The relationship between productivity and multiple aspects of biodiversity in six grassland communities

Biodiversity is a multifaceted concept but most studies examining the association between the biodiversity of a community and its productivity focus only on species richness. Consequently, studies are needed to examine how other facets of biodiversity vary with productivity if we want to have a better understanding of the distribution of biodiversity across our planet. We evaluated how a number of biodiversity measures (species richness, evenness, dominance, rarity, Simpson’s diversity, and Shannon–Weiner diversity) varied across natural productivity gradients at 6 grassland sites in the continental US. Variation in productivity did not account for a substantial amount of variation in any measure of biodiversity at small spatial scales (≈1 m²) at most sites. When productivity accounted for substantial variation in biodiversity, different measures of biodiversity responded to productivity in different ways. For example, dominance changed in a U-shaped fashion along a productivity gradient whereas richness increased in an asymptotic fashion. Consequently, diversity indices, which account for both species richness and evenness, varied in a hump-shaped fashion along the productivity gradient. Our results highlight that an exclusive focus on the association between species richness and productivity provides an incomplete picture of how a community’s biodiversity is related to its functioning.     

Similarity of mammalian body size across the taxonomic hierarchy and across space and time

Although it is commonly assumed that closely related animals are similar in body size, the degree of similarity has not been examined across the taxonomic hierarchy. Moreover, little is known about the variation or consistency of body size patterns across geographic space or evolutionary time. Here, we draw from a data set of terrestrial, nonvolant mammals to quantify and compare patterns across the body size spectrum, the taxonomic hierarchy, continental space, and evolutionary time. We employ a variety of statistical techniques including "sib-sib" regression, phylogenetic autocorrelation, and nested ANOVA. We find an extremely high resemblance (heritability) of size among congeneric species for mammals over approximately 18 g; the result is consistent across the size spectrum. However, there is no significant relationship among the body sizes of congeneric species for mammals under approximately 18 g. We suspect that life-history and ecological parameters are so tightly constrained by allometry at diminutive size that animals can only adapt to novel ecological conditions by modifying body size. The overall distributions of size for each continental fauna and for the most diverse orders are quantitatively similar for North America, South America, and Africa, despite virtually no overlap in species composition. Differences in ordinal composition appear to account for quantitative differences between continents. For most mammalian orders, body size is highly conserved, although there is extensive overlap at all levels of the taxonomic hierarchy. The body size distribution for terrestrial mammals apparently was established early in the Tertiary, and it has remained remarkably constant over the past 50 Ma and across the major continents. Lineages have diversified in size to exploit environmental opportunities but only within limits set by allometric, ecological, and evolutionary constraints.     

Functional Gene Hybridization Patterns of Terrestrial Ammonia-Oxidizing Bacteria

Abstract The biochemical pathway and genetics of autotrophic ammonia oxidation have been studied almost exclusively in Nitrosomonas europaea. Terrestrial autotrophic ammonia-oxidizing bacteria (AAOs), however, comprise two distinct phylogenetic groups in the beta-Proteobacteria, the Nitrosomonas and Nitrosospira groups. Hybridization patterns were used to assess the potential of functional probes in non-PCR-based molecular analysis of natural AAO populations and their activity. The objective of this study was to obtain an overview of functional gene homologies by hybridizing probes derived from N. europaea gene sequences ranging in size from 0.45 to 4.5 kb, and labeled with 32P to Southern blots containing genomic DNA from four Nitrosospira representatives. Probes were specific for genes encoding ammonia monooxygenase (amoA and amoB), hydroxylamine oxidoreductase (hao), and cytochrome c-554 (hcy). These probes produced hybridization signals, at low stringency (30 degreesC), with DNA from each of the four representatives; signals at higher stringency (42 degreesC) were greatly reduced or absent. The hybridization signals at low stringency ranged from 20 to 76% of the total signal obtained with N. europaea DNA. These results indicate that all four functional genes in the ammonia oxidation pathway have diverged between the Nitrosomonas and Nitrosospira groups. The hao probe produced the most consistent hybridization intensities among the Nitrosospira representatives, suggesting that hao sequences would provide the best probes for non-PCR-based molecular analysis of terrestrial AAOs. Since N. europaea can also denitrify, an additional objective was to hybridize genomic DNA from AAOs with probes for Pseudomonas genes involved in denitrification. These probes were specific for genes encoding heme-type dissimilatory nitrite reductase (dNir), Cu-type dNir, and nitrous oxide reductase (nosz). No hybridization signals were observed from probes for the heme-type dNir or nosz, but Nitrosospira sp. NpAV and Nitrosolobus sp. 24-C hybridized, under low-stringency conditions, with the Cu-type dNir probe. These results indicate that AAOs may also differ in their mechanisms and capacities for denitrification.     

