Academic literature on the topic 'Evolution and diversity across photosynthetic organisms'

Abstract. Permafrost thaw lakes (thermokarst lakes) are widely distributed across the northern landscape, and are known to be biogeochemically active sites that emit large amounts of carbon to the atmosphere as CH4 and CO2. However, the abundance and composition of the photosynthetic communities that fix CO2 have been little explored in this ecosystem type. In order to identify the major groups of phototrophic organisms and their controlling variables, we sampled 12 permafrost thaw lakes along a permafrost degradation gradient in northern Québec, Canada. Additional samples were taken from five rock-basin reference lakes in the region to determine if the thaw lakes differed in limnological properties and phototrophs. Phytoplankton community structure was determined by high-performance liquid chromatography analysis of their photoprotective and photosynthetic pigments, and autotrophic picoplankton concentrations were assessed by flow cytometry. One of the black-colored lakes located in a landscape of rapidly degrading palsas (permafrost mounds) was selected for high-throughput 18S rRNA sequencing to complement conclusions based on the pigment and cytometry analyses. The results showed that the limnological properties of the thaw lakes differed significantly from the reference lakes, and were more highly stratified. However, both waterbody types contained similarly diverse phytoplankton groups, with dominance of the pigment assemblages by fucoxanthin-containing taxa, as well as chlorophytes, cryptophytes and cyanobacteria. Chlorophyll a concentrations (Chl a) were correlated with total phosphorus (TP), and both were significantly higher in the thaw lakes (overall means of 3.3 µg Chl a L−1 and 34 µg TP L−1) relative to the reference lakes (2.0 µg Chl a L−1 and 8.2 µg TP L−1). Stepwise multiple regression of Chl a against the other algal pigments showed that it was largely a function of alloxanthin, fucoxanthin and Chl b (R2 = 0.85). The bottom waters of two of the thaw lakes also contained high concentrations of bacteriochlorophyll d, showing the presence of green photosynthetic sulphur bacteria. The molecular analyses indicated a relatively minor contribution of diatoms, while chrysophytes, dinoflagellates and chlorophytes were well represented; the heterotrophic eukaryote fraction was dominated by numerous ciliate taxa, and also included Heliozoa, Rhizaria, chytrids and flagellates. Autotrophic picoplankton occurred in biovolume concentrations up to 3.1 × 105 µm3 picocyanobacteria mL−1 and 1.9 × 106 µm3 picoeukaryotes mL−1, with large variations among lakes. Both groups of picophytoplankton were positively correlated with total phytoplankton abundance, as measured by Chl a; picocyanobacteria were inversely correlated with dissolved organic carbon, while picoeukaryotes were inversely correlated with conductivity. Despite their net heterotrophic character, subarctic thaw lakes are rich habitats for diverse phototrophic communities.

