Molecular Analysis of Shower Curtain Biofilm Microbes

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 “soap scum,” which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the α-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.     

Microbial diversity of biofilms in dental unit water systems

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

Desmids and Biofilms of Freshwater Wetlands: Development and Microarchitecture

Freshwater wetlands constitute important ecosystems, and their benthic, attached microbial communities, including biofilms, represent key habitats that contribute to primary productivity, nutrient cycling, and substrate stabilization. In many wetland biofilms, algae constitute significant parts of the microbial population, yet little is known about their activities in these communities. An analysis of wetland biofilms from the Adirondack region of New York (USA) was performed with special emphasis on desmids, a group of evolutionarily advanced green algae commonly found in these habitats. Desmids constituted as much as 23.7% of the total algal and cyanobacterial flora of the biofilms during the July and August study periods. These algae represented some of the first eukaryotes to colonize new substrates, and during July their numbers correlated with fluctuations in general biofilm parameters such as biofilm thickness and dry weight as well as total carbohydrate. Significant numbers of bacteria were associated with both the EPS sheaths and cell wall surfaces of the desmids. Colonization of new substrates and development of biofilms were rapid and were followed by various fluctuations in microbial community structure over the short- and long-term observations. In addition to desmids, diatoms, filamentous green algae and transient non-motile phases of flagellates represented the photosynthetic eukaryotes of these biofilms.     

Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis

In patients afflicted with cystic fibrosis (CF), morbidity and mortality are primarily associated with the adverse consequences of chronic microbial bronchial infections, which are thought to be caused by a few opportunistic pathogens. However, recent evidence suggests the presence of other microorganisms, which may significantly affect the course and outcome of the infection. Using a combination of 16S rRNA gene clone libraries, bacterial culturing and pyrosequencing of barcoded 16S rRNA amplicons, the microbial communities present in CF patient sputum samples were examined. In addition to previously recognized CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus, >60 phylogenetically diverse bacterial genera that are not typically associated with CF pathogenesis were also detected. A surprisingly large number of fermenting facultative and obligate anaerobes from multiple bacterial phyla was present in each sample. Many of the bacteria and sequences found were normal residents of the oropharyngeal microflora and with many containing opportunistic pathogens. Our data suggest that these undersampled organisms within the CF lung are part of a much more complex microbial ecosystem than is normally presumed. Characterization of these communities is the first step in elucidating potential roles of diverse bacteria in disease progression and to ultimately facilitate advances in CF therapy.     

Effects of polymicrobial communities on host immunity and response

Microorganisms grow as members of microbial communities in unique niches, such as the mucosal surfaces of the human body. These microbial communities, containing both commensals and opportunistic pathogens, serve to keep individual pathogens 'in check' through a variety of mechanisms and complex interactions, both between the microorganisms themselves and the microorganisms and the host. Recent studies shed new light on the diversity of microorganisms that form the human microbial communities and the interactions these microbial communities have with the host to stimulate immune responses. This occurs through their recognition by dendritic cells or their ability to induce differential cytokine and defensin profiles. The differential induction of defensins by commensals and pathogens and the ability of the induced defensins to interact with the antigens from these microorganisms may attenuate proinflammatory signaling and trigger adaptive immune responses to microbial antigens in a multistep process. Such an activity may be a mechanism that the host uses to sense what is on its mucosal surfaces, as well as to differentiate among commensals and pathogens.     

Microbial biofilms on facial prostheses

The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.     

Microbial biofilms on facial prostheses

The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.     