Phyllostomid Bats of Lowland Amazonia: Effects of Habitat Alteration on Abundance

Habitat fragmentation and conversion are among the human activities that pose the greatest threat to species persistence and conservation of biodiversity. This is particularly true in the Neotropics, where bats represent important components of biodiversity from taxonomic and functional perspectives, and provide critical ecosystem services ( e.g ., seed dispersal and pollination). We assessed the degree to which conversion of lowland Amazonian rain forest to agriculture, and its subsequent abandonment and secondary succession, affect the abundances of populations of phyllostomid bats in the vicinity of Iquitos, Perú. During 90,720 net-m-h of sampling, we captured 3789 bats of five families; of these 3764 were phyllostomids representing 44 species, 23 genera, and three feeding guilds. We focus on the 24 most abundant species of phyllostomids. In terms of abundance, frugivores dominated assemblages in all habitat types and seasons. Eight species consistently responded to habitat conversion, two species consistently responded to season, two species responded consistently to both habitat and season, and five species responded to habitat conversion in a season-specific manner. Frugivores and nectarivores were abundant in areas that had been converted to agriculture, which suggests that these bats are resilient to extant levels of disturbance and may be important in promoting secondary succession. However, this result may be scale- or context-dependent. If habitat conversion continues and dramatically reduces the areal extent and increases fragmentation of mature forest, then a complex metacommunity dynamic may characterize the region and source populations of bats may become threatened or extirpated locally.     

Matrix composition and landscape heterogeneity structure multiple dimensions of biodiversity in temperate forest birds

Quantifying how human-modified landscapes shape the distribution of biodiversity is critical for developing effective conservation strategies. To address this, we evaluated three hypotheses (habitat area, habitat configuration and matrix heterogeneity hypotheses) that predict responses of biodiversity to landscape structure in human-modified landscapes. We compared characteristics of landscape structure that influence taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions of biodiversity of breeding birds in temperate forests. Relationships between biodiversity and landscape structure were assessed at multiple spatial scales for 20 forest interior sites in northeastern USA. We assessed if relationships with landscape structure were consistent among dimensions and assemblages of different groups (residents, migrants and all birds). Relationships between dimensions of biodiversity and landscape structure were more prevalent for FD and PD than for TD. Forest amount and configuration were rarely associated with any dimensions of biodiversity. In contrast, the identity of the matrix and heterogeneity of the landscape were frequently associated with biodiversity, but relationships differed among groups of birds. For example, FD of all birds was associated positively with landscape diversity but FD of residents was associated negatively with landscape diversity, suggesting that landscape diversity surrounding forests may increase overall FD of birds but that not all groups of species respond similarly. Indeed, biodiversity of migrants was only weakly related to landscape structure. Differences among relationships to landscape structure for bird groups and spatial scales suggests that management plans should consider local decisions within a regional framework to balance potentially conflicting needs of species groups in human-dominated landscapes.     

Cross-Scale Responses of Biodiversity to Hurricane and Anthropogenic Disturbance in a Tropical Forest

