Niche Boundaries Research Articles

Unveiling intra-population functional variability patterns in a European beech (Fagus sylvatica L.) population from the southern range edge: drought resistance, post-drought recovery and phenotypic plasticity.

Understanding covariation patterns of drought resistance, post-drought recovery and phenotypic plasticity, and their variability at the intra-population level are crucial for predicting forest vulnerability to increasing aridity. This knowledge is particularly urgent at the trailing range edge since, in these areas, tree species are proximal to their ecological niche boundaries. While this proximity increases their susceptibility, these populations are recognized as valuable genetic reservoirs against environmental stressors. The conservation of this genetic variability is critical for the adaptive capacity of the species in the current context of climate change. Here we examined intra-population patterns of stem basal growth, gas exchange and other leaf functional traits in response to an experimental drought in seedlings of 16 open-pollinated families within a marginal population of European beech (Fagus sylvatica L.) from its southern range edge. We found a high degree of intra-population variation in leaf functional traits, photosynthetic performance, growth patterns and phenotypic plasticity in response to water availability. Low phenotypic plasticity was associated with higher resistance to drought. Both drought resistance and post-drought recovery of photosynthetic performance varied between maternal lines. However, drought resistance and post-drought recovery exhibited independent variation. We also found intra-population variation in stomatal sensitivity to soil drying, but it was not associated with either drought resistance or post-drought recovery. We conclude that an inverse relationship between phenotypic plasticity and drought resistance is not necessarily a sign of maladaptive plasticity, but rather it may reflect stability of functional performance and hence adaptation to withstand drought. The independent variation found between drought resistance and post-drought recovery should facilitate to some extent microevolution and adaption to increasing aridity. The observed variability in stomatal sensitivity to soil drying was consistent with previous findings at other scales (e.g., inter-specific variation, inter-population variation) that challenge the iso-anisohydric concept as a reliable surrogate of drought tolerance.

Positive fungal interactions are key drivers in Antarctic endolithic microcosms at the boundaries for life sustainability.

In the ice-free areas of Victoria Land in continental Antarctica, where the conditions reach the limits for life sustainability, highly adapted and extreme-tolerant microbial communities exploit the last habitable niches inside porous rocks (i.e. cryptoendolithic communities). These guilds host the main standing biomass and principal, if not sole, contributors to environmental/biogeochemical cycles, driving ecosystem processes and functionality in these otherwise dead lands. Although knowledge advances on their composition, ecology, genomic and metabolic features, a large-scale perspective of occurring interactions and interconnections within and between endolithic fungal assemblages is still lacking to date. Unravelling the tight relational network among functional guilds in the Antarctic cryptoendolithic communities may represent a main task. Aiming to fill this knowledge gap, we performed a correlation-network analysis based on amplicon-sequencing data of 74 endolithic microbiomes collected throughout Victoria Land. Endolithic communities' compositional pattern was largely dominated by Lichenized fungi group (83.5%), mainly represented by Lecanorales and Lecideales, followed by Saprotrophs (14.2%) and RIF+BY (2.4%) guilds led by Tremellales and Capnodiales respectively. Our findings highlighted that fungal functional guilds' relational spectrum was dominated by cooperative interactions led by lichenised and black fungi, deeply engaged in community trophic sustain and protection, respectively. On the other hand, a few negative correlations found may help in preserving niche boundaries between microbes living in such strict spatial association.

Gestures and Adaptive Niches

This proposal presents an evolutionary analysis of three types of co-speech gestures: symbolic emblems, indexical pointing gestures and iconic representational gesticulations. Synthesizing insights from a range of published sources in gestural studies, general linguistics and sign language linguistics, primate studies and analyses of biological evolution, these gestures are analyzed as evolved traits adapted to particular niches or roles within broader systems. Niche boundaries are comprised of an element’s distinct properties and functions, routes of learning and transmission and degrees of innateness and evolvability within populations. Rather than elements distributed along a flat productive-analytical continuum or as stages along diachronic pathways, these gestural traits are analyzed in terms of adaptive peaks and valleys with a landscape representing the broader system comprising human gesture and language. The same evolutionary processes are used to analyze gestures in speaking populations and the linguistic traits derived from gestures in signing populations. This approach offers new ways of approaching proposed linguistic universals and long-standing issues such as listability in sign languages, while offering a formal approach to gestures.

High resolution thermal remote sensing and the limits of species' tolerance.

