Belowground and aboveground consequences of interactions between live plant species mixtures and dead organic substrate mixtures

In all terrestrial ecosystems, plant‐derived resources mainly enter the belowground subsystem in two ways – as dead plant parts (i.e. organic substrates) and as resources released from the rhizosphere of live plants. While the effects of identity of live plants or dead plant parts on aboveground and belowground properties have been well studied, much remains unknown about the effects of combinations of live plant species and dead plant‐derived substrates. In particular, no study to date has experimentally investigated the effects of simultaneously varying the composition or diversity of both live plants and dead plant parts. We performed a pot experiment consisting of a full factorial of 12 organic substrate addition treatments by eight live plant treatments, in which the composition and diversity of both substrates and live plants were varied. The 12 substrate treatments consisted of no substrates added, each of the four substrates represented singly (four treatments), each of the possible pairwise combinations of the four substrates (six treatments), and all four substrates added together. As expected, substrate and live plant identity both had important effects both above‐ and belowground. Mixtures of plant species always had effects that could be explained by the effects of the component plant species grown singly. Usually mixtures of substrates also had effects that could be predicted by the effects of component substrates added singly, but there were instances in which mixtures of certain substrates (notably mixtures containing Populus tremula leaf litter) had synergistic effects both belowground and aboveground, with especially strong effects on the growth of Pinus sylvestris seedlings. However, there was never any evidence of interactive effects between live plant species diversity or composition and added substrate diversity or composition, either aboveground or belowground. This means that whatever effects added substrates have on ecological properties operates independently of the influence of live plants, and vice versa. In total, this study shows that most resources entering the belowground subsystem have effects that are independent of the effects of other resources, though there are isolated instances in which strong (and potentially ecologically meaningful) synergistic interactions may occur for specific combinations of dead organic substrates.     

Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel,pseudoconvergent evolution of polyamine biosynthesis

Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5′-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.     

The effects of substrate composition, quantity, and diversity on microbial activity

Variation in organic matter inputs caused by differences in plant community composition has been shown to affect microbial activity, although the mechanisms controlling these effects are not entirely understood. In this study we determine the effects of variation in substrate composition, quantity, and diversity on soil extracellular enzyme activity and respiration in laboratory microcosms. Microbial respiration responded predictably to substrate composition and quantity and was maximized by the addition of labile substrates and greater substrate quantity. However, there was no effect of substrate diversity on respiration. Substrate composition significantly affected enzyme activity. Phosphatase activity was maximized with addition of C and N together, supporting the common notion that addition of limiting resources increases investment in enzymes to acquire other limiting nutrients. Chitinase activity was maximized with the addition of chitin, suggesting that some enzymes may be stimulated by the addition of the substrate they degrade. In contrast, activities of glucosidase and peptidase were maximized by the addition of the products of these enzymes, glucose and alanine, respectively, for reasons that are unclear. Substrate diversity and quantity also stimulated enzyme activity for three and four of the six enzymes assayed, respectively. We found evidence of complementary (i.e., non-additive) effects of additions of different substrates on activity for three of the six enzymes assayed; for the remaining enzymes, effects of adding a greater diversity of substrates appeared to arise from the substrate-specific effects of those substrates included in the high-diversity treatment. Finally, in a comparison of measures of microbial respiration and enzyme activity, we found that labile C and nutrient-acquiring enzymes, not those involved in the degradation of recalcitrant compounds, were the best predictors of respiration rates. These results suggest that while composition, quantity, and diversity of inputs to microbial communities all affect microbial enzyme activity, the mechanisms controlling these relationships are unique for each particular enzyme.     

Diversity in ABC transporters: Type I,II and III importers

Abstract

ATP-binding cassette transporters are multi-subunit membrane pumps that transport substrates across membranes. While significant in the transport process, transporter architecture exhibits a range of diversity that we are only beginning to recognize. This divergence may provide insight into the mechanisms of substrate transport and homeostasis. Until recently, ABC importers have been classified into two types, but with the emergence of energy-coupling factor (ECF) transporters there are potentially three types of ABC importers. In this review, we summarize an expansive body of research on the three types of importers with an emphasis on the basics that underlie ABC importers, such as structure, subunit composition and mechanism.     