Abstract In studies of biodiversity, considerations of scale—the spatial or temporal domain to which data provide inference—are important because of the non-arithmetic manner in which species richness increases with area (and total abundance) and because fine-scale mechanisms (for example, recruitment, growth, and mortality of species) can interact with broad scale patterns (for example, habitat patch configuration) to influence dynamics in space and time. The key to understanding these dynamics is to consider patterns of environmental heterogeneity, including patterns produced by natural and anthropogenic disturbance. We studied how spatial variation in three aspects of biodiversity of terrestrial gastropods (species richness, species diversity, and nestedness) on the 16-ha Luquillo Forest Dynamics Plot (LFDP) in a tropical forest of Puerto Rico was affected by disturbance caused by Hurricanes Hugo and Georges, as well as by patterns of historic land use. Hurricane-induced changes in spatial organization of species richness differed from those for species diversity. The gamma components of species richness changed after the hurricanes and were significantly different between Hurricanes Hugo and Georges. Alpha and two beta components of species richness, one related to turnover among sites within areas of similar land use and one related to variation among areas of different land use, varied randomly over time after both hurricanes. In contrast, gamma components of species diversity decreased in indistinguishable manners after both hurricanes, whereas the rates of change in the alpha component of species diversity differed between hurricanes. Beta components of diversity related to turnover among sites declined after both hurricanes in a consistent fashion. Those related to turnover among areas with different historic land uses varied stochastically. The immediate effect of hurricanes was to reduce nestedness of gastropod assemblages. Thereafter, nestedness increased during post-hurricane secondary succession, and did so in the same way, regardless of patterns of historic land use. The rates of change in degree of nestedness during secondary succession were different after each hurricane as a result of differences in the severity and extent of the hurricane-induced damage. Our analyses quantified temporal changes in the spatial organization of biodiversity of gastropod assemblages during forest recovery from hurricane-induced damage in areas that had experienced different patterns of historic human land use, and documented the dependence of biodiversity on spatial scale. We hypothesize that cross-scale interactions, likely those between the local demographics of species at the fine scale and the landscape configuration of patches at the broad scale, play a dominant role in affecting critical transfer processes, such as dispersal, and its interrelationship with aspects of biodiversity. Cross-scale interactions have significant implications for the conservation of biodiversity, as the greatest threats to biodiversity arise from habitat modification and fragmentation associated with disturbance arising from human activities.     

Does species diversity limit productivity in natural grassland communities?

Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where competitive feedbacks and complex environmental influences affect diversity–productivity relationships. In this study, we evaluated diversity–productivity relationships while statistically controlling for environmental influences in 12 natural grassland ecosystems. Because diversity–productivity relationships are conspicuously nonlinear, we developed a nonlinear structural equation modeling (SEM) methodology to separate the effects of diversity on productivity from the effects of productivity on diversity. Meta-analysis was used to summarize the SEM findings across studies. While competitive effects were readily detected, enhancement of production by diversity was not. These results suggest that the influence of small-scale diversity on productivity in mature natural systems is a weak force, both in absolute terms and relative to the effects of other controls on productivity.     

Pertinent cell population to characterize periodontal disease

The purpose of this in situ study is to quantify the inflammatory cell subsets and the area fraction (AA%) occupied by collagen fibers in human healthy and diseased (four different stages) gingival connective tissue in order to establish a possible correlation between periodontal disease resulting in collagen breakdown and specific inflammatory cell subsets.Paraffin gingival tissue sections from eight healthy controls (group 0), 10 patients with gingivitis (group 1), 10 patients with moderate periodontitis (group 2) and 10 patients with severe periodontitis (group 3) were immunohistochemically investigated using antibodies against CD-45+, CD-3+, CD-8+, CD-20+, CD-68+, and EMA+ (plasma cells).The AA% occupied by gingival collagen fibers significantly decreased from 54.12% in group (0) to 38.58% in group (1), to 31.87% in group (2), and to 25.46% in group (3). In progressive lesions of periodontal disease, CD-3+ and CD-8+ cell numbers were increased in early stages within the connective tissue, while CD-20+ cell numbers were increased only in late stages. On the other hand, EMA+, CD-68+ and CD-45+ cell numbers were progressively increased from group (0) to group (3). We demonstrated that CD-68+ monocyte/macrophages, CD-45+ leukocyte common antigen and notably EMA+ plasma cells are pertinently correlated with the severity of periodontal disease and related collagen breakdown.     

