Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome

Copepod-bacteria interactions include permanent and transient epi- and endobiotic associations that may play roles in copepod health, transfer of elements in the food web, and biogeochemical cycling. Microbiomes of three temperate copepod species (Acartia longiremis, Centropages hamatus, and Calanus finmarchicus) from the Gulf of Maine were investigated during the early summer season using high throughput amplicon sequencing. The most prominent stable component of the microbiome included several taxa within Gammaproteobacteria, with Pseudoalteromonas spp. especially abundant across copepod species. These Gammaproteobacteria appear to be promoted by the copepod association, likely benefitting from nutrient enriched microenvironments on copepods, and forming a more important part of the copepod-associated community than Vibrio spp. during the cold-water season in this temperate system. Taxon-specific associations included an elevated relative abundance of Piscirickettsiaceae and Colwelliaceae on Calanus, and Marinomonas sp. in Centropages. The communities in full and voided gut copepods had distinct characteristics, thus the presence of a food-associated microbiome was evident, including higher abundance of Rhodobacteraceae and chloroplast sequences in the transient communities. The observed variability was partially explained by collection date that may be linked to factors such as variable time since molting, gender differences, and changes in food availability and type over the study period. While some taxon-specific and stable associations were identified, temporal changes in environmental conditions, including food type, appear to be key in controlling the composition of bacterial communities associated with copepods in this temperate coastal system during the early summer.     

Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia

The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Most of these ETs were present at only one or two time periods and were considered transients; however, one resident ET was particularly abundant (64 of the 217 isolates [29.4%]) and was found at all time points except day 32. The mean genetic diversity of the entire population was 0.520, and the index of association (a measure of multilocus linkage disequilibrium) was 1.33. These results, taken in conjunction with a previous study focusing on spatial patterns of genetic diversity in lotic B. cepacia, show that these bacterial populations exhibit greater variability among sites than within a site over time, suggesting relative stability over short time periods.     

Temporal Stability of Genetic Variability and Differentiation in the Three-Spined Stickleback (Gasterosteus aculeatus)

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (N_e) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, N_es were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the N_e estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable – at least over periods of few generations – across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.     

Genetic and Physiological Adaptation of the Copepod EURYTEMORA AFFINIS to Seasonal Temperatures

Evidence of significant additive genetic (genic) variance in temperature tolerance of the copepod Eurytemora affinis was derived from several sources. Differences were observed between average tolerances of progeny of animals exposed and not exposed to heat shock in a power plant. Genic variance was estimated using offspring-parent regressions, full-sib, and half-sib covariances, with quite consistent results. Expressed genic variance between male progeny was always higher than that among female progeny.—The pairs of estimates obtained were as follows: female heritabilities first, 0.40 ± 0.09 and 0.84 ± 0.35 (half-sibs); 0.20 ± 0.09 and 0.79 ± 0.24 (full-sibs); 0.11 ± 0.10 and 0.89 ± 0.45 (full-sibs); 0.28 ± 0.18 and 0.78 ± 0.29 (full-sibs); 0.11 ± 0.44 and 0.72 ± 0.26 (offspring-parent regression). There was no evidence of either nonadditive genetic variance or common environmental (maternal and brood) effects, implying that the genetic variance was mostly additive and was not maintained because of heterozygous advantage.—The presence of so much genetic variance is surprising in view of the high physiological adaptation found earlier, especially in females.     

Quantifying Auditory Temporal Stability in a Large Database of Recorded Music

“Moving to the beat” is both one of the most basic and one of the most profound means by which humans (and a few other species) interact with music. Computer algorithms that detect the precise temporal location of beats (i.e., pulses of musical “energy”) in recorded music have important practical applications, such as the creation of playlists with a particular tempo for rehabilitation (e.g., rhythmic gait training), exercise (e.g., jogging), or entertainment (e.g., continuous dance mixes). Although several such algorithms return simple point estimates of an audio file’s temporal structure (e.g., “average tempo”, “time signature”), none has sought to quantify the temporal stability of a series of detected beats. Such a method-a “Balanced Evaluation of Auditory Temporal Stability” (BEATS)–is proposed here, and is illustrated using the Million Song Dataset (a collection of audio features and music metadata for nearly one million audio files). A publically accessible web interface is also presented, which combines the thresholdable statistics of BEATS with queryable metadata terms, fostering potential avenues of research and facilitating the creation of highly personalized music playlists for clinical or recreational applications.     

