Microbial metabolism of mandelate: a microcosm of diversity

Abstract This review highlights the diversity of prokaryotic and eukaryotic microorganisms that can metabolise mandelate and it describes how a wide range of compounds related to mandelate is formed in many environments. The chief aspects that are summarised include the various pathways whereby mandelate and its structural analogues are converted into catechol or protocatechuate, the properties of the enzymes that are involved in the pathways, and the regulation and genetics of the pathways. The review incorporates the idea that the study of peripheral metabolic pathways is particularly useful for illuminating evolutionary speculations and it concludes with a list of questions that need to be answered.     

Microbial diversity of hypersaline environments: a metagenomic approach

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Habitat patchiness affects decomposition and faunal diversity: a microcosm experiment on forest floor

Environmental heterogeneity has been intensively studied, but little is known about relationships between habitat patchiness and soil processes. The aim of this study was to investigate (1) the impact of patchiness of the litter layer on the decomposer community and litter decomposition rate, and (2) whether the impact of soil fauna on the rates of processes differs in relation to patchiness. An experiment was carried out in microcosms with coniferous forest humus and four kinds of litter with different C:N ratios or stages of decomposition, either separately (i.e. in patches) or mixed with each other. Microarthropod species diversity was better maintained in the patchy systems. In the absence of soil fauna, community respiration was higher in the patchy microcosms, but in the presence of fauna the opposite pattern was observed. The contribution of soil fauna to the rate of decomposition was clearly greater in the mixed litter systems. Based on the results, a hypothesis is presented that in the patchy litter layer the soil fungi can create connections between different materials located some centimeters apart, thus enhancing decomposition, while in the mixed litter the scale of millimeters is more appropriate for the soil fauna, known to accelerate the process rates. Received: 10 November 1997 / Accepted: 20 April 1998     

Microbial genomes: dealing with diversity

We have now complete genome sequences of several pairs of closely related prokaryotes (conspecific strains or congeneric species). Surprisingly, even strains of the same species can differ by as much as 20% in gene content. Conceptual and methodological approaches for dealing with such diversity are now being developed, and should transform microbial genomics.     

Microbial diversity of a mesophilic hydrogen-producing sludge

A hydrogen-producing sludge degraded 99% of glucose at 36 degrees C and pH 5.5, producing a methane-free biogas (comprising 64% hydrogen) and an effluent comprising mostly butyrate, acetate, and ethanol. The yield was 0.26 l H2 g(-1) glucose and the production rate per gram of volatile suspended solids was 4.6 1 H2 day(-1). A 16S rDNA library was constructed from the sludge for microbial species determination. A total of 96 clones were selected for plasmids recovery, screened by denaturing gradient gel electrophoresis, and sequenced for rDNA. Based on the phylogenetic analysis of the rDNA sequences, 64.6% of all the clones were affiliated with three Clostridium species (Clostridiaceae), 18.8% with Enterobacteriaceae, and 3.1% with Streptococcus bovis (Streptococcaceae). The remaining 13.5% belonged to eight operational taxonomic units, the affiliations of which were not identified.     

Microbial diversity as a source of useful biopolymers

Conclusions The few examples presented here, taken from research performed in my laboratory during the last 15 years, provide additional evidence that bacteria are a rich source of highly specialized polymers, many of which have potential commercial applications. Although modern molecular genetics is a valuable tool for modifying and overproducing proteins, the wonderful diversity of the microbial world remains the major source for discovering new and useful biopolymers. More than ever, the rate-limiting steps in discovering these microbial materials are imagination and techniques for enriching and screening for microorganisms that produce the desired products.     

Microbial degradation of four Nigerian crude oils in an estuarine microcosm

Four Nigerian crude oils (Bonny Light, Bonny Medium, Escravos Light and Forcados Blend) that differ substantially in fractional composition were exposed to the Lagos Lagoon waters in microcosm experiments with oil-impregnated membrane filters. Changes in microbial numbers on the membranes and in the residual oil concentration showed a relationship between the fractional composition and the biodegradation rates of the oils, with the lighter oils disappearing more rapidly. After 10 weeks exposure in the lagoon, only 15% (w/w) of the Bonny Light crude remained on the filters as compared with 20, 32 and 45% (w/w) for Escravos Light, Bonny Medium and Forcados Blend respectively. The hydrocarbon-utilizing microbial colonizers of the oil-impregnated membranes were Micrococcus, Bacillus, Pseudomonas, Flavobacterium, Alcaligenes and Aspergillus niger.     

Microbial diversity of soda lakes

Soda lakes are highly alkaline extreme environments that form in closed drainage basins exposed to high evaporation rates. Because of the scarcity of Mg²⁺ and Ca²⁺ in the water chemistry, the lakes become enriched in CO₃ ²⁻ and Cl⁻, with pHs in the range 8 to >12. Although there is a clear difference in prokaryotic communities between the hypersaline lakes where NaCl concentrations are >15% w/v and more dilute waters, i.e., NaCl concentrations about 5% w/v, photosynthetic primary production appears to be the basis of all nutrient recycling. In both the aerobic and anaerobic microbial communities the major trophic groups responsible for cycling of carbon and sulfur have in general been identified. Systematic studies have shown that the microbes are alkaliphilic and many represent separate lineages within accepted taxa, while others show no strong relationship to known prokaryotes. Although alkaliphiles are widespread it seems probable that these organisms, especially those unique to the hypersaline lakes, evolved separately within an alkaline environment. Although present-day soda lakes are geologically quite recent, they have probably existed since archaean times, permitting the evolution of independent communities of alkaliphiles since an early period in the Earth's history. Received: January 22, 1998 / Accepted: February 16, 1998     