Nanoscopy of Filamentous Actin in Cortical Dendrites of a Living Mouse

We demonstrate superresolution fluorescence microscopy (nanoscopy) of protein distributions in a mammalian brain in vivo. Stimulated emission depletion microscopy reveals the morphology of the filamentous actin in dendritic spines down to 40 μm in the molecular layer of the visual cortex of an anesthetized mouse. Consecutive recordings at 43–70 nm resolution reveal dynamical changes in spine morphology.The postsynaptic part of most excitatory synapses in the brain is formed by dendritic spines, which are small protrusions along the dendrites that are highly dynamic during development, but also undergo morphological changes in adulthood (1,2). A prime candidate for regulating these dynamics is the neuronal actin network (3). Filamentous (F-) actin is also important for anchoring postsynaptic receptors and modulating synaptic activities, e.g., through the organization of the postsynaptic density (3). Clearly, the actin dynamics of dendritic spines is best studied in vivo, e.g., in a living mouse, and with confocal and multiphoton microscopy because these techniques can provide three-dimensional optical sectioning several 100 μm inside brain tissue (4). However, because necks of dendritic spines are on the 50–150-nm scale, their details are beyond the 250–400-nm resolution afforded by these diffraction-limited techniques. Fortunately, the diffraction resolution barrier of lens-based fluorescence microscopy has recently been overcome by causing the fluorophores of nearby features to emit sequentially (5). One of the techniques relying on this principle, stimulated emission depletion (STED) microscopy, has recently resolved dendritic spines in the cortex of a living mouse (6). In that initial, in vivo superresolution study, the dendrites were only volume-labeled, and consequently, the spatial arrangements of specific cytoskeletal proteins could not be imaged. On the other hand, F-actin has actually been imaged in living brain slices (7), but in vivo imaging of these structures has not yet been attained.Compared to other superresolution or nanoscopy techniques, STED microscopy bears a number of advantages for imaging spines in the living brain. Implemented as a beam scanning confocal microscope, STED nanoscopy offers optical sectioning and measurements at greater depth. In addition, motion artifacts of the dynamic structures can be minimized by fast scanning. And last but not least, STED can be performed with standard fluorescent proteins. Therefore, we here apply STED nanoscopy to noninvasively uncover the actin cytoskeleton in the living mouse brain. In particular, we show that the 43–70-nm resolution obtained by STED visualizes rearrangements of the dendritic spines in vivo.We took on the challenge of labeling the actin cytoskeleton in the living mouse cortex. We utilized Lifeact-EYFP, a fusion protein consisting of a small peptide and the yellow fluorescent protein EYFP, which directly binds to F-actin without disturbing its polymerization (8). The labeling itself was accomplished by viral infection. To this end, adeno-associated viral particles (AAV) of serotype 2, facilitated by the neuron specific human synapsin promoter hSYN (9) and Semliki Forest viruses (SFV), were created to express Lifeact-EYFP in neurons. For virus injection, the mouse was anesthetized and the head was fixed in a model No. SG-4N head holder (Narishige International USA, East Meadow, NY). A 5-mm incision of the skin of the head enabled drilling a 0.5-mm-diameter hole into the skull. The hole was positioned 0.5 mm outside the prospective imaging center in the visual cortex. The AAVs were injected with a micropipette connected to a pressure generator (Tooheyspritzer; Toohey Company, Fairfield, NJ). Thus, we were able to inject ∼750 nL of concentrated AAV at an angle of 30° over a time of ∼5 min to the layer of pyramidal cells in the prospective imaging center. After injection and 5-min pause, the pipette was retracted with a 5-min break at the half-way point to allow the virus to diffuse into the tissue. The skin was closed with three stitches and the mouse kept on a heating plate in an anesthetic recovery box until wake-up.After 10 days the mouse was prepared for in vivo STED nanoscopy, according to Berning et al. (6) (see also the Supporting Material). At this point, the skin had completely healed and the mouse showed no sign of obvious behavioral abnormality. Optical access was provided by a glass-sealed hole of ∼2 mm in diameter, exposing the visual cortex (Fig. 1 a). STED nanoscopy was performed with an upright beam-scanning microscope similar to that described by Berning et al. (6), with short optical paths and good vibration-damping (Fig. 1 b and see the Supporting Material). The coaligned excitation and STED beams were focused onto the mouse brain using a 1.3 numerical-aperture glycerol immersion lens. The correction collar of the lens allowed compensation