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

A 34-year survey under phosphorus decline and warming: Consequences on stoichiometry and functional trait composition of freshwater macroinvertebrate communities

Worldwide, freshwater systems are subjected to increasing temperatures and nutrient changes. Under phosphorus and nitrogen enrichment consumer communities are often thought to shift towards fast-growing and P-rich taxa, supporting the well-known link between growth rate and body stoichiometry. While these traits are also favoured under warming, the temperature effect on stoichiometry is less clear. As recently shown, there is a general link between functional traits and body stoichiometry, which makes the integration of stoichiometric traits a promising tool to help understanding the mechanisms behind taxonomic and functional community responses to nutrient changes and/or warming. Yet, such approaches have been scarcely developed at community level and on a long-term perspective. In this study, we investigated long-term responses in stoichiometry and functional trait composition of macroinvertebrate communities to nutrient changes (decreasing water P; increasing water N:P) and warming over a 34-year period in the Middle Loire River (France), testing the potentially opposing responses to these drivers. Both drivers should cause shifts in species composition, which will alter the overall community stoichiometry and functional composition following assumptions from ecological stoichiometry theory. We found that the macroinvertebrate community shifted towards P-poor taxa, causing significant trends in overall community stoichiometry which indicates long-term changes in the nutrient pool provided by these consumers (i.e. decrease in %N and %P, increase in N:P). Further, while the former high-P conditions favoured traits associated to detritus feeding and fast development (i.e. small maximum body size, short life duration), recent conditions favoured predators and slow-developing taxa. These results suggest nutrients to be a more important driver than temperature over this period. By providing a pivotal link between environmental changes and functional trait composition of communities, approaches based on stoichiometric traits offer sound perspectives to investigate ecological relationships between multiple drivers operating at various scales and ecosystem functioning.

A new era of isotope ecology: Nitrogen isotope ratio of amino acids as an approach for unraveling modern and ancient food web

Food web research is rapidly expanding through study of natural fractional abundance of 15N in individual amino acids. This paper overviews the principles of this isotope approach, and from my perspective, reanalyzes applications, and further extends the discussion. It applies kinetic isotope effects that enriches 15N in certain amino acids associated with the metabolic processes, which was clearly demonstrated by observations of both natural ecosystem and laboratory experiments. In trophic processes 'trophic amino acids' such as glutamic acid that significantly enrich 15N, whereas 'source amino acids' such as phenylalanine and methionine show little 15N enrichment. Through various applications conducted over the years, the principles of the method have shown to operate well and disentangle complex food webs and relevant problems. Applications include food chain length estimate, nitrogen resource assessment, tracking fish migration, and reconstruction of paleodiet. With this approach, considerations of a wide range of classical issues have been reinvigorated, while in the same time, new challenging frontiers are emerging.

Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities

Metatranscriptomics allows profiling of community messenger RNA (mRNA) and ribosomal RNA (rRNA) transcript abundance under certain environmental conditions. However, variations in the proportion of RNA transcripts across different community size structures remain less explained, thus limiting the possible applications of metatranscriptomics in community studies. Here, we extended the assumptions of the growth-rate hypothesis (GRH) and the metabolic theory of ecology (MTE) to validate the allometric scaling of interspecific RNA transcript (mRNA and rRNA) abundance through metatranscriptomic analysis of mock communities consisting of model organisms. Results suggest that body size imposes significant constraints on RNA transcript abundance. Interestingly, the relationship between the total mitochondrial transcript abundance (mRNA and rRNA slopes were -0.30 and -0.28, respectively) and body size aligned with the MTE assumptions with slopes close to -¼, while the nuclear transcripts displayed much steeper slopes (mRNA and rRNA slopes were -0.33 and -0.40, respectively). The assumed temperature dependence was not observed in this study. At the gene level, the allometric slopes range from 0 to -1. Overall, the above results showed that larger individuals have lesser RNA transcript abundance per tissue mass than smaller ones regardless of temperature. Analyses of field-collected microcrustacean zooplankton samples demonstrated that the correction of size effect, using the allometric exponents derived from the model organism mock community, explains better the patterns of interspecific RNA transcripts abundance within the metatranscriptome. Integrating allometry with metatranscriptomics can extend the use of RNA transcript reads in estimating ecological processes within complex communities.

