biocides tested, the biocidal potency of HOCl was the most susceptible to the change brought about by biofilm formation. By CLSM observation, differences in biofilm conformation were revealed between the microbial species. The efficacy of the biocide tested varied with the structure of biofilms formed. The assay method developed in the present study would be useful for further investigation on biofilm disinfection. PMID:16169570

Tachikawa, Mariko; Tezuka, Masakatsu; Morita, Masahiro; Isogai, Katsuhisa; Okada, Shoji

2005-09-16

48

Spatial Organization of Microbial Biofilm Communities  

Microsoft Academic Search

The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into\\u000a the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation,\\u000a chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions\\u000a and the activities of the different biofilm members. Thereby resource utilization becomes

T. Tolker-Nielsen; S. Molin

2000-01-01

49

Leitbakteria of microbial biofilm communities causing occlusion of biliary stents.  

PubMed

Biliary stents inserted to relieve obstructive jaundice caused by biliary or pancreatic malignancies inevitably become occluded by microbial growth in the form of diverse microbial community biofilms. The scarce information available on these communities is based on cultivation methods, but such methods usually provide distorted overviews of community composition, so commonalities and differences in biliary stent communities are uncertain. We extracted DNA and RNA from the microbial communities of 11 biliary stents explanted from nine patients in hospitals from two different countries, amplified 16S rRNA and rDNA sequences, analysed the amplicons by the single-strand conformation polymorphism (SSCP) method, and sequenced and deduced phylogenetic assignments of the major amplicons representing the major biofilm community members. We used a Modified Robbins Device (MRD) to study de novo development of a stent biofilm from a patient stent microbial community. Single-strand conformation polymorphism fingerprinting revealed the same six abundant bacterial species, here designated Leitbakteria, namely Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Enterobacter aerogenes, and two unculturable bacteria distantly related to E. coli and Shigella sonnei, in all of the stent biofilm communities. In the experimental biliary stent system, a sequential colonization of the stent surface was observed, with P. aeruginosa being the pioneer colonizer, followed by K. pneumoniae and one of the unculturable Leitbakteria, followed by the remainder of the community. The overview of microbial biofilm communities of biliary stents gained by the use of culture-independent methods revealed new unculturable bacteria as major members of biliary stent biofilms, and the diversity of the abundant members of the stent biofilms is considerably lower than suggested from earlier studies based on cultivation methods, and that communities from different stents from different patients in different countries are remarkably similar and have similar major members, the stent Leitbakteria. PMID:14510839

Wenderoth, Dirk F; Ferslev, Björn; Macarri, Giampiero; Molinari, Gabriella; Lünsdorf, Heinrich; Timmis, Kenneth N

2003-10-01

50

Dynamic microbial response of sulfidogenic wastewater biofilm to nitrate.  

PubMed

Nitrate is one of the chemicals often added to wastewater to control hydrogen sulfide production by sulfate-reducing bacteria (SRB). While the effect of nitrate in various SRB pure cultures is well documented, the effect observed in mixed microbial communities is not consistent. This study investigates the response of mixed SRB communities to nitrate, by examining the changes in activity and community composition of sulfidogenic wastewater biofilm over a 10-day period with 10 mmol L(-1) nitrate exposure. Biofilms were enriched in SRB belonging to the Desulfobacter, Desulfobulbus, Desulfomicrobium, and Desulfovibrio genera. Nitrate exposure decreased dsrB transcription within 4 h, and sulfate consumption within 10 days, but it did not fully eliminate sulfide production in the biofilms. The effect of nitrate on SRB was genus specific; Desulfobacter and Desulfobulbus disappeared while Desulfovibrio and Desulfomicrobium persisted in the biofilms. Nitrate exposure also led to the rapid proliferation of nitrate-reducing bacteria within the biofilms, and increased the biofilm thickness. Nitrate consumption began within 2 h of nitrate exposure and gradually increased in rate over time. Transcription of the nitrate reductase napA, and the diversity of nitrate reductase genes narG and napA also increased concurrently. Our results demonstrate that some SRB, presumably those able to tolerate or detoxify nitrite, will persist in sulfidogenic wastewater biofilms despite continuous exposure to high levels of nitrate. Nitrate is therefore unlikely to provide lasting hydrogen sulfide suppression in wastewater biofilms harboring Desulfovibrio or Desulfomicrobium populations. PMID:21611797

Mohanakrishnan, Janani; Kofoed, Michael Vedel Wegener; Barr, Jeremy; Yuan, Zhiguo; Schramm, Andreas; Meyer, Rikke Louise

2011-05-25

51

Laser Microbial Killing and Biofilm Disruption  

NASA Astrophysics Data System (ADS)

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.

Krespi, Yosef P.; Kizhner, Victor

2009-06-01

52

Role of discontinuous chlorination on microbial production by drinking water biofilms  

Microsoft Academic Search

Microbial quality in water distribution systems is strongly affected by the development of microbial biofilms. Production and release of microbial cells by the biofilm affect microbial levels in the water column and in some cases this fact constitutes a public health concern. In this study, we attempt to analyze in which way the existence of different episodes of chlorine depletion

Francesc Codony; Jordi Morató; Jordi Mas

2005-01-01

53

ORAL MICROBIAL COMMUNITIES: Biofilms, Interactions, and Genetic Systems1  

Microsoft Academic Search

? Abstract Oral microbial-plaque communities are biofilms composed of numer- ous genetically distinct types of bacteria that live in close juxtaposition on host surfaces. These bacteria communicate through physical interactions called coaggregation and coadhesion, as well as other physiological and metabolic interactions. Streptococci and actinomyces are the major initial colonizers of the tooth surface, and the inter- actions between them

Paul E. Kolenbrander

2000-01-01

54

Theoretical Aspects of Antibiotic Diffusion into Microbial Biofilms  

Microsoft Academic Search

Antibiotic penetration into microbial biofilm was investigated theoretically by the solution of mathematical equations describing various combinations of the processes of diffusion, sorption, and reaction. Unsteady material balances on the antibiotic and on a reactive or sorptive biomass constituent, along with associated boundaryandinitialconditions,constitutethemathematicalformulations.Fivecaseswereexamined:diffusion of a noninteracting solute; diffusion of a reversibly sorbing, nonreacting solute; diffusion of an irreversibly sorbing, nonreacting

PHILIP S. STEWART

1996-01-01

55

Molecular Analysis of Microbial Communities in Endotracheal Tube Biofilms  

PubMed Central

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 2.1×108 colony forming units (cfu)/cm2 of endotracheal tube (mean 1.4×107 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.

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

56

Biofilm formation by Campylobacter jejuni in controlled mixed-microbial populations  

Microsoft Academic Search

This study was to screen the ability of biofilm formation by Campylobacter jejuni strains found in New Zealand, and investigate the biofilm growth of C. jejuni in a controlled mixed-microbial population that includes five different bacteria. The ability of C. jejuni to form a biofilm in monoculture and mixed-microbial populations was measured in a laboratory assay using a microtiter plate

Koon Hoong Teh; Steve Flint; Nigel French

2010-01-01

57

A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models  

Microsoft Academic Search

A review of the basic structure of microbial biofilm reveals that at least three conceptual models exist: (i) heterogeneous mosaic biofilm, (ii) penetrated water-channel biofilm and (iii) dense confluent biofilm. When consideration is given to the effects of growth resource, it may be that all three variants are correct but form at widely different substrate concentrations. Experimental research with bacterial

Julian W. T. Wimpenny; Ric Colasanti

1997-01-01

58

Microbial Diversity of Biofilms in Dental Unit Water Systems  

PubMed Central

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 ? and ?, but not the ?, 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.

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

2003-01-01

59

Adhesion and formation of microbial biofilms in complex microfluidic devices  

SciTech Connect

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.

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

2012-01-01

60

High-throughput metal susceptibility testing of microbial biofilms  

PubMed Central

Background Microbial biofilms exist all over the natural world, a distribution that is paralleled by metal cations and oxyanions. Despite this reality, very few studies have examined how biofilms withstand exposure to these toxic compounds. This article describes a batch culture technique for biofilm and planktonic cell metal susceptibility testing using the MBEC assay. This device is compatible with standard 96-well microtiter plate technology. As part of this method, a two part, metal specific neutralization protocol is summarized. This procedure minimizes residual biological toxicity arising from the carry-over of metals from challenge to recovery media. Neutralization consists of treating cultures with a chemical compound known to react with or to chelate the metal. Treated cultures are plated onto rich agar to allow metal complexes to diffuse into the recovery medium while bacteria remain on top to recover. Two difficulties associated with metal susceptibility testing were the focus of two applications of this technique. First, assays were calibrated to allow comparisons of the susceptibility of different organisms to metals. Second, the effects of exposure time and growth medium composition on the susceptibility of E. coli JM109 biofilms to metals were investigated. Results This high-throughput method generated 96-statistically equivalent biofilms in a single device and thus allowed for comparative and combinatorial experiments of media, microbial strains, exposure times and metals. By adjusting growth conditions, it was possible to examine biofilms of different microorganisms that had similar cell densities. In one example, Pseudomonas aeruginosa ATCC 27853 was up to 80 times more resistant to heavy metalloid oxyanions than Escherichia coli TG1. Further, biofilms were up to 133 times more tolerant to tellurite (TeO32-) than corresponding planktonic cultures. Regardless of the growth medium, the tolerance of biofilm and planktonic cell E. coli JM109 to metals was time-dependent. Conclusion This method results in accurate, easily reproducible comparisons between the susceptibility of planktonic cells and biofilms to metals. Further, it was possible to make direct comparisons of the ability of different microbial strains to withstand metal toxicity. The data presented here also indicate that exposure time is an important variable in metal susceptibility testing of bacteria.

Harrison, Joe J; Turner, Raymond J; Ceri, Howard

2005-01-01

61

Microbial Biofilm Growth on Irradiated, Spent Nuclear Fuel Cladding  

SciTech Connect

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.

S.M. Frank

2009-02-01

62

The calculative nature of microbial biofilms and bioaggregates.  

PubMed

Biological proliferation is optimized at various levels of organization, including the molecule (e.g. nucleic acids, prions), the cell (e.g. prokaryotic cells, eukaryotic cells), and the community (e.g. microbial biofilms, bioaggregates). Although it was initially assumed that this occurred through the genesis of information within DNA alone, it now appears that innovative design originates at other levels of organization in addition to DNA. For example, the recombination of community structures affects the proliferation rate of genetic structures; and the recombination of genetic structures affects the proliferation rate of community structures. This feedback mechanism computes compromises between the form and function of both community and nucleic acid. A nested series of proliferating objects (e.g. genetic structure, cell structure, community structure) is thus capable of continually updating the form of each object in the series. This accounts for the calculative nature of prokaryotic cells, eukaryotic cells, biofilms, bioaggregates, microbial consortia, and most other complex adaptive systems. PMID:12207211

Caldwell, Douglas E

2002-07-18

63

Theoretical aspects of antibiotic diffusion into microbial biofilms.  

PubMed Central

Antibiotic penetration into microbial biofilm was investigated theoretically by the solution of mathematical equations describing various combinations of the processes of diffusion, sorption, and reaction. Unsteady material balances on the antibiotic and on a reactive or sorptive biomass constituent, along with associated boundary and initial conditions, constitute the mathematical formulations. Five cases were examined: diffusion of a noninteracting solute; diffusion of a reversibly sorbing, nonreacting solute; diffusion of an irreversibly sorbing, nonreacting solute; diffusion of a stoichiometrically reacting solute; and diffusion of a catalytically reacting solute. A noninteracting solute was predicted to penetrate biofilms of up to 1 mm in thickness relatively quickly, within a matter of seconds or minutes. In the case of a solute that does not sorb or react in the biofilm, therefore, the diffusion barrier is not nearly large enough to account for the reduced susceptibility of biofilms to antibiotics. Reversible and irreversible sorption retards antibiotic penetration. On the basis of data available in the literature at this point, the extent of retardation of antibiotic diffusion due to sorption does not appear to be sufficient to account for reduced biofilm susceptibility. A catalytic (e.g., enzymatic) reaction, provided it is sufficiently rapid, can lead to severe antibiotic penetration failure. For example, calculation of beta-lactam penetration indicated that the reaction-diffusion mechanism may be a viable explanation for failure of certain of these agents to control biofilm infections. The theory presented in this study provides a framework for the design and analysis of experiments to test these mechanisms of reduced biofilm susceptibility to antibiotics.

Stewart, P S

1996-01-01

64

Microbial exopolymers link predator and prey in a model yeast biofilm system.  

PubMed

Protistan grazing on biofilms is potentially an important conduit enabling energy flow between microbial trophic levels. Contrary to the widely held assumption that protistan feeding primarily involves ingestion of biofilm cells, with negative consequences for the biofilm, this study demonstrated preferential grazing on the noncellular biofilm matrix by a ciliate, with selective ingestion of yeast and bacterial cells of planktonic origin over attached and biofilm-derived planktonic cells. Introducing a ciliate to two biofilm-forming Cryptococcus species, as well as two bacterial species in a model biofilm system, fluorescent probes were applied to determine ingestion of cellular and noncellular biofilm fractions. Fluoromicroscopy, as well as photometric quantification, confirmed that protistan grazing enhanced yeast biofilm metabolism, and an increase in biofilm biomass and viability. We propose that the extracellular polymeric matrix of biofilms may act as an interface regulating interaction between predator and prey, while serving as source of nutrients and energy for protists. PMID:16897306

Joubert, L-M; Wolfaardt, G M; Botha, A

2006-08-08

65

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

PubMed Central

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.

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

2009-01-01

66

Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms ? †  

PubMed Central

We examined the chemical composition of extracellular polymeric substances (EPS) extracted from two natural microbial pellicle biofilms growing on acid mine drainage (AMD) solutions. The EPS obtained from a mid-developmental-stage biofilm (DS1) and a mature biofilm (DS2) were qualitatively and quantitatively compared. More than twice as much EPS was derived from DS2 as from DS1 (approximately 340 and 150 mg of EPS per g [dry weight] for DS2 and DS1, respectively). Composition analyses indicated the presence of carbohydrates, metals, proteins, and minor quantities of DNA and lipids, although the relative concentrations of these components were different for the two EPS samples. EPS from DS2 contained higher concentrations of metals and carbohydrates than EPS from DS1. Fe was the most abundant metal in both samples, accounting for about 73% of the total metal content, followed by Al, Mg, and Zn. The relative concentration profile for these metals resembled that for the AMD solution in which the biofilms grew, except for Si, Mn, and Co. Glycosyl composition analysis indicated that both EPS samples were composed primarily of galactose, glucose, heptose, rhamnose, and mannose, while the relative amounts of individual sugars were substantially different in DS1 and DS2. Additionally, carbohydrate linkage analysis revealed multiply linked heptose, galactose, glucose, mannose, and rhamnose, with some of the glucose in a 4-linked form. These results indicate that the biochemical composition of the EPS from these acidic biofilms is dependent on maturity and is controlled by the microbial communities, as well as the local geochemical environment.

Jiao, Yongqin; Cody, George D.; Harding, Anna K.; Wilmes, Paul; Schrenk, Matthew; Wheeler, Korin E.; Banfield, Jillian F.; Thelen, Michael P.

2010-01-01

67

Microbial biofilms and breast tissue expanders.  

PubMed

We previously developed and validated a vortexing-sonication technique for detection of biofilm bacteria on the surface of explanted prosthetic joints. Herein, we evaluated this technique for diagnosis of infected breast tissue expanders and used it to assess colonization of breast tissue expanders. From April 2008 to December 2011, we studied 328 breast tissue expanders at Mayo Clinic, Rochester, MN, USA. Of seven clinically infected breast tissue expanders, six (85.7%) had positive cultures, one of which grew Propionibacterium species. Fifty-two of 321 breast tissue expanders (16.2%, 95% CI, 12.3-20.7%) without clinical evidence of infection also had positive cultures, 45 growing Propionibacterium species and ten coagulase-negative staphylococci. While vortexing-sonication can detect clinically infected breast tissue expanders, 16 percent of breast tissue expanders appear to be asymptomatically colonized with normal skin flora, most commonly, Propionibacterium species. PMID:23956974

Karau, Melissa J; Greenwood-Quaintance, Kerryl E; Schmidt, Suzannah M; Tran, Nho V; Convery, Phyllis A; Jacobson, Steven R; Bite, Uldis; Clay, Ricky P; Petty, Paul M; Johnson, Craig H; Mandrekar, Jayawant; Patel, Robin

2013-07-16

68

High resolution gravimetric, optical and electrochemical investigations of microbial biofilm formation in aqueous systems  

Microsoft Academic Search

The formation of microbial biofilms on metallic surfaces was studied by combination of gravimetric, optical and electrochemical methods with high local resolution in dependence on colonization time and biofilm thickness. The use of electrochemical quartz crystal microbalance (EQCM) flowcells allowed simultaneous and continuous in situ monitoring of biofilm formation and resulting open circuit potential UR. Combination of macroscopic and microscopic

A. Bressel; J. W. Schultze; W. Khan; G. M. Wolfaardt; H.-P. Rohns; R. Irmscher; M. J. Schöning

2003-01-01

69

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

Microsoft Academic Search

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

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

2011-01-01

70

Tobacco smoke mediated induction of sinonasal microbial biofilms.  

PubMed

Cigarette smokers and those exposed to second hand smoke are more susceptible to life threatening infection than non-smokers. While much is known about the devastating effect tobacco exposure has on the human body, less is known about the effect of tobacco smoke on the commensal and commonly found pathogenic bacteria of the human respiratory tract, or human respiratory tract microbiome. Chronic rhinosinusitis (CRS) is a common medical complaint, affecting 16% of the US population with an estimated aggregated cost of $6 billion annually. Epidemiologic studies demonstrate a correlation between tobacco smoke exposure and rhinosinusitis. Although a common cause of CRS has not been defined, bacterial presence within the nasal and paranasal sinuses is assumed to be contributory. Here we demonstrate that repetitive tobacco smoke exposure induces biofilm formation in a diverse set of bacteria isolated from the sinonasal cavities of patients with CRS. Additionally, bacteria isolated from patients with tobacco smoke exposure demonstrate robust in vitro biofilm formation when challenged with tobacco smoke compared to those isolated from smoke naïve patients. Lastly, bacteria from smoke exposed patients can revert to a non-biofilm phenotype when grown in the absence of tobacco smoke. These observations support the hypothesis that tobacco exposure induces sinonasal biofilm formation, thereby contributing to the conversion of a transient and medically treatable infection to a persistent and therapeutically recalcitrant condition. PMID:21253587

Goldstein-Daruech, Natalia; Cope, Emily K; Zhao, Ke-Qing; Vukovic, Katarina; Kofonow, Jennifer M; Doghramji, Laurel; González, Bernardo; Chiu, Alexander G; Kennedy, David W; Palmer, James N; Leid, Jeffery G; Kreindler, James L; Cohen, Noam A

2011-01-06

71

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

NASA Astrophysics Data System (ADS)

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.

Das Gupta, S.; Fang, J.

2008-12-01

72

Biofilm formation at warming temperature: acceleration of microbial colonization and microbial interactive effects.  

PubMed

River biofilms that grow on wet benthic surface are mainly composed of bacteria, algae, cyanobacteria and protozoa embedded in a polysaccharide matrix. The effects of increased river water temperature on biofilm formation were investigated. A laboratory experiment was designed employing two temperatures (11.1-13.2°C, night-day; 14.7-16.0°C, night-day) and two nutrient levels (0.054 mg P l(-1), 0.75 mg N l(-1); 0.54 mg P l(-1), 7.5 mg N l(-1)). Biofilm formation at the higher temperature was faster, while the biomass of the mature biofilm was mainly determined by nutrient availability. The specific response of the three microbial groups that colonized the substrata (algae, bacteria and ciliates) was modulated by interactions between them. The greater bacterial growth rate and earlier bacterial colonization at the higher temperature and higher nutrient status was not translated into the accrual of higher bacterial biomass. This may result from ciliates grazing on the bacteria, as shown by an earlier increase in peritrichia at higher temperatures, and especially at high nutrient conditions. Temperature and ciliate grazing might determine the growth of a distinctive bacterial community under warming conditions. Warmer conditions also produced a thicker biofilm, while functional responses were much less evident (increases in the heterotrophic utilization of polysaccharides and peptides, but no increase in primary production and respiration). Increasing the temperature of river water might lead to faster biofilm recolonization after disturbances, with a distinct biofilm community structure that might affect the trophic web. Warming effects would be expected to be more relevant under eutrophic conditions. PMID:21113861

Diaz Villanueva, Veronica; Font, Jordi; Schwartz, Thomas; Romani, Anna M

2011-01-01

73

Evaluation of microscopic techniques to observe iron precipitation in a natural microbial biofilm  

Microsoft Academic Search

Iron biomineralization in a microbial biofilm consortium from Canadian Shield groundwaters has been investigated with different microscopic techniques. The advantages and disadvantages of the different methods of observing a biofilm growing on an opaque mineral surface are discussed. Scanning electron microscopy was able to show the initial attachment and dispersion of bacteria on the mineral surfaces, whereas transmission electron microscopy

D. Ann Brown; Terry J Beveridge; C. William Keevil; Barbara L Sherriff

1998-01-01

74

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

Microsoft Academic Search

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

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

2009-01-01

75

Detection of microbial Life in the Subsurface  

NASA Astrophysics Data System (ADS)

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.

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

2007-08-01

76

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device  

PubMed Central

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore, three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy (CLSM) of biofilms grown on polystyrene pegs in the Calgary Biofilm Device (CBD). Furthermore, a procedure is described for image processing of CLSM data stacks using amira™, a virtual reality tool, to create surface and/or volume rendered 3D visualizations of biofilm microorganisms. The combination of microscopy with microbial cultivation in the CBD – an apparatus that was designed for high-throughput susceptibility testing – allows for structure-function analysis of biofilms under multivariate growth and exposure conditions.

Harrison, Joe J.; Ceri, Howard; Yerly, Jerome; Stremick, Carol A.; Hu, Yaoping; Martinuzzi, Robert

2006-01-01

77

Microbial structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment  

NASA Astrophysics Data System (ADS)

The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their "extra-terrestrial" conditions such as darkness and mostly extreme physicochemical state they are also of astrobiological interest. The slightly radioactive thermal spring at Bad Gastein (Austria) was therefore examined for the occurrence of subsurface microbial communities. The surfaces of the submerged rocks in this warm spring were overgrown by microbial mats. Scanning electron microscopy (SEM) performed by the late Dr. Wolfgang Heinen revealed an interesting morphological diversity in biofilms found in this environment (1, 2). Molecular analysis of the community structure of the radioactive subsurface thermal spring was performed by Weidler et al. (3). The growth of these mats was simulated using sterile glass slides which were exposed to the water stream of the spring. Those mats were analysed microscopically. Staining, using fluorescent dyes such as 4',6-Diamidino-2-phenylindol (DAPI), gave an overview of the microbial diversity of these biofilms. Additional SEM samples were prepared using different fixation protocols. Scanning confocal laser microscopy (SCLM) allowed a three dimensional view of the analysed biofilms. This work presents some electron micrographs of Dr. Heinen and additionally new microscopic studies of the biofilms formed on the glass slides. The appearances of the new SEM micrographs were compared to those of Dr. Heinen that were done several years ago. The morphology and small-scale distribution in the microbial mat was analyzed by fluorescence microscopy. The examination of natural biomats and biofilms grown on glass slides using several microscopical techniques suggest that the thermal springs in the Central Alps near Bad Gastein represent a novel and unique habitat for microbial life. Results obtained during these studies revealed reproducibility of Dr. Heinen's micrographs. Hollow reticulated filaments and flat ribbons with parallel hexagonal chambers (web-structures) were found repeatedly. Given the chance that subsurface environments represent a potent opportunity to detect life on planetary bodies it is of big interest to search for representative biosignatures found on earth today. References: 1. Lauwers A. M. & Heinen W. (1985) Mikroskopie (Wien) 42, 94-101. 2. Heinen W. & Lauwers A. M. (1985) Mikroskopie (Wien) 42, 124-134. 3. Weidler G. W., Dornmayr-Pfaffenhuemer M., Gerbl F. W., Heinen W., Stan-Lotter H. (2007) AEM 73, 259-270.

Dornmayr-Pfaffenhuemer, Marion; Pierson, Elisabeth; Janssen, Geert-Jan; Stan-Lotter, Helga

2010-05-01

78

Oral microbial biofilms and plaque-related diseases: microbial communities and their role in the shift from oral health to disease  

Microsoft Academic Search

Many oral pathologies, such as dental caries, periodontal disease and peri-implantitis are plaque-related. Dental plaque is a microbial biofilm formed by organisms tightly bound to a solid substrate and each other by means of an exopolymer matrix. Bacteria exhibit different properties when contained within a biofilm. Knowing the mechanisms controlling the formation and development of biofilms can help to understand

Ludovico Sbordone; Claudia Bortolaia

2003-01-01

79

Potential Antibacterial Activity of Carvacrol-Loaded Poly(DL-lactide-co-glycolide) (PLGA) Nanoparticles against Microbial Biofilm  

PubMed Central

The ability to form biofilms contributes significantly to the pathogenesis of many microbial infections, including a variety of ocular diseases often associated with the biofilm formation on foreign materials. Carvacrol (Car.) is an important component of essential oils and recently has attracted much attention pursuant to its ability to promote microbial biofilm disruption. In the present study Car. has been encapsulated in poly(dl-lactide-co-glycolide (PLGA) nanocapsules in order to obtain a suitable drug delivery system that could represent a starting point for developing new therapeutic strategies against biofilm-associated infections, such as improving the drug effect by associating an antimicrobial agent with a biofilm viscoelasticity modifier.

Iannitelli, Antonio; Grande, Rossella; Di Stefano, Antonio; Di Giulio, Mara; Sozio, Piera; Bessa, Lucinda Janete; Laserra, Sara; Paolini, Cecilia; Protasi, Feliciano; Cellini, Luigina

2011-01-01

80

Biofilm ecology: On-line methods bring new insights into mic and microbial biofouling.  

PubMed

Microbial biofilms were formed on coupons with defined coatings in once-through laminar flow fields of controlled bulk-phase composition and shear. Dilute media were utilized to select for biofilm growth. The formation, succession, and stability of the biofilms were monitored with non-destructive on-line methods (fluorescence, bioluminescence, attenuated total reflectance Fourier transform infrared spectrometry [ATR-FTIR] and electrochemical impedance spectroscopy) and by high resolution destructive analysts (viable and direct counts and phospholipid fatty acid signature methods) at the termination of the experiments. Biofilms of reproducible composition can be formed and the order of inoculation of multi-component biofilms affects their composition at harvest. The corrosion rates of mild steel depended on the biofilm composition but not the attached biomass. Examination of biofilms with the scanning vibrating electrode in a microscope field showed effects of heterogeneity in biofilm structure which promoted localized anodic activity. Pseudomonas stains were engineered to contain the lux gene cassette as a "reporter"; and the formation of the exopolymer alginate was shown not to promote attachment of the strain or secondary colonization by Vibrio. Examination of mutants forming different alginate structures showed differential attachment and biofilm structure. Studies of mutants of lipopolysaccharide structure showed differential attachment to substrata. Specific antifouling and fouling-release coatings showed a wide range of attachment and release properties as well as sublethal toxicity. PMID:22115099

White, D C; Arrage, A A; Nivens, D E; Palmer, R J; Rice, J F; Sayler, G S

1996-01-01

81

A biofilm enhanced miniature microbial fuel cell using Shewanella oneidensis DSP10 and oxygen reduction cathodes  

Microsoft Academic Search

A miniature-microbial fuel cell (mini-MFC, chamber volume: 1.2mL) was used to monitor biofilm development from a pure culture of Shewanella oneidensis DSP10 on graphite felt (GF) under minimal nutrient conditions. ESEM evidence of biofilm formation on GF is supported by substantial power density (per device cross-section) from the mini-MFC when using an acellular minimal media anolyte (1500mW\\/m2). These experiments demonstrate

Justin C. Biffinger; Jeremy Pietron; Ricky Ray; Brenda Little; Bradley R. Ringeisen

2007-01-01

82

Response of Estuarine Biofilm Microbial Community Development to Changes in Dissolved Oxygen and Nutrient Concentrations  

Microsoft Academic Search

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water\\u000a quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms\\u000a were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater\\u000a treatment plant (WWTP) outfall and a nearby

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

2007-01-01

83

The role of microbial biofilms in deterioration of space station candidate materials.  

PubMed

Formation of microbial biofilms on surfaces of a wide range of materials being considered as candidates for use on the International Space Station was investigated. The materials included a fibre-reinforced polymeric composite, an adhesive sealant, a polyimide insulation foam, teflon cable insulation, titanium, and an aliphatic polyurethane coating. They were exposed to a natural mixed population of bacteria under controlled conditions of temperature and relative humidity (RH). Biofilms formed on the surfaces of the materials at a wide range of temperatures and RHs. The biofilm population was dominated by Pseudomonas aeruginosa, Ochrobactrum anthropi, Alcaligenes denitrificans, Xanthomonas maltophila, and Vibrio harveyi. The biocide, diiodomethyl-p-tolyl sulfone, impregnated in the polyurethane coating, was ineffective against microbial colonization and growth. Degradation of the polyurethane coatings was monitored with electrochemical impedance spectroscopy (EIS). The impedance spectra indicated that microbial degradation of the coating occurred in several stages. The initial decreases in impedance were due to the transport of water and solutes into the polymeric matrices. Further decreases were a result of polymer degradation by microorganisms. Our data showed that these candidate materials for space application are susceptible to biofilm formation and subsequent degradation. Our study suggests that candidate materials for use in space missions need to be carefully evaluated for their susceptibility to microbial biofilm formation and biodegradation. PMID:11541393

Gu, J D; Roman, M; Esselman, T; Mitchell, R

1998-01-01

84

Microbial Composition and Structure of Aerobic Granular Sewage Biofilms  

Microsoft Academic Search

Received 30 April 2007\\/Accepted 23 July 2007 Aerobic activated sludge granules are dense, spherical biofilms which can strongly improve purification efficiency and sludge settling in wastewater treatment processes. In this study, the structure and development of different granule types were analyzed. Biofilm samples originated from lab-scale sequencing batch reactors which were operated with malthouse, brewery, and artificial wastewater. Scanning electron

S. D. Weber; W. Ludwig; K.-H. Schleifer; J. Fried

2007-01-01

85

Significance of microbial biofilms in food industry: a review  

Microsoft Academic Search

Biofilms have been of considerable interest in the context of food hygiene. Of special significance is the ability of microorganisms to attach and grow on food and food-contact surfaces under favourable conditions. Biofilm formation is a dynamic process and different mechanisms are involved in their attachment and growth. Extracellular polymeric substances play an important role in the attachment and colonization

C. Ganesh Kumar; S. K Anand

1998-01-01

86

Biopolymer and Water Dynamics in Microbial Biofilm Extracellular Polymeric Substance  

PubMed Central

Nuclear magnetic resonance (NMR) is a noninvasive and nondestructive tool able to access several observable quantities in biofilms such as chemical composition, diffusion, and macroscale structure and transport. Pulsed gradient spin echo (PGSE) NMR techniques were used to measure spectrally resolved biomacromolecular diffusion in biofilm biomass, extending previous research on spectrally resolved diffusion in biofilms. The dominant free water signal was nulled using an inversion recovery modification of the traditional PGSE technique in which the signal from free water is minimized in order to view the spectra of components such as the rotationally mobile carbohydrates, DNA, and proteins. Diffusion data for the major constituents obtained from each of these spectral peaks demonstrate that the biomass of the biofilm contains both a fast and slow diffusion component. The dependence of diffusion on antimicrobial and environmental challenges suggests the polymer molecular dynamics measured by NMR are a sensitive indicator of biofilm function.