In Vitro Modulation of E. coli Community Behavior and Human Innate Immune System by Lantibiotic Nisin

Biofilms are microbial communities with genetically divergent microorganisms. Such communal behavior is known to provide survival benefit to the unicellular organisms in adverse conditions. Pathogenicity of opportunistic bacterial pathogens largely depends on their success in proper quorum establishment and biofilm formation. Thus molecules causing quorum-sensing attenuation, preventing the biofilm formation or instigating preformed biofilm dislodgement could serve as attractive drugs/drug supplements. Here we investigate the effect of nisin??type A lantibiotic naturally produced by Lactococcus lactis??on laboratory developed Escherichia coli biofilms and on isolated human neutrophils. Activity evaluation was done on the biofilms of clinical isolates of E. coli, developed on glass slides in a simple static bioreactor design. Nisin not only inhibited the formation but also effectively dislodged the preformed E. coli biofilms developed on glass surfaces. Presence of nisin also demonstrated a significant decrease in the expression of E. coli virulence factors viz. hemolysin and curli expression. The microorganisms dislodged from the biofilms and set free in the circulation of infected host might later reassociate to form new biofilms after nisin clearance from circulation. Thus complete eradication of infective bacterium will depend on stimulatory effect of nisin (if any) on human immune system cells. Therefore modulation of human neutrophil activity by nisin was also evaluated. Presence of nisin induced neutrophil extracellular trap (NET) formation or NETosis in a manner similar to that demonstrated by LPS (lipopolysaccharide) in vitro. Our results thus present nisin as a plausible molecule to be used in treatment of chronic bacterial infections as it indicated increased fitness for the same.     

Biofilms, infectious agents, and dental unit waterlines: a review

Aquatic biofilms, which are widespread not only in nature but also in medical and dental devices, can be the source of serious nosocomial infections. In these hardy microbial communities, pathogens like nontuberculous mycobacteria, Pseudomonas aeruginosa, Legionella pneumophila, and other bacteria not only survive but proliferate and lie in wait for susceptible hosts. Not only are these organisms intrinsically resistant to high temperatures and biocides, but the biofilms they inhabit enhance their resistance. This should be of concern to infection control practitioners. The bacterial colonization of dental unit waterlines can be used as a model to investigate the problem of waterborne biofilms in health care settings.     

Enterococci in the Environment

Summary: Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.     

