nils-herrmann/clean_scirepeval huggingface dataset:
Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria
Venue: Science

A common plant pathogen induces the growth of disease-suppressive microbes in local soil communities. Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.
Structural analysis of hydrophobins.
Venue: Micron

Hydrophobins are a remarkable class of small cysteine-rich proteins found exclusively in fungi. They self-assemble to form robust polymeric monolayers that are highly amphipathic and play numerous roles in fungal biology, such as in the formation and dispersal of aerial spores and in pathogenic and mutualistic interactions. The polymeric form can be reversibly disassembled and is able to reverse the wettability of a surface, leading to many proposals for nanotechnological applications over recent years. The surprising properties of hydrophobins and their potential for commercialization have led to substantial efforts to delineate their morphology and molecular structure. In this review, we summarize the progress that has been made using a variety of spectroscopic and microscopic approaches towards understanding the molecular mechanisms underlying hydrophobin structure.
CO2 mineralization induced by fungal nitrate assimilation.
Venue: Bioresource Technology

Formation of CaCO3 induced by fungal physiological activities is a potential way to sequestrate atmospheric CO2 in ecosystem. Alternaria sp. is a saprophytic fungus isolated from a forest soil. We examined the precipitation of CaCO3 induced by the fungus in response to different levels of Ca(NO3)2 or CaCl2 in agar media, and the biogenesis of CaCO3 was verified by low δ13C value. The formed CaCO3 was identified as calcite by X-ray diffraction analysis. Square, rectangular and rhombic CaCO3 crystals and amorphous calcium carbonate were observed around mycelia at higher levels of Ca(NO3)2. Acidification occurred in media at low concentrations (0 and 0.0002 M) of Ca(NO3)2, and no CaCO3 formed in these media. The quantities of CaCO3 formed in media increased with increasing concentrations of Ca(NO3)2 and were significantly correlated to fungal biomass, pH value and nitrite concentrations. No CaCO3 was formed in media with CaCl2 at all levels. These results collectively indicated that the formation of CaCO3 can be induced by the fungal assimilation of nitrate. The study also revealed that biogenic crystal of CaCO3 tended to grow on a silicon nucleus and the amorphous calcium carbonate (ACC) was the transient stage of CaCO3 crystal.
Explosive flowering, nectar production, breeding systems, and pollinators of New Zealand mistletoes (Loranthaceae)
Venue: New Zealand Journal of Botany

The six New Zealand loranthaceous mis- tletoes fall into two groups based on pollination bi- ology. Four (Alepis flavida, Peraxilla colensoi, P. tetrapetala, and Trilepidea adamsii) are bird polli- nated with hermaphrodite flowers while the other two (Ileostylus micranthus and Tupeia antarctica) are dioecious or sub-dioecious and insect pollinated. We provide data on the pollination biology of the five extant species (Trilepidea is extinct). The two Peraxilla species and Trilepidea have recently been shown to have explosive flowers. Here we show that Alepis has weakly facultatively explo- sive flowers. The world distribution of explosive mistletoe flowers suggests that the syndrome has arisen a number of times independently within the family, and is found in about half the putatively ancestral genera. The principal avian visitors to the bird-pollinated species were tui and bellbirds; introduced species are numerically unimportant as pollinators. The nectar production schedules of Alepis and Peraxilla encour- age single-visit pollination as little nectar is produced after the flowers open. However, when bird densi- ties are high, buds of Peraxilla may be forced open prematurely, encouraging multiple visits.
Wood frog adaptations to overwintering in Alaska: new limits to freezing tolerance
Venue: The Journal of Experimental Biology

We investigated the ecological physiology and behavior of free-living wood frogs [Lithobates (Rana) sylvaticus] overwintering in Interior Alaska by tracking animals into natural hibernacula, recording microclimate, and determining frog survival in spring. We measured cryoprotectant (glucose) concentrations and identified the presence of antifreeze glycolipids in tissues from subsamples of naturally freezing frogs. We also recorded the behavior of wood frogs preparing to freeze in artificial hibernacula, and tissue glucose concentrations in captive wood frogs frozen in the laboratory to −2.5°C. Wood frogs in natural hibernacula remained frozen for 193±11 consecutive days and experienced average (October–May) temperatures of −6.3°C and average minimum temperatures of −14.6±2.8°C (range −8.9 to −18.1°C) with 100% survival (N=18). Mean glucose concentrations were 13-fold higher in muscle, 10-fold higher in heart and 3.3-fold higher in liver in naturally freezing compared with laboratory frozen frogs. Antifreeze glycolipid was present in extracts from muscle and internal organs, but not skin, of frozen frogs. Wood frogs in Interior Alaska survive freezing to extreme limits and durations compared with those described in animals collected in southern Canada or the Midwestern United States. We hypothesize that this enhancement of freeze tolerance in Alaskan wood frogs is due to higher cryoprotectant levels that are produced by repeated freezing and thawing cycles experienced under natural conditions during early autumn.
Short-amplitude high-frequency wing strokes determine the aerodynamics of honeybee flight.
Venue: Proceedings of the National Academy of Sciences of the United States of America

