Seasonal variations in abundance and activity of nitrifiers in four arable cropping systems

Ammonium and nitrite oxidizers were counted with the most probable number (MPN) method and potential ammonium- and nitrite-oxidation rates were determined with a chlorate inhibition technique in an arable soil over a 3-year period. Samples were taken from the topsoil once a month for 2 years and a few times during a third year in four cropping systems: unfertilized lucerne ley and barley, and nitrate fertilized grass ley and barley. The distribution of nitrifiers was determined and their activities measured at various soil depths and between and within plant rows of fertilized barley.The numbers and activities of ammonium oxidizers were highest in the spring and autumn samples. Numbers of ammonium oxidizers ranged from 0.2 to 19×10⁴ and nitrite oxidizers from 3 to 870×10⁴ cells g^–1 dry soil. Potential ammonium-oxidizer activities ranged from 120 to 1,060 and nitrite-oxidizer activities ranged from 280 to 680 ng N g^–1 dry soil hour^–1. Lucerne and grass leys generally showed the highest, whereas unfertilized barley had the lowest, abundances and activities.Abundance estimates and activities were 10–20 times higher in the plow layer than in underlying sand and clay layers. A strong correlation was found between organic matter content vs numbers and activities of both ammonium and nitrite oxidizers. Only nitrite oxidizer counts were significantly higher within plant rows compared to between plant rows.     

Effects of small mammal and invertebrate herbivory on plant species richness and abundance in tallgrass prairie

Summary A factorial field experiment was designed to test the effects of small mammals and above- and below-ground invertebrates on plant species richness and composition in native tallgrass prairie at Konza Prairie Research Natural Area, northeast Kansas. Over a 4-year period, Microtus ochrogaster densities were maintained by live-trapping in fenced plots, and invertebrate levels were reduced using the pesticides carbaryl for above-ground invertebrates and an organophosphate (isofenphos) for belowground invertebrates. ANOVA according to a split-plot design of plant species biomass data harvested in 1984 and 1986 revealed few significant effects of either small mammal densities or pesticide application. Of 54 species harvested from both sample dates, only 10 were significantly affected by either treatment. Analysis of species richness according to 8 life-form classes provided a clearer pattern of response than did biomass either by species or life-form class. For example, numbers of C4 grasses were reduced by increasing small mammal densities, whereas numbers of C4 annual forbs were lowest when above-ground herbivory was reduced. While consumers have been shown to have strong effects on successional communities, the few significant results observed in this study suggests that the manipulated levels of small mammals and insects had few effects on a mature tallgrass prairie.Deceased May, 1986     

Functional and systems biology approaches to Huntington's disease

Huntington's disease (HD) is a hereditary, progressively degenerative and fatal brain disorder classified as a rare, or 'orphan', disease. HD is caused by the extension of trinucleotide repeats encoding a stretch of glutamine residues at the amino-terminal end of the large huntingtin (HTT) protein. Since the discovery of the mutated HTT gene in 1993, the mechanisms by which the mutant HTT protein induces neurodegeneration remain poorly understood and no disease-modifying therapy is currently available. Several functional approaches combining different experimental models and experimental technologies have been used to shed some light on the mechanisms underlying this disease. This review presents these functional approaches, highlights their potential and limitations.     

Temporal patterns of diversity, abundance and evenness for invertebrate communities from coastal freshwater and brackish water rock pools

Aquatic invertebrate data were collected from 49 erosional, Jamaican,rock pools between 1989 and 1998 and used to describe temporal patterns ofspecies diversity. This unique series of pools on the north coast of Jamaica,classified as either brackish (31) or freshwater (18), was used to determinehowdiversity changes over time, whether there was a difference between poolclassifications, and the impacts of environmental variables. Mean communitymetrics (richness, diversity, evenness, abundance) were not significantlydifferent between freshwater and brackish pools. However, there weresignificantdifferences among the eight sampling dates and differences over time dependedonpool classification. Measures of diversity for freshwater pools were relativelyconstant over time, implying little change at the community level. Brackishpools showed significant differences over time in species richness, totalabundance, and evenness implying that community composition and structure werenot static but changed in response to either environmental or biotic changes(possibly initiated by environmental change).Some temporal changes in community metrics could be linked to temporal changesin environmental variables. In brackish water pools, a significant increase inpool salinity between January 1991 and January 1992 corresponded to an increasein species richness, likely due to an increase in marine fauna. Similarly,changes in abundance and evenness corresponded to changes in temperature,dissolved oxygen, and pH. In addition, physicochemical variables used in thisstudy were shown to affect community metrics and those relationships dependedonpool classification. Most relationships between community metrics andenvironmental variables were negative with the exception of Simpson's diversityindex for which positive relationships were found. This may indicate that, aspool conditions become less favorable, a few species flourish and dominate thecommunity.     

