Equilibrium between the "genuine mutualists" and "symbiotic cheaters" in the bacterial population co-evolving with plants in a facultative symbiosis

The mathematical model for evolution of the plant-microbe facultative mutualistic interactions based on the partners’ symbiotic feedbacks is constructed. Using the example of rhizobia-legume symbiosis, we addressed these feedbacks in terms of the metabolic exchange resulting in the parallel improvements of the partners’ fitness (positive feedbacks). These improvements are correlated to the symbiotic efficiency dependent on the ratio of N₂-fixing bacterial strains (“genuine mutualists”) to the non- N₂-fixing strains (“symbiotic cheaters”) in the root nodules. The computer experiments demonstrated that an interplay between the frequency-dependent selection (FDS) and the Darwinian (frequency-independent) selection pressures implemented in the partners’ populations ensures an anchoring or even domination for the newly generated host-specific mutualists (which form N₂-fixing nodules only with one of two available plant genotypes) more successfully than for the non-host-specific mutualists (which form N₂-fixing nodules with both plant genotypes). The created model allows us to consider the mutualistic symbiosis as a finely balanced polymorphic system wherein the equilibrium in bacterial population may be shifted in favor of “genuine mutualists” due to the partner-stipulated selection for an improved symbiotic efficiency implemented in the plant population.     

Beyond dual-lattice models: Incorporating plant strategies when modeling the interplay between facilitation and competition along environmental severity gradients

We introduce a spatially explicit model that evaluates how the trade-offs between the life strategies of two interacting plant species affect the outcome of their interaction along environmental severity gradients. In our model, we represent the landscape as a two-dimensional lattice, with environmental severity increasing from left to right. Two species with different strategies, a competitor and a stress-tolerant, interact in the lattice. We find that facilitation expands the realized niche of the competitor into harsh environments by suppressing the stress-tolerant species. Most of their coexisting range is dominated by a positive effect of one species on another, with a reciprocal negative effect from the species receiving the benefits on its benefactor (“+, −”), whereas mutualistic (“+, +”) interactions are only found in the harshest part of the environmental gradient. Contrarily as assumed by models commonly used in facilitation research (e.g. dual-lattice models), our results indicate that “+, +” interactions are not dominant, and that their differences with “+, −” interactions along environmental severity gradients depend on the strategies of the interacting species. By integrating the trade-off between competitive ability and stress tolerance, our model provides a new framework to investigate the interplay of facilitative and competitive interactions along environmental gradients and their impacts on processes such as population dynamics and community organization.     

A fitness based analysis of Daisyworld

The Gaia hypothesis [Lovelock, J., Margulis, L., 1974. Atmospheric homeostasis: the Gaia hypothesis. Tellus 26, 1], that the earth functions as a self-regulating system, has never sat particularly comfortably with ideas in mainstream biology [Anon, 2002. In pursuit of arrogant simplicities. Nature 416, 247]. A lack of any clear role for evolution in the model has led to claims of teleology-that self-regulation emerges because it is pre-ordained to do so [Doolittle, W.F., 1981. Is nature really motherly? CoEvol. Q. 58-63; Dawkins, R., 1979. The Extended Phenotype. Oxford University Press, Oxford]. The Daisyworld parable [Watson, A.J., Lovelock, J.E., 1983. Biological homeostasis of the global environment--the parable of Daisyworld. Tellus B 35, 284], a simple mathematical illustration of Gaia, went some way to addressing these critiques but, despite recent success in incorporating natural selection [Stocker, S.,1995. Regarding mutations in Daisyworld models. J. Theor. Biol. 175, 495; Lenton, T.M., 1998. Gaia and natural selection. Nature 394, 439; Lenton, T.M., Lovelock, J.E., 2001. Daisyworld revisited: quantifying biological effects on planetary self-regulation. Tellus B 53, 288; Wood, A.J., Ackland, G.J., Lenton, T.M., 2006. Mutation of albedo and growth response leads to oscillations in a spatial Daisyworld. J. Theor. Biol. 242, 188], it remains a widely held view that the ideas are inconsistent with biological principles. We show that standard methodology from quantitative genetics can be used to predict the stationary states and dynamic behaviour of Daisyworlds. The system regulates its temperature due to the low-level evolutionary dynamics of competition between the thermally coupled daisies, no higher level principle is invoked. A reconciliation of Gaia with evolutionary theory may allow further development of evolutionary arguments for the existence of global self-regulatory systems.     

Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers?

Recent attempts to examine the biological processes responsible for the general characteristics of mutualistic networks focus on two types of explanations: nonmatching biological attributes of species that prevent the occurrence of certain interactions (“forbidden links”), arising from trait complementarity in mutualist networks (as compared to barriers to exploitation in antagonistic ones), and random interactions among individuals that are proportional to their abundances in the observed community (“neutrality hypothesis”). We explored the consequences that simple linkage rules based on the first two hypotheses (complementarity of traits versus barriers to exploitation) had on the topology of plant–pollination networks. Independent of the linkage rules used, the inclusion of a small set of traits (two to four) sufficed to account for the complex topological patterns observed in real-world networks. Optimal performance was achieved by a “mixed model” that combined rules that link plants and pollinators whose trait ranges overlap (“complementarity models”) and rules that link pollinators to flowers whose traits are below a pollinator-specific barrier value (“barrier models”). Deterrence of floral parasites (barrier model) is therefore at least as important as increasing pollination efficiency (complementarity model) in the evolutionary shaping of plant–pollinator networks.     

Synchronized reproduction promotes species coexistence through reproductive facilitation

Theories for species coexistence often emphasize niche differentiation and temporal segregation of recruitment to avoid competition. Recent work on mutualism suggested that plant species sharing pollinators provide mutual facilitation when exhibit synchronized reproduction. The facilitation on reproduction may enhance species persistence and coexistence. Theoretical ecologists paid little attention to such indirect mutualistic systems by far. We propose a new model for a two-species system using difference equations. The model focuses on adult plants and assumes no resource competition between these well-established individuals. Our formulas include demographic parameters, such as mortality and recruitment rates, and functions of reproductive facilitation. Both recruitment and facilitation effects reach saturation levels when flower production is at high levels. We conduct mathematical analyses to assess conditions of coexistence. We establish demographical conditions permitting species coexistence. Our analyses suggest a “rescue” effect from a “superior” species to a “weaker” species under strong recruitment enhancement effect when the later is not self-sustainable. The facilitation on rare species may help to overcome Allee effect.     

Molecular genetic mechanisms used by legumes to control early stages of mutually beneficial (mutualistic) symbiosis

Recent data on the plant control of early stages of mutually beneficial (mutualistic) symbioses of legumes, the mechanisms of perception and transmission of the microsymbiont’s molecular signals in the macrosymbiont’s cells, and induction of the genetic programs of the development of symbiotic compartments and organs of the plant are summarized. It is demonstrated that the genetic system of the plant controlling the development of nitrogen-fixing symbiosis of legumes (symbiotic root nodules), which emerged 70–80 Ma ago, has undoubtedly evolved on the basis of the genetic system controlling the development of the symbiosis with arbuscular mycorrhizal fungi (which emerged 400–500 Ma ago). Interactions between genes and between gene products, as well as exchange of molecular signals, form the basis of mutually beneficial (mutualistic) plant-bacterium interactions. Even in the case of a highly specific nitrogen-fixing symbiosis of legumes (symbiotic nodules), the receptors perceiving the signal from root-nodule bacteria may function in different ways. The development of arbuscular mycorrhiza and nitrogen-fixing symbiosis in legumes is a multistep process involving hundreds of genes of both the macro- and microsymbionts. For the symbioses to develop successfully, these genes should act in a coordinated way in the newly formed superorganismal system. Further studies are necessary to shed light onto the complexity of the plant genetic control of the development of mutualistic symbioses in legumes and provide information required for improving their functions in adaptive plant-breeding systems.     

