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PubMed1996

Are bacterial biofilms constrained to Darwin's concept of evolution through natural selection?

Numerous antimicrobial agents have been developed which act at the molecular, cellular, and organismal levels. However, few have been developed which act at the community-level. This results largely from the failure of Darwinian selection theory to envision communities as units of proliferation and evolution. It is thus difficult to conceive of microbial communities as causative agents and to develop antimicrobials which are effective against them. Consequently, we find it necessary to consider a more comprehensive biological paradigm which envisions biofilm communities and other microbial associations (e.g. mixed infections, food spoilage, tooth decay) as units of existence, activity, ecology, proliferation, survival, and evolution. These communities exist in the same sense that organisms exist as units of ecological activity. This is a simpler, more comprehensive, and more unifying theory of ecology. It is simpler in that it no longer requires convoluted explanations of altruistic behavior in terms of individual selection. It is more comprehensive by not constraining evolution to the selection of any single level of biological organization (genes, races, lineages, or groups). It unifies in that it bridges the boundaries between microbial ecology, evolutionary ecology and ecosystem ecology. The basis for this theory lies in recognizing that life consists of various forms of information (order) which evolve not only through genetic recombination and mutation, but also through the recombination of organisms within communities (as well as other mechanisms, some of which are considered beyond the realm of biology). It also involves setting aside the concept of evolution through selection and competition, in favor of evolution through proliferation and association.

Bacteria↗
PubMed2001

Lipopolysaccharide is in close proximity to each of the proteins in its membrane receptor complex. transfer from CD14 to TLR4 and MD-2.

The structural features of some proteins of the innate immune system involved in mediating responses to microbial pathogens are highly conserved throughout evolution. Examples include members of the Drosophila Toll (dToll) and the mammalian Toll-like receptor (TLR) protein families. Activation of Drosophila Toll is believed to occur via an endogenous peptide rather than through direct binding of microbial products to the Toll protein. In mammals there is a growing consensus that lipopolysaccharide (LPS) initiates its biological activities through a heteromeric receptor complex containing CD14, TLR4, and at least one other protein, MD-2. LPS binds directly to CD14 but whether LPS then binds to TLR4 and/or MD-2 is not known. We have used transient transfection to express human TLRs, MD-2, or CD14 alone or in different combinations in HEK 293 cells. Interactions between LPS and these proteins were studied using a chemically modified, radioiodinated LPS containing a covalently linked, UV light-activated cross-linking group ((125)I-ASD-Re595 LPS). Here we show that LPS is cross-linked specifically to TLR4 and MD-2 only when co-expressed with CD14. These data support the contention that LPS is in close proximity to the three known proteins of its membrane receptor complex. Thus, LPS binds directly to each of the members of the tripartite LPS receptor complex.

Animals↗
PubMed1980

Alteration of Acrylonitrile-Methylacrylate-Butadiene Terpolymer by Nocardia rhodochrous and Penicillium notatum.

[C]Barex-210, a terpolymer of acrylonitrile, methylacrylate, and butadiene, was tested for bioconversion. Powdered samples of polymer, each specifically C labeled at different carbon atoms of the polymer, were incubated with either Nocardia rhodochrous or Penicillium notatum in an enriched growth medium for various periods of time. After 6 months of incubation, the C-labeled polymer was transformed from a high-molecular-weight material completely soluble in dimethyl formamide (DMF) into both a lower-molecular-weight form still soluble in DMF and a second form that was no longer soluble in DMF. The amount of C-labeled carbon atoms converted into DMF-insoluble material was 8% of the backbone carbon-carbon atoms and 12% of the side-chain nitrile and acrylate atoms from the acrylonitrile-methylacrylate copolymer and 60% of the elastomer (acrylonitrile-butadiene copolymer) atoms. Metabolism of the polymer was not established from measurements of metabolic CO(2). Evolution of CO(2) amounted to only 0.3, 0.6, 1.8, and 3.3% of these four fractions, respectively. Although the transformation of high-molecular-weight polymer into DMF-insoluble material was rapid in the early stages of microbial growth, the accompanying CO(2) evolution was much slower. Further evidence of polymer alteration was indicated by the infrared spectrum of the insoluble material, which showed a disappearance of the nitrile and methylacrylate peaks.

Journal Article↗
PubMed2001

The genetic organization and evolution of the broad host range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa.

