Mineralization of 2,4-dichlorophenoxyacetic acid in soil previously enriched with organic substrates

Samples of chernozem soil were enriched with vanillic acid, protocatechuic acid glucose, a mixture of glucose and (NH₄)₂SO₄ (C∶N = 5∶1), ethanol and 2,4-dichlorophenoxyacetic acid (2,4-D). After a 6-d (with 2,4-D 35-d) incubation during which primary oxidation of the introduced substrates occurred, the soil was supplied with a solution of 2-¹⁴C-2,4-D (50ppm; 6.7kBq) and production of¹⁴CO₂ (product of microbial degradation of 2,4-D) was measured. Previously enriched samples exhibited a higher degradation rate; both the lag phase and doubling time of mineralization activity in the exponential phase of the process were markedly higher. This reflected an overall proliferation of bacteria and the increased relative proportion of bacterial strains capable of mineralizing 2,4-D in enriched samples. The stimulation of 2,4-D degradation may involve specific adaptation and selection mechanisms (as in the case with samples previously enriched with 2,4-D or its structural analogues—aromatic monomers, ethanol) as well as nonspecific mechanisms. The extent of mineralization of 2,4-D was not affected by soil pretreatment, about 1/3 of introduced radioactive carbon being invariably transformed to¹⁴CO₂.     

Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat

Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH.     

Evidence for Lignin Oxidation by the Giant Panda Fecal Microbiome

The digestion of lignin and lignin-related phenolic compounds from bamboo by giant pandas has puzzled scientists because of the lack of lignin-degrading genes in the genome of the bamboo-feeding animals. We constructed a 16S rRNA gene library from the microorganisms derived from the giant panda feces to identify the possibility for the presence of potential lignin-degrading bacteria. Phylogenetic analysis showed that the phylotypes of the intestinal bacteria were affiliated with the phyla Proteobacteria (53%) and Firmicutes (47%). Two phylotypes were affiliated with the known lignin-degrading bacterium Pseudomonas putida and the mangrove forest bacteria. To test the hypothesis that microbes in the giant panda gut help degrade lignin, a metagenomic library of the intestinal bacteria was constructed and screened for clones that contained genes encoding laccase, a lignin-degrading related enzyme. A multicopper oxidase gene, designated as lac51, was identified from a metagenomic clone. Sequence analysis and copper content determination indicated that Lac51 is a laccase rather than a metallo-oxidase and may work outside its original host cell because it has a TAT-type signal peptide and a transmembrane segment at its N-terminus. Lac51 oxidizes a variety of lignin-related phenolic compounds, including syringaldazine, 2,6-dimethoxyphenol, ferulic acid, veratryl alcohol, guaiacol, and sinapinic acid at conditions that simulate the physiologic environment in giant panda intestines. Furthermore, in the presence of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringic acid, or ferulic acid as mediators, the oxidative ability of Lac51 on lignin was promoted. The absorbance of lignin at 445 nm decreased to 36% for ABTS, 51% for syringic acid, and 51% for ferulic acid after incubation for 10 h. Our findings demonstrate that the intestinal bacteria of giant pandas may facilitate the oxidation of lignin moieties, thereby clarifying the digestion of bamboo lignin by the animal.     

Organic acids in the rhizosphere of Zea mays and Phaseolus aureus plants

Summary Soils from rhizosphere and non-rhizosphere of maize and mung crops and an uncultivated field were analysed for organic carbon, total nitrogen, cation exchange capacity and pH. The rhizosphere soils showed higher carbon and nitrogen content than non-rhizosphere soils. Phenolic acids viz, vanillic, p-hydroxybenzoic, p-coumaric, salicylic and syringic and pyrocatechol were detected in different cultivated and uncultivated soils. Pyrocatechol was absent from rhizosphere soils of both crops while p-coumaric and salicylic acids were not detected in rhizosphere of mung crop and nonrhizosphere of maize crop respectively. Syringic acid was present only in case of maize. Gluconic, tartaric, and citric acids were also detected in different soils. re]19720712     

Enhancing the biodegradation of total petroleum hydrocarbons in oily sludge by a modified bioaugmentation strategy