Correlational patterns between invertebrate species composition and the presence of an invasive plant

It is widely assumed that the presence of invasive exotic plants causes a negative impact on native biotas. Here, we analyse the correlational patterns between the presence of one of these invasive plants, the South African Hottentot fig, Carpobrotus acinaciformis (L.) L. Bolus (Aizoaceae), and the terrestrial invertebrate species composition of a Mediterranean rocky shore. Variations in invertebrate community were estimated by determining the presence–absence of 94 species in 30 plots along a 2.5 km shoreline. Canonical correspondence analyses revealed that three environmental variables showed significant correlation with the invertebrate presence–absence matrix. Namely, distance to the nearest urban area, soil type, and vegetation type. Presence–absence of the invasive plant was correlated with these environmental variables, but no additional effect on the invertebrate community specifically attributable to the presence of the invasive plant was detected. These facts exemplify the uncertainties in linking the presence of an invasive species with its putative outcomes because they are consistent with the hypothesis that a general gradient of anthropic influence affects the invertebrate species composition, and that the supposed effects of C. acinaciformis on the invertebrate species composition are correlated with (and therefore, indiscernible from) those derived from the existence of such general gradient of anthropic influence.     

Patterns of Orthoptera abundance and lesser kestrel conservation in arable landscapes

The lesser kestrel Falco naumanni experienced a marked decline during the second half of the 20th century due to changes in land use that influenced breeding success by reducing the abundance and quality of prey. However, the factors governing spatial and temporal variation of prey abundance around lesser kestrel colonies has not yet been investigated. We sampled Orthoptera abundance in the main crop types and edge habitats surrounding six lesser kestrel colonies in southern Spain. Samplings focused on Orthoptera because they constitute the main prey during the nestling period. Only those Orthoptera species that are known to be preyed by lesser kestrels were considered in this study. We found differences in prey density among localities, and crop types. Semi-natural habitats such as grasslands, fallow land, and field margins held the highest densities. However, prey abundance showed a complex pattern that was not possible to explain solely on the basis of crop composition around colonies. Factors determining productivity in individual fields like soil type and productivity or biocide input, and mean size of agricultural fields contributed to explain this complex pattern of prey abundance. Our results highlight the key role of semi-natural and edge habitats in farmed landscapes as prey reservoirs and corridors. Higher conservation priorities for these habitats are suggested to benefit foraging lesser kestrels, but many other farmland species that also experienced steep population declines due to decreasing food supply resulting from modern agriculture.     

Moderated statistical tests for assessing differences in tag abundance

MOTIVATION: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically. Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small. RESULTS: We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts. AVAILABILITY: An R package can be accessed from http://bioinf.wehi.edu.au/resources/     

Modelling field emergence patterns in arable weeds

A model was developed to simulate weed emergence patterns after soil cultivation. In the model, the consecutive processes of dormancy release, germination and pre-emergence growth were modelled in separate modules. Input variables of the model were: date of soil cultivation, soil temperature and soil penetration resistance. Output variables of the model were: seedling density and timing of seedling emergence. The model was parameterized for Polygonum persicaria , Chenopodium album and Spergula arvensis with data from previous field and laboratory experiments. The model was evaluated with data from an experiment, in which emergence of P. persicaria , C. album and S. arvensis was monitored in field plots that were cultivated once only, at one of five dates in the spring. At the same time as the field observations on seedling emergence, seasonal changes in seed dormancy of the buried weed seeds were assessed by testing the germination of seed lots that were buried in envelopes. From a comparison between field observations and simulated data, it appeared that the model overestimated the rate of dormancy release in spring, whereas germination and pre-emergence growth were simulated well. In general, therefore, both the numbers of emerging seedlings and the timing of emergence could be predicted accurately, when dormancy was not simulated but introduced from experimental data. Improvement of predictions of field emergence of weeds should mainly focus on increasing the precision of the simulation of dormancy release. Close correlations were found between seedbed temperature and both the extent and rate of seedling emergence, but analysis with the simulation model revealed that they were only partly based on causal relationships, so that they have limited predictive value.     

Coherent patterns of abundance and size of a tropical snapper in dynamic estuary systems

Although tropical estuaries are important juvenile habitats for the snapper, Lutjanus russelli, the extent of this utilisation, and relationships to physical variation are unknown. We used fish trapsto investigate spatial and temporal patterns of distribution, abundance and size of L. russelli within and between three tropical estuaries (Cattle, Barramundi and Alligator Creeks) over a two year period. L. russelli showed no indication of spatial segregation by size along the lengths of the estauries. The probability of capturing L. russelli was similar throughout Barramundi Creek and the seaward parts of Cattle Creek. However, the probability of capture fell markedly in upstream regions of Cattle Creek. These areas where characterised by depressed salinity levels due to seasonal flooding. High probabilities of capture of L. russelli during the wet and post-wet seasons in the whole of Barramundi Creek correlated with the time of smallest modal sizes. Thisreflected the entry of large numbers of small recruits into the trappable population. Temporal patterns in mean length were consistent for both years. The major feature of the size data was a clear pattern of seasonal change in the mean fork length of L. russelli, with largest mean sizes occurring in the pre-wet and the smallest mean sizes in the wet and post-wet seasons. This pattern probably reflected the interaction of four processes; the entry of new recruits into the trappable population, growth and mortality during residence in the estuarine nursery habitats, and migration of large fish away from the estuaries. The three creeks studied provided L. russelli with a harsh and extremely variable environment. Over the three creeks, salinities ranged from extremely hyposaline (0) to very hypersaline (55.5) and varied up to 39 within a location. However, despite the substantial physical differences and the spatial separation of the three estuaries, the patterns of temporal change were clear and consistent. Overall, the annual pattern of change insize seemed to relate more to biological processes of recruitment, mortality and migration than to responses to physical variability.     