Uncoupled binding and folding of immune signaling-related intrinsically disordered proteins

The classical protein structure-function paradigm has been challenged by the emergence of intrinsically disordered proteins (IDPs), the proteins that do not adopt well-defined three-dimensional structures under physiological conditions. This development was accompanied by the introduction of a “coupled binding and folding” paradigm that suggests folding of IDPs upon binding to their partners. However, our recent studies challenge this general view by revealing a novel, previously unrecognized phenomenon – uncoupled binding and folding. This biologically important mechanism is characteristic of members of a new family of IDPs involved in immune signaling and underlies their unusual properties including: (1) specific homodimerization, (2) the lack of folding upon binding to a well-folded protein, another IDP molecule, or to lipid bilayer membranes, and (3) the “scissors-cut paradox”. The third phenomenon occurs in diverse IDP interactions and suggests that properties of IDP fragments are not necessarily additive in the context of the entire protein. The “no disorder-to-order transition” type of binding is distinct from known IDP interactions and is characterized by an unprecedented observation of the lack of chemical shift and peak intensity changes in multidimensional NMR spectra, a fingerprint of proteins, upon complex formation. Here, I focus on those interactions of IDPs with diverse biological partners where the binding phase driven by electrostatic interactions is not be necessarily followed by the hydrophobic folding phase. I also review new multidisciplinary knowledge about immune signaling-related IDPs and show how it expands our understanding of cell function with multiple applications in biology and medicine.     

SINBAD: A neocortical mechanism for discovering environmental variables and regularities hidden in sensory input

We propose that a top priority of the cerebral cortex must be the discovery and explicit representation of the environmental variables that contribute as major factors to environmental regularities. Any neural representation in which such variables are represented only implicitly (thus requiring extra computing to use them) will make the regularities more complex and therefore more difficult, if not impossible, to learn. The task of discovering such important environmental variables is not an easy one since their existence is only indirectly suggested by the sensory input patterns the cortex receives – these variables are hidden. We present a candidate computational strategy for (i) discovering regularity-simplifying environmental variables, (ii) learning the regularities, and (iii) using regularities in perceptual and decision-making tasks. The SINBAD computational model discovers useful environmental variables through a search for different, but nevertheless highly correlated, functions of any kind over nonoverlapping subsets of the known variables, this being indicative of some important environmental variable that is responsible for the correlation. We suggest that such a search is performed in the neocortex by the dendritic trees of individual pyramidal cells. According to the SINBAD model, the basic function of each pyramidal cell is to (i) discover and represent one of the regularity-simplifying environmental variables and (ii) learn to infer the state of its variable from the states of other variables, represented by other pyramidal cells. A network of such cells – each cell just attending to representation of its variable – can function as a sophisticated and useful inferential model of the outside world.     

干旱胁迫对鸭茅幼苗根系生长及光合特性的影响

以不同耐旱型鸭茅品种(系)“01998”(敏感型)和“宝兴”(耐旱型)为试材,采用盆栽控水试验方法,研究土壤干旱胁迫对鸭茅幼苗根系生长、生理特性及叶片光合作用的影响,探讨不同品种耐旱机制的差异.结果表明：干旱胁迫下,不同耐旱型鸭茅幼苗的根系活力和根系数量均呈先上升后下降的趋势,当土壤相对含水量降到30%时,根系活力和根数显著增加并达到最大值;干旱胁迫降低了两个品种鸭茅叶片的相对含水量、叶绿素含量、净光合速率、叶片蒸腾速率、气孔导度,提高了电导率和胞间CO₂浓度.干旱胁迫降低了两个品种鸭茅的单株叶面积,品种“01998”的地下及地上生物量下降,而“宝兴”无显著变化.     