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

Potential pathogens from shower water and aerosolized shower mist (i.e., shower aerosol) have been suggested as an environmental source of infection for immunocompromised patients. To quantify the microbial load in shower water and aerosol samples, we used culture, microscopic, and quantitative PCR methods to investigate four shower stalls in a stem cell transplant unit at Barnes-Jewish Hospital in St. Louis, MO. We also tested membrane-integrated showerheads as a possible mitigation strategy. In addition to quantification, a 16S rRNA gene sequencing survey was used to characterize the abundant bacterial populations within shower water and aerosols. The average total bacterial counts were 2.2 × 10⁷ cells/liter in shower water and 3.4 × 10⁴ cells/m³ in shower aerosol, and these counts were reduced to 6.3 × 10⁴ cells/liter (99.6% efficiency) and 8.9 × 10³ cells/m³ (82.4% efficiency), respectively, after membrane-integrated showerheads were installed. Potentially pathogenic organisms were found in both water and aerosol samples from the conventional showers. Most notable was the presence of Mycobacterium mucogenicum (99.5% identity) in the water and Pseudomonas aeruginosa (99.3% identity) in the aerosol samples. Membrane-integrated showerheads may protect immunocompromised patients from waterborne infections in a stem cell transplant unit because of efficient capture of vast numbers of potentially pathogenic bacteria from hospital water. However, an in-depth epidemiological study is necessary to investigate whether membrane-integrated showerheads reduce hospital-acquired infections. The microbial load in shower aerosols with conventional showerheads was elevated compared to the load in HEPA-filtered background air in the stem cell unit, but it was considerably lower than typical indoor air. Thus, in shower environments without HEPA filtration, the increase in microbial load due to shower water aerosolization would not have been distinguishable from anticipated variations in background levels.Hospital water supplies are frequently inhabited with environmental waterborne microbes, including bacteria (Legionella pneumophila, Pseudomonas aeruginosa, Mycobacterium avium, Stenotrophomonas maltophilia, and Achromobacter spp.) and fungi (Aspergillus spp. and Fusarium spp.) (4, 13, 63). Although water storage tanks may be cleaned annually and residual chlorine levels of water contents maintained, these measures alone cannot prevent the formation of biofilms along inert surfaces of the tank and piping systems. Biofilms attached to living and inert surfaces consist of complex communities of microbes that produce glycocalyx polysaccharides, which protect bacteria from desiccation, chemical treatments, and immunologic attack (25). They can form quickly and have been found in dental water lines only a few weeks after installation (14). Finally, biofilms can harbor pathogens that are periodically released through sloughing of fringe layers (25, 70). Common point-of-use sources of potential exposure to waterborne microbes contained in biofilms in the health care setting include showerheads, water tanks, faucets, aerators, water fountains, and ice machines (2, 4, 13, 31, 34, 38, 68).While microbes found in water usually pose no risk for healthy individuals, they can be opportunistic pathogens capable of causing serious and life-threatening infections in severely immunocompromised individuals. Patients with cancers of the blood, lymph, and bone marrow (leukemia, lymphoma, and myeloma) are frequently treated with intense chemotherapy, irradiation, and/or stem cell transplant, resulting in neutropenia and profound immunosuppression. Stem cell transplant patients are encouraged to bathe or shower daily before and after transplant to help maintain skin integrity; these patients also almost universally have a central venous access device for the administration of chemotherapy and other medications. Opportunistic microbes in shower water may contaminate the central venous catheter and provide a mechanism for bacterial invasion into the bloodstream (48). Once a patient has become infected, treatment of these organisms may be more difficult because of antibiotic resistance. Thus, severely immunosuppressed patients are at risk of significant morbidity and mortality from exposure to health care-acquired environmental pathogens.Although there is no data on bacteria in hospital showers, the shower environment, particularly the aerosolized shower mist (i.e., shower aerosol), has long been suspected as a source of opportunistic pathogens (4, 10). Inhalation of aerosolized pathogenic bacteria in the shower may result in respiratory infections and dissemination of organisms from the lungs into the bloodstream. The advent of high-throughput sequencing now allows for qualifying the bacterial composition in aerosols (23, 28). Angenent et al. (5) investigated the aerosols generated from an indoor therapy pool environment in which multiple staff members contracted Mycobacterium avium infections and hypersensitivity pneumonitis (i.e., swelling of alveoli due to an immunologic reaction to airborne particles). A fraction (>30%) of the bacteria in pool water was identified as M. avium, which preferentially partitioned into the aerosol (>80%) (5). In a previous study conducted by Bollin et al. (10), Legionella pneumophila isolates were collected from shower and sink aerosols; however, to our knowledge, there are no published studies that document the effectiveness of membrane-integrated showerheads in decreasing the microbial load in indoor air.We investigated whether shower stalls in a stem cell transplant unit in a hospital could be a source of potential pathogens by quantifying and qualifying the bacterial load, colony count, and bacterial DNA in shower water and air. An engineering control that consisted of a showerhead with an integrated 0.2-μm-pore-size membrane was utilized to ascertain whether conventional hospital showers aerosolize bacteria and therefore whether a significant increase in the bacterial load was observed compared to HEPA-filtered background air. A total of four shower stalls in individual rooms in a stem cell transplant unit were evaluated during two seasonal sampling periods (two stalls per season). Each shower stall was sampled for 3 days with a conventional showerhead in place and then for 3 days with a membrane-integrated showerhead installed in the same shower. Our goal was to determine the overall mitigation effectiveness of utilizing membrane-integrated showerheads in reducing the presence of potentially pathogenic bacteria from shower water and aerosols. Patient infections were not evaluated during the course of this study.     