Climate, energy and diversity

In recent years, a number of species-energy hypotheses have been developed to explain global patterns in plant and animal diversity. These hypotheses frequently fail to distinguish between fundamentally different forms of energy which influence diversity in dissimilar ways. Photosynthetically active radiation (PAR) can be utilized only by plants, though their abundance and growth rate is also greatly influenced by water. The Gibbs free energy (chemical energy) retained in the reduced organic compounds of tissue can be utilized by all heterotrophic organisms. Neither PAR nor chemical energy influences diversity directly. Both, however, influence biomass and/or abundance; diversity may then increase as a result of secondary population dynamic or evolutionary processes. Temperature is not a form of energy, though it is often used loosely by ecologists as a proxy for energy; it does, however, influence the rate of utilization of chemical energy by organisms. It may also influence diversity by allowing a greater range of energetic lifestyles at warmer temperatures (the metabolic niche hypothesis). We conclude that there is no single species/energy mechanism; fundamentally different processes link energy to abundance in plants and animals, and diversity is affected secondarily. If we are to make progress in elucidating these mechanisms, it is important to distinguish climatic effects on species' distribution and abundance from processes linking energy supply to plant and animal diversity.     

Character combinations, convergence and diversification in ectoparasitic arthropods

Different lineages of organisms diversify over time at different rates, in part as a consequence of the characteristics of the species in these lineages. Certain suites of traits possessed by species within a clade may determine rates of diversification, with some particular combinations of characters acting synergistically to either limit or promote diversification; the most successful combinations may also emerge repeatedly in different clades via convergent evolution. Here, the association between species characters and diversification is investigated amongst 21 independent lineages of arthropods ectoparasitic on vertebrate hosts. Using nine characters (each with two to four states) that capture general life history strategy, transmission mode and host-parasite interaction, each lineage was described by the set of character states it possesses. The results show, firstly, that most possible pair-wise combinations of character states have been adopted at least once, sometimes several times independently by different lineages; thus, ectoparasitic arthropods have explored most of the life history character space available to them. Secondly, lineages possessing commonly observed combinations of character states are not necessarily the ones that have experienced the highest rates of diversification (measured as a clade’s species-per-genus ratio). Thirdly, some specific traits are associated with higher rates of diversification. Using more than one host per generation, laying eggs away from the host and intermediate levels of fecundity are features that appear to have promoted diversification. These findings indicate that particular species characters may be evolutionary drivers of diversity, whose effects could also apply in other taxa.     

Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution

While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.     

Observations on the effects of morphactin EMD 7301 and EMD 7311 on the number,size, morphology and ontogeny of cotyledonary stomata ofAbelmoschus esculentus moench

Stomata on the cotyledons of Morphactin EMD 7301 and EMD 7311 treated seedlings may be anisocytic, anomocytic, paracytic, diacytio, transitional forms and haplocytic. In spite of this diversity, the most frequent type is anisocytic on both surfaces. The stomatal ontogeny may bo perigenous, mesogenous and mesoperigenous. Morphactin EMD 7301 and EMD 7311 increase the size of cotyledons in all concentrations accompanied by an increase in the number of stomata on the adaxial surface in 100, 150, 250 ppm of EMD 7301. The effect of morphactin is promotive to the size of stomata in all concentrations, but it retards the stomatal density and number of epidermal cells. This may be due to an increase in the size of the epidermal cells. The substrates, however, have no effect on the morphology and ontogeny of the stomata; probably they are inherent chracters.     

