Persistence of community structure: what happens when you change taxonomic scale?

It is common in community ecology to use the species as the taxonomic category of interest, yet in rich tropical assemblages containing guilds of very similar species this may not be appropriate. Such assemblages may be organized at the level of guilds rather than at the finer species level. In a ten-year study of assemblages of fish at One Tree Reef, Great Barrier Reef, we found species composition and the number of fish on a given lagoonal patch reef vary greatly across time (Sale and Douglas 1984; Sale et al. in preparation). The mean average proportional similarity of a reef's assemblage to itself at different times (censuses) is usually low at a value of around 0.5. This apparent variability may be ecologically irrelevant noise if organization is at the higher guild level. We have recast our database at the guild level to test this possibility. Thirteen guilds were defined by the diets, foraging habitats and times of the individual species comprising them. Similarity of an assemblage to itself at successive censuses was re-calculated using the number of individuals in each guild instead of the numbers in each species. This analysis yielded significantly higher levels of similarity (P<0.01) among censuses. To test whether this increase in similarity was due solely to the smaller number of categories used to calculate the similarity indices, 5 sets of randomly generated guilds were constructed using a Monte Carlo approach. No significant difference (P>0.05) was found between the average similarity among censuses when assemblages were classified into these null guilds and when they were classified according to the real guilds. These results indicate that shifting to the larger taxonomic scale of guilds does not reveal a significantly more persistent assemblage structure than that revealed when analysis is at the smaller scale of species. There is no evidence of an underlying organization of these assemblages at the guild level.     

Lipid composition of the pea aphid,Acyrthosiphon pisum (Harris) (homoptera: Aphididae), reared on host plant and on artificial media

Polar and neutral lipids and their constitutive fatty acids were quantified in the pea aphid, Acyrthosiphon pisum (Harris), grown on host plant or on a lipid free artificial diet. The results were compared to determine if lipids were involved in the suitability of the diet for continuous rearing of this A. pisum biotype. For apterous adults grown on plants, the lipids were characterized by a low amount of neutral lipids (2.5% weight/fresh weight) almost entirely (96.4%) composed of hexanoyl and sorboyl dimyristin. These storage lipids were higher in the alatae (3.8%), probably correlated with potential flight activity. The phospholipid amounts were identical in these two morphs (1.3–1.4% weight/fresh weight), comprised mainly of phosphatidylethanolamines (52%) and phosphatidylcholines (40.6%). These phospholipids contained a still unidentified fatty acid, with a retention time close to that of linolenic acid and synthesized by the aphid or its bacterial symbionts (not found in plants). The apterous adult aphids reared on an artificial diet showed an accumulation of neutral lipids (8.9% for the first generation); this increase was shown to be slightly greater for the hexanoyl and sorboyl triglycerides. In contrast, the phospholipids decreased in aphids reared on an artificial diet (1.1% and 0.9%, respectively, for first and second generation), correlated with a phospholipid fatty acid profile significantly deficient in C18:3 and in the unidentified peculiar fatty acid. These phospholipids are essential components of biological membranes and a diet-driven deficient synthesis in some of their components may result in the observed symptoms. © 1992 Wiley-Liss, Inc.     

Trophic relationships between Saccharomyces cerevisiae and Lactobacillus plantarum and their metabolism of glucose and citrate

Glucose and citrate are two major carbon sources in fruits or fruit juices such as orange juice. Their metabolism and the microorganisms involved in their degradation were studied by inoculating with an aliquot of fermented orange juice a synthetic model medium containing glucose and citrate. At pH 3.6, their degradation led, first, to the formation of ethanol due to the activity of yeasts fermenting glucose and, eventually, to the formation of acetate resulting from the activity of lactobacilli. The yeast population always outcompeted the lactobacilli even when the fermented orange juice used as inoculum was mixed with fermented beet leaves containing a wider variety of lactic acid bacteria. The evolution of the medium remained similar between pH 3.3 and 5.0. At pH 3.0 or below, the fermentation of citrate was totally inhibited. Saccharomyces cerevisiae and Lactobacillus plantarum were identified as the only dominant microorganisms. The evolution of the model medium with the complex microbial community was successfully reconstituted with a defined coculture of S. cerevisiae and L. plantarum. The study of the fermentation of the defined model medium with a reconstituted microbial community allows us to better understand the behavior not only of fermented orange juice but also of many other fruit fermentations utilized for the production of alcoholic beverages.     

Universal primers for amplification of three non-coding regions of chloroplast DNA

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.     

