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PubMed2002

Evolution of extracellular enzyme activities during manure composting.

AIMS: The objectives of this work were to determine the extracellular enzyme profiles during composting, relate the activities of these enzymes to the changes in microbial population and compare the enzyme profiles between two manures. METHODS AND RESULTS: API ZYM assay was used to monitor the activities of 19 extracellular enzymes during poultry and pig manure composting. Results showed an overall increase in diversity and relative abundance of enzymes present. The relative abundance and activities of enzymes were higher in poultry manure than in pig manure. Among the 19 enzymes tested, esterase, valine amino-peptidase and alpha-galactosidase were the most abundant enzymes in poultry manure, whereas it was N-acetyl-beta-glucosaminidase for the pig manure. A number of these enzymes correlated with change in numbers of different microbial groups during composting. CONCLUSIONS: The composting process represented a combined activity of a wide succession of environments, as one enzyme/microbial group overlapped the other and each emerged gradually due to the continual change in temperature and progressive breakdown of complex compounds to simpler ones. SIGNIFICANCE AND IMPACT OF THE STUDY: The results presented here show the applicability of the API ZYM test not only in monitoring the quantitative and qualitative fluctuation of the available substrate during composting, but also in revealing differences in composts and compost maturity.

Actinomycetales↗
PubMed2003

Modeling microbial consortiums as distributed metabolic networks.

Biogeochemistry is the study of how living systems in combination with abiotic reactions process and cycle mass and energy on local, regional, and global scales (Schlesinger, 1997). Understanding how these biogeochemical cycles function and respond to perturbations has become increasingly important, as anthropogenic impacts have significantly altered many of these cycles (Galloway and Cowling, 2002; Houghton et al., 2002). Biogeochemistry is strongly governed by microbial processes, and it appears to closely follow thermodynamic constraints in that electron acceptor (O(2), NO(3)(-), SO(4)(2-), etc.) utilization closely follows a priori expectations based on energetics (Vallino et al., 1996; Hoehler et al., 1998; Jakobsen and Postma, 1999; Amend and Shock, 2001). Consortiums of microorganisms seem to have evolved to exploit chemical potentials wherever they exist in the environment, as manifested by the recent discovery of anaerobic methane oxidation by sulfate (Boetius et al., 2000) or sulfide oxidation by nitrate (Schulz et al., 1999). Three and a half billion years of natural selection have produced living systems capable of degrading most chemical potentials. We may therefore ask: If all ecosystem niche space is filled, is the biogeochemistry we observe in the environment dependent on the organisms that occupy that environment, or is the biogeochemistry determined by fundamental forces, with the evolution of living systems being the implementation of those forces? Recent developments in nonequilibrium thermodynamics (NET) are beginning to support the latter alternative, and advances in genomics are allowing us to explore microbial consortiums in detail. Taking advantage of ideas being suggested by NET, we have developed a modeling framework that views microbial consortiums as an inter-species distributed metabolic network. When combined with experimental observations, the model should help us test hypotheses that govern how living systems function.

Bacteria↗
PubMed1995

Inorganic polyphosphate: toward making a forgotten polymer unforgettable.

Pursuit of the enzymes that make and degrade poly P has provided analytic reagents which confirm the ubiquity of poly P in microbes and animals and provide reliable means for measuring very low concentrations. Many distinctive functions appear likely for poly P, depending on its abundance, chain length, biologic source, and subcellular location. These include being an energy supply and ATP substitute, a reservoir for Pi, a chelator of metals, a buffer against alkali, a channel for DNA entry, a cell capsule and, of major interest, a regulator of responses to stresses and adjustments for survival in the stationary phase of culture growth and development. Whether microbe or human, we depend on adaptations in the stationary phase, which is really a dynamic phase of life. Much attention has been focused on the early and reproductive phases of organisms, which are rather brief intervals of rapid growth, but more concern needs to be given to the extensive period of maturity. Survival of microbial species depends on being able to manage in the stationary phase. In view of the universality and complexity of basic biochemical mechanisms, it would be surprising if some of the variety of poly P functions observed in microorganisms did not apply to aspects of human growth and development, such as aging and the aberrations of disease. Of theoretical interest regarding poly P is its antiquity in prebiotic evolution, which along with its high energy and phosphate content make it a plausible precursor to RNA, DNA, and proteins. Practical interest in poly P includes many industrial applications, among which is its use in the microbial depollution of P1 in marine environments.