The relationship between seed size and abundance in plant communities: model predictions and observed patterns

Recent studies have suggested that seed size and plant abundance in communities are associated. However, inconsistent patterns have emerged from these studies, with varying mechanisms proposed to explain emergent relationships. We employ a theoretical framework, based on key theory lineages of vegetation dynamics and species coexistence, to examine relationships between species abundance and seed size. From these theory lineages, we identified four models and their predictions: the Seed size/number trade‐off model (SSNTM), the Succession model (SM), the Spatial competition model (SCM), and the Lottery model (LM). We then explored empirical evidence from ten diverse plant communities for seed size and abundance patterns, and related these patterns to model predictions. The SSNTM predicts a negative correlation between seed size and abundance. The SM predicts either a negative, positive or no correlation dependent on time since disturbance, while the SCM and LM make no predictions for a relationship between seed size and abundance. We found no evidence for consistent relationships between seed size and abundance across the ten communities. There were no consistent differences in seed size and abundance relationships between communities dominated by annuals compared to perennials. In three of the ten communities a significant positive seed size and abundance correlation emerged, which falsified the SSNTM as an important determinant of abundance structure in these communities. For sites in coastal woodland, the relationships between seed size and abundance were consistent with the predictions of the SM (although generally not significant), with fire being the disturbance. We suggest that the significant positive seed size and abundance correlations found may be driven by the association between large seeds and large growth forms, as large growth forms tend to be dominant. It seems likely that patterns of seed size and abundance in communities are determined by a complex interaction between environmental factors and correlations of plant attributes that determine a species’ strategy.     

Combining population genetics and demographical approaches in evolutionary studies of plant mating systems

The striking amount of variation in the mating systems of higher plants has stimulated fruitful research by both ecologists and population geneticists. Historically, these two schools of thought have developed independent theoretical treatments and empirical approaches to account for the evolution of such diversity. We highlight the approach adopted by each field. Population geneticists have developed an approach centred on gene properties of individuals and their role on the evolution of self-fertilisation (transmission rules and the deleterious role of mutations), while ecologists have mostly focused on demographic properties of self-fertilisation (seed production, colonisation ability of selfers). As a result, the two approaches sometimes use conflicting notions of fitness. The recent empirical advances on inbreeding depression, a topic typically motivated by population genetic questions, have emphasized the need to adopt a demographical perspective for fitness. In this paper, we suggest generalizing this approach in mating system evolution and we expect further improvements by integrating demographic and genetics perspectives.     

Techniques for assessing the abundance of Brown Hares Lepus europaeus

Over the last few decades, there have been significant declines in Brown Hare Lepus europaeus numbers throughout Europe, leading to concern for their status in many countries. In Britain, there were no quantified data on the extent of this decline, on current population levels, or any baseline against which to monitor future population changes. The need for a quantified national hare survey led to this evaluation of the techniques available to assess hare numbers. Published information on counting hares is reviewed, and various techniques compared by applying them to a number of sites in southern England. Three basic approaches are available: counts of inactive hares, counts of active hares and indirect methods. Counts of inactive hares include total clearance, wide belt and line transect counts. Total clearance counts give an absolute figure, but are labour intensive and can only be applied to restricted areas. Wide-belt assessments are difficult to apply in certain habitats and even in open areas tend to produce a substantial over-estimate. Line transect counts are easy to undertake and are not labour intensive but should only be applied to large areas, or data from several small areas combined. Counts based on active hares are more problematical, because it is difficult to determine what proportion of the population is inactive at any one time. Spotlight counts based on variable circular plots are the most accurate but difficult to apply widely, and twilight counts are very subjective in their interpretation, especially when surveying small areas or areas with a large proportion of concealing habitats. Of the indirect methods, dung pellet counts can be valuable in specific areas but are difficult to apply across a range of habitats. We concluded that, of the various techniques considered, line transect counts have the greatest potential for a national survey, but need to be stratified so that enough transects are undertaken within each habitat stratum to obtain a reliable mean population estimate for each stratum.     

Functional characterization of germin and germin-like protein genes in various plant species using transgenic approaches

The important role of germins (GER) and genes coding for germin-like proteins (GLP) in responses against various stresses in both homologous and heterologous systems is well validated. This review summarizes the work on their functional validation using various biotechnological approaches. The genes are widely expressed during a specific period of plant growth and development, and exhibit a pattern of evolutionary subfunctionalization at both the intracellular and whole plant level. Their applications against various biotic and abiotic stresses, especially against fungal pathogens, are enormous. Although the validation of these proteins against various stresses has led to the development of commercially and agronomically important transgenic plants, much work is still needed to exploit this ever-expanding repertoire of genes and deploy them for commercial use. Historical progress of genetic engineering in GERs and GLPs is reviