Can Metal Nanoparticles Be a Threat to Microbial Decomposers of Plant Litter in Streams?

The extensive use of nanometal-based products increases the chance of their release into aquatic environments, raising the question whether they can pose a risk to aquatic biota and the associated ecological processes. Aquatic microbes, namely fungi and bacteria, play a key role in forested streams by decomposing plant litter from terrestrial vegetation. Here, we investigated the effects of nanocopper oxide and nanosilver on leaf litter decomposition by aquatic microbes, and the results were compared with the impacts of their ionic precursors. Alder leaves were immersed in a stream of Northwest Portugal to allow microbial colonization before being exposed in microcosms to increased nominal concentrations of nanometals (CuO, 100, 200 and 500 ppm; Ag, 100 and 300 ppm) and ionic metals (Cu²⁺ in CuCl₂, 10, 20 and 30 ppm; Ag⁺ in AgNO₃, 5 and 20 ppm) for 21 days. Results showed that rates of leaf decomposition decreased with exposure to nano- and ionic metals. Nano- and ionic metals inhibited bacterial biomass (from 68.6% to 96.5% of control) more than fungal biomass (from 28.5% to 82.9% of control). The exposure to increased concentrations of nano- and ionic metals decreased fungal sporulation rates from 91.0% to 99.4%. These effects were accompanied by shifts in the structure of fungal and bacterial communities based on DNA fingerprints and fungal spore morphology. The impacts of metal nanoparticles on leaf decomposition by aquatic microbes were less pronounced compared to their ionic forms, despite metal ions were applied at one order of magnitude lower concentrations. Overall, results indicate that the increased release of nanometals to the environment may affect aquatic microbial communities with impacts on organic matter decomposition in streams.     

Microbial Oxidation of α-Methylstyrene and β-Methylstyrene

An unidentified bacterial strain S107B1, isolated from soil by use of isopropylbenzene as a carbon source, was shown to bring about oxidation of α-methylstyrene and β-methylstyrene,

One of the oxidation products produced from α-methylstyrene was identified as the new compound, (—)-cis-23-dihydroxy-1-isopropenyl-6-cyclohexene.

The same strain S107B1 also oxidized β-methylstyrene and produced 3-phenylpropionaldehyde and benzoic acid.

From these results, the existence of reductive step for the aerobic degradation of these aromatic hydrocarbons by this strain was made clear. The initial attack on these aromatic hydrocarbons and a cyclohexenediol compound formed from α-methylstyrene were discussed.     

Microbial production and chemical transformation of poly-γ-glutamate

Poly-γ-glutamate (PGA), a novel polyamide material with industrial applications, possesses a nylon-like backbone, is structurally similar to polyacrylic acid, is biodegradable and is safe for human consumption. PGA is frequently found in the mucilage of natto, a Japanese traditional fermented food. To date, three different types of PGA, namely a homo polymer of d-glutamate (D-PGA), a homo polymer of l-glutamate (L-PGA), and a random copolymer consisting of d- and l-glutamate (DL-PGA), are known. This review will detail the occurrence and physiology of PGA. The proposed reaction mechanism of PGA synthesis including its localization and the structure of the involved enzyme, PGA synthetase, are described. The occurrence of multiple carboxyl residues in PGA likely plays a role in its relative unsuitability for the development of bio-nylon plastics and thus, establishment of an efficient PGA-reforming strategy is of great importance. Aside from the potential applications of PGA proposed to date, a new technique for chemical transformation of PGA is also discussed. Finally, some techniques for PGA and its derivatives in advanced material technology are presented.     

Microbial diversity and the “lower-limit” problem of biodiversity

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “biodiversity”: the issues of defining the units of biodiversity and of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity.     

Microbial transformation of α-pinene

Summary A bacterium capable of utilizing -pinene as a sole carbon and energy source was isolated from soil. This strain, named strain S201-1, which was identified as Pseudomonas maltophilia on the basis of its taxonomical properties, accumulated limonene, borneol, camphor, perillic acid, and 2-(4-methyl-3-cyclohexenylidene) propionic acid from -pinene in the culture broth. It was demonstrated that -pinene, -pinene, borneol, camphor, and a number of p-menthane derivatives were oxidized by this strain. Relations between the protonation of -pinene and the formation of the products by the microbe are discussed.     

Synthesis and Microbial Transformation of Ent-12β-hydroxykaur-16-ene

A study was made of the microbial transformation of cis-abienol, a main precursor of the tobacco aroma principle, by an unidentified soil bacterium JTS-162. Four new compounds were isolated from the culture broth as transformation products. They were elucidated to be (12Z)-labda-8(17),12,14-triene, (12Z)-labda-8(17),12,14-trien-18-ol, (12Z)-labda-8(17),12,14-trien-18-al and 4,18,19-tri-nor-3,4-seco-5-oxo-(12Z)-labda-8(17),12,14-trien-3-oic acid by spectrometry and syntheses. Based on experiments with a degradation sequence, the biotransformation pathway of cis-abienol by the bacterium was proposed.     

Microbial growth and production kinetics of Streptomyces antibioticus Tü 6040

Streptomyces antibioticus Tü 6040 is the producer of simocyclinones, which belong to a novel family of angucyclinone antibiotics some of which show antitumor activities. Growth and antibiotic production is dependent on the medium composition, especially on the carbon and nitrogen source, and on the fermentation conditions. The best results with respect to antibiotic productivity were achieved using a chemically defined medium with glycerol and L-lysine as carbon and nitrogen source, respectively, in an airlift fermenter with minimised shear stress at low gas flow rates withour oxygen limitation. These conditions led to a homogeneous formation of pellets of 1–2 mm in diameter and guaranteed reproducible product yields of the main compound, simocyclinone D8, in the range of 300 mg/l.     

Microbial degradation of nonylphenol and other alkylphenols—our evolving view

Because the endocrine disrupting effects of nonylphenol (NP) and octylphenol became evident, the degradation of long-chain alkylphenols (AP) by microorganisms was intensively studied. Most NP-degrading bacteria belong to the sphingomonads and closely related genera, while NP metabolism is not restricted to defined fungal taxa. Growth on NP and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. While both bacterial and fungal degradation of short-chain AP, such as cresols, and the bacterial degradation of long-chain branched AP involves aromatic ring hydroxylation, alkyl chain oxidation and the formation of phenolic polymers seem to be preferential elimination pathways of long-chain branched AP in fungi, whereby both intracellular and extracellular oxidative enzymes may be involved. The degradation of NP by sphingomonads does not proceed via the common degradation mechanisms reported for short-chain AP, rather, via an unusual ipso-substitution mechanism. This fact underlies the peculiarity of long-chain AP such as NP isomers, which possess highly branched alkyl groups mostly containing a quaternary α-carbon. In addition to physicochemical parameters influencing degradation rates, this structural characteristic confers to branched isomers of NP a biodegradability different to that of the widely used linear isomer of NP. Potential biotechnological applications for the removal of AP from contaminated media and the difficulties of analysis and application inherent to the hydrophobic NP, in particular, are also discussed. The combination of bacteria and fungi, attacking NP at both the phenolic and alkylic moiety, represents a promising perspective.     

Microbial Resolution of (±)-1 and 2-Decalols

By microorganisms or esterase they produce, (±)-1 and 2-decalyl acetates were asymmetrically hydrolyzed to (?)-1-(R)-trans,cis-1-decalol (IIa), (+)-1-(S)-cis,cis-1-decalol (IIIb), (+)-1-(R)-cis,trans-1-decalol (IVa) and (+)-1-(S)-trans,trans-2-decalol (VIIb), (?)-cis,cis-2-decalol (IXb) with the acetates of their antipodes, whereas the axial acetates of (±)-decalols were scarecely hydrolyzed.     

Does Litter Size Variation Affect Models of Terrestrial Carnivore Extinction Risk and Management?

Background

Individual variation in both survival and reproduction has the potential to influence extinction risk. Especially for rare or threatened species, reliable population models should adequately incorporate demographic uncertainty. Here, we focus on an important form of demographic stochasticity: variation in litter sizes. We use terrestrial carnivores as an example taxon, as they are frequently threatened or of economic importance. Since data on intraspecific litter size variation are often sparse, it is unclear what probability distribution should be used to describe the pattern of litter size variation for multiparous carnivores.

Methodology/Principal Findings

We used litter size data on 32 terrestrial carnivore species to test the fit of 12 probability distributions. The influence of these distributions on quasi-extinction probabilities and the probability of successful disease control was then examined for three canid species – the island fox Urocyon littoralis, the red fox Vulpes vulpes, and the African wild dog Lycaon pictus. Best fitting probability distributions differed among the carnivores examined. However, the discretised normal distribution provided the best fit for the majority of species, because variation among litter-sizes was often small. Importantly, however, the outcomes of demographic models were generally robust to the distribution used.

Conclusion/Significance

These results provide reassurance for those using demographic modelling for the management of less studied carnivores in which litter size variation is estimated using data from species with similar reproductive attributes.     

Microbial deterioration of cultural heritage and works of art — tilting at windmills?

Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.     