Extinction risks for many insect species, particularly across very broad spatial extents, have been linked to the growing frequency and severity of temperatures that exceed the boundaries of their realized niches. Measurement and mitigation of such impacts is hindered by the availability of high-resolution measurements of species-specific severity of extreme weather, especially temperature. While techniques enabling interpolation of broad-scale remote sensing metrics are vital for such efforts, direct remote sensing measurements of thermal conditions could improve habitat management by providing detailed insights that interpolative approaches cannot. Advances in unmanned aerial vehicle (UAV) technology have created opportunities to better evaluate the role of microclimates in local species extinctions. Here, we develop a method to create high-resolution maps of microclimates using UAV and thermal imaging technology that use species’ realized niche boundaries to assess potential effects of severity of extreme temperatures. We generated air temperature maps (5 cm resolution) and canopy height maps (1 cm resolution) for 15 sites in a rare alvar ecosystem in eastern Ontario. We validated these remote sensing observations against independent, in situ temperature observations using iButtons. Temperature observations were accurate and related to physical heterogeneity in alvar habitats. We converted temperature measures into estimates of proximity of thermal niche boundaries for three butterfly species found during field surveys. This is the first time that this method has been applied to high resolution remote sensing observations and offers potential to assess the availability and adequacy of microclimates within habitats at resolutions relevant for conservation management.

Parallel adaptation prompted core-periphery divergence of Ammopiptanthus mongolicus.

Range expansion requires peripheral populations to shift adaptive optima to breach range boundaries. Opportunities for range expansion can be assessed by investigating the associations of core-periphery environmental and genetic differences. This study investigates differences in the core-periphery adaptation of Ammopiptanthus mongolicus, a broad-leaved evergreen shrub species in a relatively homogeneous temperate Asian desert environment, to explore the environmental factors that limit the expansion of desert plants. Temperate deserts are characterized by severe drought, a large diurnal temperature range, and seasonality. Long-standing adaptation to the harsh desert environment may confine the genetic diversity of A. mongolicus, despite its distribution over a wide range of longitude, latitude, and altitude. Since range edges defined by climate niches may have different genetic responses to environmental extremes, we compared genome-wide polymorphisms between nine environmental core populations and ten fragmented peripheral populations to determine the “adaptive peripheral” populations. At least four adaptive peripheral populations had similar genetic-environmental association patterns. High elevations, summer drought, and winter cold were the three main determinants of converging these four adaptive peripheral populations. Elevation mainly caused similar local climates among different geographic regions. Altitudinal adaptation resulting from integrated environmental-genetic responses was a breakthrough in breaching niche boundaries. These peripheral populations are also located in relatively humid and warmer environments. Relaxation of the drought and cold constraints facilitated the genetic divergence of these peripheral populations from the core population’s adaptive legacy. We conclude that pleiotropic selection synchronized adaptative divergence to cold and drought vs. warm and humid environments between the core and peripheral populations. Such parallel adaptation of peripheral populations relies on selection under a background of abundant new variants derived from the core population’s standing genetic variation, i.e., integration of genetic surfing and local adaptation.

Interferon gamma constrains type 2 lymphocyte niche boundaries during mixed inflammation

Allergic immunity is orchestrated by group 2 innate lymphoid cells (ILC2s) and type 2 helper T (Th2) cells prominently arrayed at epithelial- and microbial-rich barriers. However, ILC2s and Th2 cells are also present in fibroblast-rich niches within the adventitial layer of larger vessels and similar boundary structures in sterile deep tissues, and it remains unclear whether they undergo dynamic repositioning during immune perturbations. Here, we used thick-section quantitative imaging to show that allergic inflammation drives invasion of lung and liver non-adventitial parenchyma by ILC2s and Th2 cells. However, during concurrent type 1 and type 2 mixed inflammation, IFNγ from broadly distributed type 1 lymphocytes directly blocked both ILC2 parenchymal trafficking and subsequent cell survival. ILC2 and Th2 cell confinement to adventitia limited mortality by the type 1 pathogen Listeria monocytogenes. Our results suggest that the topography of tissue lymphocyte subsets is tightly regulated to promote appropriately timed and balanced immunity.

Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal.

