Plant and soil microbial responses to defoliation in temperate semi-natural grassland

There is much interest in understanding the nature of feedback mechanisms between plants and soil organisms in grazed ecosystems. In this study, we examine the effects of different intensities of defoliation on the growth of three dominant grass species, and observe how these plant responses relate to the biomass and activity of the microbial community in the root zone. Our data show that grassland plants with varying tolerances to grazing have markedly different growth responses to defoliation, and that these responses vary with the intensity of cutting. Defoliation of grasses which are tolerant to grazing, namely Festuca rubra and Cynosurus cristatus, leads to a reduction in root mass and an increase in the allocation of resources to shoots. In contrast, defoliation of a grass with low tolerance to grazing, Anthoxanthum odoratum, had little effect on root mass, but increased the relative allocation of resources below-ground. In all plant species, defoliation led to an increase in soil microbial biomass and C use efficiency in the root zone. This response was greatest in the root zone of A. odoratum and is likely to be related to changes in root exudation pattern following defoliation. The significance of these changes in relation to soil nutrient dynamics and plant nutrient uptake during regrowth require further exploration. This revised version was published online in June 2006 with corrections to the Cover Date.     

Response of soil bacterial communities to moisture and grazing in the Tibetan alpine steppes on a small spatial scale

As the Third Pole of the world, the Tibetan Plateau provides a typical alpine grassland environment for soil bacteria with its unique frigid and arid climate. Owing to clear changes in spatial moisture and increased grazing intensity, moisture and livestock grazing have become key factors influencing the microbial communities. Accordingly, we investigated the diversity and composition of soil bacteria in a selected alpine grassland within the dual gradients of moisture and grazing using high-throughput sequencing. Our results showed that grazing changed the soil bacterial diversity and composition, whereas moisture only influenced the relative abundance of the segmental community at the small spatial scale. Species richness was found to be increased by moderate grazing compared with that by high or low-grazing intensity. The relative abundance of dominant species and β-diversity of soil bacteria both showed differences with heavy, moderate, and low grazing. Some dominant bacteria were altered with the moisture content. However, there were no significant differences according to the moisture gradient in terms of the overall bacterial β diversity and composition. These results might be taken account into the small spatial scale as well as the compensation of grazing to moisture on this scale. This work provides new insights into the soil bacterial response to moisture gradients and grazing intensity in alpine steppe habitat.     

Impact of soil warming and shading on colonization and community structure of arbuscular mycorrhizal fungi in roots of a native grassland community

Arbuscular mycorrhizal (AM) fungi have a major influence on the structure, responses and below‐ground C allocation of plant communities. Our lack of understanding of the response of AM fungi to factors such as light and temperature is an obstacle to accurate prediction of the impact of global climate change on ecosystem functioning. In order to investigate this response, we divided a grassland site into 24 plots, each either unshaded or partly shaded with soil either unheated or heated by 3°C at 2 cm depth. In both short‐term studies in spring and autumn, and in a 1‐year‐long study, we measured root length colonization (L_RC) by AM and non‐AM fungi. For selected root samples, DNA sequences were amplified by PCR with fungal‐specific primers for part of the small sub‐unit (SSU) rRNA gene. In spring, the total L_RC increased over 6 weeks from 12% to 25%. Shading significantly reduced AM but increased non‐AM fungal colonization, while soil warming had no effect. In the year‐long study, colonization by AM fungi peaked in summer, whereas non‐AM colonization peaked in autumn, when there was an additive effect of shading and soil warming that reduced AM but increased non‐AM fungi. Stepwise regression revealed that light received within the 7 days prior to sampling was the most significant factor in determining AM L_RC and that mean temperature was the most important influence on non‐AM L_RC. Loglinear analysis confirmed that there were no seasonal or treatment effects on the host plant community. Ten AM fungal sequence types were identified that clustered into two families of the Glomales, Glomaceae and Gigasporaceae. Three other sequence types were of non‐AM fungi, all Ascomycotina. AM sequence types showed seasonal variation and shading impacts: loglinear regression analysis revealed changes in the AM fungal community with time, and a reduction of one Glomus sp. under shade, which corresponded to a decrease in the abundance of Trifolium repens. We suggest that further research investigating any impacts of climate change on ecosystem functioning must not only incorporate their natural AM fungal communities but should also focus on niche separation and community dynamics of AM fungi.     

