How do earthworms affect microfloral and faunal community diversity?

Much of the work regarding earthworm effects on other organisms has focused on the functional significance of microbial-earthworm interactions, and little is known on the effects of earthworms on microfloral and faunal diversity. Earthworms can affect soil microflora and fauna populations directly and indirectly by three main mechanisms: (1) comminution, burrowing and casting; (2) grazing; (3) dispersal. These activities change the soil's physico-chemical and biological status and may cause drastic shifts in the density, diversity, structure and activity of microbial and faunal communities within the drilosphere. Certain organisms and species may be enhanced, reduced or not be affected at all depending on their ability to adapt to the particular conditions of different earthworm drilospheres. A large host of factors (including CaCO₃, enzymes, mucus and antimicrobial substances) influence the ability of preferentially or randomly ingested organisms to survive (or not) passage through the earthworm gut, and their resultant capacity to recover and proliferate (or not) in earthworm casts. Small organisms, particularly microflora and microfauna, with limited ability to move within the soil, may benefit from the (comparatively) long ranging movements of earthworms. Microflora and smaller fauna appear to be particularly sensitive to earthworm activities, and priming effects enhancing nutrient release, particularly in casts, are common. Larger fauna such as microarthropods, enchytraeids and Isopods may be enhanced under some conditions (e.g., in earthworm middens), but in other cases earthworm activity may lead to a decrease in their populations due to competition for food (microbes and organic materials), and spatial and temporal changes in food abundance. Nevertheless, considering the presently available data, the beneficial interactions of earthworms and microflora and fauna appear to far outweigh the potential negative effects. However, much is still unknown regarding the interactions of earthworms of different ecological categories on the diversity and function of microfloral and faunal communities, and much more interdisciplinary research is needed to assess the potential role of earthworms in regulating the diversity of microflora and fauna in soil systems and the potentially beneficial or harmful effects this regulation may have on ecosystem function and plant growth in different ecosystems.     

How do organic solvents affect peroxidase structure and function?

The effect of organic solvents on horseradish peroxidase structure and function has been studied. Some, but not complete, enzyme denaturation occurs even in low volumes of water-miscible organic solvents (e.g., greater than 30% v/v dioxane, greater than 50% v/v methanol, and greater than 20% v/v acetonitrile) as determined by the decreased difference between the fluorescence of peroxidase's sole tryptophan residue and free L-tryptophan in solution. Absorbance and electron paramagnetic resonance spectroscopies indicate exposure of peroxidase's active site to the organic solvent. This reduces the local polarity in the enzyme's active site and results in stronger hydrogen bonding of phenolic substrates to the enzyme. In extreme cases (e.g., 95% v/v dioxane, 90% v/v acetonitrile, and ethyl and butyl acetate containing 2 and 1% v/v aqueous buffer, respectively), the transition state of the enzymic reaction is sufficiently perturbed so as to alter the magnitude of the Hammett rho value. This is most likely the result of the increased strength of hydrogen bonding between electron-donating alkoxyphenols (negative sigma values) and an electrophilic group in the enzyme's active site, thereby reducing catalytic efficiencies for such substrates relative to alkyl- and chlorophenols. Perhaps the most important effect of the organic solvent, however, is the significant ground-state stabilization of phenolic substrates in organic media as opposed to aqueous buffer. This stabilization can account for nearly 4 orders of magnitude in reduction of catalytic efficiency and is manifested in increased Km's. This study indicates that enzymes can maintain much of their native active-site structure in organic media and that the effect of solvent on substrate thermodynamics must be considered.     

How do plants feel the heat?

In plants, the heat stress response (HSR) is highly conserved and involves multiple pathways, regulatory networks and cellular compartments. At least four putative sensors have recently been proposed to trigger the HSR. They include a plasma membrane channel that initiates an inward calcium flux, a histone sensor in the nucleus, and two unfolded protein sensors in the endoplasmic reticulum and the cytosol. Each of these putative sensors is thought to activate a similar set of HSR genes leading to enhanced thermotolerance, but the relationship between the different pathways and their hierarchical order is unclear. In this review, we explore the possible involvement of different thermosensors in the plant response to warming and heat stress.     

A tale of two centromeres—diversity of structure but conservation of function in plants and animals

The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.     

How do plants make mitochondria?