Photosynthetic circadian rhythmicity patterns of Symbiodium,the coral endosymbiotic algae

Biological clocks are self-sustained endogenous timers that enable organisms (from cyanobacteria to humans) to anticipate daily environmental rhythms, and adjust their physiology and behaviour accordingly. Symbiotic corals play a central role in the creation of biologically rich ecosystems based on mutualistic symbioses between the invertebrate coral and dinoflagellate protists from the genus Symbiodinium. In this study, we experimentally establish that Symbiodinium photosynthesis, both as a free-living unicellular algae and as part of the symbiotic association with the coral Stylophora pistillata, is ‘wired’ to the circadian clock mechanism with a ‘free-run’ cycle close to 24 h. Associated photosynthetic pigments also showed rhythmicity under light/dark conditions and under constant light conditions, while the expression of the oxygen-evolving enhancer 1 gene (within photosystem II) coincided with photosynthetically evolved oxygen in Symbiodinium cultures. Thus, circadian regulation of the Symbiodinium photosynthesis is, however, complicated as being linked to the coral/host that have probably profound physiochemical influence on the intracellular environment. The temporal patterns of photosynthesis demonstrated here highlight the physiological complexity and interdependence of the algae circadian clock associated in this symbiosis and the plasticity of algae regulatory mechanisms downstream of the circadian clock.     

Diversity and similarity in the tRNA world: Overall view and case study on malaria-related tRNAs

Transfer RNAs (tRNAs) are ancient macromolecules that have evolved under various environmental pressures as adaptors in translation in all forms of life but also towards alternative structures and functions. The present knowledge on both “canonical” and “deviating” signature motifs retrieved from vertical and horizontal sequence comparisons is briefly reviewed. Novel characteristics, proper to tRNAs from a given translation system, are revealed by a case study on the nuclear and organellar tRNA sets from malaria-related organisms. Unprecedented distinctive features for Plasmodium falciparum apicoplastic tRNAs appear, which provide novel routes to be explored towards anti-malarial drugs. The ongoing high-throughput sequencing programs are expected to allow for further horizontal comparisons and to reveal other signatures of either full or restricted sets of tRNAs.     

A random-walk interpretation of incentive effects in visual discrimination

Previous studies have shown that changes in stimulus discriminability and changes in reward density affect pigeon reaction-time (RT) distributions in different ways. A random-walk model (“RWP”) accounts for these differences and assigns a single parameter to each of the independent variables. This paper briefly reviews the model and illustrates its findings with hue discrimination data. A new analysis then presents fits to data showing that increased reward for stimulus “A” lengthens RT of pecks to an alternative stimulus “B”, and that this effect on RT distributions is much the same as the effect caused by reduction of reward to B. RWP account for both effects by changes in its “bias” parameter. The remainder of the paper comments on the relations between reward, RT, incentive and bias.     

Plant–microbe interactions that have impacted plant terrestrializations

Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.

Diverse plant lineages have independently colonized emerged lands over the last 450 million years and were helped in this process by mutualistic associations with fungi and potentially bacteria.     

Mutualism and parasitism: the yin and yang of plant symbioses

Plants are solar-powered sugar factories that feed a multitude of other organisms. Many of these organisms associate directly with host plants to gain access to the plant's photosynthates. Such symbioses encompass a wide collection of styles ranging from mutualistic to commensal and parasitic. Among these, the mutualistic arbuscular mycorrhizal (AM) symbiosis is one of the evolutionarily oldest symbioses of plants, relying on the formation of an intimate relationship between fungi of the Glomeromycota and roots of the majority of vascular flowering plants. In this symbiosis, the fungus intracellularly colonizes living root cells, implying the existence of an extreme form of compatibility. Interestingly, molecular events that happen in the plant in response to mycorrhizal colonization also occur in other beneficial and, as recently shown, even antagonistic plant symbioses. Thus, basic 'compatibility modules' appear to be partially conserved between mutualism and parasitism.     

Antigenic changes in human albumin caused by reactivity with the occupational allergen diphenylmethane diisocyanate

Diphenylmethane diisocyanate (MDI), the chemical commonly used as a cross-linking agent in commercial polyurethane production, is a well-recognized cause of asthma. Reaction products between MDI and “self” proteins are hypothesized to act as antigens capable of inducing airway inflammation and asthma; however, such MDI antigens remain incompletely understood. We used a variety of analytical methods to characterize the range of MDI-albumin reaction products that form under physiological conditions. Sites of MDI conjugation on antigenic MDI-albumin products, as defined by serum immunoglobulin G (IgG) from MDI-exposed workers, were determined by high-performance liquid chromatography (HPLC) followed by tandem mass spectrometry (MS/MS). The data identified 14 MDI conjugation sites (12 lysines and 2 asparagines) on human albumin and highlight reaction specificity for the second lysine in dilysine (KK) motifs, and this may be a common characteristic of “immune-sensitizing” chemicals. Several of the MDI conjugation sites are not conserved in albumin from other species, and this may suggest species differences in epitope specificity for self protein (albumin)-isocyanate conjugates. The study also describes new applications of contemporary proteomic methodology for characterizing and standardizing MDI-albumin conjugates destined for use in clinical research.     