Cloning, sequence analysis, and characterization of the 'lysyl oxidase' from Pichia pastoris

Lysyl oxidase from Pichia pastoris has been successfully overexpressed. EPR and resonance Raman experiments have shown that copper and TPQ are present, respectively. Lysyl oxidase from P. pastoris has a similar substrate specificity to the mammalian enzyme (both have been shown to oxidize peptidyl lysine residues) and is 30% identical to the human kidney diamine oxidase (the highest of any non-mammalian source). This enzyme also has a relatively broad substrate specificity compared to other amine oxidases. Molecular modeling data suggest that the substrate channel in lysyl oxidase from P. pastoris permits greater active site access than observed in structurally-characterized amine oxidases. This larger channel may account for the diversity of substrates that are turned over by this enzyme.     

Tree Diversity,Environmental Heterogeneity,and Productivity in a Mexican Tropical Dry Forest1

Species diversity–environmental heterogeneity (D–EH) and species diversity–productivity (D–P) relationships have seldom been analyzed simultaneously even though such analyses could help to understand the processes underlying contrasts in species diversity among sites. Here we analyzed both relationships at a local scale for a highly diverse tropical dry forest of Mexico. We posed the following questions: (1) are environmental heterogeneity and productivity related?; (2) what are the shapes of D–EH and D–P relationships?; (3) what are individual, and interactive, contributions of these two variables to the observed variance in species diversity?; and (4) are patterns affected by sample size, or by partitioning into average local diversity and spatial species turnover? All trees (diameter at breast height ≥5 cm) within twenty‐six 0.2‐ha transects were censused; four environmental variables associated with water availability were combined into an environmental heterogeneity index; aboveground standing biomass was used as a productivity estimator. Simple and multiple linear and nonlinear regression models were run. Environmental heterogeneity and productivity were not correlated. We found consistently positive log‐linear D–EH and D–P relationships. Productivity explained a larger fraction of among‐transect variance in species diversity than did environmental heterogeneity. No effects of sample size were found. Different components of diversity varied in sensitivity to environmental heterogeneity and productivity. Our results suggest that species' differentiation along water availability gradients and species exclusion at the lowest productivity (driest) sites occur simultaneously, independently, and in a scale‐dependent fashion on the tree community of this forest.     

Experiments in microbial evolution: new enzymes, new metabolic activities

Biological evolution has resulted in a richness and diversity of species. Among microorganisms this is most evident in the wealth and diversity of biochemical transformations. Evidence for evolutionary relationships may be obtained from comparative studies, but with microorganisms it is also possible to follow evolution in action. Microbial populations adapt rapidly to changes in the environment and the evolution of new metabolic activities can be observed in laboratory experiments. The enzymes of many catabolic pathways are synthesized in response to the presence of inducing substrates. New catabolic activities may be acquired by mutations in regulatory genes resulting in alterations in the specificity of induction, or in enzyme synthesis in the absence of inducer. Mutations in structural genes may given rise to enzymes with altered substrate specificities. In bacteria, catabolic genes may be carried on plasmids and the exchange of plasmids among bacterial populations increases the evolutionary potential. Experiments in microbial evolution have produced strains with novel catabolic activities involving regulatory or structural gene mutations, gene duplications and plasmid exchange. Enzymes studied in this way include amidase, ribitol dehydrogenase, evolved beta-galactosidase, and enzymes of the catabolic pathways for pentoses and pentitols and haloaromatic compounds.     

Synthesis of polyhydroxyalkanoate from palm oil and some new applications

Polyhydroxyalkanoate (PHA) is a potential substitute for some petrochemical-based plastics. This biodegradable plastic is derived from microbial fermentation using various carbon substrates. Since carbon source has been identified as one of the major cost-absorbing factors in PHA production, cheap and renewable substrates are currently being investigated as substitutes for existing sugar-based feedstock. Plant oils have been found to result in high-yield PHA production. Malaysia, being the world’s second largest producer of palm oil, is able to ensure continuous supply of palm oil products for sustainable PHA production. The biosynthesis and characterization of various types of PHA using palm oil products have been described in detail in this review. Besides, by-products and waste stream from palm oil industry have also demonstrated promising results as carbon sources for PHA biosynthesis. Some new applications in cosmetic and wastewater treatment show the diversity of PHA usage. With proper management practices and efficient milling processes, it may be possible to supply enough palm oil-based raw materials for human consumption and other biotechnological applications such as production of PHA in a sustainable manner.     