Hornemann, Jennifer A.; Lysova, Anna A.; Codd, Sarah L.; Seymour, Joseph D.; Busse, Scott C.; Stewart, Philip S.; Brown, Jennifer R.

2008-01-01

87

Microbial Life-Educational Resources  

NSDL National Science Digital Library

The Marine Biology Laboratory of Woods Hole, Massachusetts and Montana State University are the collaborators on this easily navigable website of educational resources about microbial life. The goal of the site is to provide expert information about microorganisms for K-12 classrooms, university educators, and the general public. They effectively accomplish their goal here, with a host of resources, in formats appropriate for different knowledge levels, in a well-organized manner. For all of the topics covered, three levels of information are provided. Resources such as newspapers, websites, and magazine articles are provided for general learners; journal articles and academic reviews are provided for advanced learners; and activities, assignments, and readings are provided for educators. Interestingly, one of the activities found in the "Teaching Methods" tab on the left side of the homepage, is how to use the Socratic Method with students, with question suggestions, rules of participation, and what to expect from the students. An interesting part of the website is its focus on the microorganisms that live in extreme environments. Visitors can learn about the many types of extremes environments, the extremophiles, and how to teach about extreme environments in K-12 classrooms, by clicking on the "Extreme Environments" tab on the left side of the homepage. The photos of the extreme environments resemble abstract art with their close ups of the microorganisms in their environment. By clicking on the "Online Resources" tab on the left hand side of the homepage, visitors will be taken to a virtual index of their resources, where they can also narrow their view by resource type, subject, environment type, and grade-level. Each category that can be used to narrow results also shows how many entries are available for that category.

2009-07-20

88

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device  

Microsoft Academic Search

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities\\u000a have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore,\\u000a three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial\\u000a systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy

Joe J. Harrison; Howard Ceri; Jerome Yerly; Carol A. Stremick; Yaoping Hu; Robert Martinuzzi; Raymond J. Turner

2006-01-01

89

EPS in Environmental Microbial Biofilms as Examined by Advanced Imaging Techniques  

NASA Astrophysics Data System (ADS)

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.

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

2006-12-01

90

Coliforms and other microbial indicators occurrence in water and biofilm in full-scale distribution systems.  

PubMed

Biofilm and microbial water quality were studied in four middle size full-scale distribution systems (DS) in France serving 5,000-30,000 inhabitants (maximum residence time 23-160h) through three sampling campaigns over 1 year. Three of these DSs were chosen because of a quite high occurrence of bacterial indicators (i.e. total coliforms), the last DS was considered as a reference. Biofilm was studied on cast iron coupons incubated for more than 1 month in devices continuously fed with water from the DS in conditions imitating those met in DS. The devices were located at different points (4-6) along each DS. The abundance of bacteria in biofilm was estimated by heterotrophic plate counts (HPC) after detachment of the biofilm from the support by sonication. Microbiological water quality was estimated in parallel; analysis of total coliforms, E. coli, enterococci and anaerobic sulphide-reducing bacteria spores (ASRB spores) was carried out in biofilm and water. Over the period of the study, 171 water samples and 57 biofilm samples were collected. Over these 171 waters, 19 (11%) were positive for at least one of the measured indicators while two biofilm samples were positive (3.5%). Significant differences were observed in the levels of contamination between the DSs. High residence time in the DS, low disinfectant residual and high temperature increased the risk of indicator occurrence in the water phase. Due to the low number of biofilm samples positive for bacterial indicators, the data collected in the present study did not allow observation of a direct association between biofilm and water contaminations, even if the occurrence of indicators in water appeared on DSs with the highest density of biofilm (HPC). PMID:17037131

Batté, M; Féliers, C; Servais, P; Gauthier, V; Joret, J C; Block, J C

2006-01-01

91

Monitoring of microbial adhesion and biofilm growth using electrochemical impedancemetry.  

PubMed

Electrochemical impedance spectroscopy was tested to monitor the cell attachment and the biofilm proliferation in order to identify characteristic events induced on the metal surface by Gram-negative (Pseudomonas aeruginosa PAO1) and Gram-positive (Bacillus subtilis) bacteria strains. Electrochemical impedance spectra of AISI 304 electrodes during cell attachment and initial biofilm growth for both strains were obtained. It can be observed that the resistance increases gradually with the culture time and decreases with the biofilm detachment. So, the applicability of electric cell-substrate impedance sensing (ECIS) for studying the attachment and spreading of cells on a metal surface has been demonstrated. The biofilm formation was also characterized by the use of scanning electron microscopy and confocal laser scanning microscopy and COMSTAT image analysis. The electrochemical results roughly agree with the microscope image observations. The ECIS technique used in this study was used for continuous real-time monitoring of the initial bacterial adhesion and the biofilm growth. It provides a simple and non-expensive electrochemical method for in vitro assessment of the presence of biofilms on metal surfaces. PMID:18330564

Dheilly, A; Linossier, I; Darchen, A; Hadjiev, D; Corbel, C; Alonso, V

2008-03-11

92

Hypersaline microbial systems of sabkhas: examples of life's survival in "extreme" conditions.  

PubMed

Life and living systems need several important factors to establish themselves and to have a continued tradition. In this article the nature of the borderline situation for microbial life under heavy salt stress is analyzed and discussed using the example of biofilms and microbial mats of sabkha systems of the Red Sea. Important factors ruling such environments are described, and include the following: (1) Microbial life is better suited for survival in extremely changing and only sporadically water-supplied environments than are larger organisms (including humans). (2) Microbial life shows extremely poikilophilic adaptation patterns to conditions that deviate significantly from conditions normal for life processes on Earth today. (3) Microbial life adapts itself to such extremely changing and only ephemerally supportive conditions by the capacity of extreme changes (a) in morphology (pleomorphy), (b) in metabolic patterns (poikilotrophy), (c) in survival strategies (poikilophily), and (d) by trapping and enclosing all necessary sources of energy matter in an inwardly oriented diffusive cycle. All this is achieved without any serious attempt at escaping from the extreme and extremely changing conditions. Furthermore, these salt swamp systems are geophysiological generators of energy and material reservoirs recycled over a geological time scale. Neither energy nor material is wasted for propagation by spore formation. This capacity is summarized as poikilophilic and poikilotroph behavior of biofilm or microbial mat communities in salt and irradiationstressed environmental conditions of the sabkha or salt desert type. We use mainly cyanobacteria as an example, although other bacteria and even eukaryotic fungi may exhibit the same potential of living and surviving under conditions usually not suitable for life on Earth. It may, however, be postulated that such poikilophilic organisms are the true candidates for life support and survival under conditions never recorded on Planet Earth. Mars and some planets of other suns may be good candidates to search for life under conditions normally not thought to be favorable for the maintenance of life. PMID:15684726

Krumbein, Wolfgang Elisabeth; Gorbushina, Anna A; Holtkamp-Tacken, Elisabeth

2004-01-01

93

Hypersaline Microbial Systems of Sabkhas: Examples of Life's Survival in "Extreme" Conditions  

NASA Astrophysics Data System (ADS)

Life and living systems need several important factors to establish themselves and to have a continued tradition. In this article the nature of the borderline situation for microbial life under heavy salt stress is analyzed and discussed using the example of biofilms and microbial mats of sabkha systems of the Red Sea. Important factors ruling such environments are described, and include the following: (1) Microbial life is better suited for survival in extremely changing and only sporadically water-supplied environments than are larger organisms (including humans). (2) Microbial life shows extremely poikilophilic adaptation patterns to conditions that deviate significantly from conditions normal for life processes on Earth today. (3) Microbial life adapts itself to such extremely changing and only ephemerally supportive conditions by the capacity of extreme changes (a) in morphology (pleomorphy), (b) in metabolic patterns (poikilotrophy), (c) in survival strategies (poikilophily), and (d) by trapping and enclosing all necessary sources of energy matter in an inwardly oriented diffusive cycle. All this is achieved without any serious attempt at escaping from the extreme and extremely changing conditions. Furthermore, these salt swamp systems are geophysiological generators of energy and material reservoirs recycled over a geological time scale. Neither energy nor material is wasted for propagation by spore formation. This capacity is summarized as poikilophilic and poikilotroph behavior of biofilm or microbial mat communities in salt and irradiationstressed environmental conditions of the sabkha or salt desert type. We use mainly cyanobacteria as an example, although other bacteria and even eukaryotic fungi may exhibit the same potential of living and surviving under conditions usually not suitable for life on Earth. It may, however, be postulated that such poikilophilic organisms are the true candidates for life support and survival under conditions never recorded on Planet Earth. Mars and some planets of other suns may be good candidates to search for life under conditions normally not thought to be favorable for the maintenance of life. Astrobiology 4, 450-459.

Krumbein, Wolfgang Elisabeth; Gorbushina, Anna A.; Holtkamp-Tacken, Elisabeth

2004-12-01

94

Initial development and structure of biofilms on microbial fuel cell anodes  

Microsoft Academic Search

BACKGROUND: Microbial fuel cells (MFCs) rely on electrochemically active bacteria to capture the chemical energy contained in organics and convert it to electrical energy. Bacteria develop biofilms on the MFC electrodes, allowing considerable conversion capacity and opportunities for extracellular electron transfer (EET). The present knowledge on EET is centred around two Gram-negative models, i.e. Shewanella and Geobacter species, as it

Suzanne T Read; Paritam Dutta; Phillip L Bond; Jürg Keller; Korneel Rabaey

2010-01-01

95

Monitoring of microbial souring in chemically treated, produced-water biofilm systems using molecular techniques  

Microsoft Academic Search

The identification of bacteria in oil production facilities has previously been based on culture techniques. However, cultivation of bacteria from these often-extreme environments can lead to errors in identifying the microbial community members. In this study, molecular techniques including fluorescence in situ hybridization, PCR, denaturing gradient gel electrophoresis, and sequencing were used to track changes in bacterial biofilm populations treated

B. V. Kjellerup; R. H. Veeh; P. Sumithraratne; T. R. Thomsen; K. Buckingham-Meyer; B. Frølund; P. Sturman

2005-01-01

96

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

PubMed Central

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.

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

2012-01-01

97

The role of microbial biofilms in deterioration of space station candidate materials  

Microsoft Academic Search

Formation of microbial biofilms on surfaces of a wide range of materials being considered as candidates for use on the International Space Station was investigated. The materials included a fibre-reinforced polymeric composite, an adhesive sealant, a polyimide insulation foam, teflon cable insulation, titanium, and an aliphatic polyurethane coating. They were exposed to a natural mixed population of bacteria under controlled

Ji-Dong Gu; Monsi Roman; Thomas Esselman; Ralph Mitchell

1998-01-01

98

Microbial diversity in biofilms on water distribution pipes of different materials.  

PubMed

The effects of pipe materials on biofilm formation potential (BFP) and microbial communities in biofilms were analyzed. Pipe coupons made of six different materials (CU, copper; CP, chlorinated poly vinyl chloride; PB, polybutylene; PE, polyethylene; SS, stainless steel; ST, steel coated with zinc) were incubated in drinking water, mixed water (inoculated with 10% (v/v) of river water) and drinking water inoculated with Escherichia coli JM109 (E. coli), respectively. The highest BFPs were observed from steel pipes, SS and ST, while CU showed the lowest BFP values. Of the plastic materials, the BFP of CP in drinking water (96 pg ATP/cm(2)) and mixed water (183 pg ATP/cm(2)) were comparable to those of CU, but the other plastic materials, PB and PE, displayed relatively high BFP. The Number of E. coli in the drinking water inoculated with cultures of E. coli strain showed similar trends with BFP values of the pipe coupons incubated in drinking water and mixed water. Molecular analysis of microbial communities indicated the presence of alpha- and beta-proteobacteria, actinobacteria and bacteroidetes in biofilm on the pipe materials. However, the DGGE profile of bacterial 16S rDNA fragments showed significant differences among different materials, suggesting that the pipe materials affect not only BFP but also microbial diversity. Some plastic materials, such as CP, would be suitable for plumbing, particularly for drinking water distribution pipes, due to its low BFP and little microbial diversity in biofilm. PMID:20057102

Yu, J; Kim, D; Lee, T

2010-01-01

99

Microbial Genomes: Blueprints for Life.  

National Technical Information Service (NTIS)

A colloquium was convened by the American Academy of Microbiology to consider issues relating to the blossoming field of microbial genomic science. The colloquium was held in New Orleans, Louisiana, on March 19-21, 1999. The advent of DNA sequencing on a ...

D. A. Relman E. Strauss

2000-01-01

100

Mineralogical footprints of microbial life  

Microsoft Academic Search

Earth's geosphere is intimately tied to its biosphere. A major link between the two lies in the microbial realm; microorganisms grow in and upon rocks and minerals, often relying on their substratum for critical compounds needed in order to produce cellular energy. The presence of a metabolizing cell on a mineral substrate has a significant effect on the mineral texture

SUSANNE DOUGLAS

2005-01-01

101

Establishment of New Genetic Traits in a Microbial Biofilm Community  

PubMed Central

Conjugational transfer of the TOL plasmid (pWWO) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. The community consisted of three species, Pseudomonas putida RI, Acinetobacter sp. strain C6, and an unidentified isolate, D8. Only P. putida RI could act as a recipient for the TOL plasmid. Cells carrying a chromosomally integrated lacIq gene and a lacp-gfp-tagged version of the TOL plasmid were introduced as donor strains in the biofilm community after its formation. The occurrence of plasmid-carrying cells was analyzed by viable-count-based enumeration of donors and transconjugants. Upon transfer of the plasmids to the recipient cells, expression of green fluorescence was activated as a result of zygotic induction of the gfp gene. This allowed a direct in situ identification of cells receiving the gfp-tagged version of the TOL plasmid. Our data suggest that the frequency of horizontal plasmid transfer was low, and growth (vertical transfer) of the recipient strain was the major cause of plasmid establishment in the biofilm community. Employment of scanning confocal laser microscopy on fixed biofilms, combined with simultaneous identification of P. putida cells and transconjugants by 16S rRNA hybridization and expression of green fluorescence, showed that transconjugants were always associated with noninfected P. putida RI recipient microcolonies. Pure colonies of transconjugants were never observed, indicating that proliferation of transconjugant cells preferentially took place on preexisting P. putida RI microcolonies in the biofilm.

Christensen, Bjarke B.; Sternberg, Claus; Andersen, Jens Bo; Eberl, Leo; M?ller, S?ren; Givskov, Michael; Molin, S?ren

1998-01-01

102

Establishment of new genetic traits in a microbial biofilm community.  

PubMed

Conjugational transfer of the TOL plasmid (pWWO) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. The community consisted of three species, Pseudomonas putida RI, Acinetobacter sp. strain C6, and an unidentified isolate, D8. Only P. putida RI could act as a recipient for the TOL plasmid. Cells carrying a chromosomally integrated lacIq gene and a lacp-gfp-tagged version of the TOL plasmid were introduced as donor strains in the biofilm community after its formation. The occurrence of plasmid-carrying cells was analyzed by viable-count-based enumeration of donors and transconjugants. Upon transfer of the plasmids to the recipient cells, expression of green fluorescence was activated as a result of zygotic induction of the gfp gene. This allowed a direct in situ identification of cells receiving the gfp-tagged version of the TOL plasmid. Our data suggest that the frequency of horizontal plasmid transfer was low, and growth (vertical transfer) of the recipient strain was the major cause of plasmid establishment in the biofilm community. Employment of scanning confocal laser microscopy on fixed biofilms, combined with simultaneous identification of P. putida cells and transconjugants by 16S rRNA hybridization and expression of green fluorescence, showed that transconjugants were always associated with noninfected P. putida RI recipient microcolonies. Pure colonies of transconjugants were never observed, indicating that proliferation of transconjugant cells preferentially took place on preexisting P. putida RI microcolonies in the biofilm. PMID:9603843

Christensen, B B; Sternberg, C; Andersen, J B; Eberl, L; Moller, S; Givskov, M; Molin, S

1998-06-01

103

Microbial characterization of biofilms in domestic drains and the establishment of stable biofilm microcosms.  

PubMed

We have used heterotrophic plate counts, together with live-dead direct staining and denaturing gradient gel electrophoresis (DGGE), to characterize the eubacterial communities that had formed as biofilms within domestic sink drain outlets. Laboratory microcosms of these environments were established using excised biofilms from two separate drain biofilm samples to inoculate constant-depth film fermentors (CDFFs). Drain biofilms harbored 9.8 to 11.3 log(10) cells of viable enteric species and pseudomonads/g, while CDFF-grown biofilms harbored 10.6 to 11.4 log(10) cells/g. Since live-dead direct staining revealed various efficiencies of recovery by culture, samples were analyzed by DGGE, utilizing primers specific for the V2-V3 region of eubacterial 16S rDNA. These analyses showed that the major PCR amplicons from in situ material were represented in the microcosms and maintained there over extended periods. Sequencing of amplicons resolved by DGGE revealed that the biofilms were dominated by a small number of genera, which were also isolated by culture. One drain sample harbored the protozoan Colpoda maupasi, together with rhabtidid nematodes and bdelloid rotifers. The microcosm enables the maintenance of stable drain-type bacterial communities and represents a useful tool for the modeling of this ecosystem. PMID:12513993

McBain, Andrew J; Bartolo, Robert G; Catrenich, Carl E; Charbonneau, Duane; Ledder, Ruth G; Rickard, Alexander H; Symmons, Sharon A; Gilbert, Peter

2003-01-01

104

Microbial Characterization of Biofilms in Domestic Drains and the Establishment of Stable Biofilm Microcosms  

PubMed Central

We have used heterotrophic plate counts, together with live-dead direct staining and denaturing gradient gel electrophoresis (DGGE), to characterize the eubacterial communities that had formed as biofilms within domestic sink drain outlets. Laboratory microcosms of these environments were established using excised biofilms from two separate drain biofilm samples to inoculate constant-depth film fermentors (CDFFs). Drain biofilms harbored 9.8 to 11.3 log10 cells of viable enteric species and pseudomonads/g, while CDFF-grown biofilms harbored 10.6 to 11.4 log10 cells/g. Since live-dead direct staining revealed various efficiencies of recovery by culture, samples were analyzed by DGGE, utilizing primers specific for the V2-V3 region of eubacterial 16S rDNA. These analyses showed that the major PCR amplicons from in situ material were represented in the microcosms and maintained there over extended periods. Sequencing of amplicons resolved by DGGE revealed that the biofilms were dominated by a small number of genera, which were also isolated by culture. One drain sample harbored the protozoan Colpoda maupasi, together with rhabtidid nematodes and bdelloid rotifers. The microcosm enables the maintenance of stable drain-type bacterial communities and represents a useful tool for the modeling of this ecosystem.

McBain, Andrew J.; Bartolo, Robert G.; Catrenich, Carl E.; Charbonneau, Duane; Ledder, Ruth G.; Rickard, Alexander H.; Symmons, Sharon A.; Gilbert, Peter

2003-01-01

105

Effect of cathodic protection on the activity of microbial biofilms  

SciTech Connect

Impressed current or sacrificial anode systems are used to protect the subsea structures of offshore oil platforms and rigs. The steel is considered protected when a potential of -850 mV(Cu:CuSO/sub 4/) is achieved, in many cases, the potential is further reduced to -950 mV to protect the steel from corrosion caused by the activity of sulfate-reducing bacteria (SRB). Therefore, some operators have questioned the presence of sulfide-containing deposits under marine macrofouling, indicating that SRB are active on structures protected to -950 mV. The decreased potential, however, is not applied to prevent the activity of SRB, but is based on a theoretical level which will allow passivity of steel in sulfide environments. This study was performed to determine the effect of a -950 mV cathodic potential on the activity of the biofilm formed, and the production of sulfide within that biofilm. 50D mild steel (BS 4360 Grade5D)/sup (1)/ corrosion coupons, both unprotected and protected with a sacrificial anode, were exposed in the estuarine waters of Aberdeen Harbor. The activities of the bacterial biofilms were determined using radiorespirometric methods. Biofilms were shown to develop on both substrata. The activity of the aerobic and anaerobic bacteria and SRB populations, however, were significantly greater on the unprotected coupons. Furthermore, sulfide could only be detected in the biofilm formed on the unprotected coupons. The results show that a potential of -950 mV does not prevent an active population of SRB developing on the metal surface. It is suggested that the lower activity of the biofilm on the protected coupon is not directly caused by any inhibitory effect of the cathodic potential; but that the greater activity on the unprotected coupon may be the result of the production of an extensive corrosion film that offers more favorable conditions for the activity of anaerobic bacteria.

Maxwell, S.

1986-11-01

106

Microbial Biofilm 2005. I National Nazionale. Istituo Superiore di Sanita. Roma 20-21 Giugno 2005. Riassunti (Microbial Biofilm 2005. I National Workshop. Istituto Superiore di Sanita. Rome, 20-21 June 2005. Abstract Book).  

National Technical Information Service (NTIS)

Microbiologists and specialists in infectious diseases, hygiene and public health have to face more and more frequently problems related to bacterial and fungal biofilm formation. In particular, benthonic microbial growth represents a critical issue in th...

2005-01-01

107

Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.  

PubMed

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

Biswas, Kristi; Turner, Susan J

2011-12-02

108

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

PubMed Central

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.

Turner, Susan J.

2012-01-01

109

Characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (MEC).  

PubMed

GeoChip (II) and single strand conformation polymorphism (SSCP) were used to characterize anode microbial communities of a microbial electrolysis cell (MEC). Biofilm communities, enriched in a two-chamber MEC (R1, 0.6 V applied) having a coulombic efficiency (CE) of 35±4% and a hydrogen yield (Y(H?))of 31±3%, were used as the inoculum for a new reactor (R2). After three months R2 achieved stable performance with CE=38±4% and (Y(H?)). Few changes in the predominant populations were observed from R1 to R2. Unlike sludge inoculation process in R1 in the beginning, little further elimination was aroused by community competitions in anode biofilm reformation in R2. Functional genes detection of biofilm indicated that cytochrome genes enriched soon in new reactor R2, and four genera (Desulfovibrio, Rhodopseudomonas, Shewanella and Geobacter) were likely to contribute to exoelectrogenic activity. This work also implied that symbiosis of microbial communities (exoelectrogens and others) contribute to system performance and stability. PMID:21939699

Liu, Wenzong; Wang, Aijie; Sun, Dan; Ren, Nanqi; Zhang, Yunqing; Zhou, Jizhong

2011-09-16

110

A comparative study of the major microbial biomass of biofilms on exteriors of buildings in Europe and Latin America  

Microsoft Academic Search

Microorganisms in biofilms on building surfaces include algae, bacteria and fungi and cause discolouration and degradation, but definitive information about preferences of microbial groups for given building substrates and how this is affected by environmental conditions is lacking. Major biomass in 230 biofilms from buildings in seven Latin American and six European countries was analysed. Substrates included composites (cement, mortar,

Christine C. Gaylarde; Peter M. Gaylarde

2005-01-01

111

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

NASA Astrophysics Data System (ADS)

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.

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

2009-05-01

112

Characterization of microbial community in an aerobic moving bed biofilm reactor applied for simultaneous nitrification and denitrification  

Microsoft Academic Search

A continuous-flow moving bed biofilm reactor (MBBR) under aerobic conditions was established for simultaneous nitrification\\u000a and denitrification (SND), and microbial communities were investigated by a combination of denaturing gel gradient electrophoresis\\u000a (DGGE) and fluorescence in situ hybridization (FISH). DGGE analysis has revealed more similar microbial community structures\\u000a formed in the biofilms with more similar carbon nitrogen (C\\/N) ratios. FISH analysis

Bo FuXiaoyi; Xiaoyi Liao; Lili Ding; Hongqiang Ren

2010-01-01

113

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

Microsoft Academic Search

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

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

2006-01-01

114

Developed microbial biofilms can restore deteriorated conventional agricultural soils  

Microsoft Academic Search

Nitrogen fixing bacteria play a key role in the growth and persistence of effective microbial communities in the soil by supplying N through biological nitrogen fixation (BNF). In the long run, chemical inputs, particularly N fertilisers are known to adversely affect N2 fixers and hence maintenance of soil fertility and crop productivity. This study examined the effect of developed microbial

G. Seneviratne; A. P. D. A. Jayasekara; M. S. D. L. De Silva; U. P. Abeysekera

2011-01-01

115

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

Microsoft Academic Search

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 nonde- structive voltammetry techniques

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

2008-01-01

116

Molecular Analysis of Microbial Communities in Endotracheal Tube Biofilms  

Microsoft Academic Search

BackgroundVentilator-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 FindingsThe aim of this study was to characterise

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

2011-01-01

117

Extraction of extracellular polymeric substances from extreme acidic microbial biofilms  

Microsoft Academic Search

The efficiency of five extraction methods for extracellular polymeric substances (EPS) was compared on three benthic eukaryotic\\u000a biofilms isolated from an extreme acidic river, Río Tinto (SW, Spain). Three chemical methods (MilliQ water, NaCl, and ethylenediamine\\u000a tetraacetic acid [EDTA]) and two physical methods (Dowex 50.8 and Crown Ether cation exchange resins) were tested. The quality\\u000a and quantity of the EPS

Angeles Aguilera; Virginia Souza-Egipsy; Patxi San Martín-Úriz; Ricardo Amils

2008-01-01

118

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

PubMed Central

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.

2012-01-01

119

Microbial extremophiles at the limits of life.  

PubMed

Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology. PMID:17653987

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

2007-01-01

120

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.  

PubMed

DNAs of two biofilms of a thermophilic two-phase leach-bed biogas reactor fed with rye silage and winter barley straw were sequenced by 454-pyrosequencing technology to assess the biofilm-based microbial community and their genetic potential for anaerobic digestion. The studied biofilms matured on the surface of the substrates in the hydrolysis reactor (HR) and on the packing in the anaerobic filter reactor (AF). The classification of metagenome reads showed Clostridium as most prevalent bacteria in the HR, indicating a predominant role for plant material digestion. Notably, insights into the genetic potential of plant-degrading bacteria were determined as well as further bacterial groups, which may assist Clostridium in carbohydrate degradation. Methanosarcina and Methanothermobacter were determined as most prevalent methanogenic archaea. In consequence, the biofilm-based methanogenesis in this system might be driven by the hydrogenotrophic pathway but also by the aceticlastic methanogenesis depending on metabolite concentrations such as the acetic acid concentration. Moreover, bacteria, which are capable of acetate oxidation in syntrophic interaction with methanogens, were also predicted. Finally, the metagenome analysis unveiled a large number of reads with unidentified microbial origin, indicating that the anaerobic degradation process may also be conducted by up to now unknown species. PMID:22126587

Rademacher, Antje; Zakrzewski, Martha; Schlüter, Andreas; Schönberg, Mandy; Szczepanowski, Rafael; Goesmann, Alexander; Pühler, Alfred; Klocke, Michael

2011-12-20

121

Biofilms.  

PubMed

Bacterial biofilms are 3-dimensional aggregates of bacteria that have been shown to play a major role in many chronic infections. Evidence is growing that bacterial biofilms may play a role in certain cases of recalcitrant chronic sinusitis that do not respond to traditional medical and surgical therapies. Novel therapies may have clinical applications to prevent and destabilize biofilms. Future research will determine if topical antimicrobials, surfactants, and other adjuvant therapies can be used to treat biofilm-associated chronic rhinosinusitis. PMID:20525507

Suh, Jeffrey D; Ramakrishnan, Vijay; Palmer, James N

2010-06-01

122

Regional hydrology controls stream microbial biofilms: evidence from a glacial catchment  

NASA Astrophysics Data System (ADS)

Glaciers are highly responsive to global warming and important agents of landscape heterogeneity. While it is well established that glacial ablation and snowmelt regulate stream discharge, linkage among streams and streamwater hydrogeochemistry, the controls of these factors on stream microbial biofilms remain insufficiently understood. We investigated glacial (metakryal, hypokryal), groundwater-fed (krenal) and snow-fed (rhithral) streams - all of them representative for alpine stream networks - and present evidence that these hydrologic and hydrogeochemical factors differentially affect sediment microbial biofilms. Average microbial biomass and bacterial carbon production were low in the glacial streams, whereas bacterial cell size, biomass, and carbon production were higher in the tributaries, most notably in the krenal stream. Whole-cell in situ fluorescence hybridization revealed reduced detection rates of the Eubacteria and higher abundance of ?-Proteobacteria in the glacial stream, a pattern that most probably reflects the trophic status of this ecosystem. Our data suggest low flow during the onset of snowmelt and autumn as a short period (hot moment) of favorable environmental conditions with pulsed inputs of allochthonous nitrate and dissolved organic carbon, and with disproportional high microbial growth. Krenal and rhithral streams with more constant and favorable environments serve as possible sources of microbes and organic matter to the main glacial channel during periods (e.g. snowmelt) of elevated hydrologic linkage among streams. Ice and snow dynamics have a crucial impact on microbial biofilms, and we thus need better understanding of the microbial ecology and enhanced consideration of critical hydrological episodes in future models predicting alpine stream communities.

Battin, T. J.; Wille, A.; Psenner, R.; Richter, A.

2004-08-01

123

Possibilities for the Detection of Microbial Life on Extrasolar Planets  

Microsoft Academic Search

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin\\/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth

Roger F. Knacke

2003-01-01

124

Microbial communities in deep Canadian shield groundwaters—an in situ biofilm experiment  

Microsoft Academic Search

Microbial biofilm communities were cultivated on stainless steel and polypropylene surfaces within brine?filled exploration boreholes in crystalline rocks of the Canadian Shield at Kidd Creek Mine (Timmins, Ontario) and Copper Cliff South Mine (Sudbury, Ontario) at depths of 1402 m and 1219 m, respectively. The calcium?sodium?chloride brines were acidic (pH 3.5–4.8) and had temperatures of 23.4°C to 18.6°C. Direct microscopic

F. Doig; B. Sherwood Lollar; F. G. Ferris

1995-01-01

125

The Microbial Community Structure of Drinking Water Biofilms Can Be Affected by Phosphorus Availability  

Microsoft Academic Search

Microbial communities in biofilms grown for 4 and 11 weeks under the flow of drinking water supplemented with 0, 1, 2, and 5 g of phosphorus liter1 and in drinking and warm waters were compared by using phospholipid fatty acids (PLFAs) and lipopolysaccharide 3-hydroxy fatty acids (LPS 3-OH-FAs). Phosphate increased the proportion of PLFAs 16:17c and 18:17c and affected LPS

Minna M. Keinanen; Leena K. Korhonen; Markku J. Lehtola; Ilkka T. Miettinen; Pertti J. Martikainen; Terttu Vartiainen; Merja H. Suutari

2002-01-01

126

Modeling how soluble microbial products (SMP) support heterotrophic bacteria in autotroph-based biofilms.  

PubMed

Multi-species biofilm modeling has been used for many years to understand the interactions between species in different biofilm systems, but the complex symbiotic relationship between species is sometimes overlooked, because models do not always include all relevant species and components. In this paper, we develop and use a mathematical model to describe a model biofilm system that includes autotrophic and heterotrophic bacteria and the key products produced by the bacteria. The model combines the methods of earlier multi-species models with a multi-component biofilm model in order to explore the interaction between species via exchange of soluble microbial products (SMP). We show that multiple parameter sets are able to describe the findings of experimental studies, and that heterotrophs growing on autotrophically produced SMP may pursue either r- or K-strategies to sustain themselves when SMP is their only substrate. We also show that heterotrophs can colonize some distance from the autotrophs and still be sustained by autotrophically produced SMP. This work defines the feasible range of parameters for utilization of SMP by heterotrophs and the nature of the interactions between autotrophs and heterotrophs in multi-species, multi-component biofilms. PMID:19481097

Merkey, Brian V; Rittmann, Bruce E; Chopp, David L

2009-05-27

127

Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy.  

