Distribution of microorganisms in soil aggregates: Effect of aggregate size

The distribution of microorganisms in soil aggregates with different diameters was determined using a “washing and sonic vibration” method. In humic rendzina the number of bacteria, actinomycetes and fungi located in aggregates measuring 3 to 1 and ≤0.5 mm was greater than in those of 7 to 5 mm.Pseudomonas were more numerous in aggregates of ≤0.5 mm than in those of 3 to 1 mm and spore-forming aerobic bacteria—in aggregates measuring 3 to 1 mm than in those of 7 to 5 mm. The number of microorganisms growing on asparagine agar andArthrobacter-Corynebacterium increased as 7-5<3-1<0.5 and 7-5<0.5<3-1 mm, respectively. In podzolic loess spore-forming aerobic bacteria inhabited preferentially aggregates measuring 7 to 5 mm,Arthrobacter-Corynebacterium aggregates of ≤0.5 mm. The number of bacteria was greater in aggregates of 3 to 1 than in those measuring ≤0.5 mm. Aggregates of various diameters differed also in the number of some microorganisms both in the outer and inner parts and the partition ratio of microorganisms between these parts. Differences were more numerous in the humic rendzina aggregates.     

Establishment of the phylogenetic relationships between the microbial producers of cyclodextrin glucanotransferases using complete amino acid sequences

A phylogenetic tree was constructed on the basis of the amino acid sequences of the known cyclodextrin glucanotransferases (CDGTs), including those deduced from the nucleotide sequences ofBacillus sp. strain 6.6.3 andPaenibacillus macerans IB-7 genes encoding α- and β-CDGTs. The tree clearly demonstrates the existence of distinct phylogenetic groups of CDGT-producing microorganisms and the divergence of the α-, β-, and γ-CDGT produced by microorganisms from the generaBacillus, Paenibacillus, Brevibacillus, andThermoanaerobacter from a common ancestor, whereas the CDGT ofKlebsiella pneumoniae is independent and results from the convergence of different ancestors. The degree of homology of the leader peptide sequences of CDGTs may serve as a criterion of intraspecies relatedness between CDGT-producing microorganisms.     

Identification of carotenoids with high antioxidant capacity produced by extremophile microorganisms

In this study, the carotenoids produced by the extremophile microorganisms Halococcus morrhuae, Halobacterium salinarium and Thermus filiformis were separated and identified by high-performance liquid chromatography connected to a diode array detector and a tandem mass spectrometer. The in vitro scavenging capacity of the carotenoid extracts against radical and non-radical species was evaluated. In halophilic microorganisms, the following carotenoids were identified: bacterioruberin, bisanhydrobacterioruberin, trisanhydrobacterioruberin and their derivatives. In the thermophilic bacterium, the carotenoids all-trans-zeaxanthin, zeaxanthin monoglucoside, thermozeaxanthins and thermobiszeaxanthins were identified. The antioxidant capacities of the carotenoid extracts of H. morrhuae (trolox equivalent antioxidant capacity = 5.07 and IC₅₀ = 0.85 μg mL⁻¹) and H. salinarium (trolox equivalent antioxidant capacity = 5.28 and IC₅₀ = 0.84 μg mL⁻¹) were similar and higher than those of the bacterium T. filiformis (trolox equivalent antioxidant capacity = 2.87 and IC₅₀ = 2.41 μg mL⁻¹). This difference is related to the presence of acyclic carotenoids with both large numbers of conjugated double bounds and of hydroxyl groups in the major carotenoid of the halophilic microorganisms.     