Polyketide-nonribosomal peptide epothilone antitumor agents: the EpoA,B, C subunits

The epothilones are a family of macrolactone natural products from the myxobacterial species Sorangium cellulosum. Similar to taxol, they are of current clinical interest as anticancer agents. Sequence analysis of the epothilone gene cluster allowed the identification of polyketide synthase and nonribosomal peptide synthetase modules involved in catalyzing epothilone biosynthesis. Given this information, it has been possible to test the predicted functions of several modules to date. EpoA ACP, EpoB, and EpoC have been overproduced in Escherichia coli, allowing in vitro reconstitution of the EpoA/B/C interface and production of the expected epothilone precursor. Further experiments probed the tolerance of EpoB and EpoC for unnatural substrates. These studies of the first three modules of the epothilone biosynthetic cluster suggest that combinatorial biosynthesis may lead to the production of a variety of epothilone analogs that incorporate diversity into the heterocycle starter unit. Additional efforts with the remaining modules, coupled with increased understanding of the macrocyclizing thioesterase domain, may lead to the production of epothilone variants with improved clinical properties.     

Colonization patterns of wood-inhabiting fungi on baits in Hong Kong rivers, with reference to the effects of organic pollution

The diversity of wood-inhabiting fungi was investigated by submerging woody baits at upstream and downstream sites of the Lam Tsuen and Tai Po Rivers in Hong Kong. The diversity of fungi in the Lam Tsuen River was also compared with that on natural woody substrates found in a previous study. There were differences in the species composition between the upstream and downstream sites, possibly reflecting natural variations along the river. The Tai Po River downstream was organically polluted, which appeared to have little effect on species diversity since more species were recorded. Organic pollution may, however, cause a shift in species composition. The fungal communities on baits and natural substrates in the Lam Tsuen River were similar, although a lower diversity was observed on baits. This may be related to the period of submergence and the fact that a single wood type was used. Cercophora spp. occurred frequently downstream in the Tai Po River, while the common species in the Lam Tsuen River were Aquaticola rhomboidea and Pseudoproboscispora aquatica. Further interpretation on the effects of organic pollution was limited because of single collection data but appropriate experimental designs – putting baits in unimpacted sites for assessing human impacts in streams – are suggested.     

Trait vs. phylogenetic diversity as predictors of competition and community composition in herbivorous marine amphipods

Field studies of community assembly patterns increasingly use phylogenetic relatedness as a surrogate for traits. Recent experiments appear to validate this approach by showing effects of correlated trait and phylogenetic distances on coexistence. However, traits governing resource use in animals are often labile. To test whether feeding trait or phylogenetic diversity can predict competition and production in communities of grazing amphipods, we manipulated both types of diversity independently in mesocosms. We found that increasing the feeding trait diversity of the community increased the number of species coexisting, reduced dominance and changed food availability. In contrast, phylogenetic diversity had no effect, suggesting that whatever additional ecological information it represents was not relevant in this context. Although community phylogenetic structure in the field may result from multiple traits with potential for phylogenetic signal, phylogenetic effects on species interactions in controlled experiments may depend on the lability of fewer key traits.     