PubMed

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. beta-, gamma-, delta-, and epsilon-proteobacteria in sulfur-cycling clades accounted for > or = 75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating delta-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 gamma-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of epsilon-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

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

2006-08-01

128

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

PubMed

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

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

2012-03-15

129

Metal Interactions with Microbial Biofilms in Acidic and Neutral pH Environments  

PubMed Central

Microbial biofilms were grown on strips of epoxy-impregnated filter paper submerged at four sites in water contaminated with metals from mine wastes. At two sample stations, the water was acidic (pH 3.1); the other sites were in a lake restored to a near neutral pH level by application of a crushed limestone slurry. During a 17-week study period, planktonic bacterial counts increased from 101 to 103 CFU/ml at all sites. Biofilm counts increased rapidly over the first 5 weeks and then leveled to 104 CFU/cm2 in the neutral pH system and 103 CFU/cm2 at the acidic sites. In each case, the biofilms bound Mn, Fe, Ni, and Cu in excess of the amounts adsorbed by control strips covered with nylon filters (pore size, 0.22 ?m) to exclude microbial growth; Co bound under neutral conditions but not under acidic conditions. Conditional adsorption capacity constants, obtained graphically from the data, showed that biofilm metal uptake at a neutral pH level was enhanced by up to 12 orders of magnitude over acidic conditions. Similarly, adsorption strength values were usually higher at elevated pH levels. In thin sections of the biofilms, encapsulated bacterial cells were commonly found enmeshed together in microcolonies. The extracellular polymers often contained iron oxide precipitates which generated weak electron diffraction patterns with characteristic reflections for ferrihydrite (Fe2O3 · H2O) at d equaling 0.15 and 0.25 nm. At neutral pH levels, these deposits incorporated trace amounts of Si and exhibited a granular morphology, whereas acicular crystalloids containing S developed under acidic conditions. Images

Ferris, F. G.; Schultze, S.; Witten, T. C.; Fyfe, W. S.; Beveridge, T. J.

1989-01-01

130

Initial development and structure of biofilms on microbial fuel cell anodes  

PubMed Central

Background Microbial fuel cells (MFCs) rely on electrochemically active bacteria to capture the chemical energy contained in organics and convert it to electrical energy. Bacteria develop biofilms on the MFC electrodes, allowing considerable conversion capacity and opportunities for extracellular electron transfer (EET). The present knowledge on EET is centred around two Gram-negative models, i.e. Shewanella and Geobacter species, as it is believed that Gram-positives cannot perform EET by themselves as the Gram-negatives can. To understand how bacteria form biofilms within MFCs and how their development, structure and viability affects electron transfer, we performed pure and co-culture experiments. Results Biofilm viability was maintained highest nearer the anode during closed circuit operation (current flowing), in contrast to when the anode was in open circuit (soluble electron acceptor) where viability was highest on top of the biofilm, furthest from the anode. Closed circuit anode Pseudomonas aeruginosa biofilms were considerably thinner compared to the open circuit anode (30 ± 3 ?m and 42 ± 3 ?m respectively), which is likely due to the higher energetic gain of soluble electron acceptors used. The two Gram-positive bacteria used only provided a fraction of current produced by the Gram-negative organisms. Power output of co-cultures Gram-positive Enterococcus faecium and either Gram-negative organisms, increased by 30-70% relative to the single cultures. Over time the co-culture biofilms segregated, in particular, Pseudomonas aeruginosa creating towers piercing through a thin, uniform layer of Enterococcus faecium. P. aeruginosa and E. faecium together generated a current of 1.8 ± 0.4 mA while alone they produced 0.9 ± 0.01 and 0.2 ± 0.05 mA respectively. Conclusion We postulate that this segregation may be an essential difference in strategy for electron transfer and substrate capture between the Gram-negative and the Gram-positive bacteria used here.

2010-01-01

131

Microbial electrocatalysis with Geobacter sulfurreducens biofilm on stainless steel cathodes  

Microsoft Academic Search

Stainless steel and graphite electrodes were individually addressed and polarized at ?0.60V vs. Ag\\/AgCl in reactors filled with a growth medium that contained 25mM fumarate as the electron acceptor and no electron donor, in order to force the microbial cells to use the electrode as electron source. When the reactor was inoculated with Geobacter sulfurreducens, the current increased and stabilized

Claire Dumas; Régine Basseguy; Alain Bergel

2008-01-01

132

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

NASA Astrophysics Data System (ADS)

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.

Arnon, Shai; Yanuka, Keren; Nejidat, Ali

2010-05-01

133

Large-scale environmental controls on microbial biofilms in high-alpine streams  

NASA Astrophysics Data System (ADS)

Glaciers are highly responsive to global warming and important agents of landscape heterogeneity. While it is well established that glacial ablation and snowmelt regulate stream discharge, linkage among streams and streamwater geochemistry, the controls of these factors on stream microbial biofilms remain insufficiently understood. We investigated glacial (metakryal, hypokryal), groundwater-fed (krenal) and snow-fed (rhithral) streams - all of them representative for alpine stream networks - and present evidence that these hydrologic and hydrogeochemical factors differentially affect sediment microbial biofilms. Average microbial biomass and bacterial carbon production were low in the glacial streams, whereas bacterial cell size, biomass, and carbon production were higher in the tributaries, most notably in the krenal stream. Whole-cell in situ fluorescence hybridization revealed reduced detection rates of the Eubacteria and higher abundance of ?-Proteobacteria in the glacial stream, a pattern that most probably reflects the trophic status of this ecosystem. Our data suggest low flow during the onset of snowmelt and autumn as a short period (hot moment) of favorable environmental conditions with pulsed inputs of allochthonous nitrate and dissolved organic carbon, and with disproportionately high microbial growth. Tributaries are relatively more constant and favorable environments than kryal streams, and serve as possible sources of microbes and organic matter to the main glacial channel during periods (e.g., snowmelt) of elevated hydrologic linkage among streams. Ice and snow dynamics - and their impact on the amount and composition of dissolved organic matter - have a crucial impact on stream biofilms, and we thus need to consider microbes and critical hydrological episodes in future models of alpine stream communities.

Battin, T. J.; Wille, A.; Psenner, R.; Richter, A.

134

[Functional microbial community in a membrane-aerated biofilm reactor operated for completely autotrophic nitrogen removal].  

PubMed

The 16S rDNA-based molecular technique was applied to investigate the functional microbial community of a membrane-aerated biofilm bioreactor (MABR) that was used for completely autotrophic nitrogen removal over nitrite (CANON). The relationships among two kinds of key bacteria responsible for CANON: aerobic ammonia-oxidizing bacteria (AOB) and ANAMMOX bacteria, and their possible distributions in the MAB were discussed based on the microbial community analysis. FISH analysis showed the existence of two visible active layers in experimental MAB. One was the partial nitrifying layer located in the region of oxygen-rich membrane-biofilm interface, dominated by NSO190-positive AOB. The other was the ANAMMOX active layer located in the region of anoxic liquid-biofilm interface, dominated by PLA46 and AMX820-positive ANAMMOX microorganisms. As a result, the AOB as well as ANAMMOX bacteria were present and active in experimental MABR, and the cooperation between AOB and ANAMMOX bacteria was considered to be responsible for CANON. PMID:19558119

Bao, Han; Zhang, Wei-Dong; Gong, Zheng; Xue, Yuan

2009-05-15

135

Microbial Biofilm Formation and Its Consequences for the CELSS Program.  

National Technical Information Service (NTIS)

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. Th...

R. Mitchell

1994-01-01

136

Influence of Support Media Characteristics on Biofilm Activity in Graywater Treatment Systems for Advanced Life Support  

Microsoft Academic Search

Advanced life support systems for long-duration space missions will require efficient recycling of water and air. Biological treatment systems may be used as the initial process in a multistep recycling system. Biofilm reactors (or biotrickling filters) have been shown to be effective for treatment of air and water. A major design consideration for these reactors is the selection of biofilm

Neepa Shah; Sybill E. Sharvelle; M. Katherine Banks

2007-01-01

137

The Microbial Community Structure of Drinking Water Biofilms Can Be Affected by Phosphorus Availability  

PubMed Central

Microbial communities in biofilms grown for 4 and 11 weeks under the flow of drinking water supplemented with 0, 1, 2, and 5 ?g of phosphorus liter?1 and in drinking and warm waters were compared by using phospholipid fatty acids (PLFAs) and lipopolysaccharide 3-hydroxy fatty acids (LPS 3-OH-FAs). Phosphate increased the proportion of PLFAs 16:1?7c and 18:1?7c and affected LPS 3-OH-FAs after 11 weeks of growth, indicating an increase in gram-negative bacteria and changes in their community structure. Differences in community structures between biofilms and drinking and warm waters can be assumed from PLFAs and LPS 3-OH-FAs, concomitantly with adaptive changes in fatty acid chain length, cyclization, and unsaturation.

Keinanen, Minna M.; Korhonen, Leena K.; Lehtola, Markku J.; Miettinen, Ilkka T.; Martikainen, Pertti J.; Vartiainen, Terttu; Suutari, Merja H.

2002-01-01

138

Identification of Biofilm Matrix-Associated Proteins from an Acid Mine Drainage Microbial Community ? †  

PubMed Central

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.

Jiao, Yongqin; D'haeseleer, Patrik; Dill, Brian D.; Shah, Manesh; VerBerkmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.; Thelen, Michael P.

2011-01-01

139

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

SciTech Connect

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.

Jiao, Yongqin [Lawrence Livermore National Laboratory (LLNL); D'Haeseleer, Patrik M [ORNL; Dill, Brian [ORNL; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley; Thelen, Michael P. [University of California, Berkeley

2011-01-01

140

Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.  

PubMed

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. PMID:21685158

Jiao, Yongqin; D'haeseleer, Patrik; Dill, Brian D; Shah, Manesh; Verberkmoes, Nathan C; Hettich, Robert L; Banfield, Jillian F; Thelen, Michael P

2011-06-17

141

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

PubMed Central

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.

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

2008-01-01

142

Interactions between microbial biofilms and marine fouling algae: a mini review.  

PubMed

Natural and artificial substrata immersed in the marine environment are typically colonized by microorganisms, which may moderate the settlement/recruitment of algal spores and invertebrate larvae of macrofouling organisms. This mini-review summarizes the major interactions occurring between microbial biofilms and marine fouling algae, including their effects on the settlement, growth and morphology of the adult plants. The roles of chemical compounds that are produced by both bacteria and algae and which drive the interactions are reviewed. The possibility of using such bioactive compounds to control macrofouling will be discussed. PMID:24047430

Mieszkin, Sophie; Callow, Maureen E; Callow, James A

2013-09-18

143

Tobacco Smoke Mediated Induction of Sinonasal Microbial Biofilms  

Microsoft Academic Search

Cigarette smokers and those exposed to second hand smoke are more susceptible to life threatening infection than non-smokers. While much is known about the devastating effect tobacco exposure has on the human body, less is known about the effect of tobacco smoke on the commensal and commonly found pathogenic bacteria of the human respiratory tract, or human respiratory tract microbiome.

Natalia Goldstein-Daruech; Emily K. Cope; Ke-Qing Zhao; Katarina Vukovic; Jennifer M. Kofonow; Laurel Doghramji; Bernardo González; Alexander G. Chiu; David W. Kennedy; James N. Palmer; Jeffery G. Leid; James L. Kreindler; Noam A. Cohen; Malcolm Gracie Semple

2011-01-01

144

Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms  

Microsoft Academic Search

BACKGROUND: The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusion of prokaryotic lineages. However, as yet there is no consensus regarding the nature of the prokaryotic group(s) ancestral to eukaryotes. Regardless of this, a hardly debatable

Gáspár Jékely

2007-01-01

145

In Situ Techniques and Digital Image Analysis Methods for Quantifying Spatial Localization Patterns of Nitrifiers and Other Microorganisms in Biofilm and Flocs  

Microsoft Academic Search

The spatial localization patterns of microorganisms in multispecies biofilms reflect numerous phenomena that influence sessile microbial life, such as substrate concentration gradients within the biofilm and biological interactions with other biofilm populations. Quantitative and population-specific in situ analyses of spatial patterns have a high potential to provide novel insights into the biology of biofilm organisms, including yet uncultured microbes, but

Holger Daims; Michael Wagner

2011-01-01

146

Microbial Life of North Pacific Oceanic Crust  

NASA Astrophysics Data System (ADS)

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep biosphere. Molecular microbial diversity is currently determined by cloning und comparative 16S rRNA gene analyses. The first results will also be presented. In summary, the low number of isolates, cultivated under aerobic conditions, is in good agreement with the common opinion that most of the bacteria within the deep biosphere are anaerobic. Thus, studies of microbial community structure in solid geological materials are feasible and constitute further evidence that continuing microbiological activity in the challenging exploration of the deep sub-seafloor biosphere environment is absolutely promising.

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

147

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

PubMed Central

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.

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

2009-01-01

148

A biofilm enhanced miniature microbial fuel cell using Shewanella oneidensis DSP10 and oxygen reduction cathodes.  

PubMed

A miniature-microbial fuel cell (mini-MFC, chamber volume: 1.2 mL) was used to monitor biofilm development from a pure culture of Shewanella oneidensis DSP10 on graphite felt (GF) under minimal nutrient conditions. ESEM evidence of biofilm formation on GF is supported by substantial power density (per device cross-section) from the mini-MFC when using an acellular minimal media anolyte (1500 mW/m2). These experiments demonstrate that power density per volume for a biofilm flow reactor MFC should be calculated using the anode chamber volume alone (250W/m3), rather than with the full anolyte volume. Two oxygen reduction cathodes (uncoated GF or a Pt/vulcanized carbon coating on GF) were also compared to a cathode using uncoated GF and a 50mM ferricyanide catholyte solution. The Pt/C-GF (2-4% Pt by mass) electrodes with liquid cultures of DSP10 produced one order of magnitude larger power density (150W/m3) than bare graphite felt (12W/m3) in this design. These advances are some of the required modifications to enable the mini-MFC to be used in real-time, long-term environmental power generating situations. PMID:16939710

Biffinger, Justin C; Pietron, Jeremy; Ray, Ricky; Little, Brenda; Ringeisen, Bradley R

2006-08-30

149

A Modern Perspective on Ancient Life: Microbial Mats in Sandy Marine Settings from the Archean Era to Today  

Microsoft Academic Search

\\u000a Most valuable paleontological studies on the ancient life in the Archean era are on fossils of bacterial cells preserved in\\u000a chert, or on the famous stromatolites we find in the oldest carbonate or silica rocks. The past decade, a new window into\\u000a Earth’s most antique worlds opened: Modern sandy coastal areas and the biofilms and microbial mats therein! The interaction

Nora Noffke

150

3.45 b.y.-old microbial associations in cherts from the Pilbara: lessons for potential Martian life  

Microsoft Academic Search

3.45 b.y.-old cherts from the Kitty's Gap locality in the Pilbara contain superbly preserved microbial biofilms that formed on an early Earth characterised by extreme conditions. They therefore represent good analogues for potential early Martian life. Volcaniclastic sediments influenced by hydrothermal activity were deposited in very shallow water to exposed conditions, as evidenced by interstratified cross-bedded and evaporite units. Two

F. Westall

2003-01-01

151

Mathematical model for microbial fuel cells with anodic biofilms and anaerobic digestion.  

PubMed

This study describes the integration of IWA's anaerobic digestion model (ADM1) within a computational model of microbial fuel cells (MFCs). Several populations of methanogenic and electroactive microorganisms coexist suspended in the anolyte and in the biofilm attached to the anode. A number of biological, chemical and electrochemical reactions occur in the bulk liquid, in the biofilm and at the electrode surface, involving glucose, organic acids, H2 and redox mediators. Model output includes the evolution in time of important measurable MFC parameters (current production, consumption of substrates, suspended and attached biomass growth). Two- and three-dimensional model simulations reveal the importance of current and biomass heterogeneous distribution over the planar anode surface. Voltage- and power-current characteristics can be calculated at different moments in time to evaluate the limiting regime in which the MFC operates. Finally, model simulations are compared with experimental results showing that, in a batch MFC, smaller electrical resistance of the circuit leads to selection of electroactive bacteria. Higher coulombic yields are so obtained because electrons from substrate are transferred to anode rather than following the methanogenesis pathway. In addition to higher currents, faster COD consumption rates are so achieved. The potential of this general modelling framework is in the understanding and design of more complex cases of wastewater-fed microbial fuel cells. PMID:18441420

Picioreanu, C; van Loosdrecht, M C M; Katuri, K P; Scott, K; Head, I M

2008-01-01

152

The root surface as the definitive detail for microbial transformation processes in constructed wetlands--a biofilm characteristic.  

PubMed

It was the goal of the investigations to characterise the biofilm on the plant roots because of the demonstrable major role of these associated bacteria. The essential criteria for the research were to look at the structure of the microbial colonisation (pattern, density) and to determine properties of the rhizoplane biofilm such as thickness and structure. The root material from a hydroponic system, planted with Glyceria maxima and used for nitrogen removal, has been used for the investigations. Several properties of the bacteria became visible due to the application of specific dyes. The evaluation of the samples was performed by scanning confocal laser microscopy (CLSM). It was shown that the microbial colonisation of the root surface of Glyceria maxima was on an unexpected high level and seems to be related mainly to the permeability and therefore to the age of the plant roots. The thickness of the rhizoplane biofilm is remarkably thin; no inactive layers could be observed in contrast to biofilm growing on technical carrier material. Caused by the untypically two-sided supply with nutrients the whole biofilm is in interaction with the surroundings. This indicates the importance of the plant roots for the microbial transformation processes in wetlands and underlines the especialness of the root as carrier for microorganisms. PMID:17802865

Münch, Ch; Neu, T; Kuschk, P; Röske, I

2007-01-01

153

Community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach  

Microsoft Academic Search

The microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (MF) and reverse osmosis (RO) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16S rDNA clone library and fluorescence in situ hybridization techniques. All methods showed that the a-Proteobacteria was the largest microbial fraction in the samples, followed by the ?-Proteobacteria. This

C.-L. Chen; W.-T. Liu; M.-L. Chong; M.-T. Wong; S. L. Ong; H. Seah; W. J. Ng

2004-01-01

154

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

NASA Astrophysics Data System (ADS)

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.

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

2005-12-01

155

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

PubMed

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

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

2012-07-13

156

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

PubMed

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 O(2) 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

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

2011-12-01

157

Biofilms as Biomarkers in Terrestrial and Extraterrestrial Materials  

Microsoft Academic Search

Biofilms consisting of microbial mucoidal substances and cells are more readily preservable in the fossil record than the bacteria, themselves, making them potentially ideal biomarkers in the search for extraterrestrial life.

F. Westall; A. Steele; C. C. Allen; D. S. McKay; E. K. Gibson; P. Morris

1999-01-01

158

Role for glycine betaine transport in Vibrio cholerae osmoadaptation and biofilm formation within microbial communities.  

PubMed

Vibrio cholerae is a halophilic facultative human pathogen found in marine and estuarine environments. Accumulation of compatible solutes is important for growth of V. cholerae at NaCl concentrations greater than 250 mM. We have identified and characterized two compatible solute transporters, OpuD and PutP, that are involved in uptake of glycine betaine and proline by V. cholerae. V. cholerae does not, however, possess the bet genes, suggesting that it is unable to synthesize glycine betaine. In contrast, many Vibrio species are able to synthesize glycine betaine from choline. It has been shown that many bacteria not only synthesize but also secrete glycine betaine. We hypothesized that sharing of compatible solutes might be a mechanism for cooperativity in microbial communities. In fact, we have demonstrated that, in high-osmolarity medium, V. cholerae growth and biofilm development are enhanced by supplementation with either glycine betaine or spent media from other bacterial species. Thus, we propose that compatible solutes provided by other microorganisms may contribute to survival of V. cholerae in the marine environment through facilitation of osmoadaptation and biofilm development. PMID:16000796

Kapfhammer, Dagmar; Karatan, Ece; Pflughoeft, Kathryn J; Watnick, Paula I

2005-07-01

159

Scanning Transmission X-Ray, Laser Scanning, and Transmission Electron Microscopy Mapping of the Exopolymeric Matrix of Microbial Biofilms  

PubMed Central

Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.

Lawrence, J. R.; Swerhone, G. D. W.; Leppard, G. G.; Araki, T.; Zhang, X.; West, M. M.; Hitchcock, A. P.

2003-01-01

160

Submersible microbial fuel cell sensor for monitoring microbial activity and BOD in groundwater: Focusing on impact of anodic biofilm on sensor applicability.  

PubMed

A sensor, based on a submersible microbial fuel cell (SUMFC), was developed for in situ monitoring of microbial activity and biochemical oxygen demand (BOD) in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Fresh anode was required for application of the sensor for microbial activity measurement, while biofilm-colonized anode was needed for utilizing the sensor for BOD content measurement. The current density of SUMFC sensor equipped with a biofilm-colonized anode showed linear relationship with BOD content, to up to 250?mg/L (?233?±?1?mA/m(2) ), with a response time of <0.67?h. This sensor could, however, not measure microbial activity, as indicated by the indifferent current produced at varying active microorganisms concentration, which was expressed as microbial adenosine-triphosphate (ATP) concentration. On the contrary, the current density (0.6?±?0.1 to 12.4?±?0.1?mA/m(2) ) of the SUMFC sensor equipped with a fresh anode showed linear relationship, with active microorganism concentrations from 0 to 6.52?nmol-ATP/L, while no correlation between the current and BOD was observed. It was found that temperature, pH, conductivity, and inorganic solid content were significantly affecting the sensitivity of the sensor. Lastly, the sensor was tested with real contaminated groundwater, where the microbial activity and BOD content could be detected in <3.1?h. The microbial activity and BOD concentration measured by SUMFC sensor fitted well with the one measured by the standard methods, with deviations ranging from 15% to 22% and 6% to 16%, respectively. The SUMFC sensor provides a new way for in situ and quantitative monitoring contaminants content and biological activity during bioremediation process in variety of anoxic aquifers. Biotechnol. Bioeng. © 2011 Wiley Periodicals, Inc. PMID:21557205

Zhang, Yifeng; Angelidaki, Irini

2011-05-01

161

Biofilms  

Microsoft Academic Search

Cell signaling in Escherichia coli biofilms is more important than originally known, in that au toinducer two (AI-2), AI-1 (N-acylhomoserine lactones), indole, hydroxylated indoles, nore pinephrine, and epinephrine are all functional signals in this organism. This gives the bacterium the ability to monitor not only the presence of cells of its own species (through AI-2 and indole) but also the

David Stickler; H. Vlamakis; R. Kolter

1999-01-01

162

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

PubMed

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

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

2012-03-01

163

High-Yield and Phylogenetically Robust Methods of DNA Recovery for Analysis of Microbial Biofilms Adherent to Plant Biomass in the Herbivore Gut  

Microsoft Academic Search

Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other\\u000a herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by\\u000a metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential\\u000a recovered is biologically valid. To that end, we

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

2011-01-01

164

Eukaryotic life in biofilms formed in a uranium mine.  

PubMed

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

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

2012-06-01

165

Eukaryotic life in biofilms formed in a uranium mine  

PubMed Central

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.

Zirnstein, Isabel; Arnold, Thuro; Krawczyk-Barsch, Evelyn; Jenk, Ulf; Bernhard, Gert; Roske, Isolde

2012-01-01

166

Non-destructive monitoring of microbial biofilms at solid-liquid interfaces using on-line devices  

SciTech Connect

Corrosion, biofouling, and related problems have been an impetus for investigating interactions between microorganisms and solid surfaces. In recent years, a number of studies have been performed to assess the damages caused by microbial influenced corrosion (MIC). In a number of these studies, electrochemical techniques have monitored the performance of metal surfaces exposed to bacteria. However, most of these methods can only indirectly detect the presence of biofilms. In this paper, two non-destructive on-line monitoring devices, attenuated total reflection Fourier transform infrared spectroscopy (ATR-FT/IR) and the quartz crystal microbalance (QCM) were used to directly monitor biofilm formation. These devices have been developed to study the initial fouling process and subsequent biofilm development and not merely the effects of the living film on the host material. The ATR-FT/IR technique provides information about biomass, exopolymer production, and the nutritional status of microbial biofilms. The QCM provides a direct measure of biomass. ATR-FT/IR and QCM detect 10{sup 6} and 10{sup 4} Caulobacter crescentus cells/cm{sup 2}, respectively. Both techniques can be coupled with electrochemical methods for deeper insight into mechanisms of MIC. 20 refs., 2 figs.

Nivens, D.E. (Tennessee Univ., Knoxville, TN (USA). Dept. of Chemistry Tennessee Univ., Knoxville, TN (USA). Inst. for Applied Microbiology); Chambers, J.Q. (Tennessee Univ., Knoxville, TN (USA). Dept. of Chemistry); White, D.C. (Tennessee Univ., Knoxville, TN (USA). Inst. for Applied Microbiology Tennessee Univ., Knoxville, TN (USA). Dept. of Microbiology Oak Ridge National Lab., TN (USA))

1990-01-01

167

Pressure as an environmental parameter for microbial life - A review.  

PubMed

Microbial life has been prevailing in the biosphere for the last 3.8Ga at least. Throughout most of the Earth's history it has experienced a range of pressures; both dynamic pressure when the young Earth was heavily bombarded, and static pressure in subsurface environments that could have served as a refuge and where microbial life nowadays flourishes. In this review, we discuss the extent of high-pressure habitats in early and modern times and provide a short overview of microbial survival under dynamic pressures. We summarize the current knowledge about the impact of microbial activity on biogeochemical cycles under pressures characteristic of the deep subsurface. We evaluate the possibility that pressure can be a limiting parameter for life at depth. Finally, we discuss the open questions and knowledge gaps that exist in the field of high-pressure geomicrobiology. PMID:23891571

Picard, Aude; Daniel, Isabelle

2013-07-01

168

COD removal from expanded granular sludge bed effluent using a moving bed biofilm reactor and their microbial community analysis  

Microsoft Academic Search

The bioreactor performance of a moving bed biofilm reactor (MBBR) as post-treatment of expanded granular sludge bed (EGSB)\\u000a effluent was investigated. Moreover, the microbial communities of the two bioreactors during different operation periods were\\u000a studied. The MBBR was efficient for COD removal with the mean efficiency of 82.4%, and produced an effluent with high and\\u000a stable quality against shock loading

Bo Fu; Xiaoyi Liao; Rui Liang; Lili Ding; Ke Xu; Hongqiang Ren

2011-01-01

169

Detection of heavy metals in bacterial biofilms and microbial flocs with the fluorescent complexing agent Newport Green  

Microsoft Academic Search

  The complexing agent Newport Green fluoresces upon binding of nickel, zinc or cobalt. It was used to detect nickel or zinc\\u000a in MOPS buffer, in gel-like matrices, and in natural biofilms and microbial flocs cultivated in the laboratory. The response\\u000a curves for increasing nickel concentrations indicated an equimolar binding capacity of Newport Green for nickel in MOPS buffer,\\u000a whereas zinc

S Wuertz; E Müller; R Spaeth; P Pfleiderer; H-C Flemming

2000-01-01

170

Possibilities for the Detection of Microbial Life on Extrasolar Planets  

NASA Astrophysics Data System (ADS)

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

Knacke, Roger F.

2003-11-01

171

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

PubMed

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

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

2011-01-24

172

Effect of different operational conditions on biofilm development, nitrification, and nitrifying microbial population in moving-bed biofilm reactors.  

PubMed

In this study, the effect of different operational conditions on biofilm development and nitrification in three moving-bed biofilm reactors (MBBRs) was investigated: two reactors were operated in a continuously fed regime and one in sequencing-batch mode. The presence of organic carbon reduced the time required to form stable nitrifying biofilms. Subsequent stepwise reduction of influent COD caused a decrease in total polysaccharide and protein content, which was accompanied by a fragmentation of the biofilm, as shown by scanning electron microscopy, and by an enrichment of the biofilm for nitrifiers, as observed by fluorescent in situ hybridization (FISH) analysis. Polysaccharide and protein concentrations proved to be good indicators of biomass development and detachment in MBBR systems. Ammonium- and nitrite-oxidizing bacteria activities were affected when a pulse feeding of 4 g of NH(4)-N/(m(2)·day) was applied. Free nitrous acid and free ammonia were likely the inhibitors for ammonium- and nitrite-oxidizing bacteria. PMID:22243035

Bassin, J P; Kleerebezem, R; Rosado, A S; van Loosdrecht, M C M; Dezotti, M

2012-01-26

173

The universe: a cryogenic habitat for microbial life  

Microsoft Academic Search

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

Chandra Wickramasinghe

2004-01-01

174

Microbial life in ridge flank crustal fluids.  

PubMed

To determine the microbial community diversity within old oceanic crust, a novel sampling strategy was used to collect crustal fluids at Baby Bare Seamount, a 3.5 Ma old outcrop located in the north-east Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Stainless steel probes were driven directly into the igneous ocean crust to obtain samples of ridge flank crustal fluids. Genetic signatures and enrichment cultures of microorganisms demonstrate that these crustal fluids host a microbial community composed of species indigenous to the subseafloor, including anaerobic thermophiles, and species from other deep-sea habitats, such as seawater and sediments. Evidence using molecular techniques indicates the presence of a relatively small but active microbial population, dominated by bacteria. The microbial community diversity found in the crustal fluids may indicate habitat variability in old oceanic crust, with inputs of nutrients from seawater, sediment pore-water fluids and possibly hydrothermal sources. This report further supports the presence of an indigenous microbial community in ridge flank crustal fluids and advances our understanding of the potential physiological and phylogenetic diversity of this community. PMID:16343325

Huber, Julie A; Johnson, H Paul; Butterfield, David A; Baross, John A

2006-01-01

175

Microbial Life in a Liquid Asphalt Desert  

NASA Astrophysics Data System (ADS)

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.

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

176

Preliminary studies on the microbial community structure of membrane-aerated biofilms treating municipal wastewater  

Microsoft Academic Search

Membrane-aerated biofilm reactors (MABRs) support biofilms that receive oxygen and nutrients from opposite sides of the biofilm and thus should behave differently than the activated sludge process. Population modeling predicted the simultaneous presence of aerobic heterotrophs, nitrifying bacteria, denitrifying bacteria, and acetoclastic methanogens in a membrane-supported biofilm. Community analysis by PCR-DGGE demonstrated that a pilot-scale MABR supported a significantly different

Alina C. Cole; John W. Shanahan; Michael J. Semmens; Timothy M. LaPara

2002-01-01

177

Medical Biofilms  

PubMed Central

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.

2009-01-01

178

Microbial Astronauts: Assembling Microbial Communities for Advanced Life Support Systems  

Microsoft Academic Search

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

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

2004-01-01

179

Microbial life in antarctic permafrost and ice  

Microsoft Academic Search

Antarctic permafrost, ground ices and ice sheet are the best natural models for development of methodologies for conducting astrobiological research relevant to the study of icy bodies of the Solar System and in particular of Mars. The method employed in this research is the in-situ investigation (SEM, AFM, epifluorescence microscopy, lipid biomarkers analysis) of microbial extremophiles in the Arctic and

E. Vorobyova; A. Philimonova; G. Osipov; A. Bolshakova; L. Yaminsky

2002-01-01

180

Microbial life in a liquid asphalt desert.  