Plant mitochondria can differ in size, shape, number and protein content across different tissue types and over development. These differences are a result of signaling and regulatory processes that ensure mitochondrial function is tuned in a cell-specific manner to support proper plant growth and development. In the last decade, the processes involved in mitochondrial biogenesis are becoming clearer, including; how dormant seeds transition from empty promitochondria to fully functional mitochondria with extensive cristae structures and various biochemical activities, the regulation of nuclear genes encoding mitochondrial proteins via regulators of the diurnal cycle in plants, the mitochondrial stress response, the targeting of proteins to mitochondria and other organelles and connections between the respiratory chain and protein import complexes. All these findings indicate that mitochondrial function is a part of an integrated cellular network, and communication between mitochondria and other cellular processes extends beyond the known exchange or transport of metabolites. Our current knowledge now needs to be used to gain more insight into the molecular components at various levels of this hierarchical and complex regulatory and communication network, so that mitochondrial function can be predicted and modified in a rational manner.     

How do biomolecular systems speed up and regulate rates?

The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.     

Diversity of arbuscular mycorrhizal fungi in the rhizosphere of three host plants in the farming–pastoral zone, north China

The spatial diversity and distribution of AM fungi were investigated in three plots located in farming–pastoral zone, north China. The rhizospheres of Caragana korshinskii, Artemisia sphaerocephala and Salix psammophila were sampled and thirty AM fungal species belonging to five genera were isolated. The study demonstrated that AM fungal diversity and distribution differed significantly among the three host plants and the three studied plots. Spore density of AM fungi ranged between 2 and 22 spores per g^?1 of soil and species richness between 8 and 23. Correlation coefficient analysis demonstrated that spore density was significantly and positively correlated with soil organic matter and available N (P?<?0.01). Species richness was significantly and positively correlated with soil organic matter and available P (P?<?0.01), but significantly and negatively correlated with soil pH (P?<?0.01). Finally, the Shannon–Weiner index was significantly and positively correlated with soil organic matter (P?<?0.05). In this farming–pastoral zone, Glomus reticulatum and G.melanosporum may be more adaptable to the arid conditions than other AM fungal species. This research into AM fungal diversity may lead to exploitation of AM fungi for the mitigation of soil erosion and desertification using mycorrhizal plants, such as C.korshinskii, A.sphaerocephala and S. psammophila. The results of this study support the conclusion that diversity and distribution of AM fungi might be useful to monitor desertification and soil degradation.     

How do Abl family kinases regulate cell shape and movement?

Genetic analysis and studies of normal and leukemia cells in culture have shown that Abl family nonreceptor tyrosine kinases regulate cell morphogenesis and motility. Abl family kinases, which include Drosophila (D-) Abl and the vertebrate Abl and Arg proteins, relay signals from cell surface growth-factor and adhesion receptors to promote cytoskeletal rearrangements. Recent biochemical and crystallographic analyses have clarified the mechanisms by which growth-factor and adhesion receptors might regulate the activity of Abl family kinases. When activated, Abl family kinases can regulate cytoskeletal dynamics by phosphorylating several known cytoskeletal regulatory proteins. In addition, the C-terminal half of Abl family kinases has several domains that bind to cytoskeletal components. Emerging evidence suggests that Abl family kinases can use these domains to directly organize cytoskeletal structure in vivo.     

How past and present influence the foraging of clonal plants?

Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.     

When do arbuscular mycorrhizal fungi protect plant roots from pathogens?