Molecular characterization of subject-specific oral microflora during initial colonization of enamel

The initial microbial colonization of tooth surfaces is a repeatable and selective process, with certain bacterial species predominating in the nascent biofilm. Characterization of the initial microflora is the first step in understanding interactions among community members that shape ensuing biofilm development. Using molecular methods and a retrievable enamel chip model, we characterized the microbial diversity of early dental biofilms in three subjects. A total of 531 16S rRNA gene sequences were analyzed, and 97 distinct phylotypes were identified. Microbial community composition was shown to be statistically different among subjects. In all subjects, however, 4-h and 8-h communities were dominated by Streptococcus spp. belonging to the Streptococcus oralis/Streptococcus mitis group. Other frequently observed genera (comprising at least 5% of clone sequences in at least one of the six clone libraries) were Actinomyces, Gemella, Granulicatella, Neisseria, Prevotella, Rothia, and Veillonella. Fluorescence in situ hybridization (FISH) confirmed that the proportion of Streptococcus sp. sequences in the clone libraries coincided with the proportion of streptococcus probe-positive organisms on the chip. FISH also revealed that, in the undisturbed plaque, not only Streptococcus spp. but also the rarer Prevotella spp. were usually seen in small multigeneric clusters of cells. This study shows that the initial dental plaque community of each subject is unique in terms of diversity and composition. Repetitive and distinctive community composition within subjects suggests that the spatiotemporal interactions and ecological shifts that accompany biofilm maturation also occur in a subject-dependent manner.     

Bacterial composition of biofilms formed on dairy-processing equipment

Abstract

Polymicrobial biofilms often form on the surfaces of food-processing machinery, causing equipment damage and posing a contamination risk for the foods processed by the system. The composition of the microbial communities that make up these biofilms is largely unknown, especially in the dairy industry. To address this deficit, we investigated the bacterial composition of biofilms that form on the surfaces of equipment during dairy processing using Illumina MiSeq sequencing and culture-dependent methods. Illumina sequencing identified eight phyla, comprising six classes, ten orders, fifteen families, eighteen genera, and eighteen species. In contrast, only eight species were isolated from the same samples using the culture-based method. To determine the ability of the identified bacteria to form biofilms, biofilm formation analysis via crystal violet staining was performed. Five of the eight culturable species, Acinetobacter baumannii, Acinetobacter junii, Enterococcus faecalis, Corynebacterium callunae, and Stenotrophomonas maltophilia, were able to form biofilms. Since most of the identified bacteria are potential food-borne or opportunistic pathogens, this study provides guidance for quality control of products produced in dairy processing facilities.     

A glimpse under the rim – the composition of microbial biofilm communities in domestic toilets

Aim: To determine the microbial composition of biofilms in domestic toilets by molecular means. Methods and Results: Genomic DNA was extracted from six biofilm samples originating from households around Düsseldorf, Germany. While no archaeal 16S rRNA or fungal ITS genes were detected by PCR, fingerprinting of bacterial 16S rRNA genes revealed a diverse community in all samples. These communities also differed considerably between the six biofilms. Using the Ribosomal Database Project (RDP) classifier tool, 275 cloned 16S rRNA gene sequences were assigned to 11 bacterial phyla and 104 bacterial genera. Only 15 genera (representing 121 sequences affiliated with Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes and Proteobacteria) occurred in at least half of the samples or contributed at least 10% of the sequences in a single biofilm. These sequences were defined as ‘typical’ for toilet biofilms, and they were examined in more detail. On a 97% sequence similarity level, these sequences represented 56 species. Twelve of these were closely related to well‐described bacterial species, and only two of them were categorized as belonging to risk group 2. No 16S rRNA genes of typical faecal bacteria were detected in any sample. Virtually all ‘typical’ clones were found to be closely related to bacteria or to sequences obtained from environmental sources, implicating that the flushing water is the main source of recruitment. Conclusion: In view of the great diversity of mostly yet‐uncultured bacteria and the considerable differences between individual toilets, very general strategies appear to be most suited for the removal and prevention of toilet biofilms. Significance and Impact of the Study: For the first time, a molecular fingerprinting and cloning approach was used to monitor the species composition in biofilm samples taken from domestic toilets. Knowledge about the microbial composition of biofilms in domestic toilets is a prerequisite for developing and evaluating strategies for their removal and prevention.     