PubMed

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

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

2011-04-11

181

Shearing of biofilms enables selective layer based microbial sampling and analysis.  

PubMed

Granules are large, self-supporting biofilms that form naturally in high-rate anaerobic treatment systems and are extremely important to reactor functionality. Granules exhibit functional and phylogenetic layering, interesting to both scientists and technologists. Until now, it has only been possible to analyze layering through sectioning and microscopic analysis with fluorescent in situ hybridization, or to analyze the whole granule through DNA extraction and microbial community profiling methods. This means different functional and spatial layers cannot be analyzed separately, including next generation sequencing techniques, such as pyrotag sequencing. In this work, we describe a method to remove microbes selectively from successive spatial layers through hydraulic shearing and demonstrate its application on anaerobic granules of three different types (VFA-, carbohydrate-, protein-fed) in size ranges 0.6-2?mm. Outer layers in particular could be selectively sheared as confirmed by FISH. TRFLP was used as an example bulk DNA method on selectively sheared fractions. A shift in dominant population was found from presumptive acidogens (such as Bacteroidetes and Anaerolinea) in outer layers to syntrophs (such as Syntrophomonas and Geobacter) in inner layers, with progressive changes through the depth. The strength of the shear-bulk molecular method over FISH was that a deeper phylogenetic profile could be obtained, even with TRFLP, and that prior knowledge of the community is not required. PMID:23616338

Lu, Yang; Slater, Frances; Bello-Mendoza, Ricardo; Batstone, Damien J

2013-05-16

182

Limits for Microbial Life at Subzero Temperatures  

Microsoft Academic Search

The limitations of terrestrial life are not well-defined or understood and have primarily been advanced through exploration\\u000a and discovery of organisms living in “extreme” environments where life was not thought possible. Identifying the limits of\\u000a life is hampered by our inability to define the essential nature of life, rather than just describing its properties (organization,\\u000a energy use, growth, adaptation, response

Corien Bakermans

183

Microbial Life Detection with Minimal Assumptions  

Microsoft Academic Search

ABSTRACT 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. T he Life Detection Array(LIDA), an instrument proposed for the 2007 NASA Mars Scout

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

184

Microbial life detection with minimal assumptions  

Microsoft Academic Search

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,

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

2002-01-01

185

Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity  

PubMed Central

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.

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

2013-01-01

186

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

PubMed

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

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

2013-08-06

187

Microbial life in the deep terrestrial subsurface  

SciTech Connect

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.

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

1988-12-31

188

Modern analogues and the early history of microbial life  

Microsoft Academic Search

Revealing the geological history of microbial life is very challenging. Microbes rarely are preserved with morphological fidelity, and even when they are, morphology is a poor guide to phylogeny and metabolism. Biological studies of environments considered analogous to those of paleobiological interest on the ancient Earth can inform interpretations and suggest new approaches. This paper reviews recent advances in our

Brendan P. Burns; Roberto Anitori; Philip Butterworth; Ruth Henneberger; Falicia Goh; Michelle A. Allen; Raquel Ibañez-Peral; Peter L. Bergquist; Malcolm R. Walter; Brett A. Neilan

2009-01-01

189

Microbial spoilage of portuguese chouriço along shelf life period  

PubMed Central

Microbial flora of portuguese chouriço (Alentejano (A) and Ribatejano (R)) with abnormal sensorial characteristics along shelf life was studied. Mesophilic anaerobic bacteria, enterococci, mesophilic sporeformers, coliforms, coagulase-positive staphylococci, sulphite reducing clostridia, Clostridium perfringens, moulds and yeasts were the most representative in both types of chouriço.

de Jesus da Silva Matos, Teresa; Bruno-Soares, Arminda; Azevedo, Antonio Amaral

2013-01-01

190

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

Microsoft Academic Search

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

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

2009-01-01

191

Removal of microbial multi-species biofilms from the paper industry by enzymatic treatments  

Microsoft Academic Search

This study aimed to characterize biofilms from the paper industry and evaluate the effectiveness of enzymatic treatments in reducing them. The extracellular polymeric substances (EPS) extracted from six industrial biofilms were studied. EPS were mainly proteins, the protein to polysaccharide ratio ranging from 1.3 to 8.6 depending on where the sampling point was situated in the paper making process. Eight

C. E. Marcato-Romain; Y. Pechaud; E. Paul; E. Girbal-Neuhauser; V. Dossat-Létisse

2012-01-01

192

A Fatty Acid Messenger Is Responsible for Inducing Dispersion in Microbial Biofilms  

Microsoft Academic Search

It is well established that in nature, bacteria are found primarily as residents of surface-associated com- munities called biofilms. These structures form in a sequential process initiated by attachment of cells to a surface, followed by the formation of matrix-enmeshed microcolonies, and culminating in dispersion of the bacteria from the mature biofilm. In the present study, we have demonstrated that,

David G. Davies; Claudia N. H. Marques

2009-01-01

193

Disruption of Microbial Biofilms by an Extracellular Protein Isolated from Epibiotic Tropical Marine Strain of Bacillus licheniformis  

PubMed Central

Background Marine epibiotic bacteria produce bioactive compounds effective against microbial biofilms. The study examines antibiofilm ability of a protein obtained from a tropical marine strain of Bacillus licheniformis D1. Methodology/Principal Findings B. licheniformis strain D1 isolated from the surface of green mussel, Perna viridis showed antimicrobial activity against pathogenic Candida albicans BH, Pseudomonas aeruginosa PAO1 and biofouling Bacillus pumilus TiO1 cultures. The antimicrobial activity was lost after treatment with trypsin and proteinase K. The protein was purified by ultrafiltration and size-exclusion chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis revealed the antimicrobial agent to be a 14 kDa protein designated as BL-DZ1. The protein was stable at 75°C for 30 min and over a pH range of 3.0 to 11.0. The sequence alignment of the MALDI-fingerprint showed homology with the NCBI entry for a hypothetical protein (BL00275) derived from B. licheniformis ATCC 14580 with the accession number gi52082584. The protein showed minimum inhibitory concentration (MIC) value of 1.6 µg/ml against C. albicans. Against both P. aeruginosa and B. pumilus the MIC was 3.12 µg/ml. The protein inhibited microbial growth, decreased biofilm formation and dispersed pre-formed biofilms of the representative cultures in polystyrene microtiter plates and on glass surfaces. Conclusion/Significance We isolated a protein from a tropical marine strain of B. licheniformis, assigned a function to the hypothetical protein entry in the NCBI database and described its application as a potential antibiofilm agent.

Dusane, Devendra H.; Damare, Samir R.; Nancharaiah, Yarlagadda V.; Ramaiah, N.; Venugopalan, Vayalam P.; Kumar, Ameeta Ravi; Zinjarde, Smita S.

2013-01-01

194

The universe: a cryogenic habitat for microbial life.  

PubMed

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

Wickramasinghe, Chandra

2004-04-01

195

Seasonal variation in nutrient limitation of microbial biofilms colonizing organic and inorganic substrata in streams  

Microsoft Academic Search

Humans have increased the availability of nutrients including nitrogen and phosphorus worldwide; therefore, understanding\\u000a how microbes process nutrients is critical for environmental conservation. We examined nutrient limitation of biofilms colonizing\\u000a inorganic (fritted glass) and organic (cellulose sponge) substrata in spring, summer, and autumn in three streams in Michigan,\\u000a USA. Biofilms were enriched with nitrate (NO3\\u000a ?), phosphate (PO4\\u000a 3?), ammonium

Timothy J. Hoellein; Jennifer L. Tank; John J. Kelly; Emma J. Rosi-Marshall

2010-01-01

196

Quantitative Analysis of Three Hydrogenotrophic Microbial Groups, Methanogenic Archaea, Sulfate-Reducing Bacteria, and Acetogenic Bacteria, within Plaque Biofilms Associated with Human Periodontal Disease  

Microsoft Academic Search

Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H2- metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of

M. E. Vianna; S. Holtgraewe; I. Seyfarth; G. Conrads; H. P. Horz

2008-01-01

197

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)

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.

Fang, J.

2009-12-01

198

Effect of formation of biofilms and chemical scale on the cathode electrode on the performance of a continuous two-chamber microbial fuel cell.  

PubMed

A two-chamber MFC system was operated continuously for more than 500 days to evaluate effects of biofilm and chemical scale formation on the cathode electrode on power generation. A stable power density of 0.57 W/m(2) was attained after 200 days operation. However, the power density decreased drastically to 0.2 W/m(2) after the cathodic biofilm and chemical scale were removed. As the cathodic biofilm and chemical scale partially accumulated on the cathode, the power density gradually recovered with time. Microbial community structure of the cathodic biofilm was analyzed based on 16S rRNA clone libraries. The clones closely related to Xanthomonadaceae bacterium and Xanthomonas sp. in the Gammaproteobacteria subdivision were most frequently retrieved from the cathodic biofilm. Results of the SEM-EDX analysis revealed that the cation species (Na(+) and Ca(2+)) were main constituents of chemical scale, indicating that these cations diffused from the anode chamber through the Nafion membrane. However, an excess accumulation of the biofilm and chemical scale on the cathode exhibited adverse effects on the power generation due to a decrease in the active cathode surface area and an increase in diffusion resistance for oxygen. Thus, it is important to properly control the formation of chemical scale and biofilm on the cathode during long-term operation. PMID:20923722

Chung, Kyungmi; Fujiki, Itto; Okabe, Satoshi

2010-05-23

199

Biofilm formation in Escherichia coli is affected by 3-(N-morpholino)propane sulfonate (MOPS)  

Microsoft Academic Search

In most natural environments, association with a surface in a structure known as a biofilm is the prevailing microbial life-style. Escherichia coli has been a useful model for the study of biofilm formation. Here we analyzed the amounts of biofilm formed when E. coli was cultured in the presence of MOPS [3-(N-morpholino)propane sulfonate]. We used the “O'Toole and Kolter” method,

F. Paola Corona-Izquierdo; Jorge Membrillo-Hernández

2002-01-01

200

Microbial biofilms on the surface of intravaginal rings worn in non-human primates  

PubMed Central

Millions of intravaginal rings (IVRs) are used by women worldwide for contraception and for the treatment of vaginal atrophy. These devices also are suitable for local and systemic sustained release drug delivery, notably for antiviral agents in human immunodeficiency virus pre-exposure prophylaxis. Despite the widespread use of IVRs, no studies have examined whether surface-attached bacterial biofilms develop in vivo, an important consideration when determining the safety of these devices. The present study used scanning electron microscopy, fluorescence in situ hybridization and confocal laser scanning microscopy to study biofilms that formed on the surface of IVRs worn for 28 days by six female pig-tailed macaques, an excellent model organism for the human vaginal microbiome. Four of the IVRs released the nucleotide analogue reverse transcriptase inhibitor tenofovir at a controlled rate and the remaining two were unmedicated. Large areas of the ring surfaces were covered with monolayers of epithelial cells. Two bacterial biofilm phenotypes were found to develop on these monolayers and both had a broad diversity of bacterial cells closely associated with the extracellular material. Phenotype I, the more common of the two, consisted of tightly packed bacterial mats approximately 5 µm in thickness. Phenotype II was much thicker, typically 40 µm, and had an open architecture containing interwoven networks of uniform fibres. There was no significant difference in biofilm thickness and appearance between medicated and unmedicated IVRs. These preliminary results suggest that bacterial biofilms could be common on intravaginal devices worn for extended periods of time.

Gunawardana, Manjula; Moss, John A.; Smith, Thomas J.; Kennedy, Sean; Kopin, Etana; Nguyen, Cali; Malone, Amanda M.; Rabe, Lorna; Schaudinn, Christoph; Webster, Paul; Srinivasan, Priya; Sweeney, Elizabeth D.; Smith, James M.

2011-01-01

201

Microbial interactions and differential protein expression in Staphylococcus aureus -Candida albicans dual-species biofilms  

PubMed Central

The fungal species Candida albicans and the bacterial species Staphylococcus aureus are responsible for a majority of hospital-acquired infections and often coinfect critically ill patients as complicating polymicrobial biofilms. To investigate biofilm structure during polymicrobial growth, dual-species biofilms were imaged with confocal scanning laser microscopy. Analyses revealed a unique biofilm architecture where S. aureus commonly associated with the hyphal elements of C. albicans. This physical interaction may provide staphylococci with an invasion strategy because candidal hyphae can penetrate through epithelial layers. To further understand the molecular mechanisms possibly responsible for previously demonstrated amplified virulence during coinfection, protein expression studies were undertaken. Differential in-gel electrophoresis identified a total of 27 proteins to be significantly differentially produced by these organisms during coculture biofilm growth. Among the upregulated staphylococcal proteins was l-lactate dehydrogenase 1, which confers resistance to host-derived oxidative stressors. Among the downregulated proteins was the global transcriptional repressor of virulence factors, CodY. These findings demonstrate that the hyphae-mediated enhanced pathogenesis of S. aureus may not only be due to physical interactions but can also be attributed to the differential regulation of specific virulence factors induced during polymicrobial growth. Further characterization of the intricate interaction between these pathogens at the molecular level is warranted, as it may aid in the design of novel therapeutic strategies aimed at combating fungal–bacterial polymicrobial infection.

Peters, Brian M; Jabra-Rizk, Mary Ann; Scheper, Mark A; Leid, Jeff G; Costerton, John William; Shirtliff, Mark E

2010-01-01

202

Dynamic modelling of cell death during biofilm development.  

PubMed

Biofilms are currently recognised as the predominant bacterial life-style and it has been suggested that biofilm development is influenced by a number of different processes such as adhesion, detachment, mass transport, quorum sensing, cell death and active dispersal. One of the least understood processes and its effects on biofilm development is cell death. However, experimental studies suggest that bacterial death is an important process during biofilm development and many studies show a relationship between cell death and dispersal in microbial biofilms. We present a model of the process of cell death during biofilm development, with a particular focus on the spatial localisation of cell death or cell damage. Three rules governing cell death or cell damage were evaluated which compared the effects of starvation, damage accumulation, and viability during biofilm development and were also used to design laboratory based experiments to test the model. Results from model simulations show that actively growing biofilms develop steep nutrient gradients within the interior of the biofilm that affect neighbouring microcolonies resulting in cell death and detachment. Two of the rules indicated that high substrate concentrations lead to accelerated cell death, in contrast to the third rule, based on the accumulation of damage, which predicted earlier cell death for biofilms grown with low substrate concentrations. Comparison of the modelling results with experimental results suggests that cell death is favoured under low nutrient conditions and that the accumulation of damage may be the main cause of cell death during biofilm development. PMID:22100489

Fagerlind, Magnus G; Webb, Jeremy S; Barraud, Nicolas; McDougald, Diane; Jansson, Andreas; Nilsson, Patric; Harlén, Mikael; Kjelleberg, Staffan; Rice, Scott A

2011-11-11

203

Community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach.  

PubMed

The microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (MF) and reverse osmosis (RO) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16S rDNA clone library and fluorescence in situ hybridization techniques. All methods showed that the alpha-Proteobacteria was the largest microbial fraction in the samples, followed by the gamma-Proteobacteria. This suggested that members of these two groups could be responsible for the biofouling on the membranes studied. Furthermore, the microbial community structures between the MF and RO samples were considerably different in composition of the most predominant 16S rDNA clones and bacterial isolates from the alpha-Proteobacteria and only shared two common groups ( Bradyrhizobium, Bosea) out of more than 17 different bacterial groups observed. The MF and RO samples further contained Planctomycetes and Fibroacter/ Acidobacteria as the second predominant bacterial clones, respectively, and differed in minor bacterial clones and isolates. The community structure differences were mainly attributed to differences in feed water, process configurations and operating environments, such as the pressure and hydrodynamic conditions present in the water purification systems. PMID:12682791

Chen, C-L; Liu, W-T; Chong, M-L; Wong, M-T; Ong, S L; Seah, H; Ng, W J

2003-04-08

204

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

PubMed Central

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 ?m) 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.

Kuhl, Michael; J?rgensen, Bo Barker

1992-01-01

205

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...

206

Systemic Diseases in Association with Microbial Species in Oral Biofilm from Elderly Requiring Care  

Microsoft Academic Search

Background: The oral cavity is a reservoir for colonization and infection of systemic organs by pathogenic bacteria. It is understood that aging, tooth eruption, hormonal changes, active disease, oral hygiene, and other factors have an influence on biofilm formation and bacterial accumulation in the oral cavity. Objective: To understand the influence of systemic health care on microfloral changes, we conducted

H. Senpuku; A. Sogame; E. Inoshita; Y. Tsuha; H. Miyazaki; N. Hanada

2003-01-01

207

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

SciTech Connect

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.

Holden, Patricia; Neu, Mary P.

2005-06-01

208

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

SciTech Connect

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.

Holden, Patricia

2006-06-01

209

Metagenomics of microbial life in extreme temperature environments.  

PubMed

Microbial life in extreme environments is attracting broad scientific interest. Knowledge about it helps in defining the boundaries for life to exist, and organisms living under extreme conditions are also interesting sources for enzymes with unusual and desirable properties. The tremendous progress in DNA sequencing technologies now makes it relatively easy to gain a representative overview of the composition of such communities, and many community studies have in the last decade applied metagenomics to characterize habitats extreme in, for example, temperature, salt and acidity. The future challenges in the field are likely to become more and more related to the conversion of the expected massive amounts of sequence information into an understanding of the corresponding biological community functions. PMID:23146837

Lewin, Anna; Wentzel, Alexander; Valla, Svein

2012-11-09

210

Methanogenic Activity and Structural Characteristics of the Microbial Biofilm On a Needle-Punched Polyester Support  

PubMed Central

In a downflow stationary fixed-film anaerobic reactor receiving a swine waste influent, few bacteria were observed to be tightly adherent to the surfaces of the needle-punched polyester support material. However, there was a morphologically complex, dense population of bacteria trapped within the matrix. Frequently large microcolonies of a uniform morphological type of bacteria were observed. These were particularly evident for methanosarcina-like bacteria which grew forming large aggregates of unseparated cells. Leafy deposits of electron-dense, calcium- and phosphorus-enriched material coated the polyester matrix and some cells. As the biofilm matured there was more extensive mineral deposition which completely entrapped cells. The entrapped cells appeared to autolyze, and many were partially degraded. Further impregnation of the matrix with minerals and apparent cell death may eventually have a deleterious effect on the methanogenic activity of the biofilm. Images

Harvey, Martin; Forsberg, Cecil W.; Beveridge, Terry J.; Pos, Jack; Ogilvie, John R.

1984-01-01

211

Microsensor measurements of sulfate reduction and sulfide oxidation in compact microbial communities of aerobic biofilms  

SciTech Connect

The microzonation of O{sub 2} respiration, H{sub 2}S oxidation, and SO{sub 4}{sup 2{minus}} reduction in aerobic trickling-filter biofilms was studied by measuring concentration profiles at high spatial resolution (25 to 100 {mu}m) with microsensors for O{sub 2}, S{sup 2{minus}}, 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 H{sub 2}S produced from sulfate reduction was reoxidized by O{sub 2} in a narrow reaction zone, and no H{sub 2}S escaped to the overlying water. Turnover times of H{sub 2}S and O{sub 2} in the reaction zone were only a few seconds owing to rapid bacterial H{sub 2}S oxidation. Anaerobic H{sub 2}S oxidation with NO{sub 3}{sup {minus}} could be induced by addition of nitrate to the medium. Total sulfate reduction rates increased when the availability of SO{sub 4}{sup 2{minus}} or organic substrate increased as a result of deepening of the sulfate reduction zone or an increase in the sulfate reduction intensity, respectively.

Kuehl, M.; Joergensen, B.B. (Univ. of Aarhus (Denmark))

1992-04-01

212

Long-term, on-line monitoring of microbial biofilms using a quartz crystal microbalance  

Microsoft Academic Search

A quartz crystal microbalance was used to nondestructively monitor the formation of Pseudomonas cepacia biofilms. These experiments involved long-term monitoring over days. Long-term monitoring initially encountered problems associated with baseline drift which were not observed in short-term electrochemical experiments or studies performed in vacuum or air. The extent of baseline drift produced by fluctuations in hydrostatic pressure and temperature was

David E. Nivens; James Q. Chambers; Tina R. Anderson; David C. White

1993-01-01

213

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

PubMed Central

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 1–4 days. At 4–7 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.

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

2011-01-01

214

Comparison of the microbial composition of voice prosthesis biofilms from patients requiring frequent versus infrequent replacement.  

PubMed

This study was performed to establish a possible difference in biofilm composition in patients who require frequent versus infrequent prosthesis replacement. Only Groningen button voice prostheses that were removed because of increased airflow resistance or leakage of food or liquids through the prosthesis were considered for this study. These prostheses were selected from a total of 692 failed voice prostheses over a 2-year evaluation period. The failed voice prostheses were subdivided into a short-lifetime group, corresponding to an implantation period of less than 4 months (20 voice prostheses), and an extended-lifetime group, corresponding to an implantation period of greater than 9 months (18 voice prostheses). The biofilm was removed from the valve sides of the prostheses. The bacterial strain Rothia dentocariosa and the yeast strains Candida albicans I and Candida tropicalis were the predominant strains isolated from the biofilms on the voice prostheses in the short-lifetime group, whereas in the extended-lifetime group, R dentocariosa was found with a fourfold lower isolation frequency and C albicans I was found with a twofold lower isolation frequency. Candida tropicalis was absent from the extended-lifetime group. PMID:11915880

Elving, G Jolanda; van der Mei, Henny C; Busscher, Henk J; van Weissenbruch, Ranny; Albers, Frans W J

2002-03-01

215

A life detection problem in a High Arctic microbial community  

NASA Astrophysics Data System (ADS)

Fluorescent labeling of bacterial cell walls, DNA, and metabolic processes demonstrates high (potentially single molecule) sensitivity, is non-invasive, and in some cases can differentiate strains and species. Robust microscopes such as the custom instruments presented here can provide good image quality in the field and are potentially suitable for flight. However, ambiguous or false-positive results with bacterial stains can occur and can create difficulties in interpretation even on Earth. We present a "real" life detection problem in a sample of biofilms taken from the Canadian High Arctic. The samples consisted of numerous small sulfur-oxidizing bacteria and larger structures resembling fungi or diatoms. The identity of these latter structures remained ambiguous until electron microscopy and X-ray spectroscopy were performed, indicating that they were unusual sulfur minerals probably precipitated by the bacterial communities. While such mineral structures may possibly serve as biosignatures after the cells have disappeared, it is important that they not be mistaken for cells themselves. It is also possible that unusual mineral structures will be performed under extraterrestrial conditions, so great care is needed to differentiate cell structures from minerals.

Rogers, J. D.; Perreault, N. N.; Niederberger, T. D.; Lichten, C.; Whyte, L. G.; Nadeau, J. L.

2010-03-01

216

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

Microsoft Academic Search

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

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

2008-01-01

217

Biofilm formation and microbial activity in a biofilter system in the presence of MTBE, ETBE and TAME.  

PubMed

Emerging water contaminants derived from unleaded gasoline such as methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME), are in need of effective bioremediation technologies for restoring water resources. In order to design the conditions of a future groundwater bioremediating biofilter, this work assesses the potential use of Acinetobacter calcoaceticus M10, Rhodococcus ruber E10 and Gordonia amicalis T3 for the removal of MTBE, ETBE and TAME in consortia or as individual strains. Biofilm formation on an inert polyethylene support material was assessed with scanning electron microscopy, and consortia were also analysed with fluorescent in situ hybridisation to examine the relation between the strains. A. calcoaceticus M10 was the best coloniser, followed by G. amicalis T3, however, biofilm formation of pair consortia favoured consortium M10-E10 both in formation and activity. However, degradation batch studies determined that neither consortium exhibited higher degradation than individual strain degradation. The physiological state of the three strains was also determined through flow cytometry using propidium iodide and 3'-dihexylocarbocyanine iodide thus gathering information on their viability and activity with the three oxygenates since previous microbial counts revealed slow growth. Strain E10 was observed to have the highest physiological activity in the presence of MTBE, and strain M10 activity with TAME was only maintained for 24 h, thus we believe that biotransformation of MTBE occurs within the active periods established by the cytometry analyses. Viable cell counts and oxygenate removal were determined in the presence of the metabolites tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA), resulting in TBA biotransformation by M10 and E10, and TAA by M10. Our results show that A. calcoaceticus M10 and the consortium M10-E10 could be adequate inocula in MTBE and TAME bioremediating technologies. PMID:21774959

Purswani, Jessica; Juárez, Belén; Rodelas, Belén; Gónzalez-López, Jesús; Pozo, Clementina

2011-07-19

218

In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs.  

PubMed

The spatial localization patterns of microorganisms in multispecies biofilms reflect numerous phenomena that influence sessile microbial life, such as substrate concentration gradients within the biofilm and biological interactions with other biofilm populations. Quantitative and population-specific in situ analyses of spatial patterns have a high potential to provide novel insights into the biology of biofilm organisms, including yet uncultured microbes, but such approaches have been developed and used in a few studies only. Here, we outline digital image analysis methods to quantify the coaggregation, mutual avoidance, or random distribution of microbial populations in biofilm and flocs. A protocol is provided for fluorescence in situ hybridization with rRNA-targeted probes, which preserves the three-dimensional biofilm architecture for confocal microscopy and image analysis, and the combined use of these approaches is demonstrated by spatial analyses of nitrifying bacteria in complex biofilm samples. PMID:21514465

Daims, Holger; Wagner, Michael

2011-01-01

219

Continuous power generation and microbial community structure of the anode biofilms in a three-stage microbial fuel cell system  

Microsoft Academic Search

A mediator-less three-stage two-chamber microbial fuel cell (MFC) system was developed and operated continuously for more\\u000a than 1.5 years to evaluate continuous power generation while treating artificial wastewater containing glucose (10 mM) concurrently.\\u000a A stable power density of 28 W\\/m3 was attained with an anode hydraulic retention time of 4.5 h and phosphate buffer as the cathode electrolyte. An overall\\u000a dissolved organic carbon removal

Kyungmi Chung; Satoshi Okabe

2009-01-01

220

Search for microbial life in the deep sub-seafloor: preliminary results from ODP Leg 201  

Microsoft Academic Search

Studies of microbial life in the deep marine subsurface can be used as a model system for the detection of possible microbial life on Mars. Focussed on the methodology, we tested four different approaches to evaluate the number, the identity and the function of the existing microorganisms in deep-sea sediments from the Peru Margin. Specifically, we applied the combined microscopic\\/molecular

Rolf Warthmann; Patrick Meister; Laurie Mauclaire; Antonis Chatzinotas; Lev Neretin; Stefano Bernasconi; Crisogono Vasconcelos; Judith A. McKenzie

2004-01-01

221

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...

222

Exploration of deep intraterrestrial microbial life: current perspectives.  

PubMed

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

Pedersen, K

2000-04-01

223

Fluids from aging ocean crust that support microbial life.  

PubMed

Little is known about the potential for life in the vast, low-temperature (<100 degrees C) reservoir of fluids within mid-ocean ridge flank and ocean basin crust. Recently, an overpressured 300-meter-deep borehole was fitted with an experimental seal (CORK) delivering crustal fluids to the sea floor for discrete and large-volume sampling and characterization. Results demonstrate that the 65 degrees C fluids from 3.5-million-year-old ocean crust support microbial growth. Ribosomal RNA gene sequence data indicate the presence of diverse Bacteria and Archaea, including gene clones of varying degrees of relatedness to known nitrate reducers (with ammonia production), thermophilic sulfate reducers, and thermophilic fermentative heterotrophs, all consistent with fluid chemistry. PMID:12511653

Cowen, James P; Giovannoni, Stephen J; Kenig, Fabien; Johnson, H Paul; Butterfield, David; Rappé, Michael S; Hutnak, Michael; Lam, Phyllis

2003-01-01

224

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

PubMed

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

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

2006-02-21

225

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

PubMed

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 2.0±0.29mg/m(2) (mean±se). Dry matter content was 16.0±13.1g/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

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

2011-03-21

226

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

Microsoft Academic Search

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

S. Das Gupta; J. Fang

2008-01-01

227

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...

228

Antifungal therapy with an emphasis on biofilms.  

PubMed

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

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

2013-09-04

229

Microbial Research: Progress and Potential. NSF Microbial Observatory/Life in Extreme Environments Principal Investigators' Workshop. Held in Arlington, Virginia on September 22-24, 2002.  

National Technical Information Service (NTIS)

The National Science Foundation (NSF) Microbial Observatory (MO) and Life in Extreme Environments (LExEn) programs have fostered significant advances in microbial ecosystems research in a wide variety of natural environments. The investigators funded by t...

M. A. Moran S. L. Cady

2002-01-01

230

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

PubMed

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 (170days) 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 (<1kDa) and lower percentage of large molecular size (>100kDa) 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

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

2013-09-02

231

Anti-Microbial, Anti-Biofilm Activities and Cell Selectivity of the NRC-16 Peptide Derived from Witch Flounder, Glyptocephalus cynoglossus  

PubMed Central

Previous studies had identified novel antimicrobial peptides derived from witch flounder. In this work, we extended the search for the activity of peptide that showed antibacterial activity on clinically isolated bacterial cells and bacterial biofilm. Pseudomonas aeruginosa was obtained from otitis media and cholelithiasis patients, while Staphylococcus aureus was isolated from otitis media patients. We found that synthetic peptide NRC-16 displays antimicrobial activity and is not sensitive to salt during its bactericidal activity. Interestingly, this peptide also led to significant inhibition of biofilm formation at a concentration of 4–16 ?M. NRC-16 peptide is able to block biofilm formation at concentrations just above its minimum inhibitory concentration while conventional antibiotics did not inhibit the biofilm formation except ciprofloxacin and piperacillin. It did not cause significant lysis of human RBC, and is not cytotoxic to HaCaT cells and RAW264.7 cells, thereby indicating its selective antimicrobial activity. In addition, the peptide’s binding and permeation activities were assessed by tryptophan fluorescence, calcein leakage and circular dichroism using model mammalian membranes composed of phosphatidylcholine (PC), PC/cholesterol (CH) and PC/sphingomyelin (SM). These experiments confirmed that NRC-16 does not interact with any of the liposomes but the control peptide melittin did. Taken together, we found that NRC-16 has potent antimicrobial and antibiofilm activities with less cytotoxicity, and thus can be considered for treatment of microbial infection in the future.

Gopal, Ramamourthy; Lee, Jun Ho; Kim, Young Gwon; Kim, Myeong-Sun; Seo, Chang Ho; Park, Yoonkyung

2013-01-01

232

Biofilm Susceptibility to Antimicrobials  

Microsoft Academic Search

Microbial biofilms, where organisms are intimately associated with each other and a solid substratum through binding and inclusion within an exopolymer matrix, are widely distributed in nature and disease. In the mouth, multispecies biofilms are associated not only with dental plaque and tooth decay but also with soft tissues of the buccal cavity and with most forms of periodontal disease.