The effect of successive inoculation with hydrocarbon-degrading bacteria on the dynamics of petroleum hydrocarbons degradation in soil was investigated in this study. Oily sludge was used as a source of mixed hydrocarbons pollutant. Two bacterial consortia composed of alkanes and polycyclic aromatic hydrocarbon degraders were constructed from bacteria isolated from soil and oily sludge. These consortia were applied to incubated microcosms either in one dose at the onset of the incubation or in two doses at the beginning and at day 62 of the incubation period, which lasted for 198 days. During this period, carbon mineralization was evaluated by respirometry while total petroleum hydrocarbons and its fractions were gravimetrically evaluated by extraction from soil and fractionation. Dosing the bacterial consortia resulted in more than 30% increase in the overall removal of total petroleum hydrocarbons from soil. While alkane removal was only slightly improved, aromatic and asphaltic hydrocarbon fraction removal was significantly enhanced by the addition of the second consortium. Polar compounds (resins) were enriched only as a result of aromatics and asphaltene utilization. Nonetheless, their concentration declined back to the original level by the end of the incubation period.     

Detection of Listeria monocytogenes in foods by immunomagnetic separation

Immunomagnetic separation with immunomagnetic beads was used to isolate strains of Listeria monocytogenes both from pure cultures and from heterogeneous suspensions. The monoclonal antibodies used recognized all six strains of serotype 4 but only one of three strains of serotype 1. Coating procedure, incubation time, and number of immunomagnetic beads influenced the sensitivity of the isolation method. Less than 1 x 10(2) bacteria per ml in pure cultures and less than 2 x 10(2) bacteria per ml in enriched foods could be detected. The method represents a new approach to extraction and isolation of pathogenic bacteria directly from foods, after resuscitation, or from enrichment broths.     

Detection of Listeria monocytogenes in foods by immunomagnetic separation.

Immunomagnetic separation with immunomagnetic beads was used to isolate strains of Listeria monocytogenes both from pure cultures and from heterogeneous suspensions. The monoclonal antibodies used recognized all six strains of serotype 4 but only one of three strains of serotype 1. Coating procedure, incubation time, and number of immunomagnetic beads influenced the sensitivity of the isolation method. Less than 1 x 10(2) bacteria per ml in pure cultures and less than 2 x 10(2) bacteria per ml in enriched foods could be detected. The method represents a new approach to extraction and isolation of pathogenic bacteria directly from foods, after resuscitation, or from enrichment broths.     

In Vitro Physiological Responses of Fusarium oxysporum f. sp. niveum to Exogenously Applied Syringic Acid

ABSTRACT. Plant–microbe interactions are often accompanied by allelochemicals, such as syringic acid, released from the host plant. To explore the role of phenolic acids released from crop host plants in response to pathogen invasion, we examined the allelopathic effect of an artificially applied syringic acid on Fusarium oxysporum f. sp. niveum . We demonstrated that the growth and the conidial germination rate of F. oxysporum f. sp. niveum were stimulated at lower concentrations of syringic acid, though inhibited by higher dosage compared with control. The yield of fungus mycotoxin was increased from 60.9% to 561.5%. We conclude that syringic acid can be considered as a allelochemical inducer, stimulating the relative virulence factors of invading pathogens.     

Fermentation of trihydroxybenzenes by Pelobacter acidigallici gen. nov. sp. nov., a new strictly anaerobic,non-sporeforming bacterium

Five strains of rod-shaped, Gram-negative, non-sporing, strictly anaerobic bacteria were isolated from limnic and marine mud samples with gallic acid or phloroglucinol as sole substrate. All strains grew in defined mineral media without any growth factors; marine isolates required salt concentrations higher than 1% for growth, two freshwater strains only thrived in freshwater medium. Gallic acid, pyrogallol, 2,4,6-trihydroxybenzoic acid, and phloroglucinol were the only substrates utilized and were fermented stoichiometrically to 3 mol acetate (and 1 mol CO₂) per mol with a growth yield of 10g cell dry weight per mol of substrate. Neither sulfate, sulfur, nor nitrate were reduced. The DNA base ratio was 51.8% guanine plus cytosine. A marine isolate, Ma Gal 2, is described as type strain of a new genus and species, Pelobacter acidigallici gen. nov. sp. nov., in the family Bacteroidaceae. In coculture with Acetobacterium woodii, the new isolates converted also syringic acid completely to acetate. Cocultures with Methanosarcina barkeri converted the respective substrates completely to methane and carbon dioxide.     

