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Microbialite morphostratigraphy as a tool for correlating Late Cambrian-Early Ordovician sequences.

Microbialite morphostratigraphy is a new tool for intrabasinal correlation using diverse microbialite structures (morphotypes). The recognition of the succession of morphotypes over constrained temporal intervals and broad areas is a function of the complex interactions that operate to create the structure. Because so many nonlinked variables (e.g., biotic, sedimentological, physicochemical) are involved, similar morphotypes do not reoccur over long temporal intervals. To demonstrate the technique, the upper Cambrian-lowermost Ordovician shelf strata of the Great Basin, United States, were correlated using both morphostratigraphy and standard lithostratigraphy. Six morphozones and one morphosubzone were recognized, as were four main lithologic successions. Because the boundaries between the morphozones and lithologic successions did not coincide, it is inferred that the characteristics of the various microbialite structures are not solely controlled by physical factors. The principles for establishing a morphostratigraphy outlined in this article allow for the potential to correlate along other ancient marine margins in both the same Cambrian and Ordovician interval, as well as any interval in the Phanerozoic in which diverse microbialite structures occur.

Biological Evolution↗

[Research progress and trend on grassland agroecology].

The connotation, progress, research frontiers and developmental trend of grassland agroecology are discussed in this paper. The interface theory, structure and function, coupling and discordance, and health assessment of grassland agroecosystems were recognized as the four research frontiers of the discipline. There exist three primary interfaces in a grassland agroecosystem, i.e., vegetation-site, grassland-animal and production-management. Research into a series of the ecological processes that occurred at these interfaces is the key to revealing the features of the system behavior. There are four sections in a grassland agroecosystem, i.e., pre-plant, plant, animal and post-biotic sections. System coupling and discordance are the two important concepts to describe interactions among the production sections. System coupling among the sections can lead to system improvement by exerting the potential of system capacity. Health of an ecosystem is a reflection of its structure and function, and health assessment is a measurement of its orderliness and service value.

Agriculture↗

Pseudomonas syringae pv tomato induces the expression of tomato EREBP-like genes pti4 and pti5 independent of ethylene, salicylate and jasmonate

The tomato genes Pti4 and Pti5 encode ethylene-responsive element binding protein-like transcription factors that bind to the GCC box, a conserved cis-element in many defense-related genes. The Pti proteins have previously been shown to interact with the tomato disease resistance protein Pto. Here we report that the expression of both Pti4 and Pti5 are induced by a virulent strain of Pseudomonas syringae pv tomato. The expression of Pti5 is further enhanced by the interaction of the Pto gene in tomato and the corresponding avrPto gene in the bacterium. The enhancement of Pti5 expression by Pto-avrPto interaction requires a functional Prf gene in the plant. Pti5 appears to be expressed specifically during biotic stresses, suggesting a specific role in plant defense. Pti4 and several EREBP-like genes are induced by ethylene, salicylate and wounding. However, the Pseudomonas bacterium induced a wild-type level of Pti4 and Pti5 transcripts in tomato plants carrying the nahG transgene, the Nr mutation, or the def1 mutation. In addition, the ethylene action inhibitor norbornadiene did not inhibit the induction of Pti4 and Pti5 either in the compatible or incompatible interactions. The results suggest that the Pseudomonas bacterium induces Pti4 and Pti5 expression through a pathway independent of salicylic acid, ethylene and jasmonic acid.

Journal Article↗

Hydrogen peroxide formation and decay in iron-rich geothermal waters: the relative roles of abiotic and biotic mechanisms

Hydrogen peroxide (H2O2) is widely distributed in surface waters where the primary photochemical formation pathway involves the interaction between dissolved organic carbon (DOC) and ultraviolet radiation (UVR). In laboratory studies using iron-rich water from Yellow-stone's Chocolate Pots spring, H2O2 formation depended on sample treatment (unfiltered, < 0.2 micron filtered, autoclaved) prior to irradiation, suggesting several formation pathways. Similar H2O2 formation in filtered and unfiltered water indicates that it is primarily soluble material that is responsible for H2O2 formation. H2O2 formation with soluble material probably includes only photochemical reactions with DOC and/or metals. Greater H2O2 formation in unfiltered and filtered water than in autoclaved water suggests that the agent(s) involved in H2O2 formation is (are) not stable at high temperatures and pressures and degrade to nonphotoreactive species. Such unstable agents may include DOC and/or dissolved complexes of iron or other metals. UVR absorbance occurs across the UV spectrum and, though slightly greater in the UVA range (320-400 nm), is similar to that of other surface waters. Increased UVR absorbance after autoclaving suggested degradation or alteration of some components, which in turn affected H2O2 formation. The spectral region used for irradiation affected net formation and yield. H2O2 formation in water irradiated with UVA radiation was 2.5-3 times that formed in water irradiated with UVB radiation (280-320 nm) in experiments using artificial light sources. Apparent quantum yields comparable to those reported by others could not be calculated because the instrumental designs are not the same. However, approximate quantum yields were calculated for these experiments but should be viewed with caution. Quantum yields were higher in these experiments (0.0040 mol H2O2 per mol photon at 310 nm and 0.0012 mol H2O2 per mol photon at 350 nm) than values reported by other researchers (< 0.0007 mol H2O2 per mol photon at 300 nm and < 0.0005 H2O2 per mol photon at 340 nm; [Scully, N. M., D. R. S. Lean, D. J. McQueen and W. J. Cooper (1996) Limnol. Oceanogr. 41, 540-548]). In natural solar source experiments, H2O2 formation was greater in experiments with UVA and photosynthetically active radiation (PAR; 400-700 nm) than with PAR alone or with UVB, UVA and PAR. However, H2O2 capacity (nM H2O2 W-1 h-1 m2) was greatest with UVB radiation and lowest with PAR radiation. Source regions could not be studied separately. Dark decay of H2O2 occurred via two mechanisms. The main mechanism responsible for H2O2 decay involved particulate matter (probably microorganisms), whereas a secondary mechanism involved soluble matter (i.e. DOC, metal ions and other dissolved species involved in Fenton reactions).

Journal Article↗

The Prisoner's Dilemma and polymorphism in yeast SUC genes.

The SUC multigene family of the single-celled yeast Saccharomyces cerevisiae is polymorphic, with genes varying both in number and activity. All of the genes encode invertase, an enzyme that is secreted to digest sucrose outside of the cell. This communal endeavour creates the potential for individual cells to defect (cheat) by stealing the sugar digested by their neighbours without contributing the enzyme themselves. We measured the fitness of a defector, with a deleted suc2 gene, relative to an otherwise isogenic cooperator, with a functional SUC2 gene. We manipulated the level of social interaction within the community by varying the population density and found that the defector is less fit than the cooperator at low levels of sociality but more fit in dense communities. We propose that selection for antisocial cheating causes SUC polymorphism in nature. The infamous Prisoner's Dilemma game shows that social behaviour is generally unstable, and the success of both cooperation and defection can vary continuously in time and space. The variation in SUC genes reflects constant adaptation to an ever-changing biotic environment that is a consequence of the instability of cooperation. It is interesting that social interactions can have a direct effect on molecular evolution, even in an organism as simple as yeast.

Adaptation, Biological↗

Confounding factors in the detection of species responses to habitat fragmentation.

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat. Fragmentation per se is a landscape-level phenomenon in which species that survive in habitat remnants are confronted with a modified environment of reduced area, increased isolation and novel ecological boundaries. The implications of this for individual organisms are many and varied, because species with differing life history strategies are differentially affected by habitat fragmentation. Here, we review the extensive literature on species responses to habitat fragmentation, and detail the numerous ways in which confounding factors have either masked the detection, or prevented the manifestation, of predicted fragmentation effects. Large numbers of empirical studies continue to document changes in species richness with decreasing habitat area, with positive, negative and no relationships regularly reported. The debate surrounding such widely contrasting results is beginning to be resolved by findings that the expected positive species-area relationship can be masked by matrix-derived spatial subsidies of resources to fragment-dwelling species and by the invasion of matrix-dwelling species into habitat edges. Significant advances have been made recently in our understanding of how species interactions are altered at habitat edges as a result of these changes. Interestingly, changes in biotic and abiotic parameters at edges also make ecological processes more variable than in habitat interiors. Individuals are more likely to encounter habitat edges in fragments with convoluted shapes, leading to increased turnover and variability in population size than in fragments that are compact in shape. Habitat isolation in both space and time disrupts species distribution patterns, with consequent effects on metapopulation dynamics and the genetic structure of fragment-dwelling populations. Again, the matrix habitat is a strong determinant of fragmentation effects within remnants because of its role in regulating dispersal and dispersal-related mortality, the provision of spatial subsidies and the potential mediation of edge-related microclimatic gradients. We show that confounding factors can mask many fragmentation effects. For instance, there are multiple ways in which species traits like trophic level, dispersal ability and degree of habitat specialisation influence species-level responses. The temporal scale of investigation may have a strong influence on the results of a study, with short-term crowding effects eventually giving way to long-term extinction debts. Moreover, many fragmentation effects like changes in genetic, morphological or behavioural traits of species require time to appear. By contrast, synergistic interactions of fragmentation with climate change, human-altered disturbance regimes, species interactions and other drivers of population decline may magnify the impacts of fragmentation. To conclude, we emphasise that anthropogenic fragmentation is a recent phenomenon in evolutionary time and suggest that the final, long-term impacts of habitat fragmentation may not yet have shown themselves.