Abstract. Permafrost thaw lakes (thermokarst lakes) are widely distributed across the northern landscape, and are known to be biogeochemically active sites that emit large amounts of carbon to the atmosphere as CH4 and CO2. However, the abundance and composition of the photosynthetic communities that consume CO2 have been little explored in this ecosystem type. In order to identify the major groups of phototrophic organisms and their controlling variables, we sampled 12 permafrost thaw lakes along a permafrost degradation gradient in northern Québec, Canada. Additional samples were taken from 5 rock-basin reference lakes in the region to determine if the thaw waters differed in limnological properties and phototrophs. Phytoplankton community structure was determined by high performance liquid chromatography analysis of their photoprotective and photosynthetic pigments, and autotrophic picoplankton concentrations were assessed by flow cytometry. One of the black colored lakes located in a andscape of rapidly degrading palsas (permafrost mounds) was selected for high-throughput 18S rRNA sequencing to help interpret the pigment and cytometry data. The results showed that the limnological properties of the thaw lakes differed significantly from the reference lakes, and were more highly stratified. However, both waterbody types contained similarly diverse phytoplankton groups, with dominance of the pigment assemblages by fucoxanthin-containing taxa, as well as chlorophytes, cryptophytes and cyanobacteria. Chlorophyll a concentrations (Chl a) were correlated with total phosphorus (TP), and both were significantly higher in the thaw lakes (overall means of 3.3 μg Chl a L−1 and 34 μg TP L−1) relative to the reference lakes (2.0 μg Chl a L−1 and 8.2 μg TP L−1). Stepwise multiple regression of Chl a against the other algal pigments showed that it was largely a function of lutein, fucoxanthin and peridinin (R2 = 0.78). The bottom waters of two of the thaw lakes also contained high concentrations of bacteriochlorophyll d, showing the presence of green photosynthetic sulphur bacteria. The molecular analyses indicated a relatively minor contribution of diatoms, while chrysophytes, dinoflagellates and chlorophytes were well represented; the heterotrophic eukaryote fraction was dominated by numerous ciliate taxa, and also included Heliozoa, Rhizaria, chytrids and flagellates. Autotrophic picoplankton occurred in cell concentrations up to 8.8 × 105 mL−1 (picocyanobacteria) and 4.6 × 105 mL−1 (picoeukaryotes). Both groups of picophytoplankton were positively correlated with total phytoplankton abundance, as measured by Chl a; picocyanobacteria were inversely correlated with dissolved organic carbon, while picoeukaryotes were correlated with conductivity. Despite their net heterotrophic character, subarctic thaw lakes are rich habitats for diverse phototrophic communities.

Natural photonic structures are common across the biological kingdoms, serving a diversity of functionalities. The study of implications of photonic structures in plants and other phototrophic organisms is still hampered by missing methodologies for determining in situ photonic properties, particularly in the context of constantly adapting photosynthetic systems controlled by acclimation mechanisms on the cellular scale. We describe an innovative approach to determining spatial and spectral photonic properties and photosynthesis activity, employing micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry in a combined microscope setup. Using two examples from the photosynthetic realm, the dynamic Bragg-stack-like thylakoid structures of Begonia sp. and complex 2.5 D photonic crystal slabs from the diatom Coscinodiscus granii, we demonstrate how the setup can be used for measuring self-adapting photonic-photosynthetic systems and photonic properties on single-cell scales. We suggest that the setup is well-suited for the determination of photonic–photosynthetic systems in a diversity of organisms, facilitating the cellular, temporal, spectral and angular resolution of both light distribution and combined chlorophyll fluorescence determination. As the catalogue of photonic structure from photosynthetic organisms is rich and diverse in examples, a deepened study could inspire the design of novel optical- and light-harvesting technologies.

Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.

Peroxisomes are organelles bounded by a single membrane that can be found in all major groups of eukaryotes. A single evolutionary origin of this cellular compartment is supported by the presence, in diverse organisms, of a common set of proteins implicated in peroxisome biogenesis and maintenance. Their enzymatic content, however, can vary substantially across species, indicating a high level of evolutionary plasticity. Proteomic analyses have greatly expanded our knowledge on peroxisomes in some model organisms, including plants, mammals and yeasts. However, we still have a limited knowledge about the distribution and functionalities of peroxisomes in the vast majority of groups of microbial eukaryotes. Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes.

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a “deep diversity” of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