P. Gilbert; J. Das; I. Foley

1997-01-01

233

Candida biofilm resistance  

Microsoft Academic Search

Device-related infections in most nosocomial diseases can be traced to the formation of biofilms (microbial communities encased within polysaccharide-rich extracellular matrix) by pathogens on surfaces of these devices. Candida species are the most common fungi isolated from these infections, and biofilms formed by these fungal organisms are associated with drastically enhanced resistance against most antimicrobial agents. This enhanced resistance contributes

Pranab K. Mukherjee; Jyotsna Chandra

2004-01-01

234

Molecular Analysis of Shower Curtain Biofilm Microbes  

Microsoft Academic Search

Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as \\

Scott T. Kelley; Ulrike Theisen; Largus T. Angenent; A. St. Amand; N. R. Pace

2004-01-01

235

3.45 b.y.-old microbial associations in cherts from the Pilbara: lessons for potential Martian life  

NASA Astrophysics Data System (ADS)

3.45 b.y.-old cherts from the Kitty's Gap locality in the Pilbara contain superbly preserved microbial biofilms that formed on an early Earth characterised by extreme conditions. They therefore represent good analogues for potential early Martian life. Volcaniclastic sediments influenced by hydrothermal activity were deposited in very shallow water to exposed conditions, as evidenced by interstratified cross-bedded and evaporite units. Two microbial layers with different characteristics, occurring within 2 cm of each other, have been closely studied in the field, by optical microscopy, and by high resolution SEM (+ light element EDS) of carefully etched, cut surfaces. Both layers can be traced laterally for at least a couple of meters before being broken up by a chert vein. The lower microbialite is a 2--3 mm thick stromatolite-thrombolite association. The stromatolites consist of tiny columns, 250 ?m wide and about 2 mm high, whereas the thrombolitic zones present a simple, clotted texture. They were formed by microbial colonies consisting of consortia of mostly coccoidal bacteria (two species, one <0.5 ?m and one ˜1 ?m in diameter). Most of the organisms present a turgid condition and large numbers of them exhibit cell division (fission and budding). Filamentous bacteria occur but are rare. The deflated and lysed filaments are small, 4--5 ?m and about 100 nm in width. Small amounts of EPS are associated with the colonies. The second microbialite is a fine microbial mat (tabular stromatolite) that occurs at the surface of an evaporite horizon 2 cm above the first microbialite. The 0.5 cm thick evaporite horizon consists of ghosts of carbonate and possibly halite crystals. It is coated by a <50 ?m thick microbial mat, formed by consortia of 0.5 ?m coccoidal bacteria and filaments, 0.2--0.4 ?m wide and 10--20 ?m long. Some EPS is associated with the bacteria and the sedimentary particle surfaces are coated with a nm-thick polymer layer. The filaments are characterised by a striated surface. Both coccoids and filaments exhibit some deflation due to lysis before fossilisation. The organisms in both layers have been silicified but still contain significant amounts of carbon. Silicification of these deposits appeared to be continuous, since there was also secondary replacement by silica of the evaporites and silica cementation of the volcaniclastic and evaporite particles. Shallow water to evaporitic environments influenced by hydrothermal activity would have been common on Mars during the Noachian period and possibly also later. If life ever arose on Mars, it could have left similar, macroscopic to microscopic traces that could be investigated both in situ and in returned samples.

Westall, F.

2003-04-01

236

Multilocus Sequence Typing Breathes Life into a Microbial Metagenome  

PubMed Central

Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity. However, the subsequent matching of these hypothetical metagenomes to cultivable microorganisms is a limitation of such cultivation-independent methods of population analysis. Using a nucleotide sequence-based genetic typing method, multilocus sequence typing, we were able for the first time to match clonal cultivable isolates to a published and controversial bacterial metagenome, Burkholderia SAR-1, which derived from analysis of the Sargasso Sea. The matching cultivable isolates were all associated with infection and geographically widely distributed; taxonomic analysis demonstrated they were members of Burkholderia cepacia complex Group K. Comparison of the Burkholderia SAR-1 metagenome to closely related B. cepacia complex genomes indicated that it was greater than 98% intact in terms of conserved genes, and it also shared complete sequence identity with the cultivable isolates at random loci beyond the genes sampled by the multilocus sequence typing. Two features of the extant cultivable clones support the argument that the Burkholderia SAR-1 sequence may have been a contaminant in the original metagenomic survey: (i) their growth in conditions reflective of sea water was poor, suggesting the ocean was not their preferred habitat, and (ii) several of the matching isolates were epidemiologically linked to outbreaks of infection that resulted from contaminated medical devices or products, indicating an adaptive fitness of this bacterial strain towards contamination-associated environments. The ability to match identical cultivable strains of bacteria to a hypothetical metagenome is a unique feature of nucleotide sequence-based microbial typing methods; such matching would not have been possible with more traditional methods of genetic typing, such as those based on pattern matching of genomic restriction fragments or amplified DNA fragments. Overall, we have taken the first steps in moving the status of the Burkholderia SAR-1 metagenome from a hypothetical entity towards the basis for life of cultivable strains that may now be analysed in conjunction with the assembled metagenomic sequence data by the wider scientific community.

Mahenthiralingam, Eshwar; Baldwin, Adam; Drevinek, Pavel; Vanlaere, Elke; Vandamme, Peter; LiPuma, John J.; Dowson, Chris G.

2006-01-01

237

Kinetic analysis of microbial sulfate reduction by desulfovibrio desulfuricans in an anaerobic upflow porous media biofilm reactor.  

PubMed

An anaerobic upflow porous media biofilm reactor was designed to study the kinetics and stoichiometry of hydrogen sulfide production by the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans (ATCC 5575) as the first step for the modeling and control of formation souring (H(2)S) in oil field porous media. The reactor was a packed bed (50 x 5.5 cm) tubular reactor. Sea sand (140 to 375 mum) was used as the porous media. The initial indication of souring was the appearance of well-separated black spots (precipitates of iron sulfide) in the sand bed. The blackened zones expanded radially and upward through the column. New spots also appeared and expanded into the cone shapes. Lactate (substrate) was depleted and hydrogen sulfide appeared in the effluent.Analysis of the pseudo-steady state column shows that there were concentration gradients for lactate and hydrogen sulfide along the column. The results indicate that most of the lactate was consumed at the front part of the column. Measurements of SRB biomass on the solid phase (sand) and in the liquid phase indicate that the maximum concentration of SRB biomass resided at the front part of the column while the maximum in the liquid phase occurred further downstream. The stoichiometry regarding lactate consumption and hydrogen sulfide production observed in the porous media reactor was different from that in a chemostat. After analyzing the radial dispersion coefficient for the SRB in porous media and kinetics of microbial growth, it was deduced that transport phenomena dominate the souring process in our porous media reactor system. (c) 1994 John Wiley & Sons, Inc. PMID:18615689

Chen, C I; Mueller, R F; Griebe, T

1994-02-20

238

Candida biofilm resistance.  

PubMed

Device-related infections in most nosocomial diseases can be traced to the formation of biofilms (microbial communities encased within polysaccharide-rich extracellular matrix) by pathogens on surfaces of these devices. Candida species are the most common fungi isolated from these infections, and biofilms formed by these fungal organisms are associated with drastically enhanced resistance against most antimicrobial agents. This enhanced resistance contributes to the persistence of this fungus despite antifungal therapy. Candida biofilms exhibit enhanced resistance against most antifungal agents, except echinocandins and lipid formulations of AmB. The expression of drug efflux pumps during the early phase of biofilm formation and alterations in membrane sterol composition contribute to resistance of these biofilms against azoles. Metabolic dormancy and ECM do not appear to contribute to resistance, although in a mixed-species biofilm, ECM does retard the diffusion of drugs across biofilm. These multifactorial mechanisms of resistance in fungal biofilms constitute a broad-spectrum defense that is effective against many types of antifungal agents, and represent a common theme present across microbial biofilms. PMID:15533767

Mukherjee, Pranab K; Chandra, Jyotsna

239

The Geochemistry of Hot Spring Biofilms  

NASA Astrophysics Data System (ADS)

The geochemical composition of hot spring biofilms can reveal how the organisms in the biofilm interact with their environment, and how the products of that interaction can be recorded in hydrothermal mineral deposits. To provide a geochemical framework for quantifying the direct interaction of biofilms with their environments, we collected biofilm samples and their associated waters from hot springs located in Yellowstone National Park. The springs varied in pH (2 to 9) and temperature (<45 to >90 C), and were separated by distances that ranged from one to thousands of meters. Biofilm types include filaments, mats, and stromatotherms, and include microbial communities from the strictly chemolithotrophic to those dominated by phototrophs. Elemental analysis reveals that biofilms are made up of from 1 to 15 dry wt% carbon, and <1 to 5% nitrogen, indicating that biological materials constitute a small fraction of the total dry biofilm mass. Major element analysis via electron microprobe and complimentary x-ray fluorescence show that hydrothermal biofilms, regardless of location, water composition, and temperature, are dominantly composed of silica. Analyses reported as oxide sums show that SiO2 constitutes ~60 to >85 dry wt%, with the rest made up of Al2O3 (2 to 25%), and FeO (<1 to >20%), as well as minor alkali and alkali earth oxides (<3%). Trace element concentrations (in mol/kg dry weight, by inductively-coupled plasma mass spectrometry) can range from over two orders of magnitude less than the water (mol/kg) in which the biofilm is living to over two orders of magnitude greater. Hydrothermal fluid trace element concentrations can also vary over several orders of magnitude. As a consequence, sequestration factors, the ratio of concentration of an element in dry biomass (mol/kg) divided by the concentration in the associated water (mol/kg), permit comparison of biofilms from varying hydrothermal environments. Some elements behave similarly in all biofilms, with sequestration factors of greater than 10E2 (Ti), to approximately 10E0 (Ga, Cs), to less than 10E-2 (Li, B, W, As). Other elements show sequestration factors that are highly variable (Be, Mn, Cr, Mo). These differences may characterize specific community types, which would be correlated to modern hydrothermal deposits that harbored biofilms. Ultimately, these variations can provide novel biomarkers for these systems that can be used to look for evidence of life in the rock record.

Havig, J. R.; Shock, E. L.; Prapaipong, P.; Michaud, A.; Moore, G.

2006-12-01

240

Restricting Microbial Exposure in Early Life Negates the Immune Benefits Associated with Gut Colonization in Environments of High Microbial Diversity  

PubMed Central

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

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

2011-01-01

241

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

SciTech Connect

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+.

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

2007-04-19

242

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

PubMed Central

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.

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

2013-01-01

243

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

NASA Astrophysics Data System (ADS)

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.

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

2006-12-01

244

Population dynamics and spatial distribution of microbial species in multispecies biofilms under the action of direct electric current  

Microsoft Academic Search

The metabolism, population dynamics and spatial distribution of nitrifying bacteria and heterotrophs in biofilms under the\\u000a action of direct electric current were investigated by using the micro-slicing technique. The nitrification rate of nitrifying\\u000a bacteria was severely inhibited by a current over 10 Am?2 at lower C\\/N ratios. Compared to heterotrophs, the nitrifying bacteria in the surface biofilms were severely inhibited,

Hongbin Cao; Xingang Li; Jinchuan Wu; Fangli Zhong; Yi Zhang

2003-01-01

245

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

PubMed Central

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.

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

2009-01-01

246

Storage characteristics and relationships between microbial growth parameters and shelf life of MAP sliced onions  

Microsoft Academic Search

Microbial proliferation and sensory quality aspects of sliced onions were tested at different temperatures (?2, 4 and 10°C) and atmospheric conditions (with or without 40% CO2+59% N2+1% O2). The relationships among microorganism growth parameters (the initial cell number (N0), the maximum cell number (Nmax), the maximum specific growth rate (?max) and lag-phase (?)) and the microbial or sensory shelf life

Fang Liu; Yunfei Li

2006-01-01

247

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

NASA Astrophysics Data System (ADS)

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.

Prieur, Daniel

248

Microbial life in a fjord: metagenomic analysis of a microbial mat in chilean patagonia.  

PubMed

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

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

2013-08-28

249

Physical Heterogeneity Increases Biofilm Resource Use and Its Molecular Diversity in Stream Mesocosms  

Microsoft Academic Search

BackgroundEvidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood.Methodology\\/Principal FindingsUsing six 40-m-long

Gabriel Singer; Katharina Besemer; Philippe Schmitt-Kopplin; Iris Hödl; Tom J. Battin

2010-01-01

250

Chemically Specific Cellular Imaging of Biofilm Formation  

Microsoft Academic Search

This document and the accompanying manuscripts summarize the technical accomplishments for our one-year LDRD-ER effort. Biofilm forming microbes have existed on this planet for billions of years and make up 60% of the biological mass on earth. Such microbes exhibit unique biochemical pathways during biofilm formation and play important roles in human health and the environment. Microbial biofilms have been

J L Herberg; C Schaldach; J Horn; E Gjersing; R Maxwell

2006-01-01

251

Understanding biofilm resistance to antibacterial agents  

Microsoft Academic Search

According to a public announcement by the US National Institutes of Health, “Biofilms are medically important, accounting for over 80% of microbial infections in the body”. Yet bacterial biofilms remain poorly understood and strategies for their control remain underdeveloped. Standard antimicrobial treatments typically fail to eradicate biofilms, which can result in chronic infection and the need for surgical removal of

David Davies

2003-01-01

252

The possibility of alternative microbial life on Earth  

Microsoft Academic Search

Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary

Carol E. Cleland; Shelley D. Copley

2006-01-01

253

Subgingival biofilm structure.  

PubMed

Periodontitis is an inflammatory disease of the oral cavity initiated by a microbial biofilm (or 'dental plaque'). Subgingival biofilms in periodontal pockets are not easily analyzed without the loss of structural integrity. These subgingival plaques are structured communities of microorganisms with great phylogenetic diversity embedded in a self-produced extracellular polymeric matrix. For almost three decades, knowledge of the structure of plaque located below the gingival margin has been limited to landmark studies from the 1970s that were unaware of the breadth of microbial diversity we appreciate now. Only recently has technical progress - combining histology, confocal scanning fluorescent microscopy and fluorescent in situ hybridization to localize the most abundant species from different phyla and species associated with periodontitis - provided new insights into the architecture of subgingival biofilms. This review focuses on the structure and composition of subgingival biofilms and discusses current knowledge on the nature of the extracellular matrix. We describe further structural aspects of 'subgingival' biofilms produced in vitro that are gaining considerable interest as we search for models to investigate biofilm development, resistance to antibiotics, extracellular polymeric matrix composition and function, and reciprocal host-cell-to-biofilm interactions. PMID:22142954

Zijnge, Vincent; Ammann, Thomas; Thurnheer, Thomas; Gmür, Rudolf

2011-11-11

254

Biochemical markers for measurement of predation effects on the biomass, community structure, nutritional status, and metabolic activity of microbial biofilms  

Microsoft Academic Search

Chemical measures for the biomass, community structure, nutritional status, and metabolic activities of mi- crobes in biofilms attached to detrital or sediment surfaces based on analysis of components of cells and ex- tracellular polymers represent a quantitative and sensitive method for the analysis of predation. These methods require neither the quantitative removal of the organisms from the surfaces nor the

David C. White; Robert H. Findlay

1988-01-01

255

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

PubMed Central

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.

Baquero, Fernando; Moya, Andres

2012-01-01

256

In situ biofilm coupon device  

DOEpatents

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.

Peyton, Brent M. (Kennewick, WA); Truex, Michael J. (Richland, WA)

1997-01-01

257

In situ biofilm coupon device  

DOEpatents

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.

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

1997-06-24

258

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

NASA Astrophysics Data System (ADS)

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.

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

259

Microbial fuel cells applied to the metabolically based detection of extraterrestrial life.  

PubMed

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. PMID:21162676

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

2010-12-01

260

Microbial life in martian ice: A biotic origin of methane on Mars?  

Microsoft Academic Search

Despite the fact that microbial cells are unlikely to be found in the Martian soil in the near future, this paper is written on the assumption that some of the seasonally varying concentration of Martian methane is due to ongoing methanogenesis. It is first pointed out that life might have arisen on Mars first and been transported to Earth later.

P. Buford Price

2010-01-01

261

Trace gases in the atmosphere of Mars: an indicator of microbial life  

Microsoft Academic Search

The detection of certain trace gases in the atmosphere of Mars would indicate the presence of microbial life on the surface of Mars. Candidate biogenic gases include methane (CH4), ammonia (NH3), nitrous oxide (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

J. S. Levine; C. P. Rinsland; W. L. Chameides; P. J. Boston; W. R. Cofer III; P. Brimblecombe

1989-01-01

262

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

NASA Astrophysics Data System (ADS)

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.

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

2010-12-01

263

Trace gases in the atmosphere of Mars - an indicator of microbial life  

Microsoft Academic Search

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.

Joel S. Levine; Curtis P. Rinsland; Penelope J. Boston; Wesley R. Cofer III; William L. Chameides

1989-01-01

264

ENCAPSULATION OF MICROBIAL CONTROL AGENTS FOR IMPROVING RESIDUAL ACTIVITIY AND SHELF LIFE  

Technology Transfer Automated Retrieval System (TEKTRAN)

The negative effects of chemicals to control insect pests has led to research to improve the residual activity and shelf life of microbial-based insect control agents through formulation development. Encapsulation of the active microbes in edible ingredients provides environmentally safe and effect...

265

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

PubMed Central

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.

Deatherage, Brooke L.

2012-01-01

266

Discovering Biofilms: Inquiry-Based Activities for the Classroom  

ERIC Educational Resources Information Center

|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…

Redelman, Carly V.; Marrs, Kathleen; Anderson, Gregory G.

2012-01-01

267

Selenium bioaccumulation and maternal transfer in the mayfly Centroptilum triangulifer in a life-cycle, periphyton-biofilm trophic assay.  

PubMed

Selenium contamination in aquatic ecosystems provides management challenges because bioaccumulation in animals is largely a function of dietary exposure, whereas regulatory entities have traditionally focused on direct water to organism interactions. Selenium is known to be readily absorbed by primary producers and can potentially biomagnify in food webs and elicit adverse effects in higher trophic levels. However, selenium bioaccumulation in the invertebrate prey of many predatory animals is poorly understood. Here, we used 75Se (as selenite) as a radiotracer to characterize Se bioaccumulation into natural periphyton biofilms and subsequent dietary and maternal transfer in the mayfly, Centroptilum triangulifer, in a life-cycle assay. On average periphyton biofilms bioconcentrated selenium 1113 (+/-430)-fold following 7-9 days of exposure to a range of environmentally relevant dissolved concentrations (2.4-13.9 microg L(-1)). Mayflies grown to adulthood on these diets further biomagnified Se with trophic transfer factors averaging 22 (+/-0.4)-fold in postpartum maternal tissues. Adults then transferred 46.5 (+/-8.8)% of their body burdens to eggs with an observed reduction in fecundity for mayflies fed on diets greater than approximately 11 microg g(-1). These results suggest that at environmentally feasible dietary Se concentrations insects are potentially affected by Se exposure, and that the current presumption that insects are simply conduits of Se to higher trophic levels is inaccurate. PMID:19921919

Conley, Justin M; Funk, David H; Buchwalter, David B

2009-10-15

268

Biochemical markers for measurement of predation effects on the biomass, community structure, nutritional status, and metabolic activity of microbial biofilms  

Microsoft Academic Search

Chemical measures for the biomass, community structure, nutritional status, and metabolic activities of microbes in biofilms\\u000a attached to detrital or sediment surfaces based on analysis of components of cells and extracellular polymers represent a\\u000a quantitative and sensitive method for the analysis of predation. These methods require neither the quantitative removal of\\u000a the organisms from the surfaces nor the efficient culture

David C. White; Robert H. Findlay

1988-01-01

269

Microbial life in martian ice: A biotic origin of methane on Mars?  

NASA Astrophysics Data System (ADS)

Despite the fact that microbial cells are unlikely to be found in the Martian soil in the near future, this paper is written on the assumption that some of the seasonally varying concentration of Martian methane is due to ongoing methanogenesis. It is first pointed out that life might have arisen on Mars first and been transported to Earth later. A case is made that an icy origin of life is more likely than a hot origin, especially if biomolecules take advantage of the high encounter rates and stability against hydrolysis, and that microorganisms feed on the ions that comprise eutectic solutions in ice. Although certain difficulties are avoided if RNA and DNA grow while adsorbed on clay grains, double strand-breaks of microbial DNA due to alpha radioactivity are a far greater threat to microbial survival on clay or other rock types than in ice. Developing a relation between the rate of microbial metabolism in ice and the experimentally determined rate of production of trapped gases of microbial origin, one can estimate the concentration of methanogens that could account for the methane production rate as a function of temperature of their habitat. The result, of order 1 cell cm -3 in the Martian subsurface, seems an attainable goal provided samples are taken from at least 1 or 2 m below the hostile surface of Mars. Instruments on NASA's 2011 Mars Science Lab will measure stable isotopes for methane, water, and carbon dioxide, which on Earth served to distinguish abiotic, thermogenic, and microbial origins. Future measurements of chirality of biomolecules might also provide evidence for Martian life.

Buford Price, P.

2010-08-01

270

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

PubMed

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

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

2009-02-12

271

Differentiation of microbial species and strains in coculture biofilms by multivariate analysis of laser desorption postionization mass spectra.  

PubMed

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 at 7.87 eV photon energies compared to 10.5 eV radiation. This is consistent with the expectation that the 7.87 eV photoionization 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. PMID:24067765

Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C; Carlson, Ross P; Ahmed, Musahid; Hanley, Luke

2013-10-15

272

Unraveling assembly of stream biofilm communities  

PubMed Central

Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.

Besemer, Katharina; Peter, Hannes; Logue, Jurg B; Langenheder, Silke; Lindstrom, Eva S; Tranvik, Lars J; Battin, Tom J

2012-01-01

273

Microbial Life and Temperature: A Semi Empirical Approach  

NASA Astrophysics Data System (ADS)

Many groups have examined the effect of temperature on the survival of microorganisms, resulting in the development of several models. Some of these models are based on the Arrhenius equation and the others are based on multidimensional response surface equations. We argue that the former are inadequate and the latter lack biological meaning. We show that an equation (the GLE equation) deduced from the Theory of Rate Processes is more accurate than the Arrhenius equation. The excellent standard deviation values of the apparent free energy of activation obtained with the GLE equation for microbial growth, embryogenic and other processes show that this equation is more suitable than the Arrhenius equation. The GLE equation shows how temperature affects survival. Thus, organisms survive longer at low temperatures than at normal temperatures. The recent discovery of microorganisms in Siberian permafrost samples that are several million years old, in deep oil fields, mines and other extreme habitats appears to be consistent with the GLE equation. Another example, the enhanced resistance of spores at extreme temperatures can be easily explained by their high apparent free energy of activation We also examined the implications of the GLE equation on food sterilization practices and on exobiology.

Garzón, León

2004-08-01

274

Abundance and diversity of microbial life in ocean crust.  

PubMed

Oceanic lithosphere exposed at the sea floor undergoes seawater-rock alteration reactions involving the oxidation and hydration of glassy basalt. Basalt alteration reactions are theoretically capable of supplying sufficient energy for chemolithoautotrophic growth. Such reactions have been shown to generate microbial biomass in the laboratory, but field-based support for the existence of microbes that are supported by basalt alteration is lacking. Here, using quantitative polymerase chain reaction, in situ hybridization and microscopy, we demonstrate that prokaryotic cell abundances on seafloor-exposed basalts are 3-4 orders of magnitude greater than in overlying deep sea water. Phylogenetic analyses of basaltic lavas from the East Pacific Rise (9 degrees N) and around Hawaii reveal that the basalt-hosted biosphere harbours high bacterial community richness and that community membership is shared between these sites. We hypothesize that alteration reactions fuel chemolithoautotrophic microorganisms, which constitute a trophic base of the basalt habitat, with important implications for deep-sea carbon cycling and chemical exchange between basalt and sea water. PMID:18509444

Santelli, Cara M; Orcutt, Beth N; Banning, Erin; Bach, Wolfgang; Moyer, Craig L; Sogin, Mitchell L; Staudigel, Hubert; Edwards, Katrina J

2008-05-29

275

Microbial life at high salt concentrations: phylogenetic and metabolic diversity  

Microsoft Academic Search

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 100–150 g\\/l salt for growth and structural stability. Also within the order Methanococci we

Aharon Oren

2008-01-01

276

Non-destructive monitoring of microbial biofilms at solid-liquid interfaces using on-line devices.  

National Technical Information Service (NTIS)

Corrosion, biofouling, and related problems have been an impetus for investigating interactions between microorganisms and solid surfaces. In recent years, a number of studies have been performed to assess the damages caused by microbial influenced corros...

D. E. Nivens J. Q. Chambers D. C. White

1990-01-01

277

Engineering biofilm formation and dispersal  

PubMed Central

Anywhere water is in the liquid state, bacteria will exist as biofilms, which are complex communities of cells cemented together. Although frequently associated with disease and biofouling, biofilms are also important for engineering applications, such as bioremediation, biocatalysis and microbial fuel cells. Here we review approaches to alter genetic circuits and cell signaling toward controlling biofilm formation, and emphasize utilizing these tools for engineering applications. Based on a better understanding of the genetic basis of biofilm formation, we find that biofilms may be controlled by manipulating extracellular signals and that they may be dispersed using conserved intracellular signals and regulators. Biofilms could also be formed at specific locations where they might be engineered to make chemicals or treat human disease.

Wood, Thomas K.; Hong, Seok Hoon; Ma, Qun

2011-01-01

278

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...

279

Improving the Microbial Quality and Shelf Life of Chicken Carcasses by Trisodium Phosphate and Lactic Acid Dipping  

Microsoft Academic Search

This study determined the influence of Trisodium Phosphate (TSP) and Lactic Acid (LA) dipping on the microbial load and shelf life of broiler chicken carcasses during refrigerated storage for 8 days at 2±1 C. The results indicated that both TSP (12%) and LA (2%) dipping significantly reduced the initial o microbial load of Aerobic Plate Counts (APC), Psychrotrophic Counts (PTC),

Alaa Eldin Mohammed A; Khalid Ibrahim Sallam

2009-01-01

280

A novel automated waterline cleaning system that facilitates effective and consistent control of microbial biofilm contamination of dental chair unit waterlines: a one-year study.  

PubMed

Microbial contamination of dental chair unit (DCU) output water caused by biofilm growth in dental unit waterlines (DUWs) is a universal problem and a potentially significant source of cross-infection. The microbial quality of output water from a Planmeca Compact i DCU equipped with the novel Water Management System (WMS), an integrated and automated DUW cleaning system, was investigated over a 12-month period with the hydrogen peroxide- and silver ion-containing disinfectants Planosil and Planosil Forte. Four weeks after connection to the potable-water quality mains supply the density of aerobic heterotrophic bacteria, rose from the low levels consistently found in the supply water throughout this study (mean average 77 cfu/mL) to 15,400 cfu/mL. Disinfection of DUWs once weekly with Planosil for 10 weeks resulted in a dramatic reduction in bacterial density immediately following disinfection (mean average 26 cfu/mL). Bacterial density rose steadily between disinfections and by 7 days post-disinfection, water quality failed (mean average 384 cfu/mL) the American Dental Association DCU water quality standard of biofilm, but deterioration of water quality following disinfection was associated with its regrowth. The most common bacterial species cultured from the mains water and the DCU output water were Microcococcus luteus and Sphingomonas spp., respectively, the latter of which are known opportunistic pathogens. The findings of this study show that the Planmeca Compact i DCU equipped with the easy to use and automated WMS, that requires minimal effort on the part of the operator, consistently provides output water that passes the ADA quality standard of

O'Donnell, M J; Shore, A C; Coleman, D C

2006-01-24

281

Effects of UltraHigh Pressure Homogenization on Microbial and Physicochemical Shelf Life of Milk  

Microsoft Academic Search

The effect of ultra-high pressure homogenization (UHPH) on microbial and physicochemical shelf life of milk during storage at 4°C was studied and compared with a conventional heat preservation technology used in industry. Milk was standardized at 3.5% fat and was processed using a Stansted high-pressure homog- enizer. High-pressure treatments applied were 100, 200, and 300 MPa (single stage) with a

J. Pereda; V. Ferragut; J. M. Quevedo; B. Guamis; A. J. Trujillo

2007-01-01

282

Towards Determining the Upper Temperature Limits to Life on Earth: An In-situ Sulfide-Microbial Incubator  

NASA Astrophysics Data System (ADS)

Determining the maximum conditions under which life thrives, survives, and expires is critical to understanding how and where life might have evolved on our planet and for investigation of life in extraterrestrial environments. Submarine black smoker systems are optimal sites to study such questions because thermal gradients are extreme and accessible within the chimney walls under high-pressure conditions. Intact cells containing DNA and ribosomes have been observed even within the most extreme environments of sulfide structure walls bounded by 300\\deg C fluids. Membrane lipids from archaea have been detected in sulfide flanges and chimneys where temperatures are believed to be 200-300\\deg C. However, a balanced inquiry into the limits of life must focus on characterization of the actual conditions in a given system that favor reactions necessary to initiate and/or sustain life. At present, in-situ instrumentation of sulfide deposits is the only effective way to gain direct access to these natural high-temperature environments for documentation and experimentation. With this goal in mind, three prototype microbial incubators were developed with funding from the NSF, University of Washington, and the W.M. Keck Foundation. The incubators were deployed in 2003 in the walls of active black smoker chimneys in the Mothra Hydrothermal Field, Endeavour Segment of the Juan de Fuca Ridge. All instruments were successfully recovered in 2004, and one was redeployed for a short time-series experiment. Each 53-cm-long titanium assembly houses 27 temperature sensors that record temperatures from 0 to 500\\deg C within three discrete incubation chambers. Data are logged in a separate housing and inductively coupled links provide access to the data loggers without removal of the instruments. During the initial deployment, data were collected from 189 to 245 days, with up to ˜478° K temperature measurements completed for an individual instrument. Temperatures within the chimney walls ranged from near ambient conditions to ˜280° C. Distinct thermal gradients were delineated extremely well in each of the three discrete environmental chambers in all instruments. In one instrument numerous perturbations were recorded simultaneously on all 27 probes showing temperature increases of up to ˜30° C. Smaller-scale fluctuations resulting from tidal perturbations were ubiquitous in all instruments. Tidal pumping that mixes oxygenated seawater and reduced, volatile-rich hydrothermal fluids may be critical for development of dense and diverse microbial communities within the outer chimney walls. Preliminary examination of some sterile mineral surfaces emplaced within the chambers shows extensive biofilm development. Culturing experiments are ongoing and DNA has been successfully extracted from many of the chambers for genetic characterization. This experiment is a component of the W.M. Keck Foundation-funded proto-NEPTUNE Observatory and Ridge R2K program at Endeavour.

Kelley, D.; Baross, J.; Delaney, J.; Girguis, P.; Schrenk, M.

2004-12-01

283

Biofilm roughness determines Cryptosporidium parvum retention in environmental biofilms.  

