Quantifying individual‐ and community‐level effects of competition using experimentally‐determined null species pools

Abstract. The effects of competition on individual fitness and species diversity were investigated in a first‐year old field by comparing the natural community to an experimentally‐determined null community. The species pool for the null community was estimated from low‐density plots, and hypothetical sample plots in the null community were constructed by random sampling from the species pool. Individual plants were larger in low‐density plots than control plots, indicating that competition reduced individual fitness. Competition appeared to reduce diversity in half the plots (i.e. species richness and diversity were lower than in hypothetical null community plots with the same number of individuals), but did not affect diversity in the other plots. However, the reduction in diversity could be explained as an artifact caused by spatial aggregation in control plots. The magnitude of the effects of competition on diversity did not change with plot density, and no species consistently increased or decreased in relative abundance as plot density increased. We conclude that competition had no effect on diversity in this community, despite the strong effect on individual growth.     

Scale‐dependent biases in species counts in a grassland

Abstract. Numbers of plant species were recorded in species‐rich meadows in the Bílé Karpaty Mts., SE Czech Republic, with the aim to evaluate the sampling error made by well‐trained observers. Five observers recorded vascular plants in seven plots ranging from 9.8 cm² to 4 m² independently and were not time‐limited. In larger plots a discrepancy of 10–20% was found between individual estimates, in smaller plots discrepancy increased to 33%, on average. The gain in observed species richness by combining records of individual observers (in comparison with the mean numbers estimated by single observers) decreased from the smallest plot (27–82% for two to five observers) to the largest one (13–25%). However, after misidentified and suspicious records were eliminated, the gain was much lower and became scale‐independent; two observers added 12% species, on average, and the increase by combining species lists made by three or more observers was negligible (3% more on average). It is concluded that most discrepancies between individual observers were caused by misidentification of rare seedlings and young plants. We suggest that in species‐rich meadows plants should be recorded by at least three observers together and that they should consult all problematic plant specimens together in the field, to minimize errors.     

Long‐term seed bank dynamics in a temperate forest under conversion from coppice‐with‐standards to high forest management

Questions: How do changes in forest management, i.e. in disturbance type and frequency, influence species diversity, abundance and composition of the seed bank? How does the relationship between seed bank and vegetation change? What are the implications for seed bank dynamics? Location: An ancient Quercus petraea — Carpinus betulus forest in conversion from coppice‐with‐standards to regular Quercus high forest near Montargis, France. Methods: Seed bank and vegetation were sampled in six replicated stand types, forming a chronosequence along the conversion pathway. The stand types represented mid‐successional stages of stands in transition from coppice‐with‐standards (to high forest (16 plots) and early‐ and mid‐successional high forest stands (32 plots). Results: Seed bank density and species richness decreased with time since last disturbance. Adjusting for seed density effects obscured species richness differences between stand types, but species of later seres were nested subsets of earlier seres, implying concomitant shifts in species richness and composition with time since disturbance. Later seres were characterized by species with low seed weight and high seed longevity. Seed banks of early seres were more similar to vegetation than to later seres. Conclusions: Abandonment of the coppice‐with‐standards regime altered the seed bank characteristics, as well as its relationship with vegetation. Longer management cycles under high forest yield impoverished seed banks. For their persistence, seed bank species will increasingly rely on management of permanently open areas in the forest landscape. Thus, revegetation at the beginning of new high‐forest cycles may increasingly depend on inflow from seed sources.     

MALDI‐TOF‐MS‐based species identification and typing approaches in medical mycology

MALDI‐TOF MS‐based species identification has found its place in many clinical routine diagnostic laboratories over the past years. Several well‐established commercial systems exist and these allow precise analyses not only among bacteria, but also among clinically important yeasts. This methodology shows higher precision than biochemical and microscopic methods at significantly reduced turnaround times. Furthermore, the differentiation of different filamentous fungi including most dermatophytes and zygomycetes has been established. The direct identification of yeasts from blood culture bottles will be possible in a routine fashion with new standardized procedures. In addition to species identification, the MALDI‐TOF MS technology offers several further possibilities, like assays to detect or predict resistance phenotypes in fungi as well as subtyping approaches to detect clinically relevant subgroups. The differences between the commercial systems are discussed with respect to fungi and an overview of their performances provided. Factors influencing outcome of MALDI‐TOF‐based species identification are discussed.     

Multi‐scale responses of plant species diversity in semi‐natural buffer strips to agricultural landscapes

Question: How does agricultural land usage affect plant species diversity in semi‐natural buffer strips at multiple scales? Location: Lepsämä River watershed, Nurmijärvi, Southern Finland. Methods: Species diversity indicators included both richness and evenness. Plant communities in buffer strips were surveyed in 29 sampling sites. Using ArcGIS Desktop 9.0 (ArcInfo) and Fragstats 3.3 for GIS analysis, the landscape composition around each sampling site was characterized by seven parameters in square sectors at five scales: 4, 36, 100, 196, and 324ha. For each scale, Principle Component Analysis was used to examine the importance of each structural metric to diversity indicators using multiple regression and other simple analyses. Results: For all but the smallest scales (4 ha), two structural metrics including the diversity of land cover types and percentage of arable land were positively and negatively correlated with species richness, respectively. Both metrics had the highest correlation coefficients for species richness at the second largest scale (196 ha). The density of arable field edges between the fields was the only metric that correlated with species evenness for all scales, which had highest predictive power at the second smallest scale (36 ha). Conclusions: Species richness and evenness of buffer strips had scale‐dependent relationships to land use in agricultural ecosystems. The results of this study indicated that species richness depends on the pattern of arable land use at large scales, which may relate to the regional species pool. Meanwhile, species evenness depended on the level of field edge density at small scales, which relates to how the nearby farmland was divided by the edges (e.g. many small‐scale fields with high edge density or a few big‐scale fields with low edge density). This implies that it is important to manage the biodiversity of buffer strips within a landscape context at multiple scales.     

Long‐term post‐fire changes in the northeastern boreal forest of Quebec

Abstract. Natural dynamics in the boreal forest is influenced by disturbances. Fire recurrence affects community development and landscape diversity. Forest development was studied in the northeastern boreal forest of Quebec. The objective was to describe succession following fire and to assess the factors related to the changes in forest composition and structure. The study area is located in northeastern Quebec, 50 km north of Baie‐Comeau. We used the forest inventory data gathered by the Ministère des Ressources naturelles du Québec (MRNQ). In circular plots of 400 m², the diameter at breast height (DBH) of all stems of tree species greater than 10 cm was recorded and in 40 m² subplots, stems smaller than 10 cm were measured. A total of 380 plots were sampled in an area of 6000 km². The fire history reconstruction was done based on historical maps, old aerial photographs and field sampling. A time‐since‐fire class, a deposit type, slope, slope aspect and altitude were attributed to each plot. Each plot was also described according to species richness and size structure characteristics. Traces of recent disturbance were also recorded in each plot. Changes in forest composition were described using ordination analyses (NMDS and CCA) and correlated with the explanatory variables. Two successional pathways were observed in the area and characterized by the early dominance of intolerant hardwood species or Picea mariana. With time elapsed since the last fire, composition converged towards either Picea mariana, Abies balsamea or a mixture of both species and the size structure of the coniferous dominated stands got more irregular. The environmental conditions varied between stands and explained part of the variability in composition. Their effect tended to decrease with increasing time elapsed since fire, as canopy composition was getting more similar. Gaps may be important to control forest dynamics in old successional communities.     

Changes in forest understorey vegetation in Norway related to long‐term soil acidification and climatic change

Question: Does the understorey vegetation of Norwegian boreal forests change in relation to broad‐scale, long‐term changes? Location: Norway. Methods: Permanently marked 1‐m² vegetation plots from 17 monitoring reference areas in forests dominated by Picea abies (11 areas, 620 plots) and Betula spp. (six areas, 300 plots) were analysed twice, at the start in 1988–1997 and 5 yr later (1993–2002). Species subplot frequency data were analysed separately for each area by univariate and multivariate statistical methods; 5‐yr changes in single species abundances, species number per plot and species composition were tested. Results: Two distinct patterns of change were found: 1. Abundance of several vascular plant species decreased in SE Norwegian Picea forests, most noticeably of species with a preference for richer soils, such as Oxalis acetosella. 2. Abundance of many bryophyte species as well as bryophyte species number per plot increased in forests of both types over most of Norway. Conclusions: The pattern of vascular plant changes is probably a time‐delayed response of long‐lived, mainly clonal, populations to acidified soils resulting from deposition of long‐distance airborne pollutants. The pattern bryophyte changes, with reference to the close link between climatic conditions for growth and abundance changes for Hylocomium splendens established in previous demographic studies, is related to climatic conditions favourable for bryophyte growth. We conclude that many forest understorey plants are sensitive indicators of environmental change, and that the concept used for intensive monitoring of Norwegian forests enables early detection of changes in vegetation brought about by broad‐scale, regional, impact factors.     

Unpedigreed populations and worst‐case scenarios

A population in which parentage information is not recorded is considered a pedigree “black hole” in terms of genetic management. Integration of animals from such an unpedigreed population into a genetically managed population is often accomplished by assuming a worst‐case scenario and recording all animals as highly interrelated (e.g., full siblings). The assumption that a worst‐case scenario is appropriate under a wide variety of circumstances is evaluated. It was determined that the genetic costs of overestimating relationships among animals from an unpedigreed population are always greater than the genetic costs of underestimating relationships by the same amount. This demonstrates that worst‐case scenarios, which are by definition intentional overestimates, are not generally appropriate. A method of obtaining an estimate that will yield the lowest overall genetic cost using the possible maximum and minimum levels of relatedness among animals from the unpedigreed population is presented along with two methods for implementation. Finally, for cases in which the estimated average relatedness among animals from an unpedigreed population is low, it is recommended that different analytical studbook datasets be used for calculation of inbreeding coefficients and mean kinship coefficients. This strategy would allow close estimation of average relatedness without risking inadvertent pairing of highly related animals from the unpedigreed population. Zoo Biol 20:305–314, 2001. © 2001 Wiley‐Liss, Inc.     