Agar degradation by microorganisms and agar-degrading enzymes

Agar is a mixture of heterogeneous galactans, mainly composed of 3,6-anhydro-l-galactoses (or l-galactose-6-sulfates) d-galactoses and l-galactoses (routinely in the forms of 3,6-anhydro-l-galactoses or l-galactose-6-sulfates) alternately linked by β-(1,4) and α-(1,3) linkages. It is a major component of the cell walls of red algae and has been used in a variety of laboratory and industrial applications, owing to its jellifying properties. Many microorganisms that can hydrolyze and metabolize agar as a carbon and energy source have been identified in seawater and marine sediments. Agarolytic microorganisms commonly produce agarases, which catalyze the hydrolysis of agar. Numerous agarases have been identified in microorganisms of various genera. They are classified according to their cleavage pattern into three types—α-agarase, β-agarase, and β-porphyranase. Although, in a broad sense, many other agarases are involved in complete hydrolysis of agar, most of those identified are β-agarases. In this article we review agarolytic microorganisms and their agar-hydrolyzing systems, covering β-agarases as well as α-agarases, α-neoagarobiose hydrolases, and β-porphyranases, with emphasis on the recent discoveries. We also present an overview of the biochemical and structural characteristics of the various types of agarases. Further, we summarize and compare the agar-hydrolyzing systems of two specific microorganisms: Gram-negative Saccharophagus degradans 2–40 and Gram-positive Streptomyces coelicolor A3(2). We conclude with a brief discussion of the importance of agarases and their possible future application in producing oligosaccharides with various nutraceutical activities and in sustainably generating stock chemicals for biorefinement and bioenergy.     

Ammonia removal from livestock wastewater by ammonia-assimilating microorganisms immobilized in polyvinyl alcohol

We isolated ammonia-assimilating microorganisms from the livestock manure treatment systems and evaluated their ammonia-assimilating ability. Many isolates utilized ammonia at high rates when they were purely cultivated in a nitrogen-limited medium to which sterilized lagoon extract had been added. Some isolates that were immobilized in polyvinyl alcohol (PVA) utilized ammonia present in the media containing viable lagoon microorganisms. Staining with 4′,6′-diamidino-2-phenylindole (DAPI) indicated that the immobilized high ammonia-assimilating isolates grew dominantly within the PVA beads. High ammonia-assimilating isolates in the mixed culture containing viable lagoon microorganisms were identified as Pseudomonas spp. and member of Rhizobiaceae species by partial sequencing of the 16S ribosomal DNA.     

Effects of Thymol on Ruminal Microorganisms

Thymol (5-methyl-2-isopropylphenol) is a phenolic compound that is used to inhibit oral bacteria. Because little is known regarding the effects of this compound on ruminal microorganisms, the objective of this study was to determine the effects of thymol on growth and lactate production by the ruminal bacteria Streptococcus bovis JB1 and Selenomonas ruminantium HD4. In addition, the effect of thymol on the in vitro fermentation of glucose by mixed ruminal microorganisms was investigated. Neither 45 nor 90 μg/ml of thymol had any significant effect on growth or lactate production by S. bovis JB1, but 180 μg/ml of thymol completely inhibited growth and lactate production. In the case of S. ruminantium HD4, 45 μg/ml of thymol had little effect on growth and lactate production; however, 90 μg/ml of thymol completely inhibited growth of S. ruminantium HD4. Thymol also decreased glucose uptake by whole cells of both bacteria. When mixed ruminal microorganisms were incubated in medium that contained glucose, 400 μg/ml of thymol increased final pH and the acetate to propionate ratio and decreased concentrations of methane, acetate, propionate, and lactate. In conclusion, thymol was a potent inhibitor of glucose fermentation by S. bovis JB1 and S. ruminantium HD4. Even though thymol treatment decreased methane and lactate concentrations and increased final pH in mixed ruminal microorganism fermentations of glucose, concentrations of acetate and propionate were also reduced. Received: 13 May 2000 / Accepted: 14 June 2000     

Phylogenetic Diversity and Axial Distribution of Microbes in the Intestinal Tract of the Polychaete <Emphasis Type="Italic">Neanthes glandicincta</Emphasis>