PubMed

The genus Cryptosporidium is a group of waterborne protozoan parasites that have been implicated in significant outbreaks of gastrointestinal infections throughout the world. Biofilms trap these pathogens and can contaminate water supplies through subsequent release. Biofilm microbial assemblages were collected seasonally from three streams in eastern Pennsylvania and used to grow biofilms in laboratory microcosms. Daily oocyst counts in the influx and efflux flow allowed the calculation of daily oocyst retention in the biofilm. Following the removal of oocysts from the influx water, oocyst attachment to the biofilm declined to an equilibrium state within 5 days that was sustained for at least 25 days. Varying the oocyst loading rate for the system showed that biofilm retention could be saturated, suggesting that discrete binding sites determined the maximum number of oocysts retained. Oocyst retention varied seasonally but was consistent across all three sites; however, seasonal oocyst retention was not consistent across years at the same site. No correlation between oocyst attachment and any measured water quality parameter was found. However, oocyst retention was strongly correlated with biofilm surface roughness and roughness varied among seasons and across years. We hypothesize that biofilm roughness and oocyst retention are dependent on environmentally driven changes in the biofilm community rather than directly on water quality conditions. It is important to understand oocyst transport dynamics to reduce risks of human infection. Better understanding of factors controlling biofilm retention of oocysts should improve our understanding of oocyst transport at different scales. PMID:22492449

DiCesare, E A Wolyniak; Hargreaves, B R; Jellison, K L

2012-04-06

284

Chemically Specific Cellular Imaging of Biofilm Formation  

SciTech Connect

This document and the accompanying manuscripts summarize the technical accomplishments for our one-year LDRD-ER effort. Biofilm forming microbes have existed on this planet for billions of years and make up 60% of the biological mass on earth. Such microbes exhibit unique biochemical pathways during biofilm formation and play important roles in human health and the environment. Microbial biofilms have been directly implicated in, for example, product contamination, energy losses, and medical infection that cost the loss of human lives and billions of dollars. In no small part due to the lack of detailed understanding, biofilms unfortunately are resistant to control, inhibition, and destruction, either through treatment with antimicrobials or immunological defense mechanisms of the body. Current biofilm research has concentrated on the study of biofilms in the bulk. This is primarily due to the lack of analytical and physical tools to study biofilms non-destructively, in three dimensions, and on the micron or sub-micron scale. This has hindered the development of a clear understanding of either the early stage mechanisms of biofilm growth or the interactions of biofilms with their environment. Enzymatic studies have deduced a biochemical reaction that results in the oxidation of reduced sulfur species with the concomitant reduction of nitrate, a common groundwater pollutant, to dinitrogen gas by the bacterium, Thiobacillus denitrificans (TD). Because of its unique involvement in biologically relevant environmental pathways, TD is scheduled for genome sequencing in the near future by the DOE's Joint Genome Institute and is of interest to DOE's Genomes to Life Program. As our ecosystem is exposed to more and more nitrate contamination large scale livestock and agricultural practices, a further understanding of biofilm formation by organisms that could alleviate these problems is necessary in order to protect out biosphere. However, in order to study this complicated organism, we needed to first turn our attention to a well understood organism. Pseudomonas aeruginosa (PA) is a well-studied organism and will be used to compare our results with others. Then, we will turn our attention to TD. It is expected that the research performed will provide key data to validate biochemical studies of TD and result in high profile publications in leading journals. For this project, our ultimate goal was to combine both Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Resonance (NMR) experimental analysis with computer simulations to provide unique 3D molecular structural, dynamics, and functional information on the order of microns for this DOE mission relevant microorganism, T. denitrificans. For FY05, our goals were to: (1) Determine proper media for optimal growth of PA; growth rate measurements in that media and characterization of metabolite signatures during growth via {sup 1}H and {sup 13}C NMR, (2) Determine and build mineral, metal, and implant material surfaces to support growth of PA, (3) Implementing new MRI sequences to image biofilms more efficiently and increase resolution with new hardware design, (4) Develop further diffusion and flow MRI measurements of biofilms and biofilm formation with different MRI pulse sequences and different hardware design, and (5) Develop a zero dimension model of the rate of growth and the metabolite profiles of PA. Our major accomplishments are discussed in the following text. However, the bulk of this work is described in the attached manuscript entitled, ''NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa''. This paper will be submitted to the Journal of Bacteriology in coming weeks. In addition, this one-year effort has lead to our incorporation into the Enhanced Surveillance Campaign during FY05 for some proof-of-principle MRI measurements on polymers. We are currently using similar methods to evaluate these polymers. In addition, this work on MRI measurements on polymers has lead to a paper entitled, ''Characterization of local deformation in filled

Herberg, J L; Schaldach, C; Horn, J; Gjersing, E; Maxwell, R

2006-02-09

285

Microbial biodiversity, quality and shelf life of microfiltered and pasteurized extended shelf life (ESL) milk from Germany, Austria and Switzerland.  

PubMed

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

Schmidt, Verena S J; Kaufmann, Veronika; Kulozik, Ulrich; Scherer, Siegfried; Wenning, Mareike

2011-12-13

286

"Primers" on Research Techniques Used in Geomicrobiology for Students and Novices from Microbial Life Educational Resources  

NASA Astrophysics Data System (ADS)

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.

Bruckner, M. Z.; Rice, G.; Mogk, D. W.

2007-12-01

287

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

Microsoft Academic Search

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

J. Fang

2009-01-01

288

Thermodynamic limits to microbial life at high salt concentrations.  

PubMed

Life at high salt concentrations is energetically expensive. The upper salt concentration limit at which different dissimilatory processes occur in nature appears to be determined to a large extent by bioenergetic constraints. The main factors that determine whether a certain type of microorganism can make a living at high salt are the amount of energy generated during its dissimilatory metabolism and the mode of osmotic adaptation used. I here review new data, both from field observations and from the characterization of cultures of new types of prokaryotes growing at high salt concentrations, to evaluate to what extent the theories formulated 12 years ago are still valid, need to be refined, or should be refuted on the basis of the novel information collected. Most data agree well with the earlier theories. Some new observations, however, are not easily explained: the properties of Natranaerobius and other haloalkaliphilic thermophilic fermentative anaerobes, growth of the sulfate-reducing Desulfosalsimonas propionicica with complete oxidation of propionate and Desulfovermiculus halophilus with complete oxidation of butyrate, growth of lactate-oxidizing sulfate reducers related to Desulfonatronovibrio at 346 g l(-1) salts at pH 9.8, and occurrence of methane oxidation in the anaerobic layers of Big Soda Lake and Mono Lake. PMID:21054738

Oren, Aharon

2010-11-05

289

Non-destructive monitoring of microbial biofilms at solid-liquid interfaces using on-line devices  

Microsoft Academic Search

Corrosion, biofouling, and related problems have been an impetus for investigating interactions between microorganisms and solid surfaces. In recent years, a number of studies have been performed to assess the damages caused by microbial influenced corrosion (MIC). In a number of these studies, electrochemical techniques have monitored the performance of metal surfaces exposed to bacteria. However, most of these methods

D. E. Nivens; J. Q. Chambers; D. C. White

1990-01-01

290

Towards a Miniaturized System for Microbial Monitoring of Life Support Applications  

NASA Astrophysics Data System (ADS)

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.

Abaibou, Hafid; Storrs, Michele; Broyer, Patrick; Drevet, Christophe; Guy, Michel; Mabilat, Claude; Lasseur, Christophe

291

Slime Worlds: Possibilities for Detection of Microbial Life on Extrasolar Planets  

NASA Astrophysics Data System (ADS)

We suggest that on extrasolar planets on which life has not made the transition to mult-cellular organisms, land surfaces may be covered by bacterial mats, algae, or slimes. If photosynthetic, such land-based, large-scale microbial colonies would show the well-known "red edge" of chlorophylls in their spectra. They would give much stronger spectral signatures for detection of life on extrasolar planets than microbes/algae in oceans or lakes, and their spectra would resemble the chlorophyll signatures of land vegetation. Therefore, life may be detectable on extrasolar planets early in their history, before the relatively late (if similar to Earth) advent of land plants, or if the transition to multicellular life does not occur at all. We show synthetic spectra of land microorganisms on Earth-like extrasolar planets.

Knacke, R. F.

2004-12-01

292

Inhibitory effect of cyclic trihydroxamate siderophore, desferrioxamine E, on the biofilm formation of Mycobacterium species.  

PubMed

Formation of biofilm in pathogenic bacteria defends them from antibiotics and the immune system of a host's life. Hence, investigation of the molecular mechanisms of biofilm formation and search for new substances counteracting this formation are becoming an attractive research area. In the course of our search for new inhibitors of biofilm formation in Mycobacterium species, we rediscovered a cyclic trihydroxamate siderophore, desferrioxamine E, from the culture of the marine-derived Actinomycete MS67. Desferrioxamine E inhibited biofilm formation of Mycobacterium smegmatis and M. bovis BACILLE de CALMETTE et GUÉRIN (BCG) with minimum inhibitory concentration (MIC) value of 10 µM, while no anti-microbial activity was observed up to 160 µM. Desferrioxamine E was also able to restore the anti-microbial activity of isoniazid against M. smegmatis by inhibiting biofilm formation. Mechanistic analysis of desferrioxamine E suggested that such inhibition might come from the depletion of iron in the medium, which is essential for biofilm formation in Mycobacterium species. PMID:21628895

Ishida, Shunsuke; Arai, Masayoshi; Niikawa, Hiroki; Kobayashi, Motomasa

2011-01-01

293

Deep microbial life in the Altmark natural gas reservoir: baseline characterization prior CO2 injection  

NASA Astrophysics Data System (ADS)

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.

Morozova, Daria; Shaheed, Mina; Vieth, Andrea; Krüger, Martin; Kock, Dagmar; Würdemann, Hilke

2010-05-01

294

Spatially Oscillating Activity and Microbial Succession of Mercury-Reducing Biofilms in a Technical-Scale Bioremediation System  

Microsoft Academic Search

Mercury-contaminated chemical wastewater of a mercury cell chloralkali plant was cleaned on site by a technical-scale bioremediation system. Microbial mercury reduction of soluble Hg(II) to precipitating Hg(0) decreased the mercury load of the wastewater during its flow through the bioremediation system by up to 99%. The system consisted of a packed-bed bioreactor, where most of the wastewater's mercury load was

Harald von Canstein; Ying Li; J. Leonhauser; Elke Haase; Andreas Felske; Wolf-Dieter Deckwer; I. Wagner-Dobler

2002-01-01

295

Microtiter dish biofilm formation assay.  

PubMed

Biofilms are communities of microbes attached to surfaces, which can be found in medical, industrial and natural settings. In fact, life in a biofilm probably represents the predominate mode of growth for microbes in most environments. Mature biofilms have a few distinct characteristics. Biofilm microbes are typically surrounded by an extracellular matrix that provides structure and protection to the community. Microbes growing in a biofilm also have a characteristic architecture generally comprised of macrocolonies (containing thousands of cells) surrounded by fluid-filled channels. Biofilm-grown microbes are also notorious for their resistance to a range of antimicrobial agents including clinically relevant antibiotics. The microtiter dish assay is an important tool for the study of the early stages in biofilm formation, and has been applied primarily for the study of bacterial biofilms, although this assay has also been used to study fungal biofilm formation. Because this assay uses static, batch-growth conditions, it does not allow for the formation of the mature biofilms typically associated with flow cell systems. However, the assay has been effective at identifying many factors required for initiation of biofilm formation (i.e, flagella, pili, adhesins, enzymes involved in cyclic-di-GMP binding and metabolism) and well as genes involved in extracellular polysaccharide production. Furthermore, published work indicates that biofilms grown in microtiter dishes do develop some properties of mature biofilms, such a antibiotic tolerance and resistance to immune system effectors. This simple microtiter dish assay allows for the formation of a biofilm on the wall and/or bottom of a microtiter dish. The high throughput nature of the assay makes it useful for genetic screens, as well as testing biofilm formation by multiple strains under various growth conditions. Variants of this assay have been used to assess early biofilm formation for a wide variety of microbes, including but not limited to, pseudomonads, Vibrio cholerae, Escherichia coli, staphylococci, enterococci, mycobacteria and fungi. In the protocol described here, we will focus on the use of this assay to study biofilm formation by the model organism Pseudomonas aeruginosa. In this assay, the extent of biofilm formation is measured using the dye crystal violet (CV). However, a number of other colorimetric and metabolic stains have been reported for the quantification of biofilm formation using the microtiter plate assay. The ease, low cost and flexibility of the microtiter plate assay has made it a critical tool for the study of biofilms. PMID:21307833

O'Toole, George A

2011-01-30

296

Microtiter Dish Biofilm Formation Assay  

PubMed Central

Biofilms are communities of microbes attached to surfaces, which can be found in medical, industrial and natural settings. In fact, life in a biofilm probably represents the predominate mode of growth for microbes in most environments. Mature biofilms have a few distinct characteristics. Biofilm microbes are typically surrounded by an extracellular matrix that provides structure and protection to the community. Microbes growing in a biofilm also have a characteristic architecture generally comprised of macrocolonies (containing thousands of cells) surrounded by fluid-filled channels. Biofilm-grown microbes are also notorious for their resistance to a range of antimicrobial agents including clinically relevant antibiotics. The microtiter dish assay is an important tool for the study of the early stages in biofilm formation, and has been applied primarily for the study of bacterial biofilms, although this assay has also been used to study fungal biofilm formation. Because this assay uses static, batch-growth conditions, it does not allow for the formation of the mature biofilms typically associated with flow cell systems. However, the assay has been effective at identifying many factors required for initiation of biofilm formation (i.e, flagella, pili, adhesins, enzymes involved in cyclic-di-GMP binding and metabolism) and well as genes involved in extracellular polysaccharide production. Furthermore, published work indicates that biofilms grown in microtiter dishes do develop some properties of mature biofilms, such a antibiotic tolerance and resistance to immune system effectors. This simple microtiter dish assay allows for the formation of a biofilm on the wall and/or bottom of a microtiter dish. The high throughput nature of the assay makes it useful for genetic screens, as well as testing biofilm formation by multiple strains under various growth conditions. Variants of this assay have been used to assess early biofilm formation for a wide variety of microbes, including but not limited to, pseudomonads, Vibrio cholerae, Escherichia coli, staphylocci, enterococci, mycobacteria and fungi. In the protocol described here, we will focus on the use of this assay to study biofilm formation by the model organism Pseudomonas aeruginosa. In this assay, the extent of biofilm formation is measured using the dye crystal violet (CV). However, a number of other colorimetric and metabolic stains have been reported for the quantification of biofilm formation using the microtiter plate assay. The ease, low cost and flexibility of the microtiter plate assay has made it a critical tool for the study of biofilms.

O'Toole, George A.

2011-01-01

297

Investigating the heterogeneity of cell growth in microbial colonies by FTIR microspectroscopy  

Microsoft Academic Search

Microorganisms rarely occur as individual cells in nature and are, instead, organized in complex multicellular communities\\u000a such as colonies, fruiting bodies, or biofilms. Interest in the natural microbial life-style has increased during the last\\u000a decade and a whole plethora of techniques has been used to gain insight into the development, structure and composition of\\u000a diverse microbial communities. We have developed

N. A. Ngo Thi; D. Naumann

2007-01-01

298

Genetic control of Candida albicans biofilm development.  

PubMed

Candida species cause frequent infections owing to their ability to form biofilms - surface-associated microbial communities - primarily on implanted medical devices. Increasingly, mechanistic studies have identified the gene products that participate directly in the development of Candida albicans biofilms, as well as the regulatory circuitry and networks that control their expression and activity. These studies have uncovered new mechanisms and signals that govern C. albicans biofilm development and associated drug resistance, thus providing biological insight and therapeutic foresight. PMID:21189476

Finkel, Jonathan S; Mitchell, Aaron P

2010-12-29

299

Antibiotic Tolerance and Resistance in Biofilms  

Microsoft Academic Search

\\u000a One of the most important features of microbial biofilms is their tolerance to antimicrobial agents and components of the\\u000a host immune system. The difficulty of treating biofilm infections with antibiotics is a major clinical problem. Although antibiotics\\u000a may decrease the number of bacteria in biofilms, they will not completely eradicate the bacteria in vivo which may have important\\u000a clinical consequences

Oana Ciofu; Tim Tolker-Nielsen

300

Effects of seawater ozonation on biofilm development in aquaculture tanks  

Microsoft Academic Search

Microbial biofilms developing in aquaculture tanks represent a reservoir for opportunistic bacterial pathogens, and procedures to control formation and bacterial composition of biofilms are important for the development of commercially viable aquaculture industries. This study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism Artemia. Fluorescence

Matthias Wietz; Michael R. Hall; Lone Høj

2009-01-01

301

In situ imaging of biofilm within opaque porous media (Invited)  

Microsoft Academic Search

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 in situ. Imaging biofilm within opaque porous media has historically presented

G. Iltis; Y. Davit; B. D. Wood; D. Wildenschild

2010-01-01

302

Electrical Conductivity in a Mixed-Species Biofilm  

PubMed Central

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.

Lau, Joanne; Nevin, Kelly P.; Franks, Ashley E.; Tuominen, Mark T.; Lovley, Derek R.

2012-01-01

303

Nitrogen isotope evidence of ammonia vapor assimilation by cave wall microbial biofilms in a sulfidic cave, a novel mechanism of nutrient acquisition  

NASA Astrophysics Data System (ADS)

Ammonia volatilization provides a source of fixed nitrogen to the microorganisms living at low pH on the walls of Lower Kane Cave. Sulfuric acid speleogenesis is actively enlarging this cave; hydrogen sulfide dissolved in ground water is oxidized to sulfuric acid both in the cave streams and after volatilization to the cave walls. The result of this process is replacement the host limestone with a rind of gypsum on the cave walls upon which droplets with pH values of 1-2 sulfuric acid accumulate. The radically different pH values of the cave stream and cave wall habitats results in an unusual mechanism of fixed nitrogen acquisition by the cave wall microbial community, accumulation of volatilized ammonia. The spring water entering the cave has 25 to 40 ? M NH4+ and circum-neutral pH allowing a small but significant amount this ammonium to volatilize as NH3. This gaseous ammonia may then partition into the acidic cave wall droplets accumulating to concentrations of up to 800? M where it serves as a nitrogen source to the cave wall microorganisms. The effects of this ammonia volatilization may be seen in the extremely low ? 15N value of the cave wall biofilms, as low as -16‰ . These ? 15N values are among the lowest observed in organic materials. Therefore nitrogen isotope ratios represent a marker of ammonia volatilization in subaerial sulfuric acid speleogenesis that may be applied to cave systems that were once sulfidic to delineate regions of subaerial versus subaqueous cave formation.

Stern, L. A.; Engel, A. S.; Bennett, P. C.

2003-12-01

304

12 Microbial Life in Brines, Evaporites and Saline Sediments: The Search for Life on Mars  

Microsoft Academic Search

When water on a planet begins to evaporate the dissolved minerals become more concentrated, form a brine, eventually precipitating out of solution and forming evaporite deposits. The brines and evaporites form a highly saline environment that is hostile to most life forms, but provides an ideal habitat for organisms that are osmophilic, or halophilic. Halophiles are salt “loving” organisms that

Rocco L. Mancinelli

305

Permeabilizing biofilms  

DOEpatents

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.

Soukos, Nikolaos S. (Revere, MA); Lee, Shun (Arlington, VA); Doukas,; Apostolos G. (Belmont, MA)

2008-02-19

306

Biofilm Image Segmentation Using Optimal Multilevel Thresholding  

Microsoft Academic Search

A microbial biofilm is structured mainly by a protective sticky matrix of extracellular polymeric substances. Quantifying such structures is useful for microbiologists and a correct image segmentation process helps substantially reduce errors in quantification. This paper proposes an approach to segmentation of biofilm images using optimal multilevel thresholding and indices of clustering validity. A direct comparison through Rand index and

Dar ´ io Rojas; Luis Rueda; Alioune Ngom; Homero Urrutia; Gerardo Carcamo

2009-01-01

307

Caenorhabditis elegans BAH1 Is a DUF23 Protein Expressed in Seam Cells and Required for Microbial Biofilm Binding to the Cuticle  

Microsoft Academic Search

The cuticle of Caenorhabditis elegans, a complex, multi-layered extracellular matrix, is a major interface between the animal and its environment. Biofilms produced by the bacterial genus Yersinia attach to the cuticle of the worm, providing an assay for surface characteristics. A C. elegans gene required for biofilm attachment, bah-1, encodes a protein containing the domain of unknown function DUF23. The

Kevin Drace; Stephanie McLaughlin; Creg Darby; Joy Sturtevant

2009-01-01

308

Microbial siderophores: a mini review.  

PubMed

Iron is one of the major limiting factors and essential nutrients of microbial life. Since in nature it is not readily available in the preferred form, microorganisms produce small high affinity chelating molecules called siderophores for its acquisition. Microorganisms produce a wide variety of siderophores controlled at the molecular level by different genes to accumulate, mobilize and transport iron for metabolism. Siderophores also play a critical role in the expression of virulence and development of biofilms by different microbes. Apart from maintaining microbial life, siderophores can be harnessed for the sustainability of human, animals and plants. With the advent of modern molecular tools, a major breakthrough is taking place in the understanding of the multifaceted role of siderophores in nature. This mini review is intended to provide a general overview on siderophore along with its role and applications. PMID:22733623

Saha, Ratul; Saha, Nabaneeta; Donofrio, Robert S; Bestervelt, Lorelle L

2012-06-26

309

Life at the wedge: the activity and diversity of arctic ice wedge microbial communities.  

PubMed

The discovery of polygonal terrain on Mars underlain by ice heightens interest in the possibility that this water-bearing habitat may be, or may have been, a suitable habitat for extant life. The possibility is supported by the recurring detection of terrestrial microorganisms in subsurface ice environments, such as ice wedges found beneath tundra polygon features. A characterization of the microbial community of ice wedges from the high Arctic was performed to determine whether this ice environment can sustain actively respiring microorganisms and to assess the ecology of this extreme niche. We found that ice wedge samples contained a relatively abundant number of culturable cells compared to other ice habitats (?10(5) CFU·mL(-1)). Respiration assays in which radio-labeled acetate and in situ measurement of CO(2) flux were used suggested low levels of microbial activity, though more sensitive techniques are required to confirm these findings. Based on 16S rRNA gene pyrosequencing, bacterial and archaeal ice wedge communities appeared to reflect surrounding soil communities. Two Pseudomonas sp. were the most abundant taxa in the ice wedge bacterial library (?50%), while taxa related to ammonia-oxidizing Thaumarchaeota occupied 90% of the archaeal library. The tolerance of a variety of isolates to salinity and temperature revealed characteristics of a psychrotolerant, halotolerant community. Our findings support the hypothesis that ice wedges are capable of sustaining a diverse, plausibly active microbial community. As such, ice wedges, compared to other forms of less habitable ground ice, could serve as a reservoir for life on permanently cold, water-scarce, ice-rich extraterrestrial bodies and are therefore of interest to astrobiologists and ecologists alike. . PMID:22519974

Wilhelm, Roland C; Radtke, Kristin J; Mykytczuk, Nadia C S; Greer, Charles W; Whyte, Lyle G

2012-04-01

310

Microbial structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment  

Microsoft Academic Search

The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their \\

Marion Dornmayr-Pfaffenhuemer; Elisabeth Pierson; Geert-Jan Janssen; Helga Stan-Lotter

2010-01-01

311

Detection of in-situ derivatized peptides in microbial biofilms by laser desorption 7.87 eV postionizaton mass spectrometry.  

SciTech Connect

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.

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

312

Biofilm Formation Biofilm Formation Biofilm Formation .EW#LUESIN5NDERSTANDING  

Microsoft Academic Search

he water industry has long been plagued by the effects of biofilm formation in water supplies, pipes, fittings and filters. Such biomasses lead to adverse taste, odor and possible health effects in the water and decrease the life of treatment equipment. Scientists are just beginning to solve the mystery of how and why biofilms form. New evidence indicates that microorganisms

Kelly A. Reynolds

2008-01-01

313

Characterization of the deep microbial life in the Altmark natural gas reservoir  

NASA Astrophysics Data System (ADS)

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.

Morozova, D.; Alawi, M.; Vieth-Hillebrand, A.; Kock, D.; Krüger, M.; Wuerdemann, H.

2010-12-01

314

Why Microorganisms Live in Biofilms and the Problem of Biofouling  

Microsoft Academic Search

Microbial biofouling is a problem of microbial biofilms. Biofouling occurs in very different industrial fields and is mostly\\u000a addressed individually. However, the underlying phenomenon is much more general and in order to understand the processes causing\\u000a biofouling, it is good to understand the basics of biofilm formation and development. Almost every surface can be colonized\\u000a by bacteria, forming biofilms. After

Hans-Curt Flemming

315

Evaluation of the Microbial Population in the Multibiological Life Support System Experiments  

NASA Astrophysics Data System (ADS)

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.

Fu, Yuming; Tong, Ling; Li, Ming; Hu, Enzhu; Hu, Dawei; He, Wenting; Liu, Hong

316

A new coupon design for simultaneous analysis of in situ microbial biofilm formation and community structure in drinking water distribution systems.  

PubMed

This study presents a new coupon sampling device that can be inserted directly into the pipes within water distribution systems (WDS), maintaining representative near wall pipe flow conditions and enabling simultaneous microscopy and DNA-based analysis of biofilms formed in situ. To evaluate this sampling device, fluorescent in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analyses were used to investigate changes in biofilms on replicate coupons within a non-sterile pilot-scale WDS. FISH analysis demonstrated increases in bacterial biofilm coverage of the coupon surface over time, while the DGGE analysis showed the development of increasingly complex biofilm communities, with time-specific clustering of these communities. This coupon design offers improvements over existing biofilm sampling devices in that it enables simultaneous quantitative and qualitative compositional characterization of biofilm assemblages formed within a WDS, while importantly maintaining fully representative near wall pipe flow conditions. Hence, it provides a practical approach that can be used to capture the interactions between biofilm formation and changing abiotic conditions, boundary shear stress, and turbulent driven exchange within WDS. PMID:20300747

Deines, Peter; Sekar, Raju; Husband, P Stewart; Boxall, Joby B; Osborn, A Mark; Biggs, Catherine A

2010-03-19

317

Bacterial Lysine Decarboxylase Influences Human Dental Biofilm Lysine Content, Biofilm Accumulation and Sub-Clinical Gingival Inflammation  

PubMed Central

Background Dental biofilms contain a protein that inhibits mammalian cell growth, possibly lysine decarboxylase from Eikenella corrodens. This enzyme decarboxylates lysine, an essential amino acid for dentally attached cell turnover in gingival sulci. Lysine depletion may stop this turnover, impairing the barrier to bacterial compounds. The aims of this study were to determine biofilm lysine and cadaverine contents before oral hygiene restriction (OHR), and their association with plaque index (PI) and gingival crevicular fluid (GCF) after OHR for a week. Methods Laser-induced fluorescence after capillary electrophoresis was used to determine lysine and cadaverine contents in dental biofilm, tongue biofilm and saliva before OHR and in dental biofilm after OHR. Results Before OHR, lysine and cadaverine contents of dental biofilm were similar and 10-fold greater than in saliva or tongue biofilm. After a week of OHR, the biofilm content of cadaverine increased and that of lysine decreased, consistent with greater biofilm lysine decarboxylase activity. Regression indicated that PI and GCF exudation were positively related to biofilm lysine post-OHR, unless biofilm lysine exceeded the minimal blood plasma content in which case PI was further increased but GCF exudation was reduced. Conclusions After OHR, lysine decarboxylase activity seems to determine biofilm lysine content and biofilm accumulation. When biofilm lysine exceeds minimal blood plasma content after OHR, less GCF appeared despite more biofilm. Lysine appears important for biofilm accumulation and the epithelial barrier to bacterial proinflammatory agents. Clinical Relevance Inhibiting lysine decarboxylase may retard the increased GCF exudation required for microbial development and gingivitis.

Lohinai, Z.; Keremi, B.; Szoko, E.; Tabi, T.; Szabo, C.; Tulassay, Z.; Levine, M.

2012-01-01

318

MstX and a Putative Potassium Channel Facilitate Biofilm Formation in Bacillus subtilis  

PubMed Central

Biofilms constitute the predominant form of microbial life and a potent reservoir for innate antibiotic resistance in systemic infections. In the spore-forming bacterium Bacillus subtilis, the transition from a planktonic to sessile state is mediated by mutually exclusive regulatory pathways controlling the expression of genes required for flagellum or biofilm formation. Here, we identify mstX and yugO as novel regulators of biofilm formation in B. subtilis. We show that expression of mstX and the downstream putative K+ efflux channel, yugO, is necessary for biofilm development in B. subtilis, and that overexpression of mstX induces biofilm assembly. Transcription of the mstX-yugO operon is under the negative regulation of SinR, a transcription factor that governs the switch between planktonic and sessile states. Furthermore, mstX regulates the activity of Spo0A through a positive autoregulatory loop involving KinC, a histidine kinase that is activated by potassium leakage. The addition of potassium abrogated mstX-mediated biofilm formation. Our findings expand the role of Spo0A and potassium homeostasis in the regulation of bacterial development.

Lundberg, Matthew E.; Becker, Eric C.; Choe, Senyon

2013-01-01

319

MstX and a putative potassium channel facilitate biofilm formation in Bacillus subtilis.  

PubMed

Biofilms constitute the predominant form of microbial life and a potent reservoir for innate antibiotic resistance in systemic infections. In the spore-forming bacterium Bacillus subtilis, the transition from a planktonic to sessile state is mediated by mutually exclusive regulatory pathways controlling the expression of genes required for flagellum or biofilm formation. Here, we identify mstX and yugO as novel regulators of biofilm formation in B. subtilis. We show that expression of mstX and the downstream putative K+ efflux channel, yugO, is necessary for biofilm development in B. subtilis, and that overexpression of mstX induces biofilm assembly. Transcription of the mstX-yugO operon is under the negative regulation of SinR, a transcription factor that governs the switch between planktonic and sessile states. Furthermore, mstX regulates the activity of Spo0A through a positive autoregulatory loop involving KinC, a histidine kinase that is activated by potassium leakage. The addition of potassium abrogated mstX-mediated biofilm formation. Our findings expand the role of Spo0A and potassium homeostasis in the regulation of bacterial development. PMID:23737939

Lundberg, Matthew E; Becker, Eric C; Choe, Senyon

2013-05-30

320

The roles of biofilm matrix polysaccharide Psl in mucoid Pseudomonas aeruginosa biofilms.  

PubMed

The opportunistic pathogen Pseudomonas aeruginosa causes life-threatening, persistent infections in patients with cystic fibrosis (CF). Persistence is attributed to the ability of these bacteria to form structured communities (biofilms). Biofilms rely on an extracellular polymeric substances matrix to maintain structure. Psl exopolysaccharide is a key matrix component of nonmucoid biofilms, yet the role of Psl in mucoid biofilms is unknown. In this report, using a variety of mutants in a mucoid P. aeruginosa background, we found that deletion of Psl-encoding genes dramatically decreased their biofilm formation ability, indicating that Psl is also a critical matrix component of mucoid biofilms. Our data also suggest that the overproduction of alginate leads to mucoid biofilms, which occupy more space, whereas Psl-dependent biofilms are densely packed. These data suggest that Psl polysaccharide may have significant contributions in biofilm persistence in patients with CF and may be helpful for designing therapies for P. aeruginosa CF infection. PMID:22309106

Ma, Luyan; Wang, Shiwei; Wang, Di; Parsek, Matthew R; Wozniak, Daniel J

2012-03-12

321

Microbial life in glacial ice and implications for a cold origin of life.  

PubMed

Application of physical and chemical concepts, complemented by studies of prokaryotes in ice cores and permafrost, has led to the present understanding of how microorganisms can metabolize at subfreezing temperatures on Earth and possibly on Mars and other cold planetary bodies. The habitats for life at subfreezing temperatures benefit from two unusual properties of ice. First, almost all ionic impurities are insoluble in the crystal structure of ice, which leads to a network of micron-diameter veins in which microorganisms may utilize ions for metabolism. Second, ice in contact with mineral surfaces develops a nanometre-thick film of unfrozen water that provides a second habitat that may allow microorganisms to extract energy from redox reactions with ions in the water film or ions in the mineral structure. On the early Earth and on icy planets, prebiotic molecules in veins in ice may have polymerized to RNA and polypeptides by virtue of the low water activity and high rate of encounter with each other in nearly one-dimensional trajectories in the veins. Prebiotic molecules may also have utilized grain surfaces to increase the rate of encounter and to exploit other physicochemical features of the surfaces. PMID:17328118

Price, P Buford

2007-02-01

322

Transcriptional profiling of Legionella pneumophila biofilm cells and the influence of iron on biofilm formation  

Microsoft Academic Search

In aquatic environments, biofilms constitute an ecological niche where Legionella pneumophila persists as sessile cells. However, very little information on the sessile mode of life of L. pneumophila is currently available. We report here the development of a model biofilm of L. pneumophila strain Lens and the first transcriptome analysis of L. pneumophila biofilm cells. Global gene expression analysis of

Thomas Hindre; Holger Bruggemann; Carmen Buchrieser; Yann Hechard

2008-01-01

323

DIFFUSION IN BIOFILMS RESPIRING ON ELECTRODES.  