Animals↗

Toward a scientifically rigorous basis for developing mapped ecological regions.

Despite the wide use of ecological regions in conservation and resource-management evaluations and assessments, a commonly accepted theoretical basis for ecological regionalization does not exist. This fact, along with the paucity of focus on ecological regionalization by professional associations, journals, and faculties, has inhibited the advancement of a broadly acceptable scientific basis for the development, use, and verification of ecological regions. The central contention of this article is that ecological regions should improve our understanding of geographic and ecological phenomena associated with biotic and abiotic processes occurring in individual regions and also of processes characteristic of interactions and dependencies among multiple regions. Research associated with any ecoregional framework should facilitate development of hypotheses about ecological phenomena and dominant landscape elements associated with these phenomena, how these phenomena are structured in space, and how they function in a hierarchy. Success in addressing the research recommendations outlined in this article cannot occur within an ad hoc, largely uncoordinated research environment. Successful implementation of this plan will require activities--coordination, funding, and education--that are both scientific and administrative in nature. Perhaps the most important element of an infrastructure to support the scientific work of ecoregionalization would be a national or international authority similar to the Water and Science Technology Board of the National Academy of Sciences.

Conservation of Natural Resources↗

Beaver herbivory on aquatic plants.

Herbivores have strong impacts on marine and terrestrial plant communities, but their impact is less well studied in benthic freshwater systems. For example, North American beavers (Castor canadensis) eat both woody and non-woody plants and focus almost exclusively on the latter in summer months, yet their impacts on non-woody plants are generally attributed to ecosystem engineering rather than herbivory. Here, we excluded beavers from areas of two beaver wetlands for over 2 years and demonstrated that beaver herbivory reduced aquatic plant biomass by 60%, plant litter by 75%, and dramatically shifted plant species composition. The perennial forb lizard's tail (Saururus cernuus) comprised less than 5% of plant biomass in areas open to beaver grazing but greater than 50% of plant biomass in beaver exclusions. This shift was likely due to direct herbivory, as beavers preferentially consumed lizard's tail over other plants in a field feeding assay. Beaver herbivory also reduced the abundance of the invasive aquatic plant Myriophyllum aquaticum by nearly 90%, consistent with recent evidence that native generalist herbivores provide biotic resistance against exotic plant invasions. Beaver herbivory also had indirect effects on plant interactions in this community. The palatable plant lizard's tail was 3 times more frequent and 10 times more abundant inside woolgrass (Scirpus cyperinus) tussocks than in spatially paired locations lacking tussocks. When the protective foliage of the woolgrass was removed without exclusion cages, beavers consumed nearly half of the lizard's tail leaves within 2 weeks. In contrast, leaf abundance increased by 73-93% in the treatments retaining woolgrass or protected by a cage. Thus, woolgrass tussocks were as effective as cages at excluding beaver foraging and provided lizard's tail plants an associational refuge from beaver herbivory. These results suggest that beaver herbivory has strong direct and indirect impacts on populations and communities of herbaceous aquatic plants and extends the consequences of beaver activities beyond ecosystem engineering.

Animals↗

Abscisic acid, nitric oxide and stomatal closure - is nitrate reductase one of the missing links?

Once plant endogenous nitric oxide (NO) production had been proved, NO research was directed toward both the source and the targets of this extremely bioactive molecule. As in mammals, plant NO was first thought to be generated mainly by a NO synthase-like enzymatic activity. However, nitrate reductase (NR)-dependent NO production is now receiving much of the attention because of the ubiquity of this enzyme in higher plant tissues and the precise regulation of its NO-production activity. NO has been reported to be a signal in many and diverse physiological processes, such as growth and biotic and abiotic stresses. Recently, NO has been shown to affect stomatal closure and interact with abscisic acid signaling pathways. We propose NR as a putative component in the signaling cascade of ABA-induced stomatal closure.

Abscisic Acid↗

Hydrogen peroxide homeostasis: activation of plant catalase by calcium/calmodulin.

Environmental stimuli such as UV, pathogen attack, and gravity can induce rapid changes in hydrogen peroxide (H(2)O(2)) levels, leading to a variety of physiological responses in plants. Catalase, which is involved in the degradation of H(2)O(2) into water and oxygen, is the major H(2)O(2)-scavenging enzyme in all aerobic organisms. A close interaction exists between intracellular H(2)O(2) and cytosolic calcium in response to biotic and abiotic stresses. Studies indicate that an increase in cytosolic calcium boosts the generation of H(2)O(2). Here we report that calmodulin (CaM), a ubiquitous calcium-binding protein, binds to and activates some plant catalases in the presence of calcium, but calcium/CaM does not have any effect on bacterial, fungal, bovine, or human catalase. These results document that calcium/CaM can down-regulate H(2)O(2) levels in plants by stimulating the catalytic activity of plant catalase. Furthermore, these results provide evidence indicating that calcium has dual functions in regulating H(2)O(2) homeostasis, which in turn influences redox signaling in response to environmental signals in plants.

Amino Acid Sequence↗

Enterococcus faecalis strains show culture heterogeneity in cell surface charge.

Adhesion of micro-organisms to biotic and abiotic surfaces is an important virulence factor and involves different types of interactions. Enterococcus faecalis, a human commensal and an important opportunistic pathogen, has the ability to adhere to surfaces. Biliary stents frequently become clogged with bacterial biofilms, with E. faecalis as one of the predominant species. Six E. faecalis strains isolated from clogged biliary stents were investigated for the presence of specific biochemical factors involved in their adhesion: aggregation substances (Aggs) and the enterococcal surface protein (encoded by the esp gene). In addition, physico-chemical factors involved in adhesion (zeta potential and cell surface hydrophobicity) were determined, as well as the influence of ox bile on these properties. Two-thirds of the biliary stent isolates displayed culture heterogeneity in the pH dependence of their zeta potentials. Moreover, 24 out of 46 clinical isolates of E. faecalis, including 11 laboratory strains, also displayed such heterogeneity. The culture heterogeneity was demonstrated to be a stable trait, not caused by quorum sensing, not plasmid mediated, and independent of the presence of esp and Agg. Data presented show that culture heterogeneity in zeta potential enhances adhesion to an abiotic surface. A higher prevalence of culture heterogeneity in zeta potential in pathogenic as compared to non-pathogenic isolates could indicate that this phenomenon might play a role in virulence and putatively in pathogenesis.

Animals↗

Analysis of Pseudomonas aeruginosa conditional psl variants reveals roles for the psl polysaccharide in adhesion and maintaining biofilm structure postattachment.

The ability to form biofilms in the airways of people suffering from cystic fibrosis is a critical element of Pseudomonas aeruginosa pathogenesis. The 15-gene psl operon encodes a putative polysaccharide that plays an important role in biofilm initiation in nonmucoid P. aeruginosa strains. Biofilm initiation by a P. aeruginosa PAO1 strain with disruption of pslA and pslB (DeltapslAB) was severely compromised, indicating that psl has a role in cell-surface interactions. In this study, we investigated the adherence properties of this DeltapslAB mutant using biotic surfaces (epithelial cells and mucin-coated surfaces) and abiotic surfaces. Our results showed that psl is required for attachment to a variety of surfaces, independent of the carbon source. To study the potential roles of Psl apart from attachment, we generated a psl-inducible P. aeruginosa strain (Deltapsl/p(BAD)-psl) by replacing the psl promoter region with araC-p(BAD), so that expression of psl could be controlled by addition of arabinose. Analysis of biofilms formed by the Deltapsl/p(BAD)-psl strain indicated that expression of the psl operon is required to maintain the biofilm structure at steps postattachment. Overproduction of the Psl polysaccharide led to enhanced cell-surface and intercellular adhesion of P. aeruginosa. This translated into significant changes in the architecture of the biofilm. We propose that Psl has an important role in P. aeruginosa adhesion, which is critical for initiation and maintenance of the biofilm structure.

Animals↗

Biological and chemical interactions of pesticides with soil organic matter.

There is little doubt that organic matter plays a major role in the binding of pesticides in soil, and that this phenomenon is usually the most important cause for interaction of pesticides in the soil environment. Fulvic or humic acids are the chemicals most commonly involved in the binding interactions. Binding can occur with the original pesticide or a transformation product, the reaction being caused by abiotic agents or biotic agents (microbial or plant enzymes). The reactions or processes involved appear to be the same as those responsible for the formation of humic substances, i.e. for the humification process. Binding of pesticides to organic matter can occur by sorption (Van der Waal's forces, hydrogen bonding, hydrophobic bonding), electrostatic interactions (charge transfer, ion exchange or ligand exchange), covalent bonding or combinations of these reactions. Our investigation focused primarily on the binding of substituted phenols and aromatic amines to humus monomers and humic substances. In model reactions, we demonstrated the formation of covalent linkages between pesticides and humus constituents and fulvic or humic acids in the presence of phenol oxidases or clay minerals. With chlorinated phenols and carboxylic acids, it was possible to isolate and identify cross-coupling products and to elucidate the site and type of binding. The binding of chlorinated phenols to humic substances was determined by using 14C-labelled chemicals and by measuring the uptake of radioactivity by the humic material. These experiments provide a base for explaining the formation of bound residues in certain cases and for assuming the toxic potential of the immobilized pollutants.

Adsorption↗

Crosstalk between jasmonic acid, ethylene and Nod factor signaling allows integration of diverse inputs for regulation of nodulation.

Plant hormones interact at many different levels to form a network of signaling pathways connected by antagonistic and synergistic interactions. Ethylene and jasmonic acid both act to regulate the plant's responsiveness to a common set of biotic stimuli. In addition ethylene has been shown to negatively regulate the plant's response to the rhizobial bacterial signal, Nod factor. This regulation occurs at an early step in the Nod factor signal transduction pathway, at or above Nod factor-induced calcium spiking. Here we show that jasmonic acid also inhibits the plant's responses to rhizobial bacteria, with direct effects on Nod factor-induced calcium spiking. However, unlike ethylene, jasmonic acid not only inhibits spiking but also suppresses the frequency of calcium oscillations when applied at lower concentrations. This effect of jasmonic acid is amplified in the ethylene-insensitive mutant skl, indicating an antagonistic interaction between these two hormones for regulation of Nod factor signaling. The rapidity of the effects of ethylene and jasmonic acid on Nod factor signaling suggests direct crosstalk between these three signal transduction pathways. This work provides a model by which crosstalk between signaling pathways can rapidly integrate environmental, developmental and biotic stimuli to coordinate diverse plant responses.

Calcium↗

The interaction of amphotericin B methyl ester with protoplasts of Candida albicans.

The interaction of amphotericin B methyl ester (AME) with protoplasts of Candida albicans was measured indirectly by following the incorporation of [U-14C]phenylalanine into the acid-insoluble material. The inhibitory effects of AME at the minimum inhibitory concentration were prevented by the addition of 85 mM-KCl and 45 mM-MgCl2, as shown by Liras & Lampen (1974) for Saccharomyces cerevisiae. In C. albicans, pretreatment of the yeast before anti-biotic addition was unnecessary. KCl and MgCl2 did not prevent AME from binding to the protoplast membrane. This interaction was reversed by incubating the protoplasts in the presence of the protecting salts.

Amphotericin B↗

Cloning and characterization of GLOSSY1, a maize gene involved in cuticle membrane and wax production.

The cuticle covering the aerial organs of land plants plays a protective role against several biotic and abiotic stresses and, in addition, participates in a variety of plant-insect interactions. Here, we describe the molecular cloning and characterization of the maize (Zea mays) GLOSSY1 (GL1) gene, a component of the pathway leading to cuticular wax biosynthesis in seedling leaves. The genomic and cDNA sequences we isolated differ significantly in length and in most of the coding region from those previously identified. The predicted GL1 protein includes three histidine-rich domains, the landmark of a family of membrane-bound desaturases/hydroxylases, including fatty acid-modifying enzymes. GL1 expression is not restricted to the juvenile developmental stage of the maize plant, pointing to a broader function of the gene product than anticipated on the basis of the mutant phenotype. Indeed, in addition to affecting cuticular wax biosynthesis, gl1 mutations have a pleiotropic effect on epidermis development, altering trichome size and impairing cutin structure. Of the many wax biosynthetic genes identified so far, only a few from Arabidopsis (Arabidopsis thaliana) were found to be essential for normal cutin formation. Among these is WAX2, which shares 62% identity with GL1 at the protein level. In wax2-defective plants, cutin alterations induce postgenital organ fusion. This trait is not displayed by gl1 mutants, suggesting a different role of the maize and Arabidopsis cuticle in plant development.

Amino Acid Sequence↗

[Advances in plant proteomics. II. Application of proteome techniques to plant biology research].

Proteome techniques have widely been applied to the fields of plant genetics, plant development, and plant physiology and ecology to investigate plant genetic diversity, plant development such as seed maturation and germination processes, differentiation of plant tissue and organ, separation and functional identification of novel component of various organells, mechanisms of plant adapted to abiotic or biotic stresses including high temperature, low temperature, high salt, drought, and pathogens and insects, and interaction of plant with microbe. The prospects of plant proteomics are discussed.

Biology↗

Microgeographic evolution of snail shell shape and predator behavior.

Genetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.

Adaptation, Physiological↗