Au sein des Archaeplastida (eucaryotes photosynthétiques ayant acquis un chloroplaste suite à une endosymbiose avec une cyanobactérie ancestrale) les génomes chloroplastiques et mitochondriaux des algues vertes et des plantes terrestres sont régulés de manière post-transcriptionnelle, principalement par des protéines à solénoïde alpha codées dans le noyau. Ces facteurs nucléaires sont composés de motifs répétés dégénérés (protéines PPR et OPR, respectivement pentatricopeptide repeat et octatricopeptide repeats) interagissant de façon spécifique avec une partie de la séquence de leur ARN cible et forment de grandes familles de paralogues. Les protéines PPR sont très abondantes chez les plantes terrestres tandis que les OPR le sont chez les algues vertes. Ces expansions différentielles, en parallèle de l'évolution du métabolisme des ARN dans les organites pourraient refléter des adaptations génétiques préservant la phototrophie dans diverses conditions et niches écologiques. Chez les autres Archaeplastida (algues rouges et Glaucophytes) et chez les eucaryotes issus d'une endosymbiose avec une microalgue ancestrale comme les Diatomées, la régulation des génomes des organites reste peu explorée. Un premier objectif de ma thèse a été de décrire la diversité et la dynamique évolutive des protéines à solénoïde alpha connues ou candidates pour la régulation de l'expression du génome des organites et ce, dans l'ensemble des eucaryotes photosynthétiques. Pour les identifier, j'ai développé une approche combinant détection d'homologie lointaine de séquence et classification indépendante de la similarité entre séquences. J'ai validé cette approche en retrouvant et complétant les familles OPR et PPR connues chez les espèces modèles Chlamydomonas reinhardtii et Arabidopsis thaliana. J'ai montré que les expansions d'OPR étaient restreintes au sein des Chlorophytes et qu'en dehors des algues vertes et des plantes terrestres, les protéines à PPR et à OPR étaient peu nombreuses, suggérant que d'autres acteurs de la régulation de l'expression des génomes des organites restent à découvrir. J'ai également identifié plusieurs dizaines d'autres familles de protéines à solénoïde alpha adressées aux organites dans tous les protéomes étudiés, certaines aux fonctions encore inconnues et dont la caractérisation expérimentale dans des organismes modèles serait pertinente. Dans un second temps, j'ai utilisé des approches de dynamique moléculaire pour mieux comprendre l'affinité et la spécificité des liaisons entre les PPR et leurs ARN cibles. J'ai notamment étudié la dynamique des motifs répétés et la géométrie des sites de liaison des nucléotides en fonction de leur position dans la séquence des motifs PPR, y compris les effets du nombre de répétitions et de la présence ou non des domaines N- et C-terminaux, en plus de l'évolution de la conformation globale de la protéine. Nos résultats suggèrent le rôle de la flexibilité des protéines PPR, tant au niveau de la protéine que du motif dans la liaison à sa cible ARN et sa pertinence pour l'affinité et la spécificité de la reconnaissance des nucléotides
In Archaeplastida (photosynthetic eukaryotes that acquired a chloroplast following endosymbiosis with an ancestral cyanobacterium) the chloroplast and mitochondrial genomes of green algae and land plants are regulated post-transcriptionally, mainly by alpha-solenoid proteins encoded in the nucleus. These nuclear factors are composed of degenerate repeat motifs (PPR and OPR proteins, respectively pentatricopeptide repeat and octatricopeptide repeats) that interact specifically with part of their target RNA sequence and form large families of paralogs. PPR proteins are very abundant in terrestrial plants while OPRs are abundant in green algae. These differential expansions, in parallel with the evolution of RNA metabolism in organelles, may reflect genetic adaptations that preserve phototrophy under different conditions and ecological niches. In other Archaeplastids (red algae and Glaucophytes) and in eukaryotes that originate from endosymbiosis with an ancestral microalga such as the Diatoms, the regulation of organelle genomes remains poorly explored. A first objective of my thesis was to describe the diversity and evolutionary dynamics of known or candidate alpha-solenoid proteins for the regulation of organelle genome expression in all photosynthetic eukaryotes. To identify them, I developed an approach that combines distant sequence homology detection and sequence similarity independent classification. I validated this approach by finding and completing the known OPR and PPR families in the model species Chlamydomonas reinhardtii and Arabidopsis thaliana. I showed that OPR expansions were restricted within Chlorophytes and that outside of green algae and land plants, PPR and OPR proteins were few in number, suggesting that other players in the regulation of organelle genome expression remain to be discovered. I also identified several dozen other families of organelle-addressed alpha-solenoid proteins in all the proteomes studied, some of which have as yet unknown functions and whose experimental characterisation in model organisms would be relevant. In a second step, I used molecular dynamics approaches to better understand the affinity and specificity of binding between PPRs and their target RNAs. In particular, I studied the dynamics of the repeat motifs and the geometry of the nucleotide binding sites as a function of their position in the PPR motif sequence, including the effects of the number of repeats and the presence or absence of N- and C-terminal domains, in addition to the evolution of the overall conformation of the protein. Our results suggest the role of PPR protein flexibility, both at the protein and motif level, in binding to its RNA target and its relevance to the affinity and specificity of nucleotide recognition

Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.