Structure and in vitro replication of DNA templates containing 7,8-dihydro-8-oxoadenine.

Adenine residues in DNA are oxidized under the action of ionizing radiation at the C-8 position to give 7,8-dihydro-8-oxoadenine. The formation of this lesion can be considered a cause of mutations and carcinogenesis. Oligodeoxyribonucleotides 39 and 47 bases long containing a single 7,8-dihydro-8-oxoadenine (8-hydroxyadenine) residue were synthesized by using nucleoside phosphoramidites. They were used as templates to study the copies obtained in vitro by the Klenow fragment and the thermostable Taq DNA polymerase. 7,8-Dihydro-8-oxoadenine does not block the replication and thymine is incorporated opposite the damage. The modifications of the DNA duplex conformation provoked by 7,8-dihydro-8-oxoadenine are minor. 1H-NMR spectroscopy shows that the duplex is in a B form, the sugar in a normal position in the helix and the modified base in the anti position. NMR confirms that 7,8-dihydro-8-oxoadenine exists predominantly in the keto form.     

The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics.

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three-dimensional solution structure of a 21 residue oligonucleotide capable of forming a hairpin structure with a loop of three thymidine residues. This structure is in equilibrium with a duplex form. At 33 degrees C, low ionic strength and in the presence of MgCl2 the hairpin form dominates in solution. Six Watson-Crick base pairs are formed topped by the loop structure. The residues 1-3 and 18-21 are not complementary and form dangling ends. Distance constraints have been derived from nuclear Overhauser enhancement measurements. These, together with molecular mechanics calculations, have been used to determine the structure. We do not observe stacking of thymidine residues either over the 3' or the 5' end of the stem.     

Reductive Carboxylation of Propionate to Butyrate in Methanogenic Ecosystems

During the batch degradation of sodium propionate by the anaerobic sludge from an industrial digestor, we observed a significant amount of butyrate formation. Varying the initial propionate concentrations did not alter the ratio of maximal butyrate accumulation to initial propionate concentration within a large range. By measuring the decrease in the radioactivity of [1-¹⁴C]butyrate during propionate degradation, we estimated that about 20% of the propionate was converted to butyrate. Labeled butyrate was formed from [1-¹⁴C]propionate with the same specific radioactivity, suggesting a possible direct pathway from propionate to butyrate. We confirmed this hypothesis by nuclear magnetic resonance studies with [¹³C]propionate. The results showed that [1-¹³C]-, [2-¹³C]-, and [3-¹³C]propionate were converted to [2-¹³C]-, [3-¹³C]-, and [4-¹³C]butyrate, respectively, demonstrating the direct carboxylation on the carboxyl group of propionate without randomization of the other two carbons. In addition, we observed an exchange reaction between C-2 and C-3 of the propionate, indicating that acetogensis may proceed through a randomizing pathway. The physiological significance and importance of various metabolic pathways involved in propionate degradation are discussed, and an unusual pathway of butyrate synthesis is proposed.     

Aerial Dispersal and Epiphytic Survival of Pseudomonas syringae during a Pretest for the Release of Genetically Engineered Strains into the Environment

Prospective experimental field evaluation of genetically engineered microorganisms, such as microbial pest control agents, raises issues of how to properly ascertain their fate and survival in the environment. Field trials with recombinant organisms must reflect requirements for sampling and monitoring. Field trials were conducted at Tulelake, Calif., to monitor the numbers of viable cells of a nonrecombinant strain of Pseudomonas syringae that entered the atmosphere and landed on plants and soil during and after an aerosol spray application. An exponential decrease in numbers of viable cells deposited at increasing distances from three sprayed plots was observed. The relative rate of survival of cells sprayed directly on plants was more than 10 times higher than that of cells dispersed through the air to similar adjacent plants. Results are being used to gain experience with the characteristics of a release site that influence containment or dispersal and to develop appropriate sampling methodologies for evaluating survival and dispersal characteristics of genetically engineered bacteria released into the environment. The ability to make predictions about microbial dispersal and survival will reduce the uncertainties associated with environmental releases of recombinant organisms.     

On the transposition of copia-like nomadic elements in cultured Drosophila cells

We studied the stability of the genomic distribution of six retrotransposon families in long-term and short-term cultures of Drosophila cells. In a subclone derived from Kc cells, no significant rearrangements were detected over an 8 year period. On the contrary, extensive reshuffling and amplification of transposon families were observed in recently established cell lines. These results show that in cultured Drosophila cells transposition appears to be restricted to the transition from the embryo to continuous cell lines.