Temporal Stability of Allozyme Frequencies in a Natural Population of DROSOPHILA MELANOGASTER

Seasonal patterns of allozyme variation are examined for 12 polymorphic enzyme loci in Drosophila melanogaster. The data derive from a total of 56 samples taken from a natural population in the Summer and Fall of 1978 and 1979. Samples were obtained at approximately five-day intervals and assayed for 6-phosphogluconate dehydrogenase (6Pgd), phosphoglucomutase (Pgm) and glucose-6-phosphate dehydrogenase (G6pd). The remaining nine enzymes were assayed in an average of eight samples per season. None of the loci exhibit regular seasonal cycles of gene-frequency change, although 6Pgd does show significant, but irregular, frequency oscillations. There is also little evidence for gene-frequency differences between years, although 6Pgd is again exceptional in showing significant frequency changes between years. In addition, genotypic frequency distributions are usually consistent with random mating expectations. With the notable exception of 6Pgd, the data give a strong impression of gene-frequency homogeneity within and among years, despite obvious seasonal changes in climate and in the distribution of breeding sites.     

Temporal Changes in Population Structure of a Marine Planktonic Diatom

A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses.     

Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming

Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (N _b) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience substantial genetic drift. Our results reinforce the notion that naturalized trout originated recently from a small yet genetically diverse source and that farm propagules might have played a significant role in the invasion of Rainbow Trout within a single lake with intensive trout farming. Our results also argue for proficient mitigation measures that include management of escapes and strategies to minimize unintentional releases from farm facilities.     

Copepod Population-Specific Response to a Toxic Diatom Diet

Diatoms are key phytoplankton organisms and one of the main primary producers in aquatic ecosystems. However, many diatom species produce a series of secondary metabolites, collectively termed oxylipins, that disrupt development in the offspring of grazers, such as copepods, that feed on these unicellular algae. We hypothesized that different populations of copepods may deal differently with the same oxylipin-producing diatom diet. Here we provide comparative studies of expression level analyses of selected genes of interest for three Calanus helgolandicus populations (North Sea, Atlantic Ocean and Mediterranean Sea) exposed to the same strain of the oxylipin-producing diatom Skeletonema marinoi using as control algae the flagellate Rhodomonas baltica. Expression levels of detoxification enzymes and stress proteins (e.g. glutathione S-transferase, glutathione synthase, superoxide dismutase, catalase, aldehyde dehydrogenases and heat shock proteins) and proteins involved in apoptosis regulation and cell cycle progression were analyzed in copepods after both 24 and 48 hours of feeding on the diatom or on a control diet. Strong differences occurred among copepod populations, with the Mediterranean population of C. helgolandicus being more susceptible to the toxic diet compared to the others. This study opens new perspectives for understanding copepod population-specific responses to diatom toxins and may help in underpinning the cellular mechanisms underlying copepod toxicity during diatom blooms.     

Functions of Scales and Photophores in Mesopelagic Luminescent Sharks

In sharks bioluminescence is only known from the family Squalidae. It evolved independently in two out of six squalid subfamilies, Dalatiinae and Etmopterinae. The distribution of photophores was mapped in several species. It is suggested that in the Dalatiinae, which do not school, but migrate vertically, luminescence serves as ventral countershading. The Etmopterinae school and feed close to the bottom. Their luminescence is an aid in schooling. Four different placoid scale patterns are found in luminescent sharks and they allow to accommodation the photophores in the skin.     

Temporal Stability of the Salivary Microbiota in Oral Health

Objectives

Saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. For such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal variation. The purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling.

Design

Stimulated saliva samples were collected from 5 orally healthy individuals in 4 h intervals for 24 h, and collection was repeated 7 days later (number of samples per person, n = 12, total number of samples, n = 60). Salivary microbiota was analyzed using the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using the Kruskal-Wallis test with Benjamini-Hochberg’s correction for multiple comparisons, cluster analysis, principal component analysis and correspondence analysis.

Results

From a total of 60 saliva samples, 477 probe targets were collectively identified with a mean number of probes per sample of 207 (range: 153–307). Little or no variation in microbial profiles within subjects was observed over time.

Conclusions

Although there was considerable variation between subjects, microbial profiles within subjects were stable throughout a 24 hour period and after 1 week. Since there is little or no evidence of diurnal variation of the salivary microbiome, time of sampling of saliva is not critical for perturbation or other microbial studies.     