The earth’s organic life has changed continually for more than 3.5 billion years. This evolution may have resulted partly from environmental stress generated by tectonic activity within the earth and partly from processes independent of the earth’s interior. This chapter investigates these different effects in an attempt to determine the role that continents played in the evolution of organisms. Continents and tectonics associated with them may have influenced organic evolution in both active and passive ways. Active effects include several processes that partly controlled the earth’s surface environment. Climate change was caused partly by movements of continents and construction of orogenic belts. Continental rifting increased the area of shallow seas as new continental margins subsided. Changes in volume of ocean ridges and epeiric movements of continents caused marine transgressions and regressions. Temperatures of water in shallow seas increased or decreased as continents moved across latitudes. The major passive effects of continents and supercontinents result from their influence on diversity of organisms. When continents were broadly dispersed and occupied most latitudes, as on the present earth, this isolation resulted in shallow-water and subaerial families that contained numerous genera, genera with large numbers of species, and species divided among many different varieties. This diversity was clearly smaller at times when continents were aggregated into a few landmasses and particularly low when supercontinents permitted exchange of organisms throughout most of the world’s land and shallow seas. During times of major environmental stress, these differences would have restricted extinction of organisms to local species and genera during times of high diversity but might have permitted disappearance of whole orders and classes when diversity was low. Organic evolution was almost certainly affected by species diversity, but it may have occurred without any active control by tectonic processes. Although evolution probably occurs only when changing environments place stresses on organisms that enhance the competition among them, it is also possible that competition between organisms can cause evolution even without significant environmental change. Furthermore, some environmental change probably resulted from processes that are not related to the tectonics of the solid earth.

Abstract Symbiotic associations between fungi and photosynthetic organisms are both ancient and ubiquitous (Alexopoulos et al. 1996; Berbee 2001; Heckman et al. 2001). Comprising interactions spanning mutualism to antagonism, fungi associated with living plants shape both the diversity and species composition ofa wide array of terrestrial communities (Clay and Holah 1999; Clay 2001; Wilson et al. 2001; Castelli and Casper 2003; Gilbert 2002; Gehring 2003; Packer and Clay 2003). Yet, ecological interactions have been catalogued for only an extreme minority (&lt;5%) of the 1.5 million species offungi thoughtto exist (Hawksworth 1991, 2001) with most research focusing on above- and below-ground plant pathogens (Agrios 1997) and on rhizosphere symbionts such as mycorrhizal fungi (Rygiewicz and Andersen 1994; Husband et al. 2002). In contrast, the diversity, species composition, ecological relevance, and evolutionary importance of diverse and abundant fungi occurring in the phyllosphere have not been established for most plant-fungus associations. Such is the case for fungal endophytes-those fungi that colonize and form unapparent infections in healthy plant tissues (Petrini 1991)-which are known from photosynthetic tissues in all major lineages of plants studied thus far, but which have been studied extensively in only a few focal plant clades.

Abstract The last two chapters were concerned with how natural selection can change the way a lineage looks (its phenotype). These changes have had profound effects, first on the complexity of organisms (Chapter 2), and second on the complexity of the ecology of the planet (Chapter 3). This chapter continues the theme, but deals with traits that are individually far more ordinary: life history traits. Nonetheless, they account for much of the diversity in form across species, thus collectively are of immense interest. A life history is a description of the major characteristics of an organism from its birth to its death. The traits are variables that can be measured or categorized across individuals and that collectively make up the description (Figure 4.1). In the past, most work on life history evolution proceeded on a trait-by-trait basis.