Environmental correlates of tree alpha-diversity in New Zealand primary forests

Correlations between environment and tree alpha-diversity in New Zealand's primary forests were examined using an extensive quantitative dataset (14 540 plots). Generalised additive models were used to examine relationships between species richness and temperature, solar radiation, root-zone moisture deficit, relative humidity, lithology, drainage, and plot size for all trees (112 species), and separately for broadleaved trees (88 species), conifers (17), and the genus Nothofagus (4). Diversity both for all tree species and for broadleaved trees was predicted to be highest on sites with high temperatures, high solar radiation, and high soil and atmospheric moisture, and on sedimentary and basaltic substrates. Highest conifer diversity was predicted on sites with intermediate temperatures, low solar radiation, high root-zone and atmospheric moisture, and rhyolitic and Quaternary substrates, particularly where drainage was impeded. Highest Nothofagus diversity was predicted for sites combining low temperatures, high solar radiation, high root-zone moisture but low atmospheric moisture, and on granitic substrates. Differences in diversity between the species groups on different lithologies are interpreted as rejecting both the effects of variation in large-scale disturbance histories, and the effects of confounding environmental factors associated with particular substrates. There were also significant interactions between species groups: both broadleaved tree and conifer richness were predicted to be lower on sites where one or more Nothofagus spp. — all of which have marked patchiness in their distribution — are present. Although these results are consistent with the hypothesis that tree diversity is highest on sites conducive to high productivity, history is also indicated as an important determinant of tree diversity in New Zealand.     

Inherent properties of adenylosuccinate lyase could explain S-Ado/SAICAr ratio due to homozygous R426H and R303C mutations

Adenylosuccinate lyase (ADSL) is a homotetrameric enzyme involved in the de novo purine biosynthesis pathway and purine nucleotide cycle. Missense mutations in the protein lead to ADSL deficiency, an inborn error of purine metabolism characterized by neurological and physiological symptoms. ADSL deficiency is biochemically diagnosed by elevated levels of succinylaminoimidazolecarboxamide riboside (SAICAr) and succinyladenosine (S-Ado), the dephosphorylated derivatives of the substrates. S-Ado/SAICAr ratios have been associated with three phenotypic groups. Different hypotheses to explain these ratios have been proposed. Recent studies have focused on measuring activity on the substrates independently. However, it is important to examine mixtures of the substrates to determine if mutations affect enzyme activity on both substrates similarly in these conditions. The two substrates may experience an indirect communication due to being acted upon by the same enzyme, altering their activities from the non-competitive case. In this study, we investigate this hidden coupling between the two substrates. We chose two mutations that represent extremes of the phenotype, R426H and R303C. We describe a novel electrochemical-detection method of measuring the kinetic activity of ADSL in solution with its two substrates at varying concentration ratios. Furthermore, we develop an enzyme kinetic model to predict substrate activity from a given ratio of substrate concentrations. Our findings indicate a non-linear dependence of the activities on the substrate ratios due to competitive binding, distinct differences in the behaviors of the different mutations, and S-Ado/SAICAr ratios in patients could be explained by inherent properties of the mutant enzyme.     

Large beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis>) trees as ‘lifeboats’ for lichen diversity in central European forests

The forest management practices used in central Europe in the last several centuries have led to loss of lichen diversity that may be largely attributed to a loss of substrate variability and quantity. In an attempt to obtain information enabling us to mitigate this process, we surveyed affinity of lichen species to the substrates they currently occupy in six forest areas in the Czech Republic, located between 200 and 1000 m a.s.l. Tree bases and stems represented the most important substrate for lichen species, and especially so for threatened (i.e. red-listed) species. Lichen species richness per individual tree generally increased with stem diameter, especially for beech. Stems and tree bases of large-diameter beeches provide habitats that have enabled the survival of a crucial component of the red-listed lichen species in central Europe, far outweighing other tree species. The deciduous tree species that are commonly considered as favourable for lichen diversity (e.g. maples, ash, elms) were inhabited by only a few other lichen species additional to those associated with beech. This may be due to the low frequency of these tree species in most managed forests, and also some forest reserves, at the present time. Similarly, low incidence of dead wood in managed forests has likely limited its contribution to the lichen diversity, despite the high potential for lichen diversity associated with such substrates. It is thus apparent that bark of large-diameter live beech trees comprises a keystone habitat element in the provision of lichen diversity in central European forests.