Adult stem cell niche boundaries must be precisely maintained to facilitate the segregation of stem cell and daughter cell fates. However, the mechanisms that govern this process in epithelial tissues are not fully understood. In this study, we investigated the relationship between two signals, Wnt and EGFR, that are necessary for self-renewal of the epithelial follicle stem cells (FSCs) in the Drosophila ovary, but must be downregulated in cells that have exited the niche to allow for differentiation. We found that Wingless produced by inner germarial sheath (IGS) cells acts over a short distance to activate Wnt signaling in FSCs, and that movement across the FSC niche boundary is limited. In addition, we show that Wnt signaling functions genetically upstream of EGFR signaling by activating the expression of the EGFR ligand, Spitz, and that constitutive activation of EGFR partially rescues the self-renewal defect caused by loss of Wnt signaling. Collectively, our findings support a model in which the Wnt and EGFR pathways operate in a signaling hierarchy to promote FSC self-renewal.

Revisiting niche fundamentals with Tukey depth

Abstract The first attempts to describe species ecological niches were simple geometric procedures that depict the niche boundaries directly from environmental data. The convex hull was one of such procedures, popular for its simplicity, clear ecological rational and precise definition of the niche. However, it lacked the ability to differentiate areas of the niche with different probabilities of occurrence according to environmental suitability. We incorporate the Tukey depth, a mathematical tool to measure the centrality of a point within a cloud of points on a multidimensional space, in the convex hull approach to (i) propose a new procedure (CH‐Tukey) to estimate species’ environmental suitability, and (ii) estimate niche overlap coherently. In addition to a clear ecological rational and simplicity the CH‐Tukey procedure has a number of attractive features: use of presence‐only data; independence from background data; invariance to scale; robustness to outliers; and the decomposition of the niche into a finite number of iso‐suitability levels, permitting the computation of consistent overlap indices. We illustrate the use of CH‐Tukey, using occurrence data of the main Quercus species and subspecies from Western Mediterranean Europe, comparing its outputs with BIOCLIM and MaxEnt. Results showed distinct niche geometries among the different approaches. BIOCLIM produced rectilinear niches reflecting the assumption that ecological variables are independent in their action on the species. CH‐Tukey, relaxing this assumption, adjusts niche outer boundary and the inner suitability levels to the known occurrences. MaxEnt produced unbounded niche geometries, showing abrupt shifts in the species response to the environmental variables. The niche predictions obtained with geometric approaches, BIOCLIM and CH‐Tukey, are simpler but better aligned with Hutchinson's niche concept than those obtained with MaxEnt, this latter showing ecologically implausible relationships with the environmental variables. CH‐Tukey and the related overlap measures provide an adequate tool to explore niche properties and species–environment relationships.

Microenvironment and functional‐trait context dependence predict alpine plant community dynamics

Abstract Predicting the structure and dynamics of communities is difficult. Approaches linking functional traits to niche boundaries, species co‐occurrence and demography are promising, but have so far had limited success. We hypothesized that predictability in community ecology could be improved by incorporating more accurate measures of fine‐scale environmental heterogeneity and the context‐dependent function of traits. We tested these hypotheses using long term whole‐community demography data from an alpine plant community in Colorado. Species distributions along microenvironmental gradients covaried with traits important for below‐ground processes. Positive associations between species distributions across life stages could not be explained by abiotic microenvironment alone, consistent with facilitative processes. Rates of growth, survival, fecundity and recruitment were predicted by the direct and interactive effects of trait, microenvironment, macroenvironment and neighbourhood axes. Synthesis. Context‐dependent interactions between multiple traits and microenvironmental axes are needed to predict fine‐scale community structure and dynamics.

Modeling the cost and benefit of proteome regulation in a growing bacterial cell

Escherichia coli cells differentially regulate the production of metabolic and ribosomal proteins in order to stay close to an optimal growth rate in different environments, and exhibit the bacterial growth laws as a consequence. We present a simple mathematical model of a growing-dividing cell in which an internal dynamical mechanism regulates the allocation of proteomic resources between different protein sectors. The model allows an endogenous determination of the growth rate of the cell as a function of cellular and environmental parameters, and reproduces the bacterial growth laws. We use the model and its variants to study the balance between the cost and benefit of regulation. A cost is incurred because cellular resources are diverted to produce the regulatory apparatus. We show that there is a window of environments or a ‘niche’ in which the unregulated cell has a higher fitness than the regulated cell. Outside this niche there is a large space of constant and time varying environments in which regulation is an advantage. A knowledge of the ‘niche boundaries’ allows one to gain an intuitive understanding of the class of environments in which regulation is an advantage for the organism and which would therefore favour the evolution of regulation. The model allows us to determine the ‘niche boundaries’ as a function of cellular parameters such as the size of the burden of the regulatory apparatus. This class of models may be useful in elucidating various tradeoffs in cells and in making in-silico predictions relevant for synthetic biology.