Potential applications of nonthermal plasmas against biofilm‐associated micro‐organisms in vitro

Biofilms as complex microbial communities attached to surfaces pose several challenges in different sectors, ranging from food and healthcare to desalination and power generation. The biofilm mode of growth allows microorganisms to survive in hostile environments and biofilm cells exhibit distinct physiology and behaviour in comparison with their planktonic counterparts. They are ubiquitous, resilient and difficult to eradicate due to their resistant phenotype. Several chemical‐based cleaning and disinfection regimens are conventionally used against biofilm‐dwelling micro‐organisms in vitro. Although such approaches are generally considered to be effective, they may contribute to the dissemination of antimicrobial resistance and environmental pollution. Consequently, advanced green technologies for biofilm control are constantly emerging. Disinfection using nonthermal plasmas (NTPs) is one of the novel strategies having a great potential for control of biofilms of a broad spectrum of micro‐organisms. This review discusses several aspects related to the inactivation of biofilm‐associated bacteria and fungi by different types of NTPs under in vitro conditions. A brief introduction summarizes prevailing methods in biofilm inactivation, followed by introduction to gas discharge plasmas, active plasma species and their inactivating mechanism. Subsequently, significance and aspects of NTP inactivation of biofilm‐associated bacteria, especially those of medical importance, including opportunistic pathogens, oral pathogenic bacteria, foodborne pathogens and implant bacteria, are discussed. The remainder of the review discusses majorly about the synergistic effect of NTPs and their activity against biofilm‐associated fungi, especially Candida species.     

Prevalence of potentially thermophilic microorganisms in biofilms from greenhouse-enclosed drip irrigation systems

Drip irrigation systems using reclaimed water often present clogging events of biological origin. Microbial communities in biofilms from microirrigation systems of an experimental greenhouse in Almería, SE Spain, which used two different qualities of water (treated wastewater and reclaimed water), were analyzed by denaturing gradient gel electrophoresis and subsequent sequencing of amplified 16S rRNA gene bands. The most remarkable feature of all biofilms was that regardless of water origin, sequences belonging to Firmicutes were prevalent (53.5 % of total mean band intensity) and that almost all sequences recovered had some similarity (between 80.2 and 97 %) to thermophilic microorganisms. Mainly, sequences were closely related to potentially spore-forming organisms, suggesting that microbial communities able to grow at high temperatures were selected from the microbiota present in the incoming water. These pioneer results may contribute to improve management strategies to minimize the problems associated to biofouling in irrigation systems.     

Proteogenomic approaches for the molecular characterization of natural microbial communities

At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS(2)) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.     

高温油藏生物膜内硫酸盐还原菌的腐蚀机理及防治策略

硫酸盐还原菌(sulfate-reducing bacteria,SRB)广泛分布于高温、高压及高盐的石油油藏中,在油藏硫循环中起主导作用。SRB能在油藏生物膜内生长,有微量低分子有机酸时利用硫酸盐为电子受体并将其还原成硫化氢。硫化氢会腐蚀管道,导致原油泄露等其他安全问题,每年造成的经济损失超过7 000亿元。本文首先总结了油藏生物膜内微生物菌群多样性,分析了生物膜内SRB及其相关菌群的协同腐蚀机理;然后讨论了高温油藏SRB介导的硫氮氢生物地球化学循环过程、胞外电子传递机制及其腐蚀作用,并通过几个高温油藏SRB生物膜内腐蚀的现场案例进一步阐明了SRB的腐蚀机制。在此基础上,提出了应对高温油藏生物膜内SRB腐蚀的生物纳米防治策略,这为高温油藏管道防腐提供了新思路。     

Biofilm--"City of microbes" or an analogue of multicellular organisms?

The definition of the term "biofilm" and the validity of the analogy between these structured microbial communities and multicellular organisms are discussed in the review. The mechanisms of biofilm formation, the types of interrelations of the components of biofilms, and the reasons for biofilm resistance to biocides and stress factors are considered in detail. The role of biofilms in microbial ecology and in biotechnology is discussed.