Animals↗
PubMed1986

Sex distribution, age of onset and HLA profiles in two types of multiple sclerosis. A role for sex hormones and microbial infections in the development of autoimmunity?

Fifty-four patients with clinically definite multiple sclerosis were typed for HLA-A, B, C, DR and DQ antigens. HLA-DQ was not a better disease marker than the previously described HLA-DR and B markers. The patients were subdivided according to the clinical evolution of their disease, age at onset and sex. HLA-DR2 was significantly associated with females having a relapsing-remitting course of the disease and HLA-B8 and B35 were significantly associated with males having a chronic-progressive course of the disease. A role is postulated for defects in the sex hormone balance in females and for microbial infections in males as dominant environmental triggers in the development of autoreactivity.

Adult↗
PubMed2002

Microbial arsenic: from geocycles to genes and enzymes.

Arsenic compounds have been abundant at near toxic levels in the environment since the origin of life. In response, microbes have evolved mechanisms for arsenic resistance and enzymes that oxidize As(III) to As(V) or reduce As(V) to As(III). Formation and degradation of organoarsenicals, for example methylarsenic compounds, occur. There is a global arsenic geocycle, where microbial metabolism and mobilization (or immobilization) are important processes. Recent progress in studies of the ars operon (conferring resistance to As(III) and As(V)) in many bacterial types (and related systems in Archaea and yeast) and new understanding of arsenite oxidation and arsenate reduction by respiratory-chain-linked enzyme complexes has been substantial. The DNA sequencing and protein crystal structures have established the convergent evolution of three classes of arsenate reductases (that is classes of arsenate reductases are not of common evolutionary origin). Proposed reaction mechanisms in each case involve three cysteine thiols and S-As bond intermediates, so convergent evolution to similar mechanisms has taken place.

Arsenate Reductases↗
PubMed1982

Phenotypic reversion of an IS1-mediated deletion mutation: a combined role for point mutations and deletions in transposon evolution.

We have physically characterised a deletion mutant of the R plasmid R100 which has lost all of the antibiotic resistances, including chloramphenicol resistance (Cmr), coded by its IS1-flanked r-determinant. The deletion was mediated by one of the flanking IS1 elements and terminates within the carboxyl terminus of the Cmr gene. DNA sequence analysis showed that the mutated gene would produce a protein 20 amino acids longer than the wild-type due to fusion with an open reading frame in the IS element. Surprisingly for a deletion mutation, rare, spontaneous Cmr revertants could be recovered. Two of the four revertants studied had frame shifts due to the insertion of a single AT base pair at the same position; the revertants would code for a protein five amino acids shorter than the wild-type. The other two revertants had acquired duplications of the 34-bp inverted terminal repeat sequences of the IS1 element and would direct the synthesis of a protein six amino acids longer than the wild-type. The reverted Cmr markers were still capable of transposition. These observations suggest a role for point mutations and small DNA rearrangements in the formation of new gene organisations produced by mobile genetic elements.

Base Sequence↗
PubMed1999

Decomposition and CO2 Evolution from Standing Litter of the Emergent Macrophyte Erianthus giganteus.

> Abstract Decomposition of standing litter of the emergent macrophyte Erianthus giganteus (plumegrass) was quantified in a small freshwater wetland in Alabama, USA. Living green shoots of E. giganteus were tagged and periodically retrieved for determination of leaf and culm mass loss, litter-associated fungal biomass (ergosterol), and nitrogen and phosphorus concentrations. Laboratory studies were also conducted to examine the effects of plant litter moisture content and temperature on rates of CO2 evolution from plant litter. Culm and leaf material lost 25 and 32% AFDM, respectively, during plant senescence and early litter decay. Fungal biomass, as determined by ergosterol concentrations, increased significantly in both leaf and culm litter during decomposition, with maximum biomass accounting for 3.7 and 6.7% of the total detrital weight in culm and leaf litter, respectively. Spatial differences in fungal biomass were observed along the culm axis, with upper regions of the culm accumulating significantly greater amounts of fungal mass than basal regions (p < 0.01, ANOVA). Rates of CO2 evolution from both leaf and culm litter increased rapidly after wetting (0 to 76 µg CO2-C g-1 AFDM h-1 within 5 min). In addition, rates of CO2 evolution from water saturated culms increased exponentially as the temperature was increased from 10 to 30 degrees C. These results provide evidence that considerable microbial colonization and mineralization of standing emergent macrophyte litter can occur before collapse of senescent shoot material to the water and sediment surface.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p50.html

Journal Article↗
PubMed1999

Ultraviolet radiation screening compounds.