Grazing in a porous environment: 1. The effect of soil pore structure on C and N mineralization

The porous soil environment constrains grazing of microorganisms by microbivorous nematodes. In particular, at matric potentials at which water-filled pore spaces have capillary diameters less than nematode body diameters the effect of grazing, e.g. enhanced mineralization, should be reduced ('exclusion hypothesis') because nematodes cannot access their microbial forage. We examined C and N mineralization, microbial biomass C (by fumigation-extraction), the metabolic quotient (C mineralization per unit biomass C), nematode abundance, and soil water content in intact soil cores from an old field as a function of soil matric potential (−3 to −50 kPa). We expected, in accordance with the exclusion hypothesis, that nematode abundance, N and C mineralization would be reduced as matric potential decreased, i.e. as soils became drier. N mineralization was significantly greater than zero for −3 kPa but not for −10, −20 and −50 kPa. Microbial biomass C was less at −50 kPa than at −10 kPa, but not significantly different from biomass C at −3 and −20 kPa. The metabolic quotient was greatest at −50 kPa than any of the other matric potentials. From the exclusion hypothesis we expected significantly fewer nematodes to be present at −50 and −20 kPa representing water-filled capillary pore sizes less than 6 and 15 μm, respectively, than at −3 and −10 kPa. Microbivorous (fungivorous+bacterivorous) nematode abundance per unit mass of soil was not significantly different among matric potentials. Body diameters of nematodes ranged from 9 μm to 40 μm. We discuss several alternatives to the exclusion hypothesis, such as the 'enclosure hypothesis' which states that nematodes may become trapped in large water-filled pore spaces even when capillary pore diameters (as computed from matric potential) are smaller than body diameters. One of the expected outcomes of grazing in enclosures is the acceleration of nutrient cycling. This revised version was published online in June 2006 with corrections to the Cover Date.     

Mammalian seed dispersal in Cantabrian woodland pastures: Network structure and response to forest loss

We evaluated the role of wild large mammals as dispersers of fleshy-fruited woody plants in woodland pastures of the Cantabrian range (N Spain). By searching for seeds in mammal scats across four localities, we addressed how extensive seed dispersal was in relation to the fleshy-fruited plant community, and applied a network approach to identify the relative role of mammal species in the seed dispersal process. We also tested the response of mammalian dispersers to forest availability at increasing spatial scales. Five carnivores and three ungulates dispersed seeds of eight fleshy-fruited trees and shrubs. Mammalian seed dispersal did not mirror community-wide fruit availability, as abundant fruiting trees were scarce whereas thorny shrubs were over-represented among dispersed species. The dispersal network was dominated by bramble (Rubus ulmifolius/fruticosus), the remaining plants being rarer and showing more restricted disperser coteries. Fox (Vulpes vulpes), badger (Meles meles), and wild boar (Sus scrofa) dispersed mostly bramble, whereas martens (Martes sp.) dispersed mostly wild rose (Rosa sp.). Ungulates occasionally dispersed holly (Ilex aquifolium) and hawthorn (Crataegus monogyna). The empirical network reflected a skewed distribution of interactions and some functional complementarity (as judged from the low levels of connectance and nestedness), but also some degree of specialization. Mammals overused uncovered microsites for seed deposition, and increased their disperser activity in those landscape sectors devoid of forest. Combined with previous findings on avian seed dispersal, this study suggest a strong functional complementarity coming from the low overlap in the main plant types that mammals and birds disperse – thorny shrubs and trees, respectively – and the differential patterns of seed deposition, with mammals mostly dispersing into deforested areas, and birds into forest-rich landscapes.     