Most insects are thought to fly by creating a leading-edge vortex that remains attached to the wing as it translates through a stroke. In the species examined so far, stroke amplitude is large, and most of the aerodynamic force is produced halfway through a stroke when translation velocities are highest. Here we demonstrate that honeybees use an alternative strategy, hovering with relatively low stroke amplitude (approximately 90 degrees) and high wingbeat frequency (approximately 230 Hz). When measured on a dynamically scaled robot, the kinematics of honeybee wings generate prominent force peaks during the beginning, middle, and end of each stroke, indicating the importance of additional unsteady mechanisms at stroke reversal. When challenged to fly in low-density heliox, bees responded by maintaining nearly constant wingbeat frequency while increasing stroke amplitude by nearly 50%. We examined the aerodynamic consequences of this change in wing motion by using artificial kinematic patterns in which amplitude was systematically increased in 5 degrees increments. To separate the aerodynamic effects of stroke velocity from those due to amplitude, we performed this analysis under both constant frequency and constant velocity conditions. The results indicate that unsteady forces during stroke reversal make a large contribution to net upward force during hovering but play a diminished role as the animal increases stroke amplitude and flight power. We suggest that the peculiar kinematics of bees may reflect either a specialization for increasing load capacity or a physiological limitation of their flight muscles.
Deep supercooling, vitrification and limited survival to –100°C in the Alaskan beetle Cucujus clavipes puniceus (Coleoptera: Cucujidae) larvae
Venue: The Journal of Experimental Biology

Larvae of the freeze-avoiding beetle Cucujus clavipes puniceus (Coleoptera: Cucujidae) in Alaska have mean supercooling points in winter of –35 to –42°C, with the lowest supercooling point recorded for an individual of –58°C. We previously noted that some larvae did not freeze when cooled to –80°C, and we speculated that these larvae vitrified. Here we present evidence through differential scanning calorimetry that C. c. puniceus larvae transition into a glass-like state at temperatures <–58°C and can avoid freezing to at least –150°C. This novel finding adds vitrification to the list of insect overwintering strategies. While overwintering beneath the bark of fallen trees, C. c. puniceus larvae may experience low ambient temperatures of around –40°C (and lower) when microhabitat is un-insulated because of low snow cover. Decreasing temperatures in winter are correlated with loss of body water from summer high levels near 2.0 to winter lows near 0.4 mg mg–1 dry mass and concomitant increases in glycerol concentrations (4–6 mol l–1) and thermal hysteresis. Finally, we provide direct evidence that Cucujus from Wiseman, Alaska, survive temperatures to –100°C.
Preformed and Induced Chemical Resistance of Tea Leaf Against Exobasidium vexans Infection
Venue: Journal of Chemical Ecology

Levels of (−)-epicatechin in tea cultivars resistant to blister blight leaf disease were significantly higher than those in susceptible cultivars, while the reverse was true for (−)-epigallocatechin gallate, suggesting that epicatechin was involved in the resistance mechanism. The content of the methylxanthines, caffeine and theobromine, in the leaf increased in the initial translucent stage of the disease, probably as a defense response to fungal attack. Epicatechin and epigallocatechin levels were less than in healthy tissues at this stage, but increases in the corresponding gallate esters suggested that they were being converted into esters. Although epicatechin and epigallocatechin levels decreased from translucent to mature blister stages, the decrease was not significant. The decrease in levels of epicatechin, epigallocatechin, and their esters on infection and the formation of cyanidin and delphinidin on oxidative depolymerization of the blisters suggests that proanthocyanidins may play a role in the defense mechanism. The high resistance of a purple green leafed cultivar is attributed to the additional catechin source provided by the high levels of anthocyanins present.
Variability in plant nutrients reduces insect herbivore performance
Venue: Nature

