Application of Sequence-Specific Labeled 16S rRNA Gene Oligonucleotide Probes for Genetic Profiling of Cyanobacterial Abundance and Diversity by Array Hybridization

DNA sequence information for the small-subunit rRNA gene (16S rDNA) obtained from cyanobacterial cultures was used to investigate the presence of cyanobacteria and their abundance in natural habitats. Eight planktonic communities developing in lakes characterized by relatively low algal biomass (mesotrophic) and in lakes with correspondingly high biomass (eutrophic) were selected for the study. The organismal compositions of the water samples were analyzed genetically, using multiplex sequence-specific labeling of oligonucleotide probes targeted to 16S rDNA and subsequent hybridization of the labeled probes to their respective complements spotted onto a solid support (DNA array). Ten probes were established to determine the relative abundances of the discernible cyanobacteria encountered in the selected lakes. The probes were generally specific for their targets, as determined through analyses of clone cultures. Reproducible abundance profiles were established for the lakes investigated in the subsequent analyses of natural cyanobacterial communities. The results from the genetic analyses were then compared with information obtained from standard hydrobiological and hydrochemical analyses. Qualitatively, there were relatively good correlations among the groups of organisms (Nostoc, Microcystis, and Planktothrix species) found in the different lakes. The levels of correlation were lower for the quantitative data. This may, however, be due to differences in sample processing technique. The conclusions from these comparisons are that the genetic abundance profiles may provide a foundation for separating and quantifying genetically distinct groups of cyanobacteria in their natural habitats.     

Chlamydophila abortus in a Brown Skua (Catharacta antarctica lonnbergi) from a Subantarctic Island

On Bird Island, South Georgia, a new strain of Chlamydophila abortus was detected in one Brown skua out of 37 specimens from six different seabird species. Phylogenetic analysis of the rnpB and omp1 genes indicated the strain to be more closely related to C. abortus than to 6BC, the type strain of Chlamydophila psittaci.     

Food web structure and the strength of transient indirect effects

The relative importance of direct and indirect effects in ecological communities remains unresolved. Indirect effects may diminish as they propagate through highly reticulate food webs. We tested this hypothesis by assembling replicate food webs of different complexity in laboratory microcosms, and comparing the transmission of indirect effects through these webs. By providing the top predator ( Didinium ) with either one ( Paramecium ) or two ( Paramecium and Colpidium ) species of protists as prey, we created linear or reticulate food webs where we could examine the transient response of predators to an indirect effect. Addition of Chlamydomonas , a small alga consumed by Paramecium , but not by Colpidium , perturbed the system and generated an indirect effect on Didinium . We expected the proportional response of Didinium to Chlamydomonas addition would be smaller in the reticulate web containing alternative, unperturbed prey ( Colpidium ). We measured predator response as predator yield, the maximum number of predators produced prior to overexploitation of prey and subsequent predator decline. The ratio of yield in perturbed bottles to yield in unperturbed bottles measures the proportional response of Didinium to Chlamydomonas addition. We expected this ratio to be smaller with Colpidium present. Contrary to expectations, alternative prey enhanced rather than diminished predator response to the perturbation. This resulted from competition between the prey species, a factor ignored in some simple verbal arguments. Food web complexity may have unanticipated consequences for the strength of indirect effects.     

The feeding strategies of two large marine copepods

We compared the feeding behaviour of the two copepods Paraeuchaetanorvegica and Chiridius armatus, allowing them to prey on othercalanoids in small-scale laboratory experiments. Several differenceswere found. When fed either live, free-swimming or dead, non-movingprey, P.norvegica seemed unable to locate the dead prey itemswhile C.armatus foraged heavily on them. When starved, P.norvegicaincreased its feeding rate while C.armatus reduced its feedingafter an initial increase. None of the predators changed theirfeeding rates when exposed to light. Nighttime versus daytimefeeding was tested only with P.norvegcia, which seemed to possessan endogenous feeding rhythm with increased rates at night.Chiridius armatus infected with epizooic ciliates appeared tohave increased feeding rates.     

Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.