Litter decomposing and ectomycorrhizalBasidiomycetes in an igapó forest

An igapó forest near the confluence of Rio Tarumã Mirim (Tarumãzinho) and Rio Negro has been studied. It is a typical ectotroph forest with a raw humus layer and suppressed litter decomposing activity by Higher (i.e., carpophore-producing) Fungi. The number of the latter is about one-fifth of that observed in the (anectotrophic) terra firme forest. All ectotrophically mycorrhizal fungi observed belonged in three families:Amanitaceae, Boletaceae, Russulaceae. Leguminosae are dominant, and of theseAldina latifolia andSwartzia cf.polyphylla were demonstrably ectomycorrhizal. The scarcity of mineral nutrients in the soils of igapó, campinarana and campina is overcome by direct cycling through ectomycorrhizae. This is in contrast to other black- and white-water inundated forest communities in Amazonia.Litter Decomposition and Ectomycorrhiza in Amazonian Forests3. Previous contributions seeSinger & Araujo (1979) andSinger & al. (1983).     

Microbial 1β-Hydroxylation of Digitoxigenin

l-Deoxy-l-l-proIino-d-fructose was isolated from flue-cured tobacco leaves in crystalline form. The structure was confirmed by comparison with synthetic compound.     

Ultraviolet Radiation-Absorbing “Humic Pigments” of Cyanobacteria in Microbial Mats: Their Presumptive Photoprotective Function and Relevance to Early Precambrian Microbial Ecology and Evolution

Cyanobacteria that form the primary components of microbial mats in freshwater bogs and intertidal marine environments in the Bahamas produce water-soluble brown pigments whose spectral properties imply that they are a type of humic acid. These “humic pigments” are produced by vital processes of living cyanobacteria, not by decomposition of dead ones, as shown by decreases in the concentrations of humic pigments, ultraviolet (UV) radiation-absorbing photoprotective mycosporine-like amino acids (MAAs), and chlorophyll from upper to lower layers of the mats, and by the occurrence of humic pigments in cyanobacterial cultures. Unlike MAAs, which absorb UV radiation only within limited ranges of wavelengths, humic pigments absorb radiation spanning the entire UV spectrum, and absorbance increases with decreasing wavelength. These observations suggest that the biosynthesis of humic pigments originated as a photoprotective adaptation in the early Precambrian, enabling cyanobacteria to colonize shallow-water and terrestrial environments even though the atmosphere was virtually devoid of O₂ and O₃ and therefore transparent to all solar radiation in the UV region of the spectrum. Moreover, the evolution of this photoprotective mechanism may have been linked to the evolution of photosynthesis.     

Microbial ketonization of ginsenosides F1 and C–K by Lactobacillus brevis

Ginsenosides are the major pharmacological components in ginseng. We isolated lactic acid bacteria from Kimchi to identify microbial modifications of ginsenosides. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain DCY65-1 belongs to the genus Lactobacillus and is most closely related to Lactobacillus brevis. On the basis of TLC and HPLC analysis, we found two metabolic pathways: F1 → 6α,12β-dihydroxydammar-3-one-20(S)-O-β-d-glucopyranoside and C–K → 12β-hydroxydammar-3-one-20(S)-O-β-d-glucopyranoside. These results suggest that strain DCY65-1 is capable of potent ketonic decarboxylation, ketonizing the hydroxyl group at C-3. The F1 metabolite had a more potent inhibitory effect on mushroom tyrosinase than did the substrate. Therefore, the F1 and C–K derivatives may be more pharmacologically active compounds, which should be further characterized.     

Microbial production of poly-γ-glutamic acid

Poly-γ-glutamic acid (γ-PGA) is a natural, biodegradable and water-soluble biopolymer of glutamic acid. This review is focused on nonrecombinant microbial production of γ-PGA via fermentation processes. In view of its commercial importance, the emphasis is on l-glutamic acid independent producers (i.e. microorganisms that do not require feeding with the relatively expensive amino acid l-glutamic acid to produce γ-PGA), but glutamic acid dependent production is discussed for comparison. Strategies for improving production, reducing costs and using renewable feedstocks are discussed.     

Molecular Modeling and Docking of Microbial Inulinases Towards Perceptive Enzyme–Substrate Interactions

Inulin is emerging as an extremely rare source of sugar, it is having more sweetening capacity than table sugar, has beneficial effect in diabetic patient. Inulinases mainly produced by the microorganism and it degrades inulin into fructose which is a digestible form. There are more than 58 strains of microorganisms which are involved in the production of inulinases. The present report investigates about the selectivity of inulin by inulinase and its action to produce fructose through molecular docking. We have investigated exo-inulinase and endo-inulinases from Penicillium sp. TN-88({"type":"entrez-protein","attrs":{"text":"BAC16218","term_id":"22852185","term_text":"BAC16218"}}BAC16218) and Penicillium sp. TN-88({"type":"entrez-protein","attrs":{"text":"BAA19132","term_id":"1841298","term_text":"BAA19132"}}BAA19132), respectively with different arrangement of amino acids in the active site which detect the substrate. The protein sequences described above were processed to homology modeling by Swiss model and further they were docked with 1-ketose and fructose-6-phosphate as substrate by DOCK6 software package (dock.compbio.ucsf.edu). The results of the present studies represented that fructose-6-phosphate ((2R,3R,4S) fructose-6-phosphate) was having better interaction with exo-inulinase showing grid score of −40.288094 and the conserved amino acid Asp-22, Asp 128, Asp 179 and Ser 84 of exo-inulinase are involved in the bonding. In addition to this it was also seen that 1-ketose ((3S,4R)-ketose 1-phosphate) did not shown any interaction with the conserved part of the endo-inulinase.     