The performance and population dynamics of insect herbivores depend on the nutritive and defensive traits of their host plants. The literature on plant–herbivore interactions focuses on plant trait mean values, but recent studies showing the importance of plant genetic diversity for herbivores suggest that plant trait variance may be equally important. The consequences of plant trait variance for herbivore performance, however, have been largely overlooked. Here we report an extensive assessment of the effects of within-population plant trait variance on herbivore performance using 457 performance datasets from 53 species of insect herbivores. We show that variance in plant nutritive traits substantially reduces mean herbivore performance via non-linear averaging of performance relationships that were overwhelmingly concave down. By contrast, relationships between herbivore performance and plant defence levels were typically linear, with variance in plant defence not affecting herbivore performance via non-linear averaging. Our results demonstrate that plants contribute to the suppression of herbivore populations through variable nutrient levels, not just by having low average quality as is typically thought. We propose that this phenomenon could play a key role in the suppression of herbivore populations in natural systems, and that increased nutrient heterogeneity within agricultural crops could contribute to the sustainable control of insect pests in agroecosystems.
Scale-dependent trait correlations in a temperate tree community
Venue: Austral Ecology

Recent investigations of relationships among plant traits have generated important insights into plant form and function. However, relationships involving leaf area, leaf shape and plant height remain poorly resolved. Previous work has also focused on correlations between average trait values for individual species. It is unclear whether similar relationships occur within species.We searched for novel plant trait correlations by comparing leaf area, leaf circularity, specific leaf area (SLA) and plant height among 16 common woody plant species from a temperate forest in New Zealand. Analyses were conducted both within species (intra-specifically) and among species (inter-specifically) to determine whether trait correlations were scale dependent. Leaf area was unrelated to other leaf traits inter-specifically. However, leaf area declined with plant height and increased with SLA intra- specifically. Leaf circularity decreased with plant height inter-specifically, but increased with plant height intra- specifically. SLA increased with plant height both inter- and intra-specifically. Leaf circularity increased with SLA inter-specifically, but decreased with SLA intra-specifically. Overall results showed that leaf shape, SLA and plant height are interrelated. However, intra-specific relationships often differed substantially from inter-specific rela- tionships, suggesting that the processes shaping relationships between this suite of plant traits are scale-dependent.
Convergent evolution of metabolic roles in bacterial co-symbionts of insects
Venue: Proceedings of the National Academy of Sciences of the United States of America

A strictly host-dependent lifestyle has profound evolutionary consequences for bacterial genomes. Most prominent is a sometimes-dramatic amount of gene loss and genome reduction. Recently, highly reduced genomes from the co-resident intracellular symbionts of sharpshooters were shown to exhibit a striking level of metabolic interdependence. One symbiont, called Sulcia muelleri (Bacteroidetes), can produce eight of the 10 essential amino acids, despite having a genome of only 245 kb. The other, Baumannia cicadellinicola (γ-Proteobacteria), can produce the remaining two essential amino acids as well as many vitamins. Cicadas also contain the symbiont Sulcia, but lack Baumannia and instead contain the co-resident symbiont Hodgkinia cicadicola (α-Proteobacteria). Here we report that, despite at least 200 million years of divergence, the two Sulcia genomes have nearly identical gene content and gene order. Additionally, we show that despite being phylogenetically distant and drastically different in genome size and architecture, Hodgkinia and Baumannia have converged on gene sets conferring similar capabilities for essential amino acid biosynthesis, in both cases precisely complementary to the pathways conserved in Sulcia. In contrast, they have completely divergent capabilities for vitamin biosynthesis. Despite having the smallest gene set known in bacteria, Hodgkinia devotes at least 7% of its proteome to cobalamin (vitamin B12) biosynthesis, a significant metabolic burden. The presence of these genes can be explained by Hodgkinia's retention of the cobalamin-dependent version of methionine synthase instead of the cobalamin-independent version found in Baumannia, a situation that necessitates retention of cobalamin biosynthetic capabilities to make the essential amino acid methionine.
Stabilization and swelling of hagfish slime mucin vesicles
Venue: The Journal of Experimental Biology

When agitated, Atlantic hagfish (Myxine glutinosa) produce large quantities of slime that consists of hydrated bundles of protein filaments and membrane-bound mucin vesicles from numerous slime glands. When the slime exudate contacts seawater, the thread bundles unravel and the mucin vesicles swell and rupture. Little is known about the mechanisms of vesicle rupture in seawater and stabilization within the gland, although it is believed that the vesicle membrane is permeable to most ions except polyvalent anions. We hypothesized that the most abundant compounds within the slime gland exudate have a stabilizing effect on the mucin vesicles. To test this hypothesis, we measured the chemical composition of the fluid component of hagfish slime exudate and conducted functional assays with these solutes to test their ability to keep the vesicles in a condensed state. We found K+ concentrations that were elevated relative to plasma, and Na+, Cl− and Ca2+ concentrations that were considerably lower. Our analysis also revealed high levels of methylamines such as trimethylamine oxide (TMAO), betaine and dimethylglycine, which had a combined concentration of 388 mmol l−1 in the glandular fluid. In vitro rupture assays demonstrated that both TMAO and betaine had a significant effect on rupture, but neither was capable of completely abolishing mucin swelling and rupture, even at high concentrations. This suggests that some other mechanism such as the chemical microenvironment within gland mucous cells, or hydrostatic pressure is responsible for stabilization of the vesicles within the gland.
Why some leaves are anthocyanic and why most anthocyanic leaves are red
Venue: Flora