The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.05, analysis of variance) but more rapidly from the anterior to the middle segment. Phylogenetic analysis showed that the dominating phylogenetic groups included Methanomicrobiales I: Methanosaetaceae (up to 66% of archaeal clones), δ-Proteobacteria (up to 42% of bacterial clones), and γ-Proteobacteria (up to 30% of bacterial clones) widely distributed throughout the entire gut. Other microbiota distributed in different gut sections were Methanomicrobiales II: Methanospirillaceae, Methanomicrobiales III, Thermoplasmatales, Crenarchaea, Methanobacteriaceae, and Methanosarcinales for archaea; and α-Proteobacteria, β-Proteobacteria, Fusobacteria, Clostridia, Chloroflexi, and Planctomycetes for bacteria. The results reveal a difference in microbial community structure along the gut of N. glandicincta. The various phylogenetic diversity and axial distribution of microbes along the gut might indicate an environmental gradient from anterior to posterior sections affecting the structure of the microbial community.     

Processes of liquefaction/solubilization of Spanish coals by microorganisms

Several fundamental aspects of microbial coal liquefaction/solubilization were studied. The liquefied/solubilized products from coal by microorganisms were analysed. The liquid products analysed by IR titration and UV/visible spectrometry showed some alterations with regard to the original coal. Humic acids extracted from the liquefied lignite showed a reduction in the average molecular weight and a increase in the condensation index, probably due to depolymerization caused by microorganisms. The mechanisms implicated in coal biosolubilization by two fungal strains, M2 (Trichoderma sp.) and M4 (Penicillium sp.) were also studied. Extracellular peroxidase, esterase and phenoloxidase enzymes appear to be involved in coal solubilization. Received: 15 June 1998 / Received revision: 23 November 1998 / Accepted: 29 November 1998     

Enhancement of the gas-to-water ethene transfer coefficient by a dispersed water-immiscible solvent: effect of the cells

  For a mass-transfer-limited system, it was demonstrated that the volumetric ethene transfer coefficient (k _l a) from gas to water could be enhanced by dispersing adequate amounts of a water-immiscible organic liquid, namely the perfluorocarbon FC40, in the aqueous phase. When 26% (v/v) FC40 was dispersed in a culture of Mycobacterium parafortuitum an enhancement of k _l a, calculated on a total liquid volume basis, of 1.8 times was found. Steady-state experiments in the absence of microorganisms, however, showed a 1.2-fold enhancement of k _l a at 18.5% (v/v) FC40. At all FC40 volume fractions tested, enhancement factors with cells were higher than enhancements without cells; apparently the microorganisms or their excretion products affected the interfacial areas or characteristic phase dimensions. Received: 4 December 1995 / Received revision: 7 June 1996 / Accepted: 10 June 1996     

High level expression and purification of antimicrobial human cathelicidin LL-37 in Escherichia coli

The human antimicrobial peptide LL-37 is a cationic peptide with antimicrobial activity against both Gram-positive and Gram-negative microorganisms. This work describes the development of an expression system based on Escherichia coli capable of high production of the recombinant LL-37. The fusion protein Trx-LL-37 was expressed under control of T7 promoter. The expression of T7 polymerase in the E. coli strain constructed in this work was controlled by regulation mechanisms of the arabinose promoter. The expression plasmid was stabilized by the presence of parB locus which ensured higher homology of the culture during cultivation without antibiotic selection pressure. This system was capable of producing up to 1 g of fusion protein per 1 l of culture. The subsequent semipreparative HPLC allowed us to isolate 40 mg of pure LL-37. LL-37 showed high antimicrobial activity against both Gram-negative and Gram-positive microorganisms. Its activity against Candida albicans was practically nonexistent. Minimal Inhibition Concentration (MIC) determined for E. coli was 1.65 μM; for Staphylococcus aureus 2.31 μM, and for Enterococcus faecalis 5.54 μM. The effects of cathelicidin on E. coli included the ability to permeabilize both cell membranes, as could be observed by the increase of β-galactosidase activity in extracellular space in time. Physiological changes were studied by scanning electron microscopy; Gram-positive microorganisms did not show any visible changes in cell shapes while the changes observed on E. coli cells were evident. The results of this work show that the herein designed expression system is capable of producing adequate quantities of active human antimicrobial peptide LL-37.     

From <Emphasis Type="Italic">Pichia anomala</Emphasis> killer toxin through killer antibodies to killer peptides for a comprehensive anti-infective strategy

“Antibiobodies”, antibodies (Abs) with antibiotic activity, internal image of a Pichia anomala killer toxin (PaKT) characterized by microbicidal activity against microorganisms expressing β-glucans cell-wall receptors (PaKTRs), were produced by idiotypic vaccination with a PaKT-neutralizing monoclonal Ab (PaKT-like Abs) or induced by a protein-conjugated β-glucan. Human natural PaKT-like Abs (PaKTAbs) were found in the vaginal fluid of women infected with KT-sensitive microorganisms. Monoclonal and recombinant PaKT-like Abs, and PaKTAbs proved to be protective against experimental candidiasis, cryptococcosis and aspergillosis. A killer decapeptide (KP), synthesized from the sequence of a recombinant PaKT-like Ab or produced in transgenic plants, showed a microbicidal activity in vitro, neutralized by β-glucans, a therapeutic effect in vivo, against experimental mucosal and systemic mycoses, and a prophylactic role in planta, against phytopathogenic microorganisms, respectively. KP showed fungicidal properties against all the defective mutants of a Saccharomyces cerevisiae library, inclusive of strains recognized to be resistant to conventional antifungal drugs. KP inhibited in vitro, ex vivo and/or in vivo HIV-1 and Influenza A virus replication, owing to down-regulation of CCR5 co-receptors, physical block of the gp120-receptor interaction and reduction in the synthesis of glycoproteins, HA and M1 in particular. KP modulated the expression of costimulatory and MHC molecules on murine dendritic cells, improving their capacity to induce lymphocyte proliferation. KP, proven to be devoid of cytotoxicity on human cells, showed self-assembly-releasing hydrogel-like properties, catalyzed by β 1,3 glucan. PaKT’s biotechnological derivatives may represent the prototypes of novel antifungal vaccines and anti-infective drugs characterized by different mechanisms of action.     

Dissolution of Dead Corals by Euendolithic Microorganisms Across the Northern Great Barrier Reef (Australia)

Spatial and temporal variabilities in species composition, abundance, distribution, and bioeroding activity of euendolithic microorganisms were investigated in experimental blocks of the massive coral Porites along an inshore–offshore transect across the northern Great Barrier Reef (Australia) over a 3-year period. Inshore reefs showed turbid and eutrophic waters, whereas the offshore reefs were characterized by oligotrophic waters. The euendolithic microorganisms and their ecological characteristics were studied using techniques of microscopy, petrographic sections, and image analysis. Results showed that euendolithic communities found in blocks of coral were mature. These communities were dominated by the chlorophyte Ostreobium quekettii, the cyanobacterium Plectonema terebrans, and fungi. O. quekettii was found to be the principal agent of microbioerosion, responsible for 70–90% of carbonate removal. In the offshore reefs, this oligophotic chlorophyte showed extensive systems of filaments that penetrated deep inside coral skeletons (up to 4.1 mm) eroding as much as 1 kg CaCO₃ eroded m⁻² year⁻¹. The percentage of colonization by euendolithic filaments at the surface of blocks did not vary significantly among sites, while their depths of penetration, especially that of O. quekettii (0.6–4.1 mm), increased significantly and gradually with the distance from the shore. Rates of microbioerosion (0.1–1.4 kg m⁻² after 1 year and 0.2–1.3 kg m⁻² after 3 years of exposure) showed a pattern similar to the one found for the depth of penetration of O. quekettii filaments. Accordingly, oligotrophic reefs had the highest rates of microbioerosion of up to 1.3 kg m⁻² year⁻¹, whereas the development of euendolithic communities in inshore reefs appeared to be limited by turbidity, high sedimentation rates, and low grazing pressure (rates <0.5 kg m⁻² after 3 years). Those results suggest that boring microorganisms, including O. quekettii, have a significant impact on the overall calcium carbonate budget of coral reef ecosystems, which varies according to environmental conditions.     

A cellular automata model for simulating fed-batch penicillin fermentation process

A cellular automata model to simulate penicillin fed-batch fermentation process (CAPFM) was established in this study, based on a morphologically structured dynamic penicillin production model, that is in turn based on the growth mechanism of penicillin producing microorganisms and the characteristics of penicillin fed-batch fermentation. CAPFM uses the three-dimensional cellular automata as a growth space, and a Moore-type neighborhood as the cellular neighborhood. The transition rules of CAPFM are designed based on mechanical and structural kinetic models of penicillin batch-fed fermentation processes. Every cell of CAPFM represents a single or specific number of penicillin producing microorganisms, and has various state. The simulation experimental results show that CAPFM replicates the evolutionary behavior of penicillin batch-fed fermentation processes described by the structured penicillin production kinetic model accordingly. __________ Translated from ACTA BIOPHYSICA, 2005, 21(2) [译自: 生物物理学报, 2005,21(2)]     

Aerobic cometabolic degradation of trichloroethene by methane and ammonia oxidizing microorganisms naturally associated with <Emphasis Type="Italic">Carex comosa</Emphasis> roots

The degradation potential of trichloroethene by the aerobic methane- and ammonia-oxidizing microorganisms naturally associated with wetland plant (Carex comosa) roots was examined in this study. In bench-scale microcosm experiments with washed (soil free) Carex comosa roots, the activity of root-associated methane- and ammonia-oxidizing microorganisms, which were naturally present on the root surface and/or embedded within the roots, was investigated. Significant methane and ammonia oxidation were observed reproducibly in batch reactors with washed roots incubated in growth media, where methane oxidation developed faster (2 weeks) compared to ammonia oxidation (4 weeks) in live microcosms. After enrichment, the methane oxidizers demonstrated their ability to degrade 150 μg l⁻¹ TCE effectively at 1.9 mg l⁻¹ of aqueous CH₄. In contrast, ammonia oxidizers showed a rapid and complete inhibition of ammonia oxidation with 150 μg l⁻¹ TCE at 20 mg l⁻¹ of NH₄ ⁺-N, which may be attributed to greater sensitivity of ammonia oxidizers to TCE or its degradation product. No such inhibitory effect of TCE degradation was detected on methane oxidation at the above experimental conditions. The results presented here suggest that microorganisms associated with wetland plant roots can assist in the natural attenuation of TCE in contaminated aquatic environments.     

EPR study and structural aspects of ferredoxins obtained from Thiobacillus ferrooxidans

A comparison of iron-sulfur proteins obtained from Thiobacillus ferrooxidans was carried out. The microorganisms were grown on iron(II)- or sulfur-containing nutrients. In both cases different, broad elctron paramagnetic resonance (EPR) lines, originating from an iron(III) compound, were detected. Additional EPR lines of tetrahedral iron(III) and free radicals were observed. The UV spectra of these compounds also differ. Received: 15 July 1998 / Received revision: 8 October 1998 / Accepted: 16 October 1998     

Humic acid effect on pyrene degradation: finding an optimal range for pyrene solubility and mineralization enhancement