Arbuscular mycorrhizal (AM) fungi are mainly thought to facilitate phosphorus uptake in plants, but they can also perform several other functions that are equally beneficial. Our recent study sheds light on the factors determining one such function, enhanced plant protection from root pathogens. Root infection by the fungal pathogen Fusarium oxysporum was determined by both plant susceptibility and the ability of an AM fungal partner to suppress the pathogen. The non-susceptible plant species (Allium cepa) had limited F. oxysporum infection even without AM fungi. In contrast, the susceptible plant species (Setaria glauca) was heavily infected and only AM fungi in the family Glomeraceae limited pathogen abundance. Plant susceptibility to pathogens was likely determined by contrasting root architectures between plants, with the simple rooted plant (A. cepa) presenting fewer sites for infection. AM fungal colonization, however, was not limited in the same way in part because plants with fewer, simple roots are more mycorrhizal dependent. Protection only by Glomus species also indicates that whatever the mechanism(s) of this function, it responds to AM fungal families differently. While poor at pathogen protection, AM fungal species in the family Gigasporaceae most benefited the growth of the simple rooted plant species. Our research indicates that plant trait differences, such as root architecture can determine how important each mycorrhizal function is to plant growth but the ability to provide these functions differs among AM fungi.Key words: arbuscular mycorrhizal fungi, Fusarium oxysporum, root architecture, pathogen protection, multi-functionalityArbuscular mycorrhizas (AM) represent the oldest and most widespread symbiosis with land plants.¹ Most mycorrhizal research has focused on the ability of AM fungi to facilitate nutrient uptake, particularly phosphorus.² Although researchers recognize that AM fungi are multi-functional,³ it is not clear what factors determine which function an AM fungus performs or its relative importance to the plant.⁴ Newsham et al. (1995)³ hypothesized that AM function is based on root architecture: plants with simple rooting systems are dependent on mycorrhizas for nutrient uptake, while those with complex root systems are less dependent on mycorrhizas for nutrient uptake, but are more susceptible to root pathogens because of increased numbers of infections sites.³ These two functions, phosphorus uptake and enhanced pathogen protection from mycorrhizas also depend on the identity of the fungus. Arbuscular mycorrhizal fungi in the family Gigasporaceae are more effective at enhancing plant phosphorus, while AM fungi in the Glomeraceae better protect plants from root pathogens.⁵Our results support both plant and fungal control of a common pathogen, Fusarium oxysporum, and the interaction between these two factors ultimately determined the level of pathogen infection and plant mycorrhizal benefit. We inoculated two plant species that have contrasting root architectures with one of six AM fungal species from two families (or no AM fungi). After five months of growth, plants were inoculated with F. oxysporum, grown for another month and then harvested. All plant seeds and fungi were collected in a local old field community.⁶ Allium cepa (garden onion) was not susceptible to F. oxysporum likely because it has only a few adventitious roots below the main bulb that do not present many sites for infection. In contrast, Setaria glauca (yellow foxtail) was heavily infected by F. oxysporum and has fine roots with increased numbers of branching points and lateral meristems where fungi can colonize.⁷ For the susceptible plant (S. glauca), AM fungal species from the family Glomeraceae were effective at reducing pathogen abundance while species from the Gigasporaceae were not. Forming a symbiosis with a Glomus species resulted in S. glauca plants that were as large as control plants. AM fungal species from the family Gigaspoaceae were more beneficial to growth of the simple rooted A. cepa, which had fewer roots to take up soil nutrients.Reduced rooting structures may limit pathogen infection sites, but AM fungal colonization was not limited in the same way and may actually alter plant root architecture. While the simple rooted A. cepa had limited pathogen susceptibility, it had twice the AM fungal colonization of the complex rooted S. glauca. Because the simple rooted plant has a greater dependence on mycorrhizas,⁸ it likely transmits chemical signals to rapidly initiate mycorrhizal formation,⁹ but then may have less control on the spread of AM fungi within the root. In contrast, S. glauca is more susceptible to fungal pathogens and may be less mycorrhizal dependent in nature.¹⁰ As a result, S. glauca may treat all colonizing root fungi as potential parasites. Colonization by AM fungi from the Glomeraceae was also much greater than those in the Gigasporaceae due to differences in fungal life history strategy between these families.^11,12 AM fungal colonization can reduce root branching in plants and alter plant allocation to roots, thereby increasing mycorrhizal dependence for nutrients^10,13 and potentially reducing pathogen infection sites. Mycorrhizal induced changes to plant root architecture may therefore reinforce current mycorrhizal associations and alter future fungal colonization attempts.¹⁴ An important next step is to test if AM fungal families (or species) alter plant root architecture in different ways and the degree to which these effects depend on colonization timing and the plant host.Our study did not isolate the particular mechanism by which AM fungi control pathogens, but this mechanism clearly differentiates between AM fungal families. AM fungi can control pathogens through several mechanisms including direct competition for colonization sites, indirect initiation of plant defensive responses or altering other rhizosphere biota.¹⁵ Although these AM fungal families differ in the intensity of root colonization,¹¹ percentage of root length colonized by an AM fungus is a poor predictor of pathogen limitation compared to family identity,^12,16 suggesting that direct competition for space is unlikely. AM fungi share many cell surface molecules with pathogenic fungi like Fusarium.¹⁷ These molecules can act as signals that initiate plant production of defensive compounds such as phytoalexins, phenolics and other compounds.¹⁸ While AM fungi appear to evade these defenses, only AM fungal species in the family Glomeraceae would have elicited plant responses which altered future infection by F. oxysporum. AM fungi in the Gigasporaceae may differ more from F. oxysporum in their chemical signals or not colonize roots sufficiently to induce a sustained, system-wide plant response. In addition, many rhizosphere related microbes are antagonistic to pathogenic fungi¹⁵ and may differ in their response to the different AM fungal families.¹⁹ Because rhizosphere microbes also differ among plant species, plant pathogen protection may be influenced by multiple ecological interactions that determine the specific cases when mycorrhizal pathogen protection occurs. To distinguish between these mechanisms, future experiments could test whether biochemical similarity or ecological similarity (especially with other soil biota) between an AM fungus and fungal pathogen can predict mycorrhizal induced pathogen protection.Plant and fungal identity clearly affect AM fungal function and benefit, but to accurately use AM fungi in agriculture and restoration^20,21 we must clearly understand how functional mechanisms differ. Different mycorrhizal functions may be based on common plant traits like root architecture, but ecology, colonization timing and environment may alter the specific function AM fungi provide and its importance to plants. While it may be useful to establish greenhouse rules about which fungal species perform specific mycorrhizal functions, predicting their role in more complex systems relies on understanding if other factors will enhance or negate these effects. Most AM fungal species vary in their ability to perform each function and these can be locally adapted to limiting soil nutrients.²² In plants, there is also a range to which specific mycorrhizal functions may benefit plant fitness, and these responses are based on both plant traits (which change throughout a plant''s life cycle) and the local environment.^23,24 Given this variation, it is critical to understand if AM fungi can respond to cues from the plant or the environment to identify what factors limit plant growth and whether a the most effective AM fungus shows a greater response.     