Abstract Environmental change drives evolution. If environments were constant, evolution rapidly would proceed to a rather humdrum, mostly static, equilibrium. The diversity of life we see today is the result of moderate but continual environmental challenges. Put simply, the seed of creation is the strife of organisms at odds with their changing environments. The premise of this book is that environmental variation is responsible for a spectacular suite of adaptations more intricate and labile than those for dealing with fixed environments. Phenotypic plasticity is one of those adaptations, but several others exist. Among the many adaptations organisms have to cope with environmental variability are dormancy (i.e., seed banking or diapausing), to outlast problem environments; plasticity to produce relatively fit phenotypes for the demands of alternative environments; intermediate phenotypes (generalization) and bet-hedging, both of which reduce variance in performance across environments; and dispersal, to leave when environments are unfavorable. Much theoretical literature addresses the merits of each strategy, generally, compared with ecological specialization (e.g., Levins 1968; Lewontin and Cohen 1969; Cohen 1976; Lively 1986a; Seger and Brockmann 1987; Van Tienderen 1997; reviewed in Wilson and Yoshimura 1994; chapter 6).

Despite their apparent simplicity, arid environments can be quite heterogeneous. From small-scale variation in substrate and slope to large-scale geographic variation in solar input and productivity, drylands and deserts provide organisms with a tremendous range of ecological challenges (Schmidt-Nielsen 1964, Huggett 1995). Any single species is unable to meet all of these challenges equally well. A species will do better in some environments than others because evolution in heterogeneous environments is constrained by fitness tradeoffs. Such tradeoffs prevent the evolution of a versatile species, competitively superior to all other species across the entire spectrum of heterogeneity (Rosenzweig 1987). Although fitness tradeoffs may hinder species’ evolution in heterogeneous environments, they are a blessing for biodiversity. The source of biodiversity that we address in this chapter is the interplay of heterogeneity, tradeoffs, and density dependence. While we focus on species interactions at the local scale, our presentation includes a model that predicts changes in local diversity as a function of climate. The model’s predictions are based on changes in the nature of competition wrought by changes in productivity levels and climatic regimes. Cast in terms of evolutionary stable strategies (ESSs), the predictions refer to evolutionary as well as ecological patterns. A mechanism of coexistence consists of an axis of environmental heterogeneity together with an axis that indicates a tradeoff in the abilities of species to exploit different parts of the axis. In the absence of some kind of heterogeneity, there is only one environmental type, and whatever species is best adapted to it will competitively exclude others. In the absence of a tradeoff, one species could evolve competitive superiority over the full range of heterogeneity, again resulting in a monomorphic community. Consider some examples of mechanisms of species’ coexistence from dryland communities (Kotler and Brown 1988, Brown et al. 1994). For many taxa, spatial heterogeneity in predation risk is a consequence of the pattern of bushy and open areas common in drylands. In certain rodent communities, some species are able to exploit the relatively riskier open microhabitats by virtue of antipredator morphologies (Kotler 1984).

Abstract The biochemical and biophysical properties common to all of life ultimately constrain the ways in which cells evolve. The majority of cell mass consists of water molecules, whose highly unique properties govern almost every aspect of biology. About half of dry weight is composed of carbon atoms, mostly incorporated into proteins and lipids. Only about 20 additional elements are utilized in biology, most with intracellular concentrations many orders of magnitude higher than environmental levels. Amounts of DNA and numbers of protein and messenger RNA molecules per cell scale in predictable ways with cell volume across the Tree of Life. Stochasticity in molecular numbers is a significant constraint on the evolution of small cells, whereas molecular diffusion rates can limit the biological potential of large cells. Through its influence on molecular motion and stability, temperature plays a central role in all cellular processes, and mathematical summary statements can be made on the scaling of such effects. In today’s world, almost all of biology is dependent on organic compounds produced by photosynthetic organisms, which provide both carbon skeletons and energy for growth and other cellular functions. The heat of combustion of such compounds provides a reliable indicator of their available energy content. The upper limit to the efficiency of utilization of ingested carbon is about 80%, and general statements can be made as to the rate of biomass production per unit ATP utilization.

On your next stroll outdoors, you may come across a flowering plant, enjoy its beauty, and perhaps even taste its fruits. A wandering Homo sapiens, however, is probably not the flowering plant’s primary audience; an insect pollinator is more likely the one being wooed. Indeed, the vast biodiversity of flowering plants and insects on Earth is thought to be the result of a fruitful co-evolution over several million years between these organisms (Price 1997, pp. 239–258). Bees, wasps, butterflies, flies, and several other insects are also crucial in their role as pollinators for sus­taining managed agricultural ecosystems (or agro-ecosystems; National Research Council [NRC] 2007). Honey bees (Apis mellifera), managed by beekeepers, are alone estimated to be responsible for over $15 billion worth of increased yield and quality in the United States annually (Morse and Calderone 2000). U.S. growers rent an estimated 2 million beehives each year from beekeepers to pollinate over ninety different fruit, vegetable, and fiber crops (Delaplane and Mayer 2000; NRC 2007). In the first decades of the 21st century, public and scientific attention in the United States and elsewhere has been gripped by frequent reports of declines in populations of insect pollinators (e.g., Biesmeijer et al. 2006; NRC 2007), exemplified most dramatically by the news of Colony Collapse Disorder (CCD) among managed honey bees (vanEngelsdorp et al. 2009; Pettis and Delaplane 2010). While there are ongoing scientific and public debates over the extent to which the documented declines in insect pollinators constitute a global “pollinator crisis,” whether agricultural productivity has actually declined due to these losses, and what the primary causal factors are, there is nonetheless a consensus that parts of North America and Europe continue to undergo worrying reductions in the diversity and abundance of multiple species of insect pollinators (Ghazoul 2005; Stefan-Dewenter et al. 2005; NRC 2007; Carvalheiro et al. 2013). In this chapter, I analyze the main kinds of efforts that are being taken by key institutional players to resolve the environmental problem of pollinator decline in the United States.

Abstract Our emotional feelings reflect our ability to subjectively experience certain states of the nervous system. Although conscious feeling states are universally accepted as major distinguishing characteristics of human emotions, in animal research the issue of whether other organisms feel emotions is little more than aconceptual embarrassment. Such states remain difficult-some claim impossible-to study empirically. Since we cannot directly measure the internal experiences of others, whether animal or human, the study of emotional states must be indirect and based on empirically guided theoretical inferences. Because of such difficulties, there are presently no direct metrics by which we can unambiguously quantify changes in emotional states in any living creature. All objective bodily measures, from facial expressions to autonomic changes, are only vague approximations of the underlying neural dynamics-like ghostly tracks in the bubble chamber detectors of particle physics. Indeed, all integrative psychological processes arise from the interplay of brain ciruits that can be monitored, at present, only dimly and indirectly. Obviously, a careful study of behavioral actions is the most direct way to monitor emotions. However, many investigators who study behavior have argued that emotions, especially animal emotions, are illusory concepts outside the realm of scientific inquiry. As I will seek to demonstrate, that viewpoint is incorrect. Although much of behavioral control is elaborated by unconscious brain processes, both animals and humans do have similar affective feelings that are important contributors to their future behavioral tendencies. Unfortunately, the nature of human and animal emotions cannot be understood without brain research. Fortunately, a psycho-neurological analysis of animal emotions (via a careful study of how animal brains control certain behaviors) makes it possible to conceptualize the basic underlying nature of human emotions with some precision, thereby providing new insights into the functional organization of all mammalian brains. A strategy to achieve such a cross-species synthesis will be outlined here. It is based largely on the existence of many psychoneural homologies-the fact that the intrinsic nature of basic emotional systems has been remarkably well conserved during the course of mammalian evolution. Although there is a great deal of diversity in the detailed expressions of these systems across species, the conserved features allow us to finally understand some of the fundamental sources of human nature by studying the animal brain.

The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)