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase 1 from Methicillin-Resistant Staphylococcus aureus MRSA252 Provides Novel Insights into Substrate Binding and Catalytic Mechanism

The dreaded pathogen Staphylococcus aureus is one of the causes of morbidity and mortality worldwide. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes, is irreversibly oxidized under oxidative stress and is responsible for sustenance of the pathogen inside the host. With an aim to elucidate the catalytic mechanism and identification of intermediates involved, we describe in this study different crystal structures of GAPDH1 from methicillin-resistant S. aureus MRSA252 (SaGAPDH1) in apo and holo forms of wild type, thioacyl intermediate, and ternary complexes of active-site mutants with physiological substrate d-glyceraldehyde-3-phosphate (G3P) and coenzyme NAD⁺. A new phosphate recognition site, “new P_i” site, similar to that observed in GAPDH from Thermotoga maritima, is reported here, which is 3.40 Å away from the “classical P_i” site. Ternary complexes discussed are representatives of noncovalent Michaelis complexes in the ground state. d-G3P is bound to all the four subunits of C151S.NAD and C151G.NAD in more reactive hydrate (gem-di-ol) form. However, in C151S + H178N.NAD, the substrate is bound to two chains in aldehyde form and in gem-di-ol form to the other two. This work reports binding of d-G3P to the C151G mutant in an inverted manner for the very first time. The structure of the thiaocyl complex presented here is formed after the hydride transfer. The C3 phosphate of d-G3P is positioned at the “P_s” site in the ternary complexes but at the “new P_i” site in the thioacyl complex and C1-O1 bond points opposite to His178 disrupting the alignment between itself and NE2 of His178. A new conformation (Conformation I) of the 209-215 loop has also been identified, where the interaction between phosphate ion at the “new P_i” site and conserved Gly212 is lost. Altogether, inferences drawn from the kinetic analyses and crystal structures suggest the “flip-flop” model proposed for the enzyme mechanism.     

Fish Invasions in the World's River Systems: When Natural Processes Are Blurred by Human Activities

Because species invasions are a principal driver of the human-induced biodiversity crisis, the identification of the major determinants of global invasions is a prerequisite for adopting sound conservation policies. Three major hypotheses, which are not necessarily mutually exclusive, have been proposed to explain the establishment of non-native species: the “human activity” hypothesis, which argues that human activities facilitate the establishment of non-native species by disturbing natural landscapes and by increasing propagule pressure; the “biotic resistance” hypothesis, predicting that species-rich communities will readily impede the establishment of non-native species; and the “biotic acceptance” hypothesis, predicting that environmentally suitable habitats for native species are also suitable for non-native species. We tested these hypotheses and report here a global map of fish invasions (i.e., the number of non-native fish species established per river basin) using an original worldwide dataset of freshwater fish occurrences, environmental variables, and human activity indicators for 1,055 river basins covering more than 80% of Earth's surface. First, we identified six major invasion hotspots where non-native species represent more than a quarter of the total number of species. According to the World Conservation Union, these areas are also characterised by the highest proportion of threatened fish species. Second, we show that the human activity indicators account for most of the global variation in non-native species richness, which is highly consistent with the “human activity” hypothesis. In contrast, our results do not provide support for either the “biotic acceptance” or the “biotic resistance” hypothesis. We show that the biogeography of fish invasions matches the geography of human impact at the global scale, which means that natural processes are blurred by human activities in driving fish invasions in the world's river systems. In view of our findings, we fear massive invasions in developing countries with a growing economy as already experienced in developed countries. Anticipating such potential biodiversity threats should therefore be a priority.