Amongst the diversity of methods used by organisms to reduce damage caused by ultraviolet (UV) radiation, the synthesis of UV-screening compounds is almost ubiquitous. UV-screening compounds provide a passive method for the reduction of UV-induced damage and they are widely distributed across the microbial, plant and animal kingdoms. They share some common chemical features. It is likely that on early earth strong selection pressures existed for the evolution of UV-screening compounds. Many of these compounds probably had other physiological roles, later being selected for the efficacy of UV screening. The diversity in physiological functions is one of the complications in studying UV-screening compounds and determining the true ecological importance of their UV-screening role. As well as providing protection against ambient UV radiation, species with effective screening may also be at an advantage during natural ozone depletion events. In this review the characteristics of a wide diversity of UV-screening compounds are discussed and evolutionary questions are explored. As research into the range of UV-screening compounds represented in the biosphere continues, so it is likely that the properties of many more compounds will be elucidated. These compounds, as well as providing us with insights into natural responses to UV radiation, may also have implications for the development of artificial UV-screening methods to reduce human exposure to UV radiation.

Amino Acids↗
PubMed1979

Comparison of glyoxalase I purified from yeast (Saccharomyces cerevisiae) with the enzyme from mammalian sources.

Glyoxalase I from yeast (Saccharomyces cerevisiae) purified by affinity chromatography on S-hexylglutathione-Sepharose 6B was characterized and compared with the enzyme from rat liver, pig erythrocytes and human erythrocytes. The molecular weight of glyoxalase I from yeast was, like the enzyme from Rhodospirillum rubrum and Escherichia coli, significantly less (approx. 32000) than that of the enzyme from mammals (approx. 46000). The yeast enzyme is a monomer, whereas the mammalian enzymes are composed of two very similar or identical subunits. The enzymes contain 1Zn atom per subunit. The isoelectric points (at 4 degrees C) for the yeast and mammalian enzymes are at pH7.0 and 4.8 respectively; tryptic-peptide ;maps' display corresponding dissimilarities in structure. These and some additional data indicate that the microbial and the mammalian enzymes may have separate evolutionary origins. The similarities demonstrated in mechanistic and kinetic properties, on the other hand, indicate convergent evolution. The k(cat.) and K(m) values for the yeast enzyme were both higher than those for the enzyme from the mammalian sources with the hemimercaptal adduct of methylglyoxal or phenylglyoxal as the varied substrate and free glutathione at a constant and physiological concentration (2mm). Glyoxalase I from all sources investigated had a k(cat.)/K(m) value near 10(7)s(-1).m(-1), which is close to the theoretical diffusion-controlled rate of enzyme-substrate association. The initial-velocity data show non-Michaelian rate saturation and apparent non-linear inhibition by free glutathione for both yeast and mammalian enzyme. This rate behaviour may have physiological importance, since it counteracts the effects of fluctuations in total glutathione concentrations on the glyoxalase I-dependent metabolism of 2-oxoaldehydes.

Aldehydes↗
PubMed1974

Radiation genetics in microorganisms and evolutionary considerations.

Recent knowledge of UV-resistance mechanisms in microorganisms is reviewed in perspective, with emphasis on E. coli. Dark-repair genes are classified into "excision" and "tolerance" (ability to produce a normal copy of DNA from damaged DNA). The phenotype of DNA repair is rather common among the microorganisms compared, and yet their molecular mechanisms are not universal. In contrast, DNA photoreactivation is the simplest and the most general among these three repair systems. It is proposed that DNA repair mechanisms evolved in the order: photoreactivation, excision repair, and tolerance repair. The UV protective capacity and light-inducible RNA photoreactivation possessed by some plant viruses are interpreted to be the result of solar UV selection during a rather recent era of evolution.

Biological Evolution↗
PubMed1994

Mosaic pbpX genes of major clones of penicillin-resistant Streptococcus pneumoniae have evolved from pbpX genes of a penicillin-sensitive Streptococcus oralis.