Effects of co-substrates and inhibitors on the anaerobic O-demethylation of methyl <Emphasis Type="Italic">tert</Emphasis>-butyl ether (MTBE)

Methyl tert-butyl ether (MTBE) contamination is widespread in aquifers near urban areas around the world. Since this synthetic fuel oxygenate is resistant to most physical methods of treating fuel-contaminated water, biodegradation may be a useful means of remediation. Currently, information on anaerobic MTBE degradation is scarce. Depletion has been observed in soil and sediment microcosms from a variety of locations and under several redox conditions, but the responsible organisms are unknown. We are studying anaerobic consortia, enriched from contaminated sediments for MTBE-utilizing microorganisms for over a decade. MTBE degradation occurred in the presence of other fuel components and was not affected by toluene, benzene, ethanol, methanol, or gasoline. Many aryl O-methyl ethers, such as syringic acid, that are O-demethylated by acetogenic bacteria, were also O-demethylated by the MTBE-utilizing enrichment cultures. The addition of these compounds as co-substrates increased the rate of MTBE degradation, offering a potentially useful method of stimulating the MTBE degradation rate in situ. Propyl iodide caused light-reversible inhibition of MTBE degradation, suggesting that the MTBE degradation process is corrinoid dependent. The anaerobic MTBE degradation process was not directly coupled to methanogenesis or sulfidogenesis and was inhibited by the bactericidal antibiotic, rifampicin. These results suggest that MTBE degradation is mediated by acetogenic bacteria.     

Macromolecular syntheses during biosynthesis of prodigiosin by Serratia marcescens.

Amino acids that were utilized as sole sources of carbon and nitrogen for growth of Serratia marcescens Nima resulted in biosynthesis of prodigiosin in non-proliferating bacteria. Addition of alanine, proline, or histidine to non-proliferating cells incubated at 27 C increased the rate of protein synthesis and also caused biosynthesis of prodigiosin. No increase in the rate of protein synthesis was observed upon the addition of amino acids that did not stimulate prodigiosin biosynthesis. Increased rates of synthesis of ribonucleic acid (RNA) and of deoxyribonucleic acid (DNA) (a small amount) also occurred after addition of amino acids that resulted in biosynthesis of prodigiosin. After incubation of 24 h, the total amount of protein in suspensions of bacteria to which alanine or proline was added increased 67 and 98%, respectively. Total amounts of DNA and of RNA also increased before synthesis of prodigiosin. The amounts of these macromolecules did not increase after addition of amino acids that did not induce biosynthesis of progidiosin. However, macromolecular synthesis was not related only to prodigiosin biosynthesis because the rates of DNA, RNA, and protein synthesis also increased in suspensions of bacteria incubated with proline at 39 C, at which temperature no prodigiosin was synthesized. The quantities of DNA, RNA, and protein synthesized were lower in non-proliferating cells than in growing cells. The data indicated that amino acids causing biosynthesis of prodigiosin in non-proliferating cells must be metabolized and serve as sources of carbon and of nitrogen for synthesis of macromolecules and intermediates. Prodigiosin was synthesized secondarily to these primary metabolic events.     

Enzymatic production of l-phenylalanine from acetamidocinnamic acid: breeding of an acetamidocinnamate amidohydrolase-hyperproducing mutant

To increase the productivity of l-phenylalanine from acetamidocinnamic acid, we screened bacteria containing high acetamidocinnamate amidohydrolase activity, and strain S-5 containing high activity was isolated from soil. The bacteria were identified as Corynebacterium sp. S-5.When strain S-5 was cultured in a medium containing acetamidocinnamic acid as the sole carbon source or enzyme inducer, the formation of acetamidocinnamate amidohydrolase was observed. This was controlled by catabolite repression. When the strain was cultured in a medium containing glucose and acetamidocinnamic acid as the sole nitrogen source, it showed low acetamidocinnamate amidohydrolase activity and an increased doubling time.To obtain acetamidocinnamate amidohydrolase-hyperproducing strain, we enriched cells growing faster than strain S-5 in a medium containing glucose and acetamidocinnamic acid by continuous culture of mutagenized cells. Mutant C-23 had 12-fold the enzyme production and 3-fold the growth rate of the wild-type strain in a medium containing glucose. Acetamidocinnamate amidohydrolase formation in the mutant did not require acetamidocinnamic acid as enzyme inducer and was resistant to catabolite repression.     

Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment

Abstract The effect of temperature on CH₄ production, turnover of dissolved H₂, and enrichment of H₂-utilizing anaerobic bacteria was studied in anoxic paddy soil and sediment of Lake Constance. When anoxic paddy soil was incubated under an atmosphere of H₂/CO₂, rates of CH₄ production increased 25°C, but decreased at temperatures lower than 20°C. Chloroform completely inhibited methano-genesis in anoxic paddy soil and lake sediment, but did not or only partially inhibit the turnover of dissolved H₂, especially at low incubation temperatures. Cultures with H₂ as energy source resulted in the enrichment of chemolithotrophic homoacetogenic bacteria whenever incubation temperatures were lower than 20°C. Hydrogenotrophic methanogens could only be enriched at 30°C from anoxic paddy soil. A homoacetogen     

The occurrence of glycine in bacterial lipopolysaccharides

Abstract The aminoacyl analysis of endotoxic lipopolysaccharides (LPS) isolated from several bacteria revealed essential amounts of glycine, among the inherent LPS components. Significant amounts of the glycine was detected in lipopolysaccharides isolated from over 30 strains of Escherichia, Salmonella, Hafnia, Citrobacter and Shigella species. Glycine as a single amino acid was found only in a core part of LPS. Molar ratio of glycine in core oligosaccharide fraction ranged from 0.2 to 0.6 per 3 heptoses. The oligosaccharide enriched in glycine was isolated using the HPLC. The amino acid appeared to be terminally located in a core oligosaccharide. The labelling of the lipopolysaccharide cores was achieved when the bacteria were cultivated in the presence of radioactive [¹⁴C]glycine. The labelled core oligosaccharide released the radioactivity during treatment with mild alkali or acid (0.1 M NaOH or HCl, 100°C, 4 h). The radioactivity in SDS-polyacrylamide gel electrophoresis migrated exclusively with LPS. The results indicate that amino acid is an integral constituent of core oligosaccharide in lipopolysaccharide.     

Degradation of the multiple branched alkane 2,6,10,14-tetramethyl-pentadecane (pristane) in Rhodococcus ruber and Mycobacterium neoaurum

Pristane, a highly branched hydrocarbon that also contains iso-branched termini, was used as a substrate for several alkane-metabolizing bacteria. Rhodococcus ruber and Mycobacterium neoaurum were able to utilize pristane for growth effectively. The intermediates produced by these bacteria during incubation with pristane were analyzed by gas chromatography (GC) and gas chromatography/mass spectra (GC/MS). The products revealed as products of 4-methyl pentanoic acid; methyl butanedioic acid; 2-methyl pentadioic acid; methyl propanedioic acid; 4-methyl heptanedioic acid; and 2,6,10,14-tetramethyl-pentadecan-3-one were detected in M. neoaurum cultures. In R. ruber, methyl butanedioic acid; 2-methyl pentadioic acid; 4,8-dimethylnonanoic acid, 4-methyl heptanedioic acid; 2,6,10-trimethylundecanoic acid; 3,7-dimethyl decanedioic acid; and 2,6,10,14-tetramethyl-pentadecan-3-one were detected. The occurrence of these intermediates showed that pristane could be catabolized not only via mono- but also by a di-terminal oxidation pathway. Furthermore, the presence of 2,6,10,14-tetramethyl-pentadecan-3-one; 3,7-dimethyldecandioate; and 2-methylbutandioate established a third pathway initiated by sub-terminal oxidation at the third carbon atom of pristane. Novel intermediates detected suggest simultaneous sub-terminal and di-terminal oxidation pathways.     

A new strategy for cellulases application in high temperature industrial scenarios with syringic acid assisting

In the process of bioethanol production, more stable and active cellulase in high temperature condition is required. In this study, syringic acid was applied in cellulase hydrolysis system. At 70°C, TvEG3 activity increased 201.36%, CtBglA activity decreased 72.79% by syringic acid. With syringic acid assisting, TvEG3 thermostability was improved, CtBglA thermostability was reduced. Syringic acid scarcely affected CtCBH. In hydrolysis system with the cellulases containing TvEG3, CtCBH, and CtBglA, the reducing sugar yield improved by 28.37% with syringic acid assisting. With the molecular dynamic simulation in syringic acid system, the backbone root-mean-square deviation (RMSD) and the residue root-mean-square fluctuation (RMSF) of TvEG3, CtCBH reduced, while the RMSD and RMSF of CtBglA increased. The reduction in the number of secondary structures, especially α-helix, caused the structure of CtBglA in the presence of syringic acid to collapse at high temperature. More secondary structures in TvEG3 and more α-helix in CtCBH in the presence of syringic acid make them more stable at high temperatures. These means syringic acid can stabilize TvEG3 and CtCBH structure, destabilize CtBglA structure at high temperature. In summary, this study not only provides insight into cellulase hydrolysis at high temperature with syringic acid assisting but also demonstrates the promoting mechanism of syringic acid.     