Microbial transglutaminase—a review of its production and application in food processing

Transglutaminase (EC 2.3.2.13) catalyses an acyl-transfer reaction in which the -carboxamide groups of peptide-bound glutaminyl residues are the acyl donors. The enzyme catalyses in vitro cross-linking in whey proteins, soya proteins, wheat proteins, beef myosin, casein and crude actomysin refined from mechanically deboned poultry meat. In recent years, on the basis of the enzyme's reaction to gelatinize various food proteins through the formation of cross-links, this enzyme has been used in attempts to improve the functional properties of foods. Up to now, commercial transglutaminase has been merely obtained from animal tissues. The complicated separation and purification procedure results in an extremely high price for the enzyme, which hampers a wide application in food processing. Recently studies on the production of transglutaminase by microorganisms have been started. The enzyme obtained from microbial fermentation has been applied in the treatment of food of different origins. Food treated with microbial transglutaminase appeared to have an improved flavour, appearance and texture. In addition, this enzyme can increase shelf-life and reduce allergenicity of certain foods. This paper gives an overview of the development of microbial transglutaminase production, including fermentation and down-stream processing, as well as examples of how to use this valuable enzyme in processing foods of meat, fish and plant origin.     

Hybridization Analysis of Microbial DNA from Fuel Oil–Contaminated and Noncontaminated Soil

Abstract The enrichment of several genes (xylE, nahAcd, todC1C2BA, tmoABCDE, alkB) that encode enzymes responsible for key steps in the degradation of hydrocarbons, and one gene specific to rRNA group I of the genus Pseudomonas, was studied in DNA extracted from a fuel oil–contaminated field site, and in laboratory microcosms (with the exception of alkB). Toluene, ethylbenzene, xylene, and naphthalene concentrations were related to the extent of hybridization of the genes in the field studies. Significant differences were observed in the extent of hybridization of some of the genes between contaminated and noncontaminated samples. In the microcosm studies, gasoline at rates ranging from 0.5 mg to 125 mg gasoline/g of soil as applied to soils, and the changes in hybridization intensity of these genes monitored with time. The lower threshold of gene enrichment of these genes in response to gasoline addition was below 0.5 mg/g soil. Small increases were observed at the 0.5-mg exposure level, but hybridization intensity quickly decreased to levels below detection 6–8 days after addition of the gasoline. A dose-response effect was observed from treatments with gasoline concentrations ranging from 0.5 to 35 mg/g soil. Inhibition by toxic components in gasoline was observed at 75 and 125 mg/g soil levels. Hybridization of the Pseudomonas group 1 probe to field DNA was not significantly enriched in the contaminated field site, although these sequences were enriched in the microcosm studies. Among the genes tested, xylE was the most sensitive indicator of low levels of fuel oil contamination. Received: 23 July 1996; Accepted 9 October 1996     

Microbial metabolism of quorum-sensing molecules acyl-homoserine lactones, γ-heptalactone and other lactones

The cell-to-cell communication of microorganisms is known to be via exertion of certain chemical compounds (signal molecules) and is referred to as quorum sensing (QS). QS phenomenon is widespread in microbial communities. Several Gram-positive and Gram-negative bacteria and fungi use lactone-containing compounds (e.g. acyl-homoserine lactones (AHLs), γ-heptalactone, butyrolactone-I) as signalling molecules. The ability of microorganisms to metabolise these compounds and the mechanisms they employ for this purpose are not clearly understood. Many studies, however, have focused on identifying AHL and other lactone-degrading enzymes produced by bacteria and fungi. Various strains that are able to utilise these signalling molecules as carbon and energy sources have also been isolated. In addition, several reports have provided evidence on the involvement of lactones and lactone-degrading enzymes in numerous biological functions. These studies, although focused on processes other than metabolism of lactone signalling molecules, still provide insights into further understanding of the mechanisms employed by various microorganisms to metabolise the QS compounds. In this review, we consider conceivable microbial strategies to metabolise AHL and other lactone-containing signalling molecules such as γ-heptalactones.