Biased niches - Species response curves and niche attributes from Huisman-Olff-Fresco models change with differing species prevalence and frequency.

The study aimed to examine the effects of different numbers of presences and frequencies (proportions) of occurrences of species in a plot data set of forest vegetation on the species response curves and their niche attributes, based on Huisman-Olff-Fresco models (HOF). We modeled responses of 72 to 105 herbaceous forest species along a pH gradient under 14 different random sampling scenarios by varying the number of presences and absences used for model fitting. Mean niche attributes were calculated from 100 repetitive runs for each scenario and species. Re-prediction success of HOF models among the repetitive runs was highest when the total number of plots was high and the frequency of occurrences was low. With low plot numbers and high frequencies, less complicated model types (no response or monotonically increasing/decreasing responses) predominate. Measures of species niche boundaries (limits & borders) and niche width were strongly influenced by changes in sampling characteristics. With an increasing number of presences and an increasing frequency, limits and borders shifted to more extreme values, leading to wider niches. In contrast, species optima showed almost no change between the scenarios. Thus, the detected ecological response of a species often depends on the size of the data set and the relation between presences and absences of a species. In general, high data quantities are required for reliable response curve modeling with HOF models, which prevents the assessment of the responses of many rare species. To avoid undesired bias by differing sampling characteristics when comparing niches between different species or between data sets, the data basis used for model fitting should be adjusted according to the niche attribute in question, for example by keeping the frequency of the species constant.

Effects of hypoxia and ocean acidification on the upper thermal niche boundaries of coral reef fishes.

Rising ocean temperatures are predicted to cause a poleward shift in the distribution of marine fishes occupying the extent of latitudes tolerable within their thermal range boundaries. A prevailing theory suggests that the upper thermal limits of fishes are constrained by hypoxia and ocean acidification. However, some eurythermal fish species do not conform to this theory, and maintain their upper thermal limits in hypoxia. Here we determine if the same is true for stenothermal species. In three coral reef fish species we tested the effect of hypoxia on upper thermal limits, measured as critical thermal maximum (CTmax). In one of these species we also quantified the effect of hypoxia on oxygen supply capacity, measured as aerobic scope (AS). In this species we also tested the effect of elevated CO2 (simulated ocean acidification) on the hypoxia sensitivity of CTmax We found that CTmax was unaffected by progressive hypoxia down to approximately 35 mmHg, despite a substantial hypoxia-induced reduction in AS. Below approximately 35 mmHg, CTmax declined sharply with water oxygen tension (PwO2). Furthermore, the hypoxia sensitivity of CTmax was unaffected by elevated CO2 Our findings show that moderate hypoxia and ocean acidification do not constrain the upper thermal limits of these tropical, stenothermal fishes.

Density-Dependent Selection Revisited: Mechanisms Linking Explanantia and Explananda

Interest in the most general theory of the evolutionary ecology of life histories ever proposed—that of density-independent (r) versus density-dependent (K) selection—peaked in the 1980s and 1990s respectively but declined somewhat thereafter because of arguments over its theoretical coherence and some empirical failures; although as is shown here, not so much as is commonly supposed. In this article, some conceptual analyses and clarification of terms in the conditions for its application (density relative to resources as a variable with spatial, temporal, and niche boundaries fixed), and in the explanantia of the theory (costs and frequencies, stability and instability within and among growing and declining populations, multiple levels of selection, and ultimately homogeneous and patchy environments) are presented. These make intelligible plausible mechanisms (consumption and digestion, production, and reproduction) linking the explanantia and the explananda of the theory that are both theoretically coherent and clarify what predictions it does not and does make including about senescence.

Oxygen dependence of upper thermal limits in fishes.