The salmon louse genome may be much larger than sequencing suggests

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.

Divergent nucleic acid allocation in juvenile insects of different metamorphosis modes

Nucleic acids help clarify variation in species richness of insects having different metamorphosis modes, a biological conundrum. Here we analyse nucleic acid contents of 639 specimens of aquatic insects collected from four high mountain streams of Sierra Nevada in southern Spain to test whether the allocation to RNA or DNA content differs during ontogeny between juvenile insects undergoing direct (hemimetabolous) or indirect (holometabolous) metamorphosis. The results show that RNA content as a function of body mass was negatively correlated to insect body length in four out of six and three out of six of the holometabolan and hemimetabolan taxa, respectively. Although no significant differences in RNA content were found between holometabolans and hemimetabolans, the significant interaction between body length and metamorphosis mode for RNA and RNA:DNA indicates a strong ontogenetic component to RNA allocation. In addition, our finding of lower DNA content in holometabolans relative to hemimetabolans agree with the analysis of empirical genome data in aquatic and terrestrial insects, and extend to this class of arthropods the “growth rate-genome size-nutrient limitation” hypothesis that differences in allocation between RNA and DNA may reflect fundamental evolutionary trade-off of life-history strategies associated with high growth rates (and RNA content) in holometabolans at the expense of diminished genome sizes.

Predation risk alters life history strategies in an oceanic copepod

The ubiquitous oceanic copepod Calanus finmarchicus is the major link between primary producers and important fish stocks in the North Atlantic Ocean and adjacent seas. Despite over a century of research on growth and development of this key species, the effect of predation risk on these processes remains elusive. We tested how food level and chemical cues from a fish predator influence growth and development of C. finmarchicus, using a predator naïve laboratory population. Copepods reached adult stage earlier both in response to high food and to predator cues in our experiment. High food also increased growth and lipid accumulation. In contrast, perceived predation risk triggered reduced size and lipid fullness, indicating a decoupling of growth and development rates. Our results demonstrate that chemical predator cues can influence life history strategies in C. finmarchicus, and suggest that present and future patterns in oceanic zooplankton size and population dynamics may also reflect differences in predation risk.

Allocation and stoichiometric regulation of phosphorus in a freshwater zooplankton under limited conditions: Implication for nutrient cycling

Because zooplankton is potentially limited by phosphorus (P) in freshwater, they may modify their body P distributions in different biochemical and anatomic components depending on the environmental P levels. In the present study, we quantified the distribution and regulation of P in a freshwater zooplankton Daphnia magna under P-limited conditions by using ³³P as a radiotracer. We demonstrated that the P allocation patterns in D. magna were independent of the ontogenic development. Carapace accounted for 35-54% of total body P, followed by small molecules and nucleic acids (11-30%), whereas phospholipids represented only a minor P pool. The proportion of body P allocated into carapace decreased from 51.8% in +P adults to 16.5% in the -P adults, and a lower proportion of body P was also allocated to eggs in the -P adults than in the +P adults (3.8 vs. 16.5%). Meanwhile, no difference in allocation pattern was detected in the juveniles under +P and -P conditions, demonstrating an interaction between effects of P condition and ontogeny. Furthermore, the P turnover rates of nucleic acids and phospholipids in the -P juveniles were only half of those found in the +P individuals, suggesting a reduced metabolic rate under P-deficient conditions. However, the P turnover rate of small molecules, nucleic acids and phospholipids did not vary with the P condition in adults. It appeared that the adults could maintain their basic P metabolism by down-regulating the P allocation to carapace and eggs. Our results provide an insight into the tolerance of zooplankton to P-deficiency and bear implications on involvement of Daphnia in regulation of P cycling and availability in the epilimnion.