How do bryophytes govern generative recruitment of vascular plants?

Interactions between vascular plants and bryophytes determine plant community composition in many ecosystems. Yet, little is known about the importance of interspecific differences between bryophytes with respect to their effects on vascular plants. We compared the extent to which species-specific bryophyte effects on vascular plant generative recruitment depend on the following underlying mechanisms: allelopathy, mechanical obstruction, soil moisture and temperature control. We sowed 10 vascular plant species into monospecific mats of six chemically and structurally diverse bryophytes, and examined 1-yr seedling recruitment. Allelopathic effects were also assessed in a laboratory phyto-assay. Although all bryophytes suppressed vascular plant regeneration, there were significant differences between the bryophyte species. The lack of interactions indicated the absence of species-specific adaptations of vascular plants for recruitment in bryophyte mats. Differences between bryophyte species were best explained by alterations in temperature regime under bryophyte mats, mostly by reduced temperature amplitudes during germination. The temperature regime under bryophyte mats was well predicted by species-specific bryophyte cushion thickness. The fitness of established seedlings was not affected by the presence of bryophytes. Our results suggest that climatically or anthropogenically driven changes in the species' composition of bryophyte communities have knock-on effects on vascular plant populations via generative reproduction.     

Redundant or complementary? Impact of a colonizing species on community structure and function

Recent studies suggest that species with similar functional traits will have similar effects on ecosystems, but evidence for redundancy of species impacts is limited. Here we use a long‐term experiment to gain insight into functional relationships within a desert rodent community. Experimental removal of kangaroo rats, Dipodomys spp., coupled with the recent, serendipitous colonization of a single species of large pocket mouse Chaetodipus baileyi yielded treatments that differed in the diversity of large granivorous rodents present. We evaluated functional overlap of C. baileyi and the other resident large granivores (i.e. the kangaroo rats) by comparing total energy use of granivorous rodents and total abundance and species richness of small granivores across treatments before and after the arrival of C. baileyi. We found that C. baileyi almost completely compensated for the changes in these key ecosystem‐level properties caused by kangaroo rat removal, but it differentially impacted the population dynamics of individual small granivorous rodent species. Thus, its effects were largely complementary, rather than redundant, to those of the missing kangaroo rats. Although short‐term or single‐measure analyses may suggest redundancy, our results support the longstanding dictum that niches of coexisting species are often similar but rarely, if ever, identical.     

How do cell walls regulate plant growth?

The cell wall of growing plant tissues has frequently been interpreted in terms of inextensible cellulose microfibrils 'tethered' by hemicellulose polymers attached to the microfibril surface by hydrogen bonds, with growth occurring when tethers are broken or 'peeled' off the microfibril surface by expansins. This has sometimes been described as the 'sticky network' model. In this paper, a number of theoretical difficulties with this model, and discrepancies between predicted behaviour and observations by a number of researchers, are noted. (i) Predictions of cell wall moduli, based upon the sticky network model, suggest that the cell wall should be much weaker than is observed. (ii) The maximum hydrogen bond energy between tethers and microfibrils is less than the work done in expansion and therefore breakage of such hydrogen bonds is unlikely to limit growth. (iii) Composites of bacterial cellulose with xyloglucan are weaker than pellicles of pure cellulose so that it seems unlikely that hemicelluloses bind the microfibrils together. (iv) Calcium chelators promote creep of plant material in a similar way to expansins. (v) Reduced relative 'permittivities' inhibit the contraction of cell wall material when an applied stress is decreased. Revisions of the sticky network model that might address these issues are considered, as are alternatives including a model of cell wall biophysics in which cell wall polymers act as 'scaffolds' to regulate the space available for microfibril movement. Experiments that support the latter hypothesis, by demonstrating that reducing cell wall free volume decreases extensibility, are briefly described.