Employing the biparental exogenous plasmid isolation method, conjugative plasmids conferring mercury resistance were isolated from the microbial community of the rhizosphere of field grown alfalfa plants. Five different plasmids were identified, designated pSB101-pSB105. One of the plasmids, pSB102, displayed broad host range (bhr) properties for plasmid replication and transfer unrelated to the known incompatibility (Inc) groups of bhr plasmids IncP-1, IncW, IncN and IncA/C. Nucleotide sequence analysis of plasmid pSB102 revealed a size of 55 578 bp. The transfer region of pSB102 was predicted on the basis of sequence similarity to those of other plasmids and included a putative mating pair formation apparatus most closely related to the type IV secretion system encoded on the chromosome of the mammalian pathogen Brucella sp. The region encoding replication and maintenance functions comprised genes exhibiting different degrees of similarity to RepA, KorA, IncC and KorB of bhr plasmids pSa (IncW), pM3 (IncP-9), R751 (IncP-1beta) and RK2 (IncP-1alpha), respectively. The mercury resistance determinants were located on a transposable element of the Tn5053 family designated Tn5718. No putative functions could be assigned to a quarter of the coding capacity of pSB102 on the basis of comparisons with database entries. The genetic organization of the pSB102 transfer region revealed striking similarities to plasmid pXF51 of the plant pathogen Xylella fastidiosa.

Bacteria↗
PubMed1985

Change in Microbial Numbers during Thermophilic Composting of Sewage Sludge with Reference to CO(2) Evolution Rate.

Dewatered sewage sludge was composted in a laboratory-scale autothermal reactor in which a constant temperature of 60 degrees C was kept as long as possible by regulating the air feed rate. The change in CO(2) evolution rate was measured continuously from the start up through the cessation of compositing. The succession of mesophilic bacteria, thermophilic bacteria, and thermophilic actinomycetes was also observed during the composting. Specific CO(2) evolution rates of thermophilic bacteria and actinomycetes in the constant-temperature region of 60 degrees C were assessed quantitatively. It was found that the CO(2) evolution rate was attributed to thermophilic bacteria at the initial stage of 60 degrees C and to thermophilic actinomycetes at the later stage of 60 degrees C.

Journal Article↗
PubMed2003

Linking floc structure and settling properties to activated sludge population dynamics in an SBR.

Over a period of 227 days properties of activated sludge grown in an sequencing batch reactor (SBR) operated under stable conditions were analyzed. Settling properties (sludge volume index (SVI)) of the activated sludge were compared with on-line measurements of floc size and size distribution obtained by using a laser light scattering technique (Malvern Mastersizer/S, Malvern, UK), and with measurements of microbial community dynamics analyzed by denaturing gradient gel electrophoresis (DGGE) patterns of 16S rRNA genes. In addition, microscopical observations were used to confirm the results. Three distinct stages in the SBR evolution were observed. In the first stage the structural floc properties showed predominant presence of floc-forming bacteria in the activated sludge. A good correlation between floc size, properties and microbial community evolution was observed. The second stage showed a good balance between floc-forming and filamentous bacteria, with good settling properties and a highly dynamic community in the SBR. In the third stage, an increase in the filamentous bacteria, which became predominant in the system was observed. Again, a good correlation between settling properties and floc size distribution was obtained and a new dominant species was observed in the DGGE patterns, which can be assumed to be a filamentous organism.

Bioreactors↗
PubMed2000

Compensatory evolution in rifampin-resistant Escherichia coli.

This study examines the intrinsic fitness burden associated with RNA polymerase (rpoB) mutations conferring rifampin resistance in Escherichia coli K12 (MG1655) and explores the nature of adaptation to the costs of resistance. Among 28 independent Rif(r) mutants, the per-generation fitness burden (in the absence of rifampin) ranged from 0 to 28%, with a median of 6.4%. We detected no relationship between the magnitude of the cost and the level of resistance. Adaptation to the costs of rif resistance was studied by following serial transfer cultures for several Rif(r) mutants both in the presence of rifampin and in the absence. For cultures evolved in the absence of rifampin, single clones isolated after 200 generations were more fit than their ancestor; we saw no association between increased fitness and changes in the level of rifampin resistance; and in all cases, increased fitness was due to compensatory mutations, rather than to reversion to drug sensitivity. However, in the parallel evolution experiments in the presence of rifampin, overall levels of resistance increased as did relative fitness-for all strains save one that had an initially high level of resistance. Among the evolved clones tested, five (of seven) demonstrated increased transcription efficiency (assessed using a semiquantitative RT-PCR protocol). The implications of these results for our understanding of adaptive molecular evolution and the increasing clinical problem of antibiotic resistance are discussed.

Amino Acid Sequence↗
PubMed1982

Effects of plutonium on soil microorganisms.

As a first phase in an investigation of the role of the soil microflora in Pu complex formation and solubilization in soil, the effects of Pu concentration, form, and specific activity on microbial types, colony-forming units, and CO(2) evolution rate were determined in soils amended with C and N sources to optimize microbial activity. The effects of Pu differed with organism type and incubation time. After 30 days of incubation, aerobic sporeforming and anaerobic bacteria were significantly affected by soil Pu levels as low as 1 mug/g when Pu was added as the hydrolyzable Pu(NO(3))(4) (solubility, <0.1% in soil). Other classes of organisms, except the fungi, were significantly affected at soil Pu levels of 10 mug/g. Fungi were affected only at soil Pu levels of 180 mug/g. Soil CO(2) evolution rate and total accumulated CO(2) were affected by Pu only at the 180 mug/g level. Because of the possible role of resistant organisms in complex formation, the mechanisms of effects of Pu on the soil fungi were further evaluated. The effect of Pu on soil fungal colony-forming units was a function of Pu solubility in soil and Pu specific activity. When Pu was added in a soluble, complexed form [Pu(2)(diethylenetriaminepentaacetate)(3)], effects occurred at Pu levels of 1 mug/g and persisted for at least 95 days. Toxicity was due primarily to radiation effects rather than to chemical effects, suggesting that, at least in the case of the fungi, formation of Pu complexes would result primarily from ligands associated with normal (in contrast to chemically-induced) biochemical pathways.

Journal Article↗
PubMed2005

Hexahydro-1,3,5-trinitro-1,3,5-triazine transformation by biologically reduced ferrihydrite: evolution of Fe mineralogy, surface area, and reaction rates.

Microbial respiration of Fe(III) oxides has been shown to produce reduced Fe phases that are capable of transforming a variety of oxidized contaminants. Little data, however, are available on how these Fe phases evolve over time and how this evolution may affect their ability to reduce contaminants. Here,the evolution and reactivity of biologically reduced ferrihydrite were monitored over a period of 14 months. Solids were collected from a culture of Geobacter metallireducens (GS-15) thatwas incubated with ferrihydrite (as the electron acceptor) for 0, 7, 10, 20, 75, and 400 days. Mineralogical composition and surface area of the biologically reduced solids were characterized using Mössbauer spectroscopy, X-ray diffraction, and BET with N2 adsorption. By day 10, ferrihydrite began to transform, and a nanoparticle magnetite/maghemite phase, as well as two ferrous phases, was observed. One of the ferrous phases was identified as siderite, whereas the other could not be positively identified. Likely candidates, however, include Fe(OH)2(s) or an adsorbed Fe(II) species. Over the next few months, ferrihydrite was completely reduced and evolved into a mixture containing about 70% magnetite/maghemite, 19% siderite, and 11% of the second Fe(II) phase. The effect of incubation time on the reactivity of the biologically reduced solids was evaluated by measuring the kinetics of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) transformation. The only products observed were the three reduced nitroso products. Rate coefficients (k) for RDX transformation were dramatically influenced by incubation time with half-lives of about 1 month observed in the presence of solids incubated for 10 and 20 days, 3 months with solids incubated for 75 days, and negligible removal with solids incubated for 400 days. The loss of reactivity was not directly correlated to any one mineralogical variable but may be due to particle size or surface chemistry changes in the reactive Fe phase or to cell die-off and the accumulation of cell lysis products after consumption of the electron acceptor. The dramatic effect of incubation time on the rate of RDX removal highlights a potential limitation of studying complex systems, as we have here, in batch reactors and suggests that incubation time is an important variable to consider when measuring and comparing rates of contaminant reduction.

Biotransformation↗
PubMed2000

Assessing evolutionary relationships among microbes from whole-genome analysis.

The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.

Archaea↗
PubMed2000

Molecular phylogeny: pitfalls and progress.

Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.

Artifacts↗
PubMed2000

The evolution of human pathogens: examples and clinical implications.

Recent advances in sequencing of complete bacterial genomes, molecular typing of micro-organisms, and research on microbial pathogenicity factors changed our view on the evolution of human bacterial pathogens. We review current evolutionary concepts on plague and meningococcal disease to illustrate the interplay of molecular phylogeny, epidemiology, and pathogenicity research. Furthermore, examples of the tremendous velocity of bacterial evolution under changing environmental conditions will be discussed.

Adaptation, Physiological↗
PubMed2004

Development of rationally designed nucleic acid signatures for microbial pathogens.

The detection and identification of microbial pathogens are critical challenges in clinical medicine and public health surveillance. Advances in genome analysis technology are providing an unprecedented amount of information about bacterial and viral organisms, and hold great potential for pathogen detection and identification. In this paper, a rational approach to the development and application of nucleic acid signatures is described based on phylogenetically informative sequence features, especially single nucleotide polymorphisms. The computational tools that are available to enable the development of the next generation of microbial molecular signatures for clinical diagnostics and infectious disease surveillance are reviewed and the impact on public health and national security will be discussed.

Bacteria↗
PubMed1998

Molecular mechanisms of bacteriocin evolution.

Microorganisms are engaged in a never-ending arms race. One consequence of this intense competition is the diversity of antimicrobial compounds that most species of bacteria produce. Surprisingly, little attention has been paid to the evolution of such extraordinary diversity. One class of antimicrobials, the bacteriocins, has received increasing attention because of the high levels of bacteriocin diversity observed and the use of bacteriocins as preservatives in the food industry and as antibiotics in the human health industry. However, little effort has been focused on evolutionary questions, such as what are the phylogenetic relationships among these toxins, what mechanisms are involved in their evolution, and how do microorganisms respond to such an arsenal of weapons? The focus of this review is to provide a detailed picture of our current understanding of the molecular mechanisms involved in the process of bacteriocin diversification.

Bacteriocins↗
PubMed2002

HIV mutagenesis and the evolution of antiretroviral drug resistance.

The development of antiretroviral drug resistance is a major threat to the effective treatment of human immunodeficiency virus type 1 (HIV-1) infection. Drug treatment failure is associated with accumulation of drug resistance mutations and the evolution of drug resistance. Studies from microbial systems provide evidence for a correlation between drug resistance development and increased pathogen mutation rates. Recent studies with HIV-1 have shown that drugs targeted against reverse transcriptase (RT) as well as drug-resistant RT can increase HIV-1 mutation frequencies. Furthermore, combinations of drug and drug-resistant RT have been found to increase virus mutation frequencies in a multiplicative manner. The correlation of increased HIV-1 mutation rates with the evolution of antiretroviral drug resistance indicates that drug failure could increase the likelihood of further resistance evolving from subsequent drug regimens.

Anti-HIV Agents↗
PubMed2000

Biomass evolution in porous media and its effects on permeability under starvation conditions.

The purpose of this study was to understand bacteria profile modification and its applications in subsurface biological operations such as biobarrier formation, in situ bioremediation, and microbial-enhanced oil recovery. Biomass accumulation and evolution in porous media were investigated both experimentally and theoretically. To study both nutrient-rich and carbon-source-depleted conditions, Leuconostoc mesenteroides was chosen because of its rapid growth rate and exopolymer production rate. Porous micromodels were used to study the effects of biomass evolution on the permeability of a porous medium. Bacterial starvation was initiated by switching the feed from a nutrient solution to a buffer solution in order to examine biofilm stability under nutrient-poor conditions. Four different evolution patterns were identified during the nutrient-rich and nutrient-depleted conditions used in the micromodel experiments. In phase I, the permeability of the porous micromodel decreased as a result of biomass accumulation in pore bodies and pore throats. In phase II, starvation conditions were initiated. The depletion of nutrient in the phase II resulted in slower growth of the biofilm causing the permeability to reach a minimum as all the remaining nutrients were consumed. In phase III, permeability began to increase due to biofilm sloughing caused by shear stress. In phase IV, shear stress remained below the critical shear stress for sloughing and the biofilm remained stable for long periods of time during starvation. The critical shear stress for biofilm sloughing provided an indication of biofilm strength. Shear removal of biofilms occurred when shear stress exceeded critical shear stress. A network model was used to describe the biofilm formation phenomenon and the existence of a critical shear stress. Simulations were in qualitative agreement with the experimental results, and demonstrate the existence of a critical shear stress.

Biomass↗
PubMed1998

Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria.

Microbial Resistance to antibiotics is on the rise, in part because of inappropriate use of antibiotics in human medicine but also because of practices in the agricultural industry. Intensive animal production involves giving livestock animals large quantities of antibiotics to promote growth and prevent infection. These uses promote the selection of antibiotic resistance in bacterial populations. The resistant bacteria from agricultural environments may be transmitted to humans, in whom they cause disease that cannot be treated by conventional antibiotics. The author reviews trends in antibiotic use in animal husbandry and agriculture in general. The development of resistance is described, along with the genetic mechanisms that create resistance and facilitate its spread among bacterial species. Particular aspects of resistance in bacterial species common to both the human population and the agrifood industry are emphasized. Control measures that might reverse the current trends are highlighted.

Agrochemicals↗