Penicillin-resistant clinical isolates of Streptococcus pneumoniae contain mosaic penicillin-binding protein (PBP) genes that encode PBPs with decreased affinity for beta-lactam antibiotics. The mosaic blocks are believed to be the result of gene transfer of homologous PBP genes from related penicillin-resistant species. We have now identified a gene homologous to the pneumococcal PBP2x gene (pbpX) in a penicillin-sensitive Streptococcus oralis isolate M3 from South Africa that diverged by almost 20% from pbpX of penicillin-sensitive pneumococci, and a central sequence block of a mosaic pbpX gene of Streptococcus mitis strain NCTC 10712. In contrast, it differed by only 2-4% of the 1 to 1.5 kb mosaic block in pbpX genes of three genetically unrelated penicillin-resistant S. pneumoniae isolates, two of them representing clones of serotype 6B and 23F, which are prevalent in Spain and are also already found in other countries. With low concentrations of cefotaxime, transformants of the sensitive S. pneumoniae R6 strain could be selected containing pbpX genes from either S. mitis NCTC 10712 or S. oralis M3, demonstrating that genetic exchange can already occur between beta-lactam-sensitive species. These data are in agreement with the assumption that PBPs as penicillin-resistance determinants have evolved by the accumulation of point mutations in genes of sensitive commensal species.

Amino Acid Sequence↗
PubMed1996

Evolution of drug resistance in Salmonella panama isolates in Chile.

In a search for Salmonella isolates in the environment in Chile in 1975, drug-susceptible strains of Salmonella panama were recovered for the first time from river water and vegetables in the vicinity of Santiago. Two to 3 years later, antibiotic-resistant S. panama began to appear in a variety of sources (meat, animals, vegetables, etc.), giving rise to a human epidemic that involved the entire nation. Of 139 clinical isolates studied, 7 were drug susceptible, 11 were resistant only to nitrofurans, and 3 were streptomycin, spectinomycin, and nitrofuran resistant; none of these 21 isolates harbored plasmid DNA. Most isolates (n = 107) were resistant to nitrofurans (chromosomal) and to streptomycin, spectinomycin, sulfonamides, tetracycline, and mercuric and tellurite salts; this multidrug resistance was encoded on a 218-kb plasmid classified in a number of strains as being in the IncHI2 group. From 1982 to 1993, 11 isolates acquired an additional self-transferable plasmid coding for resistance to any one of ampicillin (61 kb), ampicillin and trimethoprim (65 kb), ampicillin, trimethoprim, streptomycin, and sulfonamides (71 kb), ampicillin, gentamicin, kanamycin, and tetracycline (120 kb), or a nontransferable plasmid of approximately 6 kb encoding resistance to ampicillin or kanamycin. With the exception of ampicillin or ampicillin and trimethoprim resistance, S. panama isolates from foodstuffs, mainly pork meat products, and animals had resistance patterns that were the same as those found in clinical specimens. Remarkably, strains from goats and goat cheese and from shellfish isolated in particular rural regions were either drug susceptible or resistant only to streptomycin-spectinomycin encoded on a mobile genetic element and to nitrofurans. The report describes the arrival of a susceptible S. panama strain, its spread all over the country, and the evolution of progressively complex resistance patterns.

Chile↗
PubMed2001

Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling.

Genetic profiling techniques of microbial communities based on PCR-amplified signature genes, such as denaturing gradient gel electrophoresis or single-strand-conformation polymorphism (SSCP) analysis, are normally done with PCR products of less than 500-bp. The most common target for diversity analysis, the small-subunit rRNA genes, however, are larger, and thus, only partial sequences can be analyzed. Here, we compared the results obtained by PCR targeting different variable (V) regions (V2 and V3, V4 and V5, and V6 to V8) of the bacterial 16S rRNA gene with primers hybridizing to evolutionarily conserved flanking regions. SSCP analysis of single-stranded PCR products generated from 13 different bacterial species showed fewer bands with products containing V4-V5 (average, 1.7 bands per organism) than with V2-V3 (2.2 bands) and V6-V8 (2.3 bands). We found that the additional bands (>1 per organism) were caused by intraspecies operon heterogeneities or by more than one conformation of the same sequence. Community profiles, generated by PCR-SSCP from bacterial-cell consortia extracted from rhizospheres of field-grown maize (Zea mays), were analyzed by cloning and sequencing of the dominant bands. A total of 48 sequences could be attributed to 34 different strains from 10 taxonomical groups. Independent of the primer pairs, we found proteobacteria (alpha, beta, and gamma subgroups) and members of the genus Paenibacillus (low G+C gram-positive) to be the dominant organisms. Other groups, however, were only detected with single primer pairs. This study gives an example of how much the selection of different variable regions combined with different specificities of the flanking "universal" primers can affect a PCR-based microbial community analysis.

Bacteria↗