PubMed

The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (D(e)) 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 D(e) 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 D(e) heat maps and surface-averaged relative effective diffusion coefficient (D(rs)) depth profiles. We found that 1) D(rs) decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; 2) D(rs) at a given location decreases with G. sulfurreducens biofilm age; 3) average D(e) and D(rs) 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 D(e) values. Density, reflected by D(e), plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms. PMID:23420623

Renslow, Rs; Babauta, Jt; Majors, Pd; Beyenal, H

2012-11-15

324

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

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

Schubotz, F; Meyer-Dombard, D R; Bradley, A S; Fredricks, H F; Hinrichs, K-U; Shock, E L; Summons, R E

2013-08-28

325

Non-destructive on-line monitoring of MIC (microbially influenced corrosion)  

Microsoft Academic Search

The formation of microbial biofilms on metal surfaces with the subsequent increase in heat transfer resistance and the induction of microbially influenced corrosion (MIC) is being increasingly recognized as an extremely important economic and safety problem for industrial water systems. The development of sufficiently rugged and accurate monitoring devices by which biofilm formation and activity of microbial biofilms can be

D. C. White; D. E. Nivens; M. W. Mittelman; J. Q. Chambers; J. M. H. King; G. S. Sayler

1990-01-01

326

Model parameter uncertainties in a dual-species biofilm competition model affect ecological output parameters much stronger than morphological ones  

Microsoft Academic Search

Bacterial biofilms are complex microbial depositions on immersed interfaces that form wherever the environmental conditions sustain microbial growth. Despite their name, biofilms can develop in highly irregular structures. Recently several mathematical concepts have been introduced to model these spatially structured microbial populations. Regardless of the type of model, they all have, even for microbially relatively simple systems, many parameters which

Nasim Muhammad; Hermann J. Eberl

2011-01-01

327

Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin  

PubMed Central

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.

Merhej, Vicky; Raoult, Didier

2012-01-01

328

Linking nitrifying biofilm characteristics and nitrification performance in moving-bed biofilm reactors for polluted raw water pretreatment.  

PubMed

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

Zhang, Shuangfu; Wang, Yayi; He, Weitao; Xing, Meiyan; Wu, Min; Yang, Jian; Gao, Naiyun; Sheng, Guangyao; Yin, Daqiang; Liu, Shanhu

2013-07-26

329

Microbial Trace Fossils in Antarctica and the Search for Evidence of Early Life on Mars. Abstract Only.  

National Technical Information Service (NTIS)

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 suitab...

E. I. Friedmann R. O. Friedmann

1989-01-01

330

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

Microsoft Academic Search

Cryptoendolithic microbial communities living within Antarctic rocks are an example of survival in an extremely cold and dry environment. The extinction of these micro-organisms formerly colonizing sandstone in the Mount Fleming area (Ross Desert), was probably provoked by the hostile environment. This is considered to be a good terrestrial analogue of the first stage of the disappearance of possible life

Jacek Wierzchos; Carmen Ascaso

2002-01-01

331

Synchrotron Radiation X-Ray Fluorescence nanoanalyses of the metallome of a ~3.3 Ga-old microbial biofilm from the Barberton greenstone belt, South Africa.  

NASA Astrophysics Data System (ADS)

Combining in situ nanometer-scale techniques on the fossilized Josefsdal Chert Microbial Biofilm (JCMB) reveals a distinct vertical structural and compositional organisation: the lower part is calcified as aragonite, while the upper non-calcified kerogenous layer is characterised by up to 1% sulphur [1]. The in situ analysis of all the metals as a group represents a useful microbial fingerprint [2] and we will continue to explore it. Synchrotron Radiation X-Ray Fluorescence maps of high spatial resolution (< 0.3 µm) were recorded on a unique FIB section (15 x 10 x 3 µm3) of the JCMB. A 300 nm resolution was reached at 2500 eV on the ID21 scanning X-ray microscope (SXM) and a 120x165 (horizontal x vertical) nm at 17450 eV on ID22NI at the European Synchrotron Radiation Facility (ESRF). All maps reveal chemical heterogeneities not previously discernible by scanning the same FIB cut using micron resolution. The feasibility of high-resolution analyses with high flux on rock samples was first shown for samples that had in this respect an ideal hotspot geometry in a uniform silica matrix [3, 4]. Our FIB sample preparation ensures negligible thickness variations so quantitation of all the metals in the JCMB is presently only limited by the important intrinsic heterogeneity of the sample. Methods to deal with micrometer bulk heterogeneity have just been developed by performing redundant volumetric scans in fluorescence tomography to counterbalance the complex sample geometry [5]. An alternative methodology more adapted to the thin slice geometry is tested here. A relationship between the ratio of the Compton to Rayleigh (C-R) scatterings and the average atomic number (Zave), only established with unpolarized X-rays [6], was measured using fully polarized synchrotron beams [7]. C-R peaks measured on thick Astimex standards (1 mm) and those calculated from Monte-Carlo simulations of thick and thin (100 µm and 1 µm) samples having the same compositions were analyzed using a version of the PyMCA software [8] specially optimised for this purpose. The empirical relations of the type Zave = a•(C/R)b obtained for the three analyses sets provide a comprehensive set of calibrations suitable for any sample of any thickness. On the basis of these calibrations, we inferred positions and concentrations of undetected low-Z phases in the JCMB and further corrected the concentrations of the detected metals in the organic phases. 1. Westall F., et al., 2011. Earth & Planet. Sci. Lett., 310, 468-479. 2. Zerkle A L., et al., 2005. Am. J. Science, 305, 467-502. 3. Westphal A. J., et al., 2010. AIP Conference Proceedings, 1221, 131-138. 4. Bleuet P., et al., 2008. App. Phys. Lett., 92, 213111-1-3. 5. Golosio B., et al., 2003. Appl. Phys., 94, 145-157. 6. M. Haschke, 2003. PhD dissertation, T.U. Berlin. 7. Simionovici A. S., et al., 2010. Proceedings of the Meteoritical Society Conference, N.Y., USA. 8. Solé V.A., et al., 2006, Elsevier, 62, 63-68.

Hubert, A.; Lemelle, L.; Salome, M.; Cloetens, P.; Westall, F.; Simionovici, A.

2012-04-01

332

Role of biofilm in catheter-associated urinary tract infection  

Microsoft Academic Search

The predominant form of life for the majority of microorganisms in any hydrated biologic system is a cooperative community termed a “biofilm.” A biofilm on an indwelling urinary catheter consists of adherent microorganisms, their extracellular products, and host components deposited on the catheter. The biofilm mode of life conveys a survival advantage to the microorganisms associated with it and, thus,

Barbara W Trautner; Rabih O Darouiche

2004-01-01

333

Searching for fossil microbial biofilms on Mars: a case study using a 3.46 billion-year old example from the Pilbara in Australia  

NASA Astrophysics Data System (ADS)

With the immanent arrival of three Mars landers, one of which (Beagle 2) is dedicated to the search for life on Mars, analogue studies that are of general relevance to the search for past life on Mars are timely. We are using a 3.46 Ga, fossiliferous, sedimentary rock as a reference sample. The rock consists of laminated sediments, whose components were derived from volcanic rocks (volcaniclastic) that were deposited in a shallow water basin. Microbial mats occur at the surfaces of the sediments. This rock formed in an environment and from materials that would have existed on early Mars. Preliminary observation with the Beagle 2 camera shows that it should be possible to identify sedimentary structures, such as ripple marks and laminations, in fine detail. A 2 mm high ministromatolite/thrombolite layer was also readily visible. Further analysis using the microscope and the spectrometers would provide additional information that would lead to the choice of suitable samples, such as the ministromatolite/thrombolite layer, for chemical study with the gas analysis package. In this way details concerning the nature (and biogenicity) of the carbonaceous matter.

Westall, Frances; Hofmann, Beda; Brack, André

2004-03-01

334

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

NASA Astrophysics Data System (ADS)

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 lifethreatening infections. Other types of medical devices such as bronchoscopes and duodenoscopes account for the highest number of reported endoscopic infections where microbial biofilm is one of the major causes for these infections. We applied a hyperspectral imaging method to detect biofilm contamination on the surface of several common materials used for medical devices. Such materials include stainless steel, titanium, and stainless-steeltitanium alloy. Potential uses of hyperspectral imaging technique to monitor biofilm attachment to different material surfaces are discussed.

Kim, Do-Hyun; Kim, Moon S.; Hwang, Jeeseong

2012-02-01

335

Biofilms: Recent Developments on an Old Battle  

Microsoft Academic Search

Microbial cells are able to adhere to surfaces and through an exo-polymeric matrix they establish microbial communities known as biofilms. This form of immobilised biomass can be responsible for heat and mass transfer limitations in industrial processes and be a source of contamination and proliferation of infections in water supply systems and medical devices. Several processes to prevent and destroy

2007-01-01

336

Deliberations on Microbial Life in the Subglacial Lake Vostok, East Antarctica  

NASA Astrophysics Data System (ADS)

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.

Bulat, S.; Alekhina, I.; Lipenkov, V.; Lukin, V.; Marie, D.; Petit, J.

2004-12-01

337

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

Microsoft Academic Search

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

Hisashi Satoh; Mitsunori Odagiri; Tsukasa Ito; Satoshi Okabe

2009-01-01

338

Microbial life in cold, sulfur-rich environments: Investigations of an Arctic ecosystem and implications for life detection at Europa  

NASA Astrophysics Data System (ADS)

Exobiological investigations require a detailed understanding of life's interactions with its environment here on Earth before we can confidently recognize signs of these interactions at other worlds such as Europa. Using a cold, sulfur-based ecosystem at Borup Fiord pass in the Canadian High Arctic as a study site, I investigated how the supraglacial non-ice materials are represented across different scales in spectral data, how microbiology is influencing the mineralogy of the site, and whether the products of microbial sulfide oxidation preserve indications of their biogenic origin. A systematic scale-integrated approach was applied to query orbital (Hyperion), field, and laboratory spectra to identify sulfur-rich materials precipitated on a glacier. While sulfur, the main constituent of the deposits, is well represented in Hyperion data, minor constituents such as calcite and gypsum are partially or entirely masked. Absorption features of sulfates, where present, are shifted in wavelength due to the effects of mixing or temperature. Autonomous detection methods were successfully applied to monitor the generation and extent of the deposits, which show spectral similarities to Europa's non-ice materials. Geomicrobiological cultivation of sulfide oxidizing bacteria succeeded in demonstrating that the microbiological community present at the site has the potential to catalyze the generation of sulfur deposits. Sulfur generated in culture is present as biomineralized structures comprised of microbial filaments and sheaths along which sulfur globules are deposited. Consortia producing these structures are dominated by gamma-Proteobacteria closely related to Marinobacter, not previously known to oxidize sulfide. The sulfur structures produced by these consortia are not observed in abiotic controls and have the potential to serve as morphological biosignatures. Investigations into the biogenicity of field deposits reveal mineral assemblages with similar morphologies to those generated in culture. X-ray diffraction analyses show some evidence for rosickyite, a metastable form of biogenic sulfur. Mid-infrared laboratory spectroscopy also indicates the presence of organic functional groups diagnostic of proteins and fatty acids within the sulfur deposits. These combined investigations suggest that sulfur minerals extruded onto Europa's near surface, analogous to those of Borup Fiord pass, have the potential to contain identifiable biosignatures which low-temperature conditions could help stabilize and preserve.

Gleeson, Damhnait Fagan

2009-12-01

339

Towards a rapid and comprehensive microbial detection and identification system for life support and planetary protection applications  

NASA Astrophysics Data System (ADS)

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.

Lasseur, Christophe

340

Lava Cave Microbial Communities Within Mats and Secondary Mineral Deposits: Implications for Life Detection on Other Planets  

PubMed Central

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.

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

341

Biogeochemistry of Hot Spring Biofilms: Major and Trace Element Behavior  

NASA Astrophysics Data System (ADS)

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.

Havig, J. R.; Prapaipong, P.; Zolotova, N.; Moore, G.; Shock, E. L.

2008-12-01

342

3.5 billion years of glass bioalteration: Volcanic rocks as a basis for microbial life?  

NASA Astrophysics Data System (ADS)

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.

Staudigel, Hubert; Furnes, Harald; McLoughlin, Nicola; Banerjee, Neil R.; Connell, Laurie B.; Templeton, Alexis

2008-08-01

343

Microbial community structure across the tree of life in the extreme R?o Tinto  

PubMed Central

Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río 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.

Amaral-Zettler, Linda A; Zettler, Erik R; Theroux, Susanna M; Palacios, Carmen; Aguilera, Angeles; Amils, Ricardo

2011-01-01

344

A great leap forward in microbial ecology.  

PubMed

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds. PMID:21576878

Okabe, Satoshi; Oshiki, Mamoru; Kamagata, Yoichi; Yamaguchi, Nobuyasu; Toyofuku, Masanori; Yawata, Yutaka; Tashiro, Yosuke; Nomura, Nobuhiko; Ohta, Hiroyuki; Ohkuma, Moriya; Hiraishi, Akira; Minamisawa, Kiwamu

2010-01-01

345

Effect of nanoporous TiO2 coating and anodized Ca2+ modification of titanium surfaces on early microbial biofilm formation  

PubMed Central

Background The soft tissue around dental implants forms a barrier between the oral environment and the peri-implant bone and a crucial factor for long-term success of therapy is development of a good abutment/soft-tissue seal. Sol-gel derived nanoporous TiO2 coatings have been shown to enhance soft-tissue attachment but their effect on adhesion and biofilm formation by oral bacteria is unknown. Methods We have investigated how the properties of surfaces that may be used on abutments: turned titanium, sol-gel nanoporous TiO2 coated surfaces and anodized Ca2+ modified surfaces, affect biofilm formation by two early colonizers of the oral cavity: Streptococcus sanguinis and Actinomyces naeslundii. The bacteria were detected using 16S rRNA fluorescence in situ hybridization together with confocal laser scanning microscopy. Results Interferometry and atomic force microscopy revealed all the surfaces to be smooth (Sa ? 0.22 ?m). Incubation with a consortium of S. sanguinis and A. naeslundii showed no differences in adhesion between the surfaces over 2 hours. After 14 hours, the level of biofilm growth was low and again, no differences between the surfaces were seen. The presence of saliva increased the biofilm biovolume of S. sanguinis and A. naeslundii ten-fold compared to when saliva was absent and this was due to increased adhesion rather than biofilm growth. Conclusions Nano-topographical modification of smooth titanium surfaces had no effect on adhesion or early biofilm formation by S. sanguinis and A. naeslundii as compared to turned surfaces or those treated with anodic oxidation in the presence of Ca2+. The presence of saliva led to a significantly greater biofilm biovolume but no significant differences were seen between the test surfaces. These data thus suggest that modification with sol-gel derived nanoporous TiO2, which has been shown to improve osseointegration and soft-tissue healing in vivo, does not cause greater biofilm formation by the two oral commensal species tested than the other surfaces.

2011-01-01

346

Headwaters are critical reservoirs of microbial diversity for fluvial networks.  

PubMed

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

Besemer, Katharina; Singer, Gabriel; Quince, Christopher; Bertuzzo, Enrico; Sloan, William; Battin, Tom J

2013-10-02

347

Saturated hydraulic conductivity and biofilms: A theoretical approach linking pore and pedon scale  

NASA Astrophysics Data System (ADS)

The fate of active substances in the soil environment is shaped by soil physical properties as well as microbial life. Microorganisms degrading those substances occur in soil pores either in suspension or as biofilms on grain surfaces. At the same scale, i.e. pore scale, the soil physical properties texture, density, porosity, and water content have an impact on transport behaviour of active substances. Macroscopic parameters describe these processes at pedon scale; e.g. hydraulic conductivity summarizes the effect of named pore scale parameters. Narsilio et al. [2009] derived a relationship between the saturated hydraulic conductivity and pore scale water velocity fields based on Navier-Stokes equation for incompressible fluids. However, they did not analyse the influence of heterogeneity and microbial activity, whereas microorganisms, especially biofilms, do have an impact on hydraulic conductivity [Vandevivere and Baveye, 1992]. Biofilms alter the pore geometry while growing. This alteration directly influences the soil water flow field and hence the convective transport of active substances. Here, we present a way to couple the saturated hydraulic conductivity at macro scale to biomass population dynamics and pore space. The hydraulic conductivity will be analysed with regard to heterogeneous soils. The model combining fluid flow, reactive transport, and biofilm dynamics is applied to investigate the degradation and transport behaviour of pesticides in heterogeneous soils.

Richter, M.; Moenickes, S.; Richter, O.; Schröder, T.

2012-04-01

348

Bacterial Biofilms as Complex Communities  

NASA Astrophysics Data System (ADS)

Many microbial populations form surface-associated multicellular communities known as biofilms. These multicellular communities are encased in a self-produced extracellular matrix composed of polysaccharides and proteins. Division of labor is a key feature of these communities and different cells serve distinct functions. We have found that in biofilms of the bacterium Bacillus subtilis, different cell types including matrix-producing and sporulating cells coexist and localize to distinct regions within the structured community. We were interested in understanding how these different cell types arise. Using fluorescence reporters under the control of promoters that are specific for distinct cell types we were able to follow the dynamics of differentiation throughout biofilm development. We found that a series of extracellular signals leads to differentiation of distinct cell types during biofilm formation. In addition, we found that extracellular matrix functions as a differentiation signal for timely sporulation within a biofilm and mutants unable to produce matrix were delayed in sporulation. Our results indicate that within a biofilm, cell-cell signaling is directional in that one cell type produces a signal that is sensed by another distinct cell type. Furthermore, once differentiated, cells become resistant to the action of other signaling molecules making it possible to maintain distinct cell populations over prolonged periods.

Vlamakis, Hera

2010-03-01

349

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning  

NASA Astrophysics Data System (ADS)

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.

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

350

Microbial Biofilm Studies of the Environmental Control and Life Support System Water Recovery Test for Space Station Freedom.  

National Technical Information Service (NTIS)

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 t...

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

1992-01-01

351

Application of an iterative approach for development of a microbial model predicting the shelf-life of packed fish  

Microsoft Academic Search

An iterative approach was used to develop a microbial model for shelf-life prediction of cod fillets packed in modified atmospheres. The effect of temperature (0–15°C) and CO2 (0–100%) on growth of the specific spoilage organism, Photobacterium phosphoreum, was studied in packed cod and in liquid media. P. phosphoreum was a dominant part of the spoilage microflora of packed cod stored

Paw Dalgaard; Ole Mejlholm; Hans Henrik Huss

1997-01-01

352

Impairment of the Bacterial Biofilm Stability by Triclosan  

PubMed Central

The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (<63 µm) and exposed to a range of triclosan concentrations (control, 2 – 100 µg L?1) was monitored over time by Magnetic Particle Induction (MagPI). In parallel, bacterial cell numbers, division rate, community composition (DGGE) and EPS (extracellular polymeric substances: carbohydrates and proteins) secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI) of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality) were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of ecosystem effects.

Hubas, Cedric; Behrens, Sebastian; Ricciardi, Francesco; Paterson, David M.

2012-01-01

353

Impairment of the bacterial biofilm stability by triclosan.  

PubMed

The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition--isolated from sediments of the Eden Estuary (Scotland, UK)--on non-cohesive glass beads (<63 µm) and exposed to a range of triclosan concentrations (control, 2-100 µg L(-1)) was monitored over time by Magnetic Particle Induction (MagPI). In parallel, bacterial cell numbers, division rate, community composition (DGGE) and EPS (extracellular polymeric substances: carbohydrates and proteins) secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI) of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality) were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of ecosystem effects. PMID:22523534

Lubarsky, Helen V; Gerbersdorf, Sabine U; Hubas, Cédric; Behrens, Sebastian; Ricciardi, Francesco; Paterson, David M

2012-04-16

354

Biofilm formation of Malassezia pachydermatis from dogs.  

PubMed

Yeasts of the genus Malassezia are commensals of the normal skin microbial flora of humans and animals. These yeasts may become pathogenic under certain circumstances and their pathogenic role may be related to host immune system as well to yeast virulence factors (e.g., phospholipase production and biofilm formation). This study aims to evaluate the in vitro ability of M. pachydermatis strains to produce biofilm, and its relationship with phospholipase activity and the genetic make-up of isolates from lesioned (n=32) and healthy (n=30) dog skin. The production of biofilm was determined by crystal violet staining and scanning electronic microscopy (SEM). Biofilm was produced by almost all M. pachydermatis isolates (95.2%) from dogs with and without skin lesions at variable level and different structure. At the SEM, biofilm matrix presented adhering blastoconidia clustered in multi- or monolayer structures with variable quantity of extracellular production. Of the three genotypes detected, genotype B showed the lowest ability to produce biofilm. Of the 59 isolates producing biofilm, 33 (55.9%) produced phospholipase, with a higher biofilm formation (p<0.05) in strains collected from animals with skin lesions. It is here suggested that phospholipase production might act in synergism with the biofilm formation by inducing or exacerbating skin lesions in dogs. The results provide evidences for a better understanding of the interactions between yeasts and host immune system, toward revealing the pathogenicity of M. pachydermatis in animals. PMID:22682201

Figueredo, Luciana A; Cafarchia, Claudia; Desantis, Salvatore; Otranto, Domenico

2012-05-18

355

Imperfect asymmetry of life: earth microbial communities prefer D-lactate but can use L-lactate also.  

PubMed

Asymmetrical utilization of chiral compounds has been sought on Mars as evidence for biological activity. This method was recently validated in glucose. Earth organisms utilize D-glucose, not L-glucose, a perfect asymmetry. In this study, we tested the method in lactate and found utilization of both enantiomers. Soil-, sediment-, and lake-borne microbial communities prefer D-lactate but can consume L-lactate if given extra time to acclimate. This situation is termed imperfect asymmetry. Future life-detection mission investigators need to be aware of imperfect asymmetry so as not to miss relatively subtle signs of life. PMID:20528194

Moazeni, Faegheh; Zhang, Gaosen; Sun, Henry J

2010-05-01

356

Fungal Biofilms in the Clinical Lab Setting  

Microsoft Academic Search

Device-related infections are often associated with biofilms (microbial communities encased within polysaccharide-rich extracellular\\u000a matrix) formed by pathogens on surfaces of these devices. Candida species are the most common fungi isolated from infections associated with catheters and dentures, and both Candida and Fusarium are commonly isolated from contact lens–related infections such as fungal keratitis. These biofilms exhibit decreased susceptibility\\u000a to most

Jyotsna Chandra; Pranab K. Mukherjee; Mahmoud A. Ghannoum

2010-01-01

357

Basaltic glass as a habitat for microbial life: Implications for astrobiology and planetary exploration  

Microsoft Academic Search

Recent studies have demonstrated that terrestrial subaqueous basalts and hyaloclastites are suitable microbial habitats. During subaqueous basaltic volcanism, glass is produced by the quenching of basaltic magma upon contact with water. On Earth, microbes rapidly begin colonizing the glassy surfaces along fractures and cracks that have been exposed to water. Microbial colonization of basaltic glass leads to the alteration and

M. R. M. Izawa; N. R. Banerjee; R. L. Flemming; N. J. Bridge; C. Schultz

2010-01-01

358

Efflux Pump Inhibitor Potentiates Antimicrobial Photodynamic Inactivation of Enterococcus faecalis Biofilm  

PubMed Central

Microbial biofilm architecture contains numerous protective features including extracellular polymeric material that render biofilms impermeable to conventional antimicrobial agents. This study evaluated the efficacy of antimicrobial photodynamic inactivation (aPDI) of Enterococcus faecalis biofilms. The ability of a cationic, phenothiazinium photosensitizer, methylene blue (MB) and an anionic, xanthene photosensitizer, rose bengal (RB) to inactivate biofilms of E. faecalis (OGIRF and FA 2-2) and disrupt the biofilm structure was evaluated. Bacterial cells were tested as planktonic suspensions, intact biofilms and biofilm-derived suspensions obtained by the mechanical disruption of biofilms. The role of a specific microbial efflux pump inhibitor (EPI), verapamil hydrochloride in the MB-mediated aPDI of E. faecalis biofilms was also investigated. The results showed that E. faecalis biofilms exhibited significantly higher resistance to aPDI when compared to E. faecalis in suspension (P < 0.001). aPDI with cationic MB produced superior inactivation of E. faecalis strains in a biofilm along with significant destruction of biofilm structure when compared to anionic RB (P < 0.05). The ability to inactivate biofilm bacteria was further enhanced when the EPI was used with M B (P < 0.001). These experiments demonstrated the advantage of a cationic phenothiazinium photosensitizer combined with an EPI to inactivate biofilm bacteria and disrupt biofilm structure.

Kishen, Anil; Upadya, Megha; Tegos, George P.; Hamblin, Michael R.

2010-01-01

359

Genetic Dissection of an Exogenously Induced Biofilm in Laboratory and Clinical Isolates of E. coli  

Microsoft Academic Search

Microbial biofilms are a dominant feature of many human infections. However, developing effective strategies for controlling biofilms requires an understanding of the underlying biology well beyond what currently exists. Using a novel strategy, we have induced formation of a robust biofilm in Escherichia coli by utilizing an exogenous source of poly-N- acetylglucosamine (PNAG) polymer, a major virulence factor of many

Sasan Amini; Hani Goodarzi; Saeed Tavazoie

2009-01-01

360

Biofilm and Nanowire Production Leads to Increased Current in Geobacter sulfurreducens Fuel Cells  

Microsoft Academic Search

Geobacter sulfurreducens developed highly structured, multilayer biofilms on the anode surface of a microbial fuel cell converting acetate to electricity. Cells at a distance from the anode remained viable, and there was no decrease in the efficiency of current production as the thickness of the biofilm increased. Genetic studies demonstrated that efficient electron transfer through the biofilm required the presence

Gemma Reguera; Kelly P. Nevin; Julie S. Nicoll; Sean F. Covalla; Trevor L. Woodard; Derek R. Lovley

2006-01-01

361

Dispersion as an Important Step in the Candida albicans Biofilm Developmental Cycle  

Microsoft Academic Search

Biofilms are dynamic microbial communities in which transitions between planktonic and sessile modes of growth occur interchangeably in response to different environmental cues. In the last decade, early events associated with C. albicans biofilm formation have received considerable attention. However, very little is known about C. albicans biofilm dispersion or the mechanisms and signals that trigger it. This is important

Priya Uppuluri; Ashok K. Chaturvedi; Anand Srinivasan; Mohua Banerjee; Anand K. Ramasubramaniam; Julia R. Köhler; David Kadosh; Jose L. Lopez-Ribot

2010-01-01

362

The essential role of hydrodynamic shear force in the formation of biofilm and granular sludge  

Microsoft Academic Search

Biofilm and granular sludge processes are promising biotechnology for wastewater treatment. The formation, structure and metabolism of immobilized microbial community are associated very closely with hydrodynamic shear force in reactors. Therefore, this paper attempts to review the essential role of shear force in the formation and performance of biofilm and granular sludge. More compact, stable and denser biofilms, aerobic and

Yu Liu; Joo-Hwa Tay

2002-01-01

363

Effect of Growth Rate on Resistance of Candida albicans Biofilms to Antifungal Agents  

Microsoft Academic Search

A perfused biofilm fermentor, which allows growth-rate control of adherent microbial populations, was used to assess whether the susceptibility of Candida albicans biofilms to antifungal agents is dependent on growth rate. Biofilms were generated under conditions of glucose limitation and were perfused with drugs at a high concentration (20 times the MIC). Amphotericin B produced a greater reduction in the

GEORGE S. BAILLIE; L. JULIA DOUGLAS

1998-01-01

364

For Peer Review Only A mixed-culture model of a probiotic biofilm control system  

Microsoft Academic Search

We present a mathematical model and computer simulations for the control of a pathogenic biofilm by a probiotic biofilm. This is a substantial extension of a previous model of con- trol of a pathogenic biofilm by microbial control agents that are suspended in the aque- ous bulk phase (Khassehkhan and Eberl, Comp. Math. Meth. Med, 9(1):47-67, 2008). The mathematical model

Hermann J. Eberl; Hassan Khassehkhan; Laurent Demaret

365

Quantification ofDehalospirillum multivoransin Mixed-Culture Biofilms with an Enzyme-Linked Immunosorbent Assay  

Microsoft Academic Search

A fast, highly selective and sensitive method to quantify specific biomasses in mixed-culture biofilms is described. It consists of detachment of a biofilm from its support material, resolution of the detached biofilm flocs in order to separate the enclosed cells and antigens, and quantification of specific biomass by an enzyme-linked immunosorbent assay. Quantification of microbial biomass is an important factor

PETRA BAUER-KREISEL; MARTINA EISENBEIS; ANDHEIDRUN SCHOLZ-MURAMATSU

1996-01-01

366

Characterization of artificially dried biofilms for air biofiltration studies  

Microsoft Academic Search

One of the main problems associated with the operation of air biofilters is the loss of performance caused by drying of the bioactive support, as the removal capacity of contaminants by the microorganisms is dependent on their water content. In this work, biofilms from a microbial consortium adapted to toluene were grown on stainless steel slides. The biofilms were dried

Bibiana Cercado; Richard Auria; Beatriz Cardenas; Sergio Revah

2012-01-01

367

Bacterial biofilms: from the Natural environment to infectious diseases  

Microsoft Academic Search

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 (?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

Luanne Hall-Stoodley; J. William Costerton; Paul Stoodley

2004-01-01

368

Quantification of biofilm structures by the novel computer program COMSTAT  

Microsoft Academic Search

The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as

Arne Heydorn; Alex Toftgaard Nielsen; Morten Hentzer; Claus Sternberg; Michael Givskov; Bjarne Kjær Ersbøll; Søren Molin

2000-01-01

369

Biofilms in infectious disease and on medical devices  

Microsoft Academic Search

Microbial biofilms constitute a major reason for infections to occur and persist at various sites in the human body, especially in association with medical devices. The organisms invariably form these biofilms on surfaces which have host proteins and other substances coating them. Once adherent, the bacteria multiply and anchor themselves in quite intricate structures which appear to allow for communication

G Reid

1999-01-01

370

Effects of Bacteriocins on Methicillin-Resistant Staphylococcus aureus Biofilm.  