AusRivAS: using macroinvertebrates to assess ecological condition of rivers in Western Australia

1. AusRivAS (Australian River Assessment Scheme) models were developed, using macroinvertebrates as indicators, to assess the ecological condition of rivers in Western Australia as part of an Australia-wide program. The models were based on data from 188 minimally disturbed reference sites and are similar to RIVPACS models used in Britain. The major habitats in the rivers (macrophyte, channel) were sampled separately and macroinvertebrates collected were identified to family level. 2. Laboratory sorting of preserved macroinvertebrate samples recovered about 90% of families present when 150 animals were collected, whereas live picking in the field recovered only 76%. 3. Reference sites clustered into five groups on the basis of macroinvertebrate families present. Using seven physical variables, a discriminant function allocated 73% of sites to the correct classification group. A discriminant function based on seven physical and two chemical variables allocated 81% of sites to the correct group. However, when the same reference sites were re-sampled the following year, the nine variable discriminant function misallocated more sites than the seven variable function, owing to annual fluctuations in water chemistry that were not accompanied by changes in fauna. 4. In preliminary testing, the wet season channel model correctly assessed 80% of reference sites as undisturbed in the year subsequent to model building (10% of sites were expected to rate as disturbed because the 10th percentile was used as the threshold for disturbance). Nine sites from an independent data set, all thought to be disturbed, were assessed as such by the model. Results from twenty test sites, chosen because they represented a wide range of ecological condition, were less clear-cut. In its current state the model reliably distinguishes undisturbed and severely disturbed sites. Subtle impacts are either detected inconsistently or do not affect ecological condition.     

Long-term Perspectives on Lagged Ecosystem Responses to Climate Change: Permafrost in Boreal Peatlands and the Grassland/Woodland Boundary

Changes in climate could have far-reaching consequences for ecosystems sensitive to changes in temperature and precipitation, such as boreal permafrost peatlands and grassland/woodland boundaries. The long-term data from our studies in these ecosystems suggest that transient responses of permafrost and vegetation to climate change may be difficult to predict due to lags and positive feedbacks related to vegetation and disturbance. Boreal permafrost peatlands comprise an ecosystem with strong local controls on microclimate that influence the formation and thaw of permafrost. These local controls may preserve permafrost during the transient stages of climate warming, producing lagged responses. The prairie–forest border region of the northern Great Plains has experienced frequent change and has complex dynamics involving transitions in the grassland composition of prairie and in the degree of woodiness in bordering forests. Fire frequency interacts with fuel loading and tree recruitment in ways that affect the timing and direction of change. Lags and thresholds could lead to sudden large responses to future climate change that are not readily apparent from current vegetation. The creation of adequate models to characterize transient ecosystem changes will require an understanding of the linkages among processes operating at the scale of 10s of meters and over long time periods. Received 14 December 1999; accepted 7 July 2000.     

Variations in the microalgal structure in paddy soil in Osaka, Japan: comparison between surface and subsurface soils

Seasonal variations in microalgal communities were compared between surface and subsurface paddy soils in Osaka, Japan. Soil samples were collected from depths of 0–1 (surface), 8–9, and 17–18 cm. Diatom cells were counted directly, and the numbers of other microalgae were estimated using a culture method. The microalgal community as well as the soil properties changed drastically in the surface soil as a consequence of alternate flooding and drainage. In the soil collected at a depth of 0–1 cm, the cell density of diatoms and the viable count of other microalgae markedly increased, and Chlorella spp., Nitzschia spp., and Navicula spp. were predominant during the flooding period, whereas Scenedesmus spp. and Hantzschia spp. were predominant during the drainage period. In contrast, in the soils collected at depths of 8–9 and 17–18 cm, the cell density of diatoms and the viable count of other microalgae remained constant. Despite the unavailability of light, a large number of microalgae were present in these subsurface soils throughout the annual cultivation cycle, and Scenedesmus spp. and Nitzschia spp. were always dominant. Cyanophytes were also present at all the depths but had low relative frequencies. These results suggest that the algae that are predominant in paddy soil can survive not only drastic changes in water content but also complete darkness.     

Response of grassland soil arthropod community to biological and conventional control of a native moth: using Beauveria bassiana and lambda-cyhalothrin for Dalaca pallens (Lepidoptera: Hepialidae) suppression

Conventional and biological control of a native moth, Dalaca pallens (Blanchard) (Lepidoptera: Hepialidae), were evaluated in Southern Chile in relation to changes on community metrics (diversity, species richness, evenness and dominance) of a soil-dwelling invertebrate assemblage. Two experiments were conducted (in winter and spring) to compare non-target effects of Beauveria bassiana (Balsamo) Vuillemin and lambda-cyhalothrin insecticide. The invertebrate community was sampled before and after spraying by extracting soil cores. Estimates of diversity (Shannon index), species richness, evenness (Hurlbert’s Probability of Interspecific Encounter) and dominance indicated that the invertebrate assemblage was strongly disturbed by lambda-cyhalothrin treatment but not by B. bassiana applied in winter, over the sampling period (40 days). Spring results revealed that diversity and evenness at control and at B. bassiana plots were similar between them and higher than at lambda-cyhalothrin plots, while there were no differences between sites 30 days after treatment in species richness. Inundative biological control using B. bassiana strain QU-B931 was considered to pose lower ecological risk than lambda-cyhalothrin, currently one of the most frequently used insecticides for D. pallens control.     

Ecological biogeography of North American mammals: species density and ecological structure in relation to environmental gradients

Aim To evaluate the relationship of climate and physiography to species density and ecological diversity of North American mammals. Location North America, including Mexico and Central America. Methods Species density, size structure and trophic structure of mammalian faunas and nine environmental variables were documented for quadrats covering the entire continent. Spatial autocorrelation of species density and the environmental variables illustrated differences in their spatial structure at the continental scale. We used principal component analysis to reduce the dimensionality of the climatic variables, linear multiple regression to determine which environmental variables best predict species density for the continent and several regions of the continent, and canonical ordination to evaluate how well the environmental variables predict ecological structure of mammalian faunas over North America. Results In the best regression model, five environmental variables, representing seasonal extremes of temperature, annual energy and moisture, and elevation, predicted 88% of the variation in species density for the whole continent. Among different regions of North America, the environmental variables that predicted species density vary. Changes in the size and trophic structure of mammalian faunas accompany changes in species density. Redundancy analysis demonstrated that environmental variables representing winter temperature, frostfree period, potential and actual evapotranspiration, and elevation account for 77% of the variation in ecological structure. Main conclusions The latitudinal gradient in mammalian species density is strong, but most of it is explained by variation in the environmental variables. Each ecological category peaks in species richness under particular environmental conditions. The changes of greatest magnitude involve the smallest size categories (< 10 g, 11–100 g), aerial insectivores and frugivores. Species in these categories, mostly bats, increase along a gradient of decreasing winter temperature and increasing annual moisture and frostfree period, trends correlated with latitude. At the opposite end of this gradient, species in the largest size category (101–1000 kg) increase in frequency. Species in size categories 3 (101–1000 g), 5 (11–100 kg) and 6 (101–1000 kg), herbivores, and granivores increase along a longitudinal gradient of increasing annual potential evapotranspiration and elevation. Much of the spatial pattern is consistent with ecological sorting of species ranges along environmental gradients, but differential rates of speciation and extinction also may have shaped the ecological diversity of extant North American mammals.     

Carbon flow in an upland grassland: effect of liming on the flux of recently photosynthesized carbon to rhizosphere soil

The effect of liming on the flow of recently photosynthesized carbon to rhizosphere soil was studied using ¹³CO₂ pulse labelling, in an upland grassland ecosystem in Scotland. The use of ¹³C enabled detection, in the field, of the effect of a 4‐year liming period of selected soil plots on C allocation from plant biomass to soil, in comparison with unlimed plots. Photosynthetic rates and carbon turnover were higher in plants grown in limed soils than in those from unlimed plots. Higher δ¹³C‰ values were detected in shoots from limed plants than in those from unlimed plants in samples clipped within 15 days of the end of pulse labelling. Analysis of the aboveground plant production corresponding to the 4‐year period of liming indicated that the standing biomass was higher in plots that received lime. Lower δ¹³C‰ values in limed roots compared with unlimed roots were found, whereas no significant difference was detected between soil samples. Extrapolation of our results indicated that more C has been lost through the soil than has been gained via photosynthetic assimilation because of pasture liming in Scotland during the period 1990–1998. However, the uncertainty associated with such extrapolation based on this single study is high and these estimates are provided only to set our findings in the broader context of national soil carbon emissions.     

Understanding the contribution of native tracheobronchial structure to lung function: CT assessment of airway morphology in never smokers

Background

Computed tomographic (CT) airway lumen narrowing is associated with lower lung function. Although volumetric CT measures of airways (wall volume [WV] and lumen volume [LV]) compared to cross sectional measures can more accurately reflect bronchial morphology, data of their use in never smokers is scarce. We hypothesize that native tracheobronchial tree morphology as assessed by volumetric CT metrics play a significant role in determining lung function in normal subjects. We aimed to assess the relationships between airway size, the projected branching generation number (BGN) to reach airways of <2mm lumen diameter –the site for airflow obstruction in smokers- and measures of lung function including forced expiratory volume in 1 second (FEV₁) and forced expiratory flow between 25% and 75% of vital capacity (FEF 25–75).

Methods

We assessed WV and LV of segmental and subsegmental airways from six bronchial paths as well as lung volume on CT scans from 106 never smokers. We calculated the lumen area ratio of the subsegmental to segmental airways and estimated the projected BGN to reach a <2mm-lumen-diameter airway assuming a dichotomized tracheobronchial tree model. Regression analysis was used to assess the relationships between airway size, BGN, FEF 25–75, and FEV₁.

Results

We found that in models adjusted for demographics, LV and WV of segmental and subsegmental airways were directly related to FEV₁ (P <0.05 for all the models). In adjusted models for age, sex, race, LV and lung volume or height, the projected BGN was directly associated with FEF 25–75 and FEV₁ (P = 0.001) where subjects with lower FEV₁ had fewer calculated branch generations between the subsegmental bronchus and small airways. There was no association between airway lumen area ratio and lung volume.

Conclusion

We conclude that in never smokers, those with smaller central airways had lower airflow and those with lower airflow had less parallel airway pathways independent of lung size. These findings suggest that variability in the structure of the tracheobronchial tree may influence the risk of developing clinically relevant smoking related airway obstruction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0181-y) contains supplementary material, which is available to authorized users.     

Protein cell surface display in Gram-positive bacteria: from single protein to macromolecular protein structure

In the course of evolution, Gram-positive bacteria, defined here as prokaryotes from the domain Bacteria with a cell envelope composed of one biological membrane (monodermita) and a cell wall composed at least of peptidoglycan and covalently linked teichoic acids, have developed several mechanisms permitting to a cytoplasmic synthesized protein to be present on the bacterial cell surface. Four major types of cell surface displayed proteins are currently recognized: (i) transmembrane proteins, (ii) lipoproteins, (iii) LPXTG-like proteins and (iv) cell wall binding proteins. The subset of proteins exposed on the bacterial cell surface, and thus interacting with extracellular milieu, constitutes the surfaceome. Here, we review exhaustively the current molecular mechanisms involved in protein attachment within the cell envelope of Gram-positive bacteria, from single protein to macromolecular protein structure.