Intra-Population Genetic Variation in the Temporal Pattern of Egg Maturation in a Parasitoid Wasp

Parasitoid wasps are taxonomically and biologically extremely diverse. A conceptual framework has recently been developed for understanding life-history evolution and diversification in these animals, and it has confirmed that each of two linked life-history traits – the mode of larval development and the temporal pattern of egg maturation – acts as an organiser of life-history. The framework has been predicated on the assumption that there exists sufficient genetic variation in the latter trait to allow it to be shaped by natural selection. Focusing on the parasitoid wasp Trichogramma brassicae, our aim was to test the validity of that assumption, using established quantitative genetic methods. We demonstrate the existence of a statistically significant degree of intra-population polygenic variation in the temporal pattern of egg production within the wasp population we studied. Furthermore, our results, together with published data on clinal variation in the egg maturation pattern of another species, suggest that intra-specific evolutionary shifts in the temporal pattern of egg maturation of parasitoid wasps can result from a change in allocation to egg production either before, or very shortly after adult emergence, without there being an accompanying change in lifetime fecundity. As well as opening new avenues of research into the reproductive strategies, behaviour, community organisation and biological control potential of parasitoid wasps, this discovery also has implications for studies of life-history evolution and diversification in insects generally.     

Copepod feeding in a tuna fishery area of the tropical Atlantic Ocean

Biomass, feeding and metabolic rates of planktonic copepods were studied in an oligotrophic area of the tropical Atlantic Ocean during an instability wave period (boreal summer) and a stratified period (boreal winter). In summer, zooplankton biomass was higher than in winter, showing a positive effect of the instability wave. Moreover, feeding equilibrated metabolic expenditures of copepods in most cases during the instability. In contrast, in stratified conditions copepods did not equilibrate their metabolic budget. Our results suggest that the microbial loop was the dominant trophic pathway during both periods but with a quicker cycling during the instability.     

一类具有阶段结构的传染病模型的全局分析

通过建立一类具有阶段结构的传染病模型,得到了系统解的永久持续性,并通过构造Liapunov函数和定性分析得到了各类平衡点的全局稳定性的充分条件.     

Genetic Structure of a Population Occupying a Circular Habitat

The geographical structure of a finite population distributed continuously and homogeneously along a circular habit is explored. Selection is supposed to be absent, and the analysis is restricted to a single locus with discrete, non-overlapping generations. Assuming every mutant is new to the population, the rate of decay of genetic variability is obtained, and the probability that two homologous genes separated by a given distance are different alleles is calculated. If moments of the migration function higher than second are neglected, the eigenvalue equation is shown to be a simple trigonometric one, and the Fourier series giving the transient and stationary probabilities of allelism are summed in terms of elementary functions. The proportion of homozygotes, the effective number of alleles maintained in the population, and the amount of local differentiation of gene frequencies are discussed.     

Copepod grazing in a summer cyanobacteria bloom in the Gulf of Finland

Blooms of the cyanobacteria Nodularia spumigena and Aphanizomenon flos-aquae dominated the phytoplankton assemblages of the western Gulf of Finland and the eastern side of the northern Baltic Sea in late July–August, 1992. The bloom overlapped the peak seasonal contributions of the dominant mesozooplankton herbivores in the region, the copepods Acartia bifilosa and Eurytemora affinis and the cladoceran Bosmina longispina maritima. Using radio-labelling techniques; the copepods were offered one of the cyanobacteria, Nodularia, as well as the 10–54 µm fraction of the natural phytoplankton assemblage. In general, incorporation rates of the labelled phytoplankton into the copepods declined with increasing contributions of the cyanobacteria. For both copepods, incorporation was inversely related to total phytoplankton biomass, whether measured as chlorophyll, total cells or cyanobacteria biomass. The very low rates for Acartia (< 0.8 µl [copepod h]^–1) indicated that this copepod was likely starving in the cyanobacteria bloom, consistent with the generally poor condition of the animal observed in the laboratory. The other major mesozooplanktor, B. longispina maritima, ingested substantially more cyanobacterial biomass than the two copepods, based on HPLC-identified cyanobacteria-specific pigment echinenone in the gut. Bloom carbon provided < 1% and < 4% of the daily rations for Acartia and Eurytemora, respectively. Total copepod demand in the cyanobacteria blooms was trivial, < 1% of bloom biomass consumed daily. These results suggest that copepod herbivory is relatively unimportant in dissipating summer cyanobacteria blooms in the Gulf of Finland.     

Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol

Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of copepods.