PubMed

Control of biofilms formed by microbial pathogens is an important subject for medical researchers, since the development of biofilms on foreign-body surfaces often causes biofilm-associated infections in patients with indwelling medical devices. The present study examined the effects of different kinds of bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by certain bacteria, on biofilms formed by a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA). The activities and modes of action of three bacteriocins with different structures (nisin A, lacticin Q, and nukacin ISK-1) were evaluated. Vancomycin, a glycopeptide antibiotic used in the treatment of MRSA infections, showed bactericidal activity against planktonic cells but not against biofilm cells. Among the tested bacteriocins, nisin A showed the highest bactericidal activity against both planktonic cells and biofilm cells. Lacticin Q also showed bactericidal activity against both planktonic cells and biofilm cells, but its activity against biofilm cells was significantly lower than that of nisin A. Nukacin ISK-1 showed bacteriostatic activity against planktonic cells and did not show bactericidal activity against biofilm cells. Mode-of-action studies indicated that pore formation leading to ATP efflux is important for the bactericidal activity against biofilm cells. Our results suggest that bacteriocins that form stable pores on biofilm cells are highly potent for the treatment of MRSA biofilm infections. PMID:23979748

Okuda, Ken-Ichi; Zendo, Takeshi; Sugimoto, Shinya; Iwase, Tadayuki; Tajima, Akiko; Yamada, Satomi; Sonomoto, Kenji; Mizunoe, Yoshimitsu

2013-08-26

371

Planetary Biology and Microbial Ecology. Biochemistry of Carbon and Early Life.  

National Technical Information Service (NTIS)

Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of compariso...

L. Margulis K. H. Nealson I. Taylor

1983-01-01

372

Indole affects biofilm formation in bacteria.  

PubMed

Biofilm is bacterial population adherent to each other and to surfaces or interfaces, often enclosed by a matrix. Various biomolecules contribute to the establishment of biofilms, yet the process of building a biofilm is still under active investigation. Indole is known as a metabolite of amino acid tryptophan, which, however, has recently been proved to participate in various aspects of bacterial life including virulence induction, cell cycle regulation, acid resistance, and especially, signaling biofilm formation. Moreover, indole is also proposed to be a novel signal involved in quorum sensing, a bacterial cooperation behavior sometimes concerning the biofilm formation. Here the signaling role and molecular mechanism of indole on bacterial biofilm formation are reviewed, as well discussed is its relation to bacterial living adaptivity. PMID:22282601

Hu, Mingxi; Zhang, Can; Mu, Yufei; Shen, Qianwei; Feng, Yongjun

2011-01-21

373

Impact of microbial attachment on intravascular catheter-related infections.  

PubMed

Intravascular catheters (IVCs) are the most frequently used medical devices in hospitals. However, they are associated with life-threatening IVC-related bloodstream infection (IVC-BSI), which is one of the main hospital-acquired infections, and continue to be associated with morbidity, mortality and additional medical cost. Most published studies focus on measuring the rate of IVC-BSIs and addressing their importance, but only a few studies have mentioned the possible routes for microbes entering the bloodstream, which would help in developing effective prevention methods, and large trial studies are lacking. Some studies on IVC-BSIs have reported the most frequently isolated microbes, but caution needs to be made since many fastidious microbes are not isolated under current laboratory conditions. Although it is known that microbes colonise IVC surfaces and develop biofilms, leading to IVC-BSI, the relationships of microbial biofilms with patients' symptoms or outcomes remain unclear. Here we discuss the knowledge gained from microbial research in other (non-IVC) medical and non-medical applications that may be helpful in understanding the IVC context. In addition, published theory and data regarding microbial colonisation and biofilm development specifically in IVCs are reviewed. More research is needed to explore mechanisms of IVC-BSI and to provide superior prevention strategies. PMID:21435841

Zhang, Li; Gowardman, John; Rickard, Claire M

2011-03-23

374

Elucidation and control of biofilm formation processes in water treatment and distribution using the Unified Biofilm Approach.  

PubMed

Controlling biological processes in water treatment and distribution is a major challenge to water supply companies. In the Netherlands, the use of chlorine-based disinfectants in water treatment is limited as much as possible and treated water is distributed without disinfectant residual in most cases. Biofilm formation processes in water treatment and distribution are studied using adenosinetriphosphate (ATP) as the parameter for active biomass. ATP measurements are applied to assess biofilm concentrations in distribution systems, in the biofilm monitor to determine the biofilm formation rate of treated water, in the biomass production potential test to determine the effect of pipe materials on microbial growth and in membrane systems to quantify biofouling. The use of a single parameter enables to compare biofilm concentrations in all situations and contributes to the understanding and control of biofilm formation processes in water treatment and distribution. This approach has been designated as the Unified Biofilm Approach. PMID:12701911

van der Kooij, D; Vrouwenvelder, J S; Veenendaal, H R

2003-01-01

375

Battling Bacterial Biofilms with Gas Discharge Plasma  

NASA Astrophysics Data System (ADS)

Most studies dealing with growth and physiology of bacteria have been carried out using free-living cells. However, most bacteria live in communities referred to as biofilms where cooperative interactions among their members make conventional methods of controlling microbial growth often ineffective. The use of gas discharge plasmas represents an alternative to traditional decontamination/sterilization methods. We studied biofilms using two organisms, Chromobacterium violaceum and Pseudomonas aeruginosa. With the first organism we demonstrated almost complete loss of cell culturability after a 5-min plasma treatment. However, additional determinations showed that non-culturable cells were still alive after short exposure times. We have recently reported the effect of plasma on P. aeruginosa biofilms grown on borosilicate coupons. In this paper, we present results for plasma treatments of 1-, 3-, and 7-day old P. aeruginosa biofilms grown on polycarbonate or stainless-steel coupons. Results indicate nearly 100% of ­biofilm inactivation after 5 min of exposure with similar inactivation kinetics for 1-, 3-, and 7-day-old biofilms, and for both materials used. The inactivation kinetics is similar for both organisms, suggesting that the method is useful regardless of the type of biofilm. AFM images show changes in biofilm structure for various plasma exposure times.

Zelaya, Anna; Vandervoort, Kurt; Brelles-Mariño, Graciela

376

The elimination of bacteria and biofilms in periodontal disease via the thermal laser  

Microsoft Academic Search

The breakdown of oral health is in almost all cases due to microbial infiltration; even in cases of neuromuscular failure due to faulty occlusion, microorganisms will take advantage of the body's stress and fatigue. Bacteria rarely travel alone or in free-floating plankton-like forms; instead they aggregate in colonies, in what are called microbial biofilms. These biofilms are nearly impossible to

Martha Cortes

2003-01-01

377

On line, non-destructive biomass determiantion of bacterial biofilms by fluorometry  

Microsoft Academic Search

Summary The lack of on-line methodology for the determination of microbial biomass and activity of attached bacteria has severely limited the study of biofilm physiology. This study showed that the fluorescent emission of aromatic amino acids in microbial biofilms can be used to determine the biomass formed on 316 stainless steel coupons. Cells resuspended from the substratum were enumerated by

Peter Angell; Andrew A. Arrage; Marc W. Mittelman; David C. White

1993-01-01

378

Seasonal Retention and Release of Cryptosporidium parvum Oocysts by Environmental Biofilms in the Laboratory ?  

PubMed Central

Cryptosporidium is a genus of waterborne protozoan parasites that causes significant gastrointestinal disease in humans. These parasites can accumulate in environmental biofilms and be subsequently released to contaminate water supplies. Natural microbial assemblages were collected each season from an eastern Pennsylvania stream and used to grow biofilms in laboratory microcosms in which influx, efflux, and biofilm retention were determined from daily oocyst counts. For each seasonal biofilm, oocysts attached to the biofilm quickly during oocyst dosing. Upon termination of oocyst dosing, the percentage of oocysts retained within the biofilm decreased to a new steady state within 5 days. Seasonal differences in biofilm retention of oocysts were observed. The spring biofilm retained the greatest percentage of oocysts, followed (in decreasing order) by the winter, summer, and fall biofilms. There was no statistically significant correlation between the percentage of oocysts attached to the biofilm and (i) any measured stream water quality parameter (including temperature, pH, conductivity, and dissolved organic carbon concentration) or (ii) experimental temperature. Seasonal differences in oocyst retention persisted when biofilms were tested with stream water from a different season. These data suggest that seasonal variation in the microbial community and resulting biofilm architecture may be more important to oocyst transport in this stream site than water quality. The biofilm attachment and detachment dynamics of C. parvum oocysts have implications for public health, and the drinking water industry should recognize that the potential exists for pathogen-free water to become contaminated during the distribution process as a result of biofilm dynamics.

Wolyniak, E. A.; Hargreaves, B. R.; Jellison, K. L.

2010-01-01

379

Performances and microbial features of an aerobic packed-bed biofilm reactor developed to post-treat an olive mill effluent from an anaerobic GAC reactor  

PubMed Central

Background Olive mill wastewater (OMW) is the aqueous effluent of olive oil producing processes. Given its high COD and content of phenols, it has to be decontaminated before being discharged. Anaerobic digestion is one of the most promising treatment process for such an effluent, as it combines high decontamination efficiency with methane production. The large scale anaerobic digestion of OMWs is normally conducted in dispersed-growth reactors, where however are generally achieved unsatisfactory COD removal and methane production yields. The possibility of intensifying the performance of the process using a packed bed biofilm reactor, as anaerobic treatment alternative, was demonstrated. Even in this case, however, a post-treatment step is required to further reduce the COD. In this work, a biological post-treatment, consisting of an aerobic biological "Manville" silica bead-packed bed aerobic reactor, was developed, tested for its ability to complete COD removal from the anaerobic digestion effluents, and characterized biologically through molecular tools. Results The aerobic post-treatment was assessed through a 2 month-continuous feeding with the digested effluent at 50.42 and 2.04 gl-1day-1 of COD and phenol loading rates, respectively. It was found to be a stable process, able to remove 24 and 39% of such organic loads, respectively, and to account for 1/4 of the overall decontamination efficiency displayed by the anaerobic-aerobic integrated system when fed with an amended OMW at 31.74 and 1.70 gl-1day-1 of COD and phenol loading rates, respectively. Analysis of 16S rRNA gene sequences of biomass samples from the aerobic reactor biofilm revealed that it was colonized by Rhodobacterales, Bacteroidales, Pseudomonadales, Enterobacteriales, Rhodocyclales and genera incertae sedis TM7. Some taxons occurring in the influent were not detected in the biofilm, whereas others, such as Paracoccus, Pseudomonas, Acinetobacter and Enterobacter, enriched significantly in the biofilter throughout the treatment. Conclusion The silica-bead packed bed biofilm reactor developed and characterized in this study was able to significantly decontaminate anaerobically digested OMWs. Therefore, the application of an integrated anaerobic-aerobic process resulted in an improved system for valorization and decontamination of OMWs.

Bertin, Lorenzo; Colao, Maria Chiara; Ruzzi, Maurizio; Marchetti, Leonardo; Fava, Fabio

2006-01-01

380

Marine bacterial isolates inhibit biofilm formation and disrupt mature biofilms of Pseudomonas aeruginosa PAO1  

Microsoft Academic Search

According to the Centers for Disease Control and Prevention, biofilms cause 65% of infections in developed countries. Pseudomonas aeruginosa biofilm cause life threatening infections in cystic fibrosis infection and they are 1,000 times more tolerant to antibiotic\\u000a than the planktonic cells. As quorum sensing, hydrophobicity index and extracellular polysaccharide play a crucial role in\\u000a biofilm formation, extracts from 46 marine

Chari Nithya; Mansur Farzana Begum; Shunmugiah Karutha Pandian

2010-01-01

381

Potential Application of Phage Therapy Against Pseudomonas aeruginosa Biofilm Infection in Cystic Fibrosis Patients  

Microsoft Academic Search

Majority of the microbial activity in humans is in the form of biofilms i.e. an Exopolysaccharide-enclosed bacterial mass. Unlike planktonic cells and the cells on the surface of the biofilm, the biofilm-embedded cells are more resistant to the effects of the antibiotics and the host cellular defense mechanisms. A combination of biofilm growth and inherent resistance prevents effective antibiotics treatment

Aditi Gurkar

2005-01-01

382

Needle-Type Multi-Analyte MEMS Sensor Arrays for In Situ Measurements in Biofilms  

Microsoft Academic Search

\\u000a Biofilms are colonies of microbial cells in a polymeric matrix. Formation of biofilms has been associated with a broad range\\u000a of industrial problems at the annual cost of billions of dollars. For example, biofilms are ubiquitous in water distribution\\u000a systems and control of their growth have been a great challenge, with many water utilities in the US reporting biofilm survival

Jin-Hwan Lee; Youngwoo Seo; Woo Hyoung Lee; Paul Bishop; Ian Papautsky

383

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells  

PubMed Central

Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological properties compared to free living microorganisms. Biofilms in nature are often difficult to investigate and reside under poorly defined conditions1. Using a transparent substratum it is possible to device a system where simple biofilms can be examined in a non-destructive way in real-time: here we demonstrate the assembly and operation of a flow cell model system, for in vitro 3D studies of microbial biofilms generating high reproducibility under well-defined conditions2,3. The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows a continuous supply of nutrients and administration of e.g. antibiotics with minimal disturbance of the cells grown in the flow chamber. Moreover, the flow conditions within the flow cell allow studies of biofilm exposed to shear stress. A bubble trapping device confines air bubbles from the tubing which otherwise could disrupt the biofilm structure in the flow cell. The flow cell system is compatible with Confocal Laser Scanning Microscopy (CLSM) and can thereby provide highly detailed 3D information about developing microbial biofilms. Cells in the biofilm can be labeled with fluorescent probes or proteins compatible with CLSM analysis. This enables online visualization and allows investigation of niches in the developing biofilm. Microbial interrelationship, investigation of antimicrobial agents or the expression of specific genes, are of the many experimental setups that can be investigated in the flow cell system.

Weiss Nielsen, Martin; Sternberg, Claus; Molin, S?ren; Regenberg, Birgitte

2011-01-01

384

Ecology and life history of an amoebomastigote, Paratetramitus jugosus, from a microbial mat: new evidence for multiple fission.  

PubMed

Five microbial habitats (gypsum crust, gypsum photosynthetic community, Microcoleus mat, Thiocapsa scum, and black mud) were sampled for the presence of the euryhaline, rapidly growing amoebomastigote, Paratetramitus jugosus. Field investigations of microbial mats from Baja California Norte, Mexico, and Salina Bido near Matanzas, Cuba, reveal that P. jugosus is most frequently found in the Thiocapsa layer of microbial mats. Various stages of the life history were studied using phase-contrast, differential-interference, and transmission electron microscopy. Mastigote stages were induced and studied by electron microscopy; mastigotes that actively feed on bacteria bear two or more undulipodia. A three-dimensional drawing of the kinetid ("basal apparatus") based on electron micrographs is presented. Although promitoses were occasionally observed, it is unlikely that they can account for the rapid growth of P. jugosus populations on culture media. Dense, refractile, spherical, and irregular-shaped bodies were seen at all times in all cultures along with small mononucleate (approximately 2-7 micrometers diameter) amoebae. Cytochemical studies employing two different fluorescent stains for DNA (DAPI, mithramycin) verified the presence of DNA in these small bodies. Chromatin-like material seen in electron micrographs within the cytoplasm and blebbing off nuclei were interpreted to the chromatin bodies. Our interpretation, consistent with the data but not proven, is that propagation by multiple fission of released chromatin bodies that become small amoebae may occur in Paratetramitus jugosus. These observations are consistent with descriptions of amoeba propagules in the early literature (Hogue, 1914). PMID:11539079

Enzien, M; McKhann, H I; Margulis, L

1989-08-01

385

Fungal Biofilms: Relevance in the Setting of Human Disease  

PubMed Central

The use of indwelling medical devices is rapidly growing and is often complicated by infections with biofilm-forming microbes that are resistant to antimicrobial agents and host defense mechanisms. Fungal biofilms have emerged as a clinical problem associated with these medical device infections, causing significant morbidity and mortality. This review discusses the recent advances in the understanding of fungal biofilms, including the role of fungal surface components in adherence, gene expression, and quorum sensing in biofilm formation. We propose novel strategies for the prevention or eradication of microbial colonization of medical prosthetic devices.

Martinez, Luis R.; Fries, Bettina C.

2011-01-01

386

Modulation of metabolism and switching to biofilm prevail over exopolysaccharide production in the response of Rhizobium alamii to cadmium.  

PubMed

Heavy metals such as cadmium (Cd(2+)) affect microbial metabolic processes. Consequently, bacteria adapt by adjusting their cellular machinery. We have investigated the dose-dependent growth effects of Cd(2+) on Rhizobium alamii, an exopolysaccharide (EPS)-producing bacterium that forms a biofilm on plant roots. Adsorption isotherms show that the EPS of R. alamii binds cadmium in competition with calcium. A metabonomics approach based on ion cyclotron resonance Fourier transform mass spectrometry has showed that cadmium alters mainly the bacterial metabolism in pathways implying sugars, purine, phosphate, calcium signalling and cell respiration. We determined the influence of EPS on the bacterium response to cadmium, using a mutant of R. alamii impaired in EPS production (MS?GT). Cadmium dose-dependent effects on the bacterial growth were not significantly different between the R. alamii wild type (wt) and MS?GT strains. Although cadmium did not modify the quantity of EPS isolated from R. alamii, it triggered the formation of biofilm vs planktonic cells, both by R. alamii wt and by MS?GT. Thus, it appears that cadmium toxicity could be managed by switching to a biofilm way of life, rather than producing EPS. We conclude that modulations of the bacterial metabolism and switching to biofilms prevails in the adaptation of R. alamii to cadmium. These results are original with regard to the conventional role attributed to EPS in a biofilm matrix, and the bacterial response to cadmium. PMID:22096497

Schue, Mathieu; Fekete, Agnes; Ortet, Philippe; Brutesco, Catherine; Heulin, Thierry; Schmitt-Kopplin, Philippe; Achouak, Wafa; Santaella, Catherine

2011-11-09

387

A novel planar flow cell for studies of biofilm heterogeneity and flow-biofilm interactions  

PubMed Central

Biofilms are microbial communities growing on surfaces, and are ubiquitous in nature, in bioreactors, and in human infection. Coupling between physical, chemical, and biological processes is known to regulate the development of biofilms; however, current experimental systems do not provide sufficient control of environmental conditions to enable detailed investigations of these complex interactions. We developed a novel planar flow cell that supports biofilm growth under complex two-dimensional fluid flow conditions. This device provides precise control of flow conditions and can be used to create well-defined physical and chemical gradients that significantly affect biofilm heterogeneity. Moreover, the top and bottom of the flow chamber are transparent, so biofilm growth and flow conditions are fully observable using non-invasive confocal microscopy and high-resolution video imaging. To demonstrate the capability of the device, we observed the growth of Pseudomonas aeruginosa biofilms under imposed flow gradients. We found a positive relationship between patterns of fluid velocity and biofilm biomass because of faster microbial growth under conditions of greater local nutrient influx, but this relationship eventually reversed because high hydrodynamic shear leads to the detachment of cells from the surface. These results reveal that flow gradients play a critical role in the development of biofilm communities. By providing new capability for observing biofilm growth, solute and particle transport, and net chemical transformations under user-specified environmental gradients, this new planar flow cell system has broad utility for studies of environmental biotechnology and basic biofilm microbiology, as well as applications in bioreactor design, environmental engineering, biogeochemistry, geomicrobiology, and biomedical research.

Zhang, Wei; Sileika, Tadas S.; Chen, Cheng; Liu, Yang; Lee, Jisun; Packman, Aaron I.

2012-01-01

388

Modified a colony forming unit microbial adherence to hydrocarbons assay and evaluated cell surface hydrophobicity and biofilm production of Vibrio scophthalmi  

Technology Transfer Automated Retrieval System (TEKTRAN)

Vibrio scophthalmi has been considered as an opportunistic pathogen of the flat fish. There is little information available on V. scophthalmi adhesion to the host, an important step in the initial infection process. The objectives of this study were to (1) develop a modified Microbial Adherence to H...

389

Microbial life in terrestrial permafrost: methanogenesis and nitrification in Gelisols as potentials for exobiological processes  

Microsoft Academic Search

The comparability of environmental and climatic conditions of the early Mars and Earth is of special interest for the actual research in astrobiology. Martian surface and terrestrial permafrost areas show similar morphological structures, which suggests that their development is based on comparable processes. Soil microbial investigations of adaptation strategies of microorganisms from terrestrial permafrost in combination with environmental, geochemical and

Dirk Wagner; Eva Spieck; Eberhard Bock; Eva-Maria Pfeiffer

2002-01-01

390

The Impact of Microbially Influenced Corrosion on Spent Nuclear Fuel and Storage Life  

SciTech Connect

A study was performed to evaluate if microbial activity could be considered a threat to spent nuclear fuel integrity. The existing data regarding the impact of microbial influenced corrosion (MIC) on spent nuclear fuel storage does not allow a clear assessment to be made. In order to identify what further data are needed, a literature survey on MIC was accomplished with emphasis on materials used in nuclear fuel fabrication, e.g., A1, 304 SS, and zirconium. In addition, a survey was done at Savannah River, Oak Ridge, Hanford, and the INEL on the condition of their wet storage facilities. The topics discussed were the SNF path forward, the types of fuel, ramifications of damaged fuel, involvement of microbial processes, dry storage scenarios, ability to identify microbial activity, definitions of water quality, and the use of biocides. Information was also obtained at international meetings in the area of biological mediated problems in spent fuel and high level wastes. Topics dis cussed included receiving foreign reactor research fuels into existing pools, synergism between different microbes and other forms of corrosion, and cross contamination.

J. H. Wolfram; R. E. Mizia; R. Jex; L. Nelson; K. M. Garcia

1996-10-01

391

Viable halobacteria from Permo-Triassic salt deposits and the possibility of extraterrestrial microbial life  

Microsoft Academic Search

The range of physico-chemical parameters for the presence of life is ever expanding, making it conceivable to search in seemingly inhospitable environments for extraterrestrial forms of life. Extremely halophilic archaebacteria (haloarchaea) were isolated from ancient salt deposits, adding another dimension - potentially exorbitant longevity - to the unusual characteristics of prokaryotic life. Distribution of haloarchaea in salt sediments appears to

H. Stan-Lotter; C. Radax; C. Gruber; A. Legat; M. Pfaffenhuemer; H. Wieland

2001-01-01

392

Characterisation of two quorum sensing systems in the endophytic Serratia plymuthica strain G3: differential control of motility and biofilm formation according to life-style  

PubMed Central

Background N-acylhomoserine lactone (AHL)-based quorum sensing (QS) systems have been described in many plant-associated Gram-negative bacteria to control certain beneficial phenotypic traits, such as production of biocontrol factors and plant growth promotion. However, the role of AHL-mediated signalling in the endophytic strains of plant-associated Serratia is still poorly understood. An endophytic Serratia sp. G3 with biocontrol potential and high levels of AHL signal production was isolated from the stems of wheat and the role of QS in this isolate was determined. Results Strain G3 classified as Serratia plymuthica based on 16S rRNA was subjected to phylogenetic analysis. Using primers to conserved sequences of luxIR homologues from the Serratia genus, splIR and spsIR from the chromosome of strain G3 were cloned and sequenced. AHL profiles from strain G3 and Escherichia coli DH5? expressing splI or spsI from recombinant plasmids were identified by liquid chromatography-tandem mass spectrometry. This revealed that the most abundant AHL signals produced by SplI in E. coli were N-3-oxo-hexanoylhomoserine lactone (3-oxo-C6-HSL), N-3-oxo-heptanoylhomoserine lactone (3-oxo-C7-HSL), N-3-hydroxy-hexanoylhomoserine lactone (3-hydroxy-C6-HSL), N-hexanoylhomoserine lactone (C6-HSL), and N-heptanoyl homoserine lactone (C7-HSL); whereas SpsI was primarily responsible for the synthesis of N-butyrylhomoserine lactone (C4-HSL) and N-pentanoylhomoserine lactone (C5-HSL). Furthermore, a quorum quenching analysis by heterologous expression of the Bacillus A24 AiiA lactonase in strain G3 enabled the identification of the AHL-regulated biocontrol-related traits. Depletion of AHLs with this lactonase resulted in altered adhesion and biofilm formation using a microtiter plate assay and flow cells coupled with confocal laser scanning microscopy respectively. This was different from the closely related S. plymuthica strains HRO-C48 and RVH1, where biofilm formation for both strains is AHL-independent. In addition, QS in G3 positively regulated antifungal activity, production of exoenzymes, but negatively regulated production of indol-3-acetic acid (IAA), which is in agreement with previous reports in strain HRO-C48. However, in contrast to HRO-C48, swimming motility was not controlled by AHL-mediated QS. Conclusions This is the first report of the characterisation of two AHL-based quorum sensing systems in the same isolate of the genus Serratia. Our results show that the QS network is involved in the global regulation of biocontrol-related traits in the endophytic strain G3. However, although free-living and endophytic S. plymuthica share some conservation on QS phenotypic regulation, the control of motility and biofilm formation seems to be strain-specific and possible linked to the life-style of this organism.

2011-01-01

393

Biofilms: United They Stand, Divided They Colonize  

NSDL National Science Digital Library

Curricular materials designed to teach parallel computational modeling to undergraduate or graduate students in science and other STEM disciplines. The module begins with the construction of a cellular automaton model of microbial biofilms using Mathematica. This model is then re-implemented with C and parallelized using MPI.

Shiflet, Angela B.; Shiflet, George W.; Ellison, Shay M.

394

Rock Surfaces as Life Indicators: New Ways to Demonstrate Life and Traces of Former Life  

NASA Astrophysics Data System (ADS)

Life and its former traces can only be detected from space when they are abundant and exposed to the planetary atmosphere at the moment of investigation by orbiters. Exposed rock surfaces present a multifractal labyrinth of niches for microbial life. Based upon our studies of highly stress-resistant microcolonial fungi of stone monument and desert rock surfaces, we propose that microbial biofilms that develop and become preserved on rock surfaces can be identified remotely by the following characteristics: (1) the existence of spectroscopically identifiable compounds that display unique adsorption, diffraction, and reflection patterns characteristic of biogenerated organic compounds (e.g., chlorophylls, carotenes, melanins, and possibly mycosporines), (2) demonstrably biogenic geomorphological features (e.g., biopitting, biochipping, and bioexfoliation), and (3) biominerals produced in association with biofilms that occupy rock surfaces (e.g., oxalates, forsterite, and special types of carbonates, sulfides, and silicates). Such traces or biosignatures of former life could provide macroscopically visible morphotypes and chemically identifiable products uniquely indicative of life. This work was supported by DFG grants Go 897/2-1 and Kr 333/30-1.

Gorbushina, A. A.; Krumbein, W. E.; Volkmann, M.

2002-12-01

395

Uranium Immobilization by Sulfate-reducing Biofilms  

SciTech Connect

Hexavalent uranium [U(VI)] was immobilized using biofilms of the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans G20. The biofilms were grown in flat-plate continuous-flow reactors using lactate as the electron donor and sulfate as the electron acceptor. U(VI) was continuously fed into the reactor for 32 weeks at a concentration of 126 íM. During this time, the soluble U(VI) was removed (between 88 and 96% of feed) from solution and immobilized in the biofilms. The dynamics of U immobilization in the sulfate-reducing biofilms were quantified by estimating: (1) microbial activity in the SRB biofilm, defined as the hydrogen sulfide (H2S) production rate and estimated from the H2S concentration profiles measured using microelectrodes across the biofilms; (2) concentration of dissolved U in the solution; and (3) the mass of U precipitated in the biofilm. Results suggest that U was immobilized in the biofilms as a result of two processes: (1) enzymatically and (2) chemically, by reacting with microbially generated H2S. Visual inspection showed that the dissolved sulfide species reacted with U(VI) to produce a black precipitate. Synchrotron-based U L3-edge X-ray absorption near edge structure (XANES) spectroscopy analysis of U precipitated abiotically by sodium sulfide indicated that U(VI) had been reduced to U(IV). Selected-area electron diffraction pattern and crystallographic analysis of transmission electron microscope lattice-fringe images confirmed the structure of precipitated U as being that of uraninite.

Beyenal, Haluk; Sani, Rajesh K.; Peyton, Brent M.; Dohnalkova, Alice; Amonette, James E.; Lewandowski, Zbigniew

2004-04-01

396

Mechanism and risk factors of oral biofilm formation.  

PubMed

Recent microbiological investigations completely changed our understanding of the role of biofilm in the formation of the mucosal immune barrier and in pathogenesis of chronic inflammation of bacterial etiology. It is now clear that formation of bacterial biofilm on dental surfaces is characteristic for existence of oral microbial communities. It has also been proved that uncontrolled biofilms on dental tissues, as well as on different biomaterials (e.g. orthodontic appliances), are the main cause of dental diseases such as dental caries and periodontitis. The aim of this paper is to explain mechanisms and consequences of orthodontic biofilm formation. We will discuss current opinions on the influence of different biomaterials employed for orthodontic treatment in biofilm formation and new strategies employed in prevention and elimination of oral biofilm ("dental plaque"). PMID:24018439

Pasich, Ewa; Walczewska, Maria; Pasich, Adam; Marcinkiewicz, Janusz

2013-08-02

397

Formation of biofilms in drinking water distribution networks, a case study in two cities in Finland and Latvia  

Microsoft Academic Search

The formation of biofilms in drinking water distribution networks is a significant technical, aesthetic and hygienic problem. In this study, the effects of assimilable organic carbon, microbially available phosphorus (MAP), residual chlorine, temperature and corrosion products on the formation of biofilms were studied in two full-scale water supply systems in Finland and Latvia. Biofilm collectors consisting of polyvinyl chloride pipes

Markku J. Lehtola; T?lis Juhna; Ilkka T. Miettinen; Terttu Vartiainen; Pertti J. Martikainen

2004-01-01

398

Differential Lipopolysaccharide Core Capping Leads to Quantitative and Correlated Modifications of Mechanical and Structural Properties in Pseudomonas aeruginosa Biofilms  

Microsoft Academic Search

Bacterial biofilms are responsible for the majority of all microbial infections and have profound impact on industrial and geochemical processes. While many studies documented phenotypic differentiation and gene regulation of biofilms, the importance of their structural and mechanical properties is poorly understood. Here we investigate how changes in lipopolysaccharide (LPS) core capping in Pseudomonas aeruginosa affect biofilm structure through modification

Peter C. Y. Lau; Theresa Lindhout; Terry J. Beveridge; John R. Dutcher; Joseph S. Lam

2009-01-01

399

Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis  

SciTech Connect

Abstract: The morphological and structural properties of microbial biofilms are influenced by internal substrate diffusion and utilization processes. In the case of microbial hydrolysis of plant cell walls, only thin and uniform biofilm structures are typically formed by cellulolytic microorganisms. In this study, we develop a hydrolysate diffusion and utilization model system to examine factors influencing cellulolytic biofilm formation. Model simulations using Caldicellulosiruptor obsidiansis as a representative organism, reveal that the growth of the cellulolytic biofilm is limited by hydrolysate utilization but not diffusion. As a consequence, the cellulolytic biofilm has a uniform growth rate, and there is a hydrolysate surplus that diffuses through the cellulolytic biofilm into the bulk solution where it is consumed by planktonic cells. Predictions based on the model were tested in a cellulose fermentation study and the results are consistent with the model and previously reported experimental data. The factors determining the rate-limiting step of biofilm growth are also analyzed.

Wang, Zhiwu [ORNL; Hamilton-Brehm, Scott [ORNL; Lochner, Adriane [ORNL; Elkins, James G [ORNL; Morrell-Falvey, Jennifer L [ORNL

2011-01-01

400

Do Inactivated Microbial Preparations Improve Life History Traits of the Copepod Acartia tonsa ?  

Microsoft Academic Search

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\\u000a and quality of copepods in culture (increased egg production and hatching success, HS). This was carried out because the use\\u000a of copepods as live prey

Guillaume Drillet; Tahina Rabarimanantsoa; Stéphane Frouël; Jacob S. Lamson; Anette M. Christensen; Sandra Kim-Tiam; Benni W. Hansen