The addition of humic acid (HA) to polycyclic aromatic hydrocarbon (PAH) contaminated systems has been shown to enhance, inhibit, or have no effect on the biodegradation of these PAHs. In this study, the surfactant effects of Elliott soil HA (ESHA) at two pH values were tested. At pH 7.0, ESHA did not behave as a surfactant. At pH 11.8, ESHA acted as a surfactant, as displayed by a decrease in surface tension with increasing concentrations of ESHA. The effect of ESHA on pyrene solubility was tested by adding 0 to 800 μg ESHA/g soil to soil-slurries. Enhancement of pyrene apparent solubility demonstrated a dose- and time-related effect. Broader doses from 0 to 10,080 μg ESHA/g soil and three higher doses from 3,360 to 10,080 μg ESHA/g soil were tested for their effects on pyrene mineralization by indigenous soil microorganisms and a novel PAH-degrading Mycobacterium sp. KMS in soil microcosms, respectively. ESHA amendments between 20 and 200 μg ESHA/g soil were found to consistently increase pyrene mineralization by indigenous microorganisms, while the 10,080 μg ESHA/g soil produced inhibition and all other doses presented no effects. Pyrene degradation by M. KMS was significantly inhibited by the addition of the highest dose of ESHA.     

Hydrocarbon degradation potential of salt marsh plant–microorganisms associations

Estuaries are often considered sinks for contaminants and the cleanup of salt marshes, sensitive ecosystems with a major ecological role, should be carried out by means of least intrusive approaches, such as bioremediation. This study was designed to evaluate the influence of plant–microorganisms associations on petroleum hydrocarbons fate in salt marshes of a temperate estuary (Lima River, NW Portugal). Sediments un-colonized and colonized (rhizosediments) by different plants (Juncus maritimus, Phragmites australis, Triglochin striata and Spartina patens) were sampled in four sites of the lower and middle estuary for hydrocarbon degrading microorganisms (HD), total cell counts (TCC) and total petroleum hydrocarbons (TPHs) assessment. In general, TPHs, HD and TCC were significantly higher (P < 0.05) in rhizosediments than in un-colonized sediments. Also recorded were differences on the abundance of hydrocarbon degraders among the rhizosediment of the different plants collected at the same site (J. maritimus < P. australis < T. striata), with statistically significant differences (P < 0.05) between J. maritimus and T. striata. Moreover, strong positive correlations—0.81 and 0.84 (P < 0.05), between biotic (HD) and abiotic (organic matter content) parameters and TPHs concentrations were also found. Our data clearly suggest that salt marsh plants can influence the microbial community, by fostering the development of hydrocarbon-degrading microbial populations in its rhizosphere, an effect observed for all plants. This effect, combined with the plant capability to retain hydrocarbons around the roots, points out that salt marsh plant–microorganisms associations may actively contribute to hydrocarbon removal and degradation in estuarine environments.     

Resistance to heavy metals by some Nigerian yeast strains

The heavy metal resistance of yeasts isolated from sugary substrates such as orange, palm wine and pineapple and identified asSaccharomyces carlsbergensis andS. cerevisiae was studied. The yeast isolates were tested against different concentrations of cadmium, copper, manganese, silver and zinc salts ranging from 1 to 20 mmol/L. Local yeasts showed resistance to 3–15 mmol/L cadmium, 18–20 copper, 16–20 manganese, 1–9 silver and 16–19 for zinc. The significance of the results is discussed in relation to the effects of heavy metals on growth of microorganisms and selection of yeasts for the brewing industry in Nigeria.     

Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid

We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E < 1 × 10⁻²) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.     

Molecular studies on isopenicillin N synthases

The isopenicillin N synthases isolated thus far are related to oxidases from other microorganisms and plants. These enzymes maintain a non-heme monoferrous-dependent catalytic centre comprising a HisXAsp(53–57)XHis motif and a crucial substrate-binding pocket with an ArgXSer motif for their functionality. The elucidation of these motifs was dependent on information collated from studies on structural chemistry, structural biology, site-directed engineered mutations and biochemical experiments. It is envisaged that these enzymes can potentially be improved through molecular breeding and protein engineering. Received: 15 December 1999 / Received revision: 26 January 2000 / Accepted: 27 January 2000