CO2 leakage simulation: Effects of the decreasing pH to the survival and reproduction of two crustacean species

The effects of CO₂-related acidification on two crustacean populations, the isopod Cyathura carinata and the amphipod Elasmopus rapax, were studied. Three pH levels were tested: artificial seawater without CO₂ injection and two levels of reduced pH. Even though RNA:DNA ratio was reduced for both species, no statistical significant differences were found between the control and the treatments. Both species experienced a reduction in survivorship, longevity and the body length of surviving animals; although the impairment observed in E. rapax was more severe than in C. carinata. The long life span isopod and the short life span amphipod experienced a high degree of impairment in the reproduction, likely due to the reallocation of resources from reproduction to body maintenance and increasing survival by postponing the brood production. Regardless of the underlying processes and the energetic pathways, both experienced failure to reproduce, which could lead to the local extinction of these species.

Nitrogen effects on the pelagic food web are modified by dissolved organic carbon

Global environmental change has altered the nitrogen (N) cycle and enhanced terrestrial dissolved organic carbon (DOC) loadings to northern boreal lakes. However, it is still unclear how enhanced N availability affects pelagic food web efficiency (FWE) and crustacean zooplankton growth in N limited boreal lakes. Here, we performed in situ mesocosm experiments in six unproductive boreal Swedish lakes, paired across a DOC gradient, with one lake in each pair fertilized with N (2011: reference year; 2012, 2013: impact years). We assessed how zooplankton growth and FWE were affected by changes in pelagic energy mobilization (PEM), food chain length (phytoplankton versus bacterial production based food chain, i.e. PP:BP), and food quality (seston stoichiometry) in response to N fertilization. Although PP, PEM and PP:BP increased in low and medium DOC lakes after N fertilization, consumer growth and FWE were reduced, especially at low DOC—potentially due to reduced phytoplankton food quality [increased C: phosphorus (P); N:P]. At high DOC, N fertilization caused modest increases in PP and PEM, with marginal changes in PP:BP and phytoplankton food quality, which, combined, led to a slight increase in zooplankton growth and FWE. Consequently, at low DOC (<12 mg L⁻¹), increased N availability lowers FWE due to mismatches in food quality demand and supply, whereas at high DOC this mismatch does not occur, and zooplankton production and FWE may increase. We conclude that the lake DOC level is critical for predicting the effects of enhanced inorganic N availability on pelagic productivity in boreal lakes.

Advances in Biochemical Indices of Zooplankton Production

Several new approaches for measuring zooplankton growth and production rates have been developed since the publication of the ICES (International Council for the Exploration of the Sea) Zooplankton Methodology Manual (Harris et al., 2000). In this review, we summarize the advances in biochemical methods made in recent years. Our approach explores the rationale behind each method, the design of calibration experiments, the advantages and limitations of each method and their suitability as proxies for in situ rates of zooplankton community growth and production. We also provide detailed protocols for the existing methods and information relevant to scientists wanting to apply, calibrate or develop these biochemical indices for zooplankton production.

Diet mixing: do animals integrate growth or resources across temporal heterogeneity?

Animals commonly experience spatial and temporal variation in resource quality, thus experiencing temporally variable diets. Methods for scaling up growth in component patches to long‐term growth across heterogeneity are seldom explicitly considered. Long‐term growth is sometimes considered to be a weighted average of growth rates on component diets (growth integration). However, if animals integrate resources across high‐ and low‐quality diets, their long‐term growth may be greater than predicted from diet‐specific growth rates (resource integration). We measured biomass growth rates of seven Daphnia species exposed to different types of diet variation in algal phosphorus (P) content. Support for resource integration was found for four of the seven species, which achieved near maximal growth when high‐P food was available for at least 12 h. In contrast, no support for resource integration was found for the other three species. These three species achieved only one‐half maximal growth rate under the same conditions and could be considered growth integrators. The type of integration could be predicted from the degree of stoichiometric homeostasis. Species with weak homeostatic regulation exhibited a capacity for resource integration. Resource integrators should have an advantage in heterogeneous environments.