Microbial diversity of Minnesota peatlands

Microbial diversity, numbers, and metabolic activities in Minnesota peatlands were investigated using a variety of microbial enrichment and enumeration procedures together with radioisotopic measurements of microbial degradative processes. Minnesota peatlands were shown to contain large microbial populations of wide metabolic diversity. Direct counts of bacteria using epifluorescence microscopy indicated bacterial populations of about 10⁸ ml^–1 of peatland water, irrespective of depth. Radioisotopic most-probable-number (MPN) counts of heterotrophs able to mineralize¹⁴C-labeled substrates to¹⁴CO₂ showed significant populations of glucose degraders (10⁴–10⁶ ml^–1) as well as degraders of benzoate (10²–10³ ml^–1), 2,4-dichlorophenoxyacetate (10²–10⁵ ml^–1), and sphagnum (10³–10⁷ ml^–1) in the various peatlands examined. The MPNs of NO₃ ^– reducers varied from 10³–10⁶ ml^–1, SO₄ ^– reducers from 10²–10³ ml^–1, methanogenic bacteria from 10³–10⁶ ml^–1, and methane oxidizers from 10³–10⁴ ml^–1, depending on sampling site and depth. Eighty pure cultures of aerobic bacteria and fungi were isolated from Minnesota peats. Most of those cultures tested were able to grow on at least 20 organic compounds (carbohydrates, aromatic molecules, hydrocarbons, etc.) as sole sources of carbon and energy. One isolate, aBacillus, was able to fix atmospheric N₂. Several of the isolates were able to mineralize¹⁴C-labeled lignin.     

Microbial metabolism of pyrene

The isolation and identification of pyrene metabolites formed from pyrene by the fungus Cunninghamella elegans is described. C. elegans was incubated with pyrene for 24 h. Six metabolites were isolated by reversed-phase high-performance liquid (HPLC) and thin-layer chromatography (TLC) and characterized by the application of UV absorption, 1H-NMR and mass spectral techniques. C. elegans hydroxylated pyrene predominantly at the 1,6- and 1,8-positions with subsequent glucosylation to form glucoside conjugates of 1-hydroxypyrene, 1,6- and 1,8-dihydroxypyrene. In addition, 1,6- and 1,8-pyrenequinones and 1-hydroxypyrene were identified as metabolites. Experiments with [4-14C]pyrene indicated that over a 24-h period, 41% of pyrene was metabolized to ethyl acetate-soluble metabolites. The glucoside conjugates of 1-hydroxypyrene, 1,6- and 1,8-dihydroxypyrene accounted for 26%, 7% and 14% of the pyrene metabolized, respectively. Pyrenequinones accounted for 22%. The results indicate that the fungus C. elegans metabolized pyrene to non-toxic metabolites (glucoside conjugates) as well as to compounds (pyrenequinones) which have been suggested to be biologically active in higher organisms. In addition, there was no metabolism at the K-region of the molecule which is a major site of enzymatic attack in mammalian systems.     

Microbial diversity of cellulose hydrolysis

Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still not clearly understood even though there is a great deal of information available about the bovine rumen. Two major problems that limit our understanding of this area are the vast diversity of organisms present in most cellulose degrading environments and the inability to culture most of them.     

Microbial metabolism of ethylene

The ethylene-oxidizing strain E20 was grown on different carbon sources to obtain information on the metabolism of ethylene from simultaneous adaptation studies and from measurements of specific activities of enzymes in cell-free extracts.From the simultaneous adaptation studies it was concluded that ethylene oxide is a product of ethylene catabolism. The bacterium was also able to grow on the epoxide. From a comparison of the specific activities of isocitrate lyase and malate synthetase in different extracts it was concluded that the glyoxylate cycle was involved in the metabolism of ethylene, indicating that acetyl-CoA is a metabolite of ethylene catabolism. The sequence of reactions leading from ethylene oxide to acetyl-CoA could not be established from the simultaneous adaptation experiments and the enzyme activities in extracts.Support for the research has come in part from grants of the N.V. Nederlandse Gasunie and the VEG Gasinstituut.     

Microbial diversity of Alcyonium digitatum

Marine multi-cellular organisms are described as sources of many newly discovered bioactive compounds. Meanwhile, it has been demonstrated repeatedly for several natural products of reputed multicellular origin that they are, in fact, produced by endophytic unicellular organisms—such as microbial fungi or bacteria. Consequently, while studying compounds isolated from a living organism, it is essential to ensure that the sample integrity is not compromised. To test the diversity of the endobiome from Alcyonium digitatum, a cold water coral found along the Atlantic coasts of the northern hemisphere, we performed a culture dependent surveyed using a phylogenetic approach. A 1 cm³ cube from the interior tissue of A. digitatum was excised under aseptic conditions, homogenized, spread onto agar-based growth medium plates and incubated in 22 °C to promote microbial growth. Colonies were transferred to secondary medium plates, incubated, and after harvesting lysed using sterile water to release DNA. 16S and 23S rDNA regions were amplified using PCR, and sequenced for systematic evaluation using phylogenetic analysis. From this survey we identified a broad selection of bacteria, predominantly of the α-proteobacterial, bacteriodete, actinobacterial and firmicute lineages, demonstrating a significant biodiversity of the coral bacterial endobiome.     

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.