Temperature-induced limitations on the capacity of the cardiorespiratory system to transport oxygen from the environment to the tissues, manifested as a reduced aerobic scope (maximum minus standard metabolic rate), have been proposed as the principal determinant of the upper thermal limits of fishes and other water-breathing ectotherms. Consequently, the upper thermal niche boundaries of these animals are expected to be highly sensitive to aquatic hypoxia and other environmental stressors that constrain their cardiorespiratory performance. However, the generality of this dogma has recently been questioned, as some species have been shown to maintain aerobic scope at thermal extremes. Here, we experimentally tested whether reduced oxygen availability due to aquatic hypoxia would decrease the upper thermal limits (i.e. the critical thermal maximum, CTmax) of the estuarine red drum (Sciaenops ocellatus) and the marine lumpfish (Cyclopterus lumpus). In both species, CTmax was independent of oxygen availability over a wide range of oxygen levels despite substantial (>72%) reductions in aerobic scope. These data show that the upper thermal limits of water-breathing ectotherms are not always linked to the capacity for oxygen transport. Consequently, we propose a novel metric for classifying the oxygen dependence of thermal tolerance; the oxygen limit for thermal tolerance (PCTmax ), which is the water oxygen tension (PwO2 ) where an organism's CTmax starts to decline. We suggest that this metric can be used for assessing the oxygen sensitivity of upper thermal limits in water-breathing ectotherms, and the susceptibility of their upper thermal niche boundaries to environmental hypoxia.

How accurately can minimum temperatures at the cold limits of tree species be extrapolated from weather station data?

Most plant physiological processes act on micro-geographic scales within meters or less and on temporal scales of minutes or less. Yet, most studies relating species distribution to climate used typical resolutions of kilometers and months at best. Commonly available climate records from weather stations or freely available coarse-resolution geographic climatic layers thus, do not reflect local climatic conditions. In this study we selected sites where eight temperate deciduous tree species are growing at their cold upper elevational and latitudinal limits in the Swiss Alps (from 1165m a.s.l. to 1804m a.s.l.) and in Sweden (from 58°18′N to 59°27′ N). At each site, temperature was recorded for 1–2 years in different conditions: at understorey height (50cm), 2-m above ground, in the top of tree canopies and at 10cm depth in the soil. We compared these biologically meaningful temperatures with the closest weather station data after correction for elevation. The data evidence that in mountain terrain, scaling from weather station data to on-site forest conditions requires month-specific lapse rates of temperatures, separated for means and extremes (e.g. minima). Besides best elevation-correction procedures, monthly absolute minimum temperatures predicted from near weather stations remained 1.4±0.2K (mean±se, 12 sites) cooler than in situ conditions during growing season (2.0±0.2K cooler during the non-growing season). At the time when 2-m air temperature reached its absolute monthly minimum, the top of the tree canopy was found 0.4±0.1K cooler (mean±se, 12 sites) during growing season and 0.9±0.1K during the non-growing season. These systematic deviations of low temperature extremes from those predicted from weather stations close the gap between geographical range limits of species, their physiological limits (e.g. freezing resistance) and meteorological information. The “thermal niche” concept of species range limits needs to account for such deviations of life conditions from meteorological data, should the niche boundaries have a functional meaning rooted in plant biology.

Climatic niche at physiological and macroecological scales: the thermal tolerance–geographical range interface and niche dimensionality

AbstractAimUnder theHutchinsonian concept of the realized niche, biotic interactions and dispersal limitation may prevent species from fully occupying areas that they could tolerate physiologically. This can hamper the translation of physiological limits into climatically defined range limits and distorts inferences of evolutionary changes of the adaptive limits (i.e. niche conservatism). In contrast, heritable physiological limits should conform more closely to the position of the niche in the climatic hyperspace. Here, we hypothesize that a measure of niche position in the climatic hyperspace is more reliable than niche boundaries to capture the variability and evolutionary pattern of physiological tolerance.LocationNeotropics andPalaeartic.MethodsWe used phylogenetic and non‐phylogenetic regressions to test the relationships between physiological requirements and macroecological niche features (i.e. based on known species distributions) among anurans. We use larval critical thermal maximum (CTmax) as a measure of physiological response and maximum temperature (Tmax), temperature variability (Tvar) and the position and breadth of niche in climatic hyperspace as measures of the realized niche in geographical space. We also compare evolutionary rates among these parameters using the phylogenetic signal representation curve.ResultsCTmaxis better correlated with niche position (r2 = 0.414) than withTvar, andCTmaxis unrelated to eitherTmaxor niche breadth.CTmaxand macroecological niche position also show similar and rapid evolutionary rates, i.e. faster thanBrownian motion, whereasTmaxandTvarevolve more slowly and niche breadth evolves at random.Main conclusionsThe transferability between thermal tolerance and realized climatic niche limits is weak. Only macroecological niche position in the multivariate climatic hyperspace correlates with physiological tolerance. It thus appears to be more suitable for describing the variability and evolutionary pattern of the species' adaptive limits. We link these results to ‘niche dimensionality’, in that multiple interacting factors outweigh single factors in demarcating the species' realized climatic niche, thereby determining the conserved upper thermal limits of the species.

