Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation.

DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress.

Nucleic acid content in crustacean zooplankton: bridging metabolic and stoichiometric predictions.

Metabolic and stoichiometric theories of ecology have provided broad complementary principles to understand ecosystem processes across different levels of biological organization. We tested several of their cornerstone hypotheses by measuring the nucleic acid (NA) and phosphorus (P) content of crustacean zooplankton species in 22 high mountain lakes (Sierra Nevada and the Pyrenees mountains, Spain). The P-allocation hypothesis (PAH) proposes that the genome size is smaller in cladocerans than in copepods as a result of selection for fast growth towards P-allocation from DNA to RNA under P limitation. Consistent with the PAH, the RNA:DNA ratio was >8-fold higher in cladocerans than in copepods, although 'fast-growth' cladocerans did not always exhibit higher RNA and lower DNA contents in comparison to 'slow-growth' copepods. We also showed strong associations among growth rate, RNA, and total P content supporting the growth rate hypothesis, which predicts that fast-growing organisms have high P content because of the preferential allocation to P-rich ribosomal RNA. In addition, we found that ontogenetic variability in NA content of the copepod Mixodiaptomus laciniatus (intra- and interstage variability) was comparable to the interspecific variability across other zooplankton species. Further, according to the metabolic theory of ecology, temperature should enhance growth rate and hence RNA demands. RNA content in zooplankton was correlated with temperature, but the relationships were nutrient-dependent, with a positive correlation in nutrient-rich ecosystems and a negative one in those with scarce nutrients. Overall our results illustrate the mechanistic connections among organismal NA content, growth rate, nutrients and temperature, contributing to the conceptual unification of metabolic and stoichiometric theories.

Do phosphorus requirements for RNA limit genome size in crustacean zooplankton?

As for most other organisms, genome size in zooplankton differs widely. This may have a range of consequences for growth rate, development, and life history strategies, yet the causes of this pronounced variability are not settled. Here we propose that small genome size may be an evolutionary consequence of phosphorus (P) allocation from DNA to RNA under P deficiency. To test this hypothesis we have compared the two major groups of zooplankton, copepods and cladocerans, that have overlapping niches and body size. Relative to the cladocerans, copepods have a more complex life history and a lower mass-specific P content, while cladocerans tend to have higher P and RNA contents and higher specific growth rates and frequently experience P-limited growth, likely due to a shortage of P for ribosome synthesis. Cladocerans also generally have smaller genomes than copepods (1C = 0.17-0.63 pg DNA.cell(-1) vs. 1C = 0.10-10 pg DNA.cell(-1)). Furthermore, cladocerans have a higher slope of the relationship of body size with DNA content (1.5 vs. 0.28 in copepods) and present almost 15-fold higher RNA:DNA ratios (24.8 in cladocerans vs. 1.6 in copepods). Hence, small genome size in cladocerans could reflect an evolutionary pressure towards "efficient" genomes to conserve a key element needed to maximize growth rate. We do not claim that this is a universal cause of genome size variability, but propose that streamlining of genomes could be related to P conservation rather than energy conservation. This could be relevant for a range of organisms that may suffer P-limited growth rates.

Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors.

Small eukaryotes (0.2-5 microm) in hyper-eutrophic conditions were described using terminal restriction fragment length polymorphism and cloning-sequencing, and were related to environmental variables both by an experimental approach and by a temporal field study. In situ analysis showed marked temporal variations in the dominant terminal restriction fragments (T-RFs), which were related to environmental variables such as nutrient concentrations and metazooplankton composition. To monitor the responses of the small-eukaryote community to top-down (absence or presence of planktivorous fish) and bottom-up (low or high nitrogen and phosphorus addition) effects, a cross-classified design mesocosm experiment was used. Depending on the type of treatment, we recorded changes in the diversity of T-RFs, as well as modifications in phylogenetic composition. Centroheliozoa and Cryptophyta were found in all types of treatment, whereas Chlorophyta were specific to enclosures receiving high nutrient loadings, and were associated either with LKM11 and 'environmental sequences'. Cercozoa and Fungi were not detected in enclosures receiving high nutrient loadings and fishes. Our results showed that resources and top-down factors are both clearly involved in shaping the structure of small eukaryotes, not only autotrophs but also heterotrophs, via complex interactions and trophic cascades within a microbial loop, notably in response to nutrient loading.

Analysis of expressed sequence tags from a naked foraminiferan Reticulomyxa filosa.

Foraminifers are a major component of modern marine ecosystems and one of the most important oceanic producers of calcium carbonate. They are a key phylogenetic group among amoeboid protists, but our knowledge of their genome is still mostly limited to a few conserved genes. Here, we report the first study of expressed genes by means of expressed sequence tag (EST) from the freshwater naked foraminiferan Reticulomyxa filosa. Cluster analysis of 1630 valid ESTs enabled the identification of 178 groups of related sequences and 871 singlets. Approximately 50% of the putative unique 1059 ESTs could be annotated using Blast searches against the protein database SwissProt + TrEMBL. The EST database described here is the first step towards gene discovery in Foraminifera and should provide the basis for new insights into the genomic and transcriptomic characteristics of these interesting but poorly understood protists.

Comment on "Nature of phosphorus limitation in the ultraoligotrophic eastern Mediterranean".

Thingstad et al. (Reports, 12 August 2005, p. 1068) reported that in situ mesoscale phosphorus enrichment of the eastern Mediterranean Sea altered selected biological parameters and concluded that the added phosphorus was rapidly transferred from bacteria to mesozooplankton. However, because of a lack of replication and a misinterpretation of their statistical analyses, that conclusion is not supported by the data.