of spherical aberrations arising from focusing beneath the brain surface (7).Open in a separate windowFigure 1STED nanoscopy of the dendritic filamentous (F-) actin cytoskeleton in the visual cortex of a living mouse. (a) Clear view of the visual cortex through an optical window. (b) Upright STED imaging of the anesthetized mouse. (c) Dendritic F-actin in the molecular layer of the visual cortex at 4, 25, and 40-μm depths. Maximum intensity projection of a stack of five (xy) images taken in 500-nm axial (z) distances. (Right) Line profile at the marked positions; average of five lines of the raw data and Lorentz fit with full width at half-maximum (FWHM); all image data are raw.Fig. 1 c shows representative parts of dendrites in the molecular layer of the visual cortex. The combination of Lifeact-EYFP labeling and superresolution displayed the dendritic actin of the living mouse neuron in unprecedented detail. Most spines have an actin-rich bulbous end, i.e., a spine head. Sometimes, the dendrite shows small areas with high actin enrichment, which presumably constitute the beginning of filopodia outgrowths (see Fig. S1 in the Supporting Material). The STED image quality was maintained down to a depth of 40 μm below the cover glass. The actin filaments in the spine neck were 43–70-nm thin (see Fig. S2), which can also be interpreted as an upper estimate (poorest value) for the resolution obtained by STED. Note that the images were not processed after recording. All dendrites appeared normal, i.e., in comparison with the morphology of volume-labeled pyramidal cells of transgenic mice (6). The STED beam average laser power was 34 mW. For somewhat greater laser power, we occasionally saw swelling of the dendrites but they were never destroyed. The maximum applicable power depends on the thickness of the dendrite and most likely on the presence of mitochondria as well.Next, we raised the expression level of Lifeact-EYFP by replacing AAV with SFV infection (7,10). We injected 750 nL of SFV (see the Supporting Material) analog to the AAV protocol and allowed the mouse to wake up and recover. After one day, we recorded in vivo STED nanoscopy images of the visual cortex. The labeling was sparser than with the AAV, i.e., fewer cells expressed Lifeact-EYFP, but the signal was brighter and highly specific to neurons. Fig. 2 shows a STED image of a part of a dendrite in the visual cortex at depth <10 μm. The actin label is brighter in the spine heads than in the body of the dendrite, showing that Lifeact-EYFP is primarily attached to F-actin. STED recording over 12 min revealed morphological changes in the actin cytoskeleton. No changes were observed after fixation (see Fig. S4). Bleaching-corrected brightness changes in the spine head inherently reflect density changes in the actin network. In contrast to AAV, SFV shuts down host cell protein synthesis, which leads to cell death after >24 h (11,12); this was not improved by the less cytotoxic SFV(PD) variant (11). Therefore, we recorded in vivo nanoscopy images one day after viral transduction where most dendrites looked healthy. To confirm the viral transduction and verify the subtype of the infected neurons, we perfused the mouse with paraformaldehyde and imaged the brain slices of the region of interest (see Fig. S5). Whereas the AAV labeled mainly neurons of the pyramidal layer, the SFV infected sparsely neurons from all layers of the cortex.Open in a separate windowFigure 2Actin rearrangement in dendritic spines at 60-nm subdiffraction spatial resolution. Image stacks reveal dynamic changes of actin in the spines. (Arrows) Shape changes of spine heads. Maximum intensity projection of five slices of 500-nm axial (z) separation; all data are raw. Average power at back-aperture of objective lens: 2.4 μW excitation and 38-mW STED.The 4–5-fold lateral resolution improvement of STED over standard confocal and multiphoton microscopy is not sufficient to resolve single actin fibers, as with platinum replica electron microscopy (13). Future refinements of both labeling and STED imaging should make this goal achievable. The resolution along the optical (z) axis was kept diffraction-limited (∼500 nm) so that the total illumination dose remained small. At depth >40 μm, scattering and aberrations compromise the image quality. Nonetheless, the molecular layer of the sensory cortex is a highly interesting target for functional optical nanoscopy, because it is the site of the first stage of cortical sensory processing.In summary, STED microscopy can be applied to study subcellular protein structures at 43–70-nm resolution down to 40 μm in the brain of a living mammal. Specifically, we showed that the dynamic actin network responsible for the morphologic plasticity in the brain can be superresolved in the living mouse. Extending in vivo STED microscopy to other protein assemblies as well as to other cell types should provide basic insights into the working principles of the brain.