Tracking of climatic niche boundaries under recent climate change

1. Global climate has changed significantly during the past 30 years and especially in northern temperate regions which have experienced poleward shifts in temperature regimes. While there is evidence that some species have responded by moving their distributions to higher latitudes, the efficiency of this response in tracking species' climatic niche boundaries over time has yet to be addressed. 2. Here, we provide a continental assessment of the temporal structure of species responses to recent spatial shifts in climatic conditions. We examined geographic associations with minimum winter temperature for 59 species of winter avifauna at 476 Christmas Bird Count circles in North America from 1975 to 2009 under three sampling schemes that account for spatial and temporal sampling effects. 3. Minimum winter temperature associated with species occurrences showed an overall increase with a weakening trend after 1998. Species displayed highly variable responses that, on average and across sampling schemes, contained a strong lag effect that weakened in strength over time. In general, the conservation of minimum winter temperature was relevant when all species were considered together but only after an initial lag period (c. 35 years) was overcome. The delayed niche tracking observed at the combined species level was likely supported by the post1998 lull in the warming trend. 4. There are limited geographic and ecological explanations for the observed variability, suggesting that the efficiency of species' responses under climate change is likely to be highly idiosyncratic and difficult to predict. This outcome is likely to be even more pronounced and time lags more persistent for less vagile taxa, particularly during the periods of consistent or accelerating warming. Current modelling efforts and conservation strategies need to better appreciate the variation, strength and duration of lag effects and their association with climatic variability. Conservation strategies in particular will benefit through identifying and maintaining dispersal corridors that accommodate diverging dispersal strategies and timetables.

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat

Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.

Dependence of the Cyanobacterium Prochlorococcus on Hydrogen Peroxide Scavenging Microbes for Growth at the Ocean's Surface

The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxygen species are continuously generated via photochemical reactions with dissolved organic matter. However, Prochlorococcus genomes lack catalase and additional protective mechanisms common in other aerobes, and this genus is highly susceptible to oxidative damage from hydrogen peroxide (HOOH). In this study we showed that the extant microbial community plays a vital, previously unrecognized role in cross-protecting Prochlorococcus from oxidative damage in the surface mixed layer of the oligotrophic ocean. Microbes are the primary HOOH sink in marine systems, and in the absence of the microbial community, surface waters in the Atlantic and Pacific Ocean accumulated HOOH to concentrations that were lethal for Prochlorococcus cultures. In laboratory experiments with the marine heterotroph Alteromonas sp., serving as a proxy for the natural community of HOOH-degrading microbes, bacterial depletion of HOOH from the extracellular milieu prevented oxidative damage to the cell envelope and photosystems of co-cultured Prochlorococcus, and facilitated the growth of Prochlorococcus at ecologically-relevant cell concentrations. Curiously, the more recently evolved lineages of Prochlorococcus that exploit the surface mixed layer niche were also the most sensitive to HOOH. The genomic streamlining of these evolved lineages during adaptation to the high-light exposed upper euphotic zone thus appears to be coincident with an acquired dependency on the extant HOOH-consuming community. These results underscore the importance of (indirect) biotic interactions in establishing niche boundaries, and highlight the impacts that community-level responses to stress may have in the ecological and evolutionary outcomes for co-existing species.

A novel particle swarm niching technique based on extensive vector operations

Several techniques have been proposed to extend the particle swarm optimization (PSO) paradigm so that multiple optima can be located and maintained within a convoluted search space. A significant number of these implementations are subswarm-based, that is, portions of the swarm are optimized separately. Niches are formed to contain these subswarms, a process that often requires user-specified parameters. The proposed technique, known as the vector-based PSO, uses a novel approach to locate and maintain niches by using additional vector operations to determine niche boundaries. As the standard PSO uses weighted vector combinations to update particle positions and velocities, the niching technique builds upon existing knowledge of the particle swarm. Once niche boundaries have been calculated, the swarm can be organized into subswarms without prior knowledge of the number of niches and their corresponding niche radii. This paper presents the vector-based PSO with emphasis on its underlying principles. Results for a number of functions with different characteristics are reported and discussed. The performance of the vector-based PSO is also compared to two other niching techniques for particle swarm optimization.