The adaptive significance of leaf reddening, as it occurs during specific developmental stages or after stress, has puzzled biologists for more than a century. Theoretically, the accumulation of a non-photosynthetic pigment competing with chlorophylls for photon capture would impose a photosynthetic cost, which should be paid off by the benefits afforded by anthocyanins under some circumstances. Hence, the proposed hypotheses presume protective functions against excess light, UV-B radiation, reactive oxygen species, water stress (osmoregulation) and herbivory. The existing arguments in favor of an anti-oxidant, anti-UV-B and osmoregulatory role are confounded by the co-occurrence in leaves of other compounds having the same properties, not absorbing visible light, attaining much higher concentrations and, in some cases, having a more appropriate location to fulfill the ascribed functions. Moreover, the excess light hypothesis should take into account that anthocyanins mainly absorb green photons, which are used photosynthetically in deeper cell layers needing less photoprotection. The more ecological, anti-herbivore hypotheses, consider red leaf color as a signal denoting high defensive commitment, as a camouflage obscuring the green reflectance indicative of a healthy leaf and/or as a device undermining the folivorous insects camouflage. The anti-herbivore hypotheses have not been thoroughly tested, yet they are compatible with the known optical preferences of insects and their underlying physiology. Overall, although a multiplicity of potential roles can be argued, the primary role may depend on the reference system, i.e. species, developmental stage or specific biotic and abiotic stressors.
Physiological and anatomical changes during the early ontogeny of the heteroblastic bromeliad, Vriesea sanguinolenta, do not concur with the morphological change from atmospheric to tank form
Venue: Plant Cell and Environment

Two distinct morphological forms characterize the ontogeny of many epiphytic bromeliads. Smaller plants exhibit an atmospheric habit, while larger plants form water-impounding tanks. The study of the functional significance of heteroblasty in epiphytes is severely hampered by considerable size-related variation in morphological, anatomical and physiological parameters. To overcome this problem, plants of varying size of both atmospheric and tank form were included in the present study with Vriesea sanguinolenta. The results show that virtually all morphological, anatomical and physiological characteristics vary during ontogeny, but changes were rarely directly related to the step change in gross morphology. Changes were either: (1) gradual from smallest atmospheric to small tank (e.g. leaf divergence angles, reduction in photosystem II efficiency during drought, speed of recovery after drought); (2) there was no change between atmospheric and small tank, but a gradual or step change within the tank form (stomatal density, relationship of leaf N and specific leaf area); or (3) developmental patterns were more complicated with decreases and increases during ontogeny (photosynthetic capacity, carbon isotope ratios, abscisic acid levels during drought). Although the comparisons between ontogenetic phases were always confounded by size differences, a hypothetical small tank plant is expected to suffer higher water loss than a real atmospheric, whereas a hypothetical, large atmospheric plant would show reduced access to resources, such as nutrients, in comparison with the real tank. The present results are consistent with the notion of heteroblasty as an adaptation of early ontogenetic stages to drought, but highlight that size-related variation greatly modifies any difference directly associated with the step change from atmospheric to tank.
Evolution of restraint in a structured rock–paper–scissors community
Venue: Proceedings of the National Academy of Sciences of the United States of America

It is not immediately clear how costly behavior that benefits others evolves by natural selection. By saving on inherent costs, individuals that do not contribute socially have a selective advantage over altruists if both types receive equal benefits. Restrained consumption of a common resource is a form of altruism. The cost of this kind of prudent behavior is that restrained individuals give up resources to less-restrained individuals. The benefit of restraint is that better resource management may prolong the persistence of the group. One way to dodge the problem of defection is for altruists to interact disproportionately with other altruists. With limited dispersal, restrained individuals persist because of interaction with like types, whereas it is the unrestrained individuals that must face the negative long-term consequences of their rapacity. Here, we study the evolution of restraint in a community of three competitors exhibiting a nontransitive (rock–paper–scissors) relationship. The nontransitivity ensures a form of negative feedback, whereby improvement in growth of one competitor has the counterintuitive consequence of lowering the density of that improved player. This negative feedback generates detrimental long-term consequences for unrestrained growth. Using both computer simulations and evolution experiments with a nontransitive community of Escherichia coli, we find that restrained growth can evolve under conditions of limited dispersal in which negative feedback is present. This research, thus, highlights a set of ecological conditions sufficient for the evolution of one form of altruism.