Microbiological Degradation of Organic Components in Oil Shale Retort Water: Organic Acids

The losses of benzoic acid and a homologous series of both mono- and dibasic aliphatic acids in oil shale retort water were monitored with time (21 days) in liquid culture (4% retort water, vol/vol) inoculated with soil. The organic acids constituted approximately 12% of the dissolved organic carbon in retort water, which served as the sole source of carbon and energy in these studies. The levels of the acids in solution were reduced by 80 to 90% within 9 days of incubation. From mass balance calculations, the decrease in dissolved organic carbon with time of incubation was equal to the formation of CO₂ and bacterial cell carbon. The decrease in the level of the acid components, either from degradation to CO₂ or incorporation into bacteria, would account for ~70% of the loss in dissolved organic carbon within the first 9 days of incubation and would account for ~50% of the loss over the entire 21-day incubation period.     

Establishment and Characterization of an Anaerobic Thermophilic (55(deg)C) Enrichment Culture Degrading Long-Chain Fatty Acids

A thermophilic, long-chain fatty acid-oxidizing culture was enriched. Stearate was used as the substrate, and methane and carbon dioxide were the sole end products. Cultivation was possible only when a fed-batch system was used or with addition of activated carbon or bentonite. The enrichment culture consisted of a short rod and two bacteria antigenically related to Methanobacterium thermoautotrophicum (Delta)H and Methanosarcina thermophila TM-1.     

Growth and metabolic flexibility in groundwater bacteria

Groundwater bacteria isolated from an oligotrophic-saturated soil showed a mixed strategy of economized metabolism and migration when grown in a continuous-flow column system simulating poor or nutrient-amended growth conditions. The cells were generally <0.5m in diameter in pure groundwater, but doubled in size when the concentration of dissolved organic carbon and phosphate in groundwater was increased 10-fold. The biomass, estimated from analysis of muramic acid (MuAc) in cell wall peptidoglucans, increased at the same time by a factor of 5 when the solid support in the columns was gravel and by a factor of 10 when it was glass beads. Bacteria in pure groundwater stored 10 times more of the energy-rich polysaccharide, poly--hydroxybutyric acid (PHB), than bacteria in enriched groundwater, and those cells that were attached to the gravel stored 10 times as much as cells in the interstitial pore water. Once phosphate was added to groundwater, stored PHB was metabolized. The proportion of free-living to attached bacteria was 2 to 10 times higher in enriched compared with pure groundwater indicating a mass transport of cells as the carrying capacity of their habitat rose.     

Use of Phospholipid Fatty Acids To Detect Previous Self-Heating Events in Stored Peat

The use of the phospholipid fatty acid (PLFA) composition of microorganisms to detect previous self-heating events was studied in naturally self-heated peat and in peat incubated under temperature-controlled conditions. An increased content of total PLFAs was found in self-heated peat compared to that in unheated peat. Two PLFAs, denoted T1 and T2, were detected only in the self-heated peat. Incubation of peat samples at 25 to 55°C for 4 days indicated that T1 and T2 were produced from microorganisms with different optimum temperatures. This was confirmed by isolation of bacteria at 55°C, which produced T2 but not T1. These bacteria produced another PLFA (denoted T3) which coeluted with 18:1ω7. T2 and T3 were identified as ω-cyclohexyltridecanoic acid and ω-cyclohexylundecanoic acid, respectively, indicating that the bacteria belonged to the genus Alicyclobacillus. T1 was tentatively identified as ω-cycloheptylundecanoic acid. T2 was detected 8 h after the peat incubation temperature was increased to 55°C, and maximum levels were found within 5 days of incubation. The PLFA 18:1ω7-T3 increased in proportion to T2. T1 was detected after 96 h at 55°C, and its level increased throughout the incubation period, so that it eventually became one of the dominant PLFAs after 80 days. In peat samples incubated at 55°C and then at 25°C, T1 and T2 disappeared slowly. After 3 months, detectable levels were still found. Incubation at 25°C after heating for 3 days at 55°C decreased the amounts of T2 and 18:1ω7-T3 faster than did incubation at 5°C. Thus, not only the duration and temperature during the heating event but also the storage temperature following heating are important for the detection of PLFAs indicating previous self-heating.