Vegetation convergence during early succession on coal wastes: a 6‐year permanent plot study

Question: Does the course of succession on a coal mine restored by hydroseeding converge with a reference community in terms of species composition and vegetation structure? What is the rate of succession on restored areas? How does the balance between local colonization and extinction rates change during succession? Which species group (native or hydroseeded) determines the successional process? Location: Large reclaimed coal mine in the north of Palencia province, northern Spain (42°50′N, 4°38′W). Methods: Between 2004 and 2009 we monitored annually vascular plant species cover in nine permanent plots (20 m² each) at a restored mine; these plots were structured to account for site aspect (north, south and flat). Three identical permanent plots were established in the surrounding reference community and monitored in 2004 and 2009. We used detrended correspondence analysis to assess successional trends and rates of succession, generalized linear mixed models to derive patterns of vegetation structural changes and turnover through time, and Huisman–Olff–Fresco modelling to illustrate response of individual species through time. Results: The three restored mine areas exhibited a successional trend towards the reference community through time, although speed of convergence differed. However, after 6 years the restored sites had diverged considerably and this was greater than the dissimilarity reduction with respect to the reference community. Richness, diversity and native species cover increased linearly through time, whereas hydroseeded species cover decreased. Success of hydroseeded species initially differed in the three areas, and this was negatively related with native species colonization rates. Response patterns through time of ten hydroseeded and 20 most common native species are described. Conclusions: Vegetation structural parameters rapidly converged with the reference community, whereas compositional convergence needed much longer. At the same time, successional composition trajectories and rates were related to site properties (here aspect).     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Scale‐dependent determinants of plant species richness in a semi‐arid fragmented agro‐ecosystem

Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large‐scale determinants of species richness in a fragmented agro‐ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured. Location: A fragmented agro‐ecosystem in the Southern Judea Lowland, Israel, within a desert–Mediterranean transition zone. Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225 m²). Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale‐dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size. Main conclusions: Species richness is determined by the combined effect of several scale‐dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi‐factorial approach and multi‐scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.     

Insights into the history of the legume‐betaproteobacterial symbiosis

The interaction between legumes and rhizobia has been well studied in the context of a mutualistic, nitrogen‐fixing symbiosis. The fitness of legumes, including important agricultural crops, is enhanced by the plants’ ability to develop symbiotic associations with certain soil bacteria that fix atmospheric nitrogen into a utilizable form, namely, ammonia, via a chemical reaction that only bacteria and archaea can perform. Of the bacteria, members of the alpha subclass of the protebacteria are the best‐known nitrogen‐fixing symbionts of legumes. Recently, members of the beta subclass of the proteobacteria that induce nitrogen‐fixing nodules on legume roots in a species‐specific manner have been identified. In this issue, Bontemps et al. reveal that not only are these newly identified rhizobia novel in shifting the paradigm of our understanding of legume symbiosis, but also, based on symbiotic gene phylogenies, have a history that is both ancient and stable. Expanding our understanding of novel plant growth promoting rhizobia will be a valuable resource for incorporating alternative strategies of nitrogen fixation for enhancing plant growth.     

Restoring riparian meadows currently dominated by Artemisa using alternative state concepts ‐ above‐ground vegetation response

Abstract. Livestock overgrazing and stream incision in the western USA often result in encroachment and dominance of Artemisia tridentata ssp. tridentata (Big sagebrush) in riparian areas that formerly supported meadows. To define the alternative states and thresholds for these ecosystems, we conducted a restoration experiment that included sites with high, intermediate or low water tables. We used a paired‐plot approach in which one plot on each site was burned and seeded with native grasses and forbs typical of naturally occurring dry meadow and Artemisia/Leymus cinereus ecological types, while adjacent unburned plots served as controls. Sites with high and intermediate water tables had greater initial abundances of perennial grasses typical of dry meadows, such as Leymus triticoides and Poa secunda ssp. juncifolia, and these species increased after the burn. In contrast, sites with low water tables were dominated by annual forbs such as Chenopo‐dium album and Descurainia pinnata after the burn. Biomass increased progressively from 1997 to 1999 on burned plots, while controls showed little change. Burning effects were microsite specific, with former Artemisia microsites exhibiting lower biomass than interspaces initially, but similar or higher biomass by the third year. Establishment of seeded species was low and species composition was determined largely by pre‐burn vegetation. Artemisia dominated sites with high water tables appear to represent an alternative state of the dry meadow ecological type, while sites with low water table sites have crossed an abiotic threshold governed by water tables and represent a new ecological type. Burning is an effective tool for restoring relatively high water table sites, but low water table sites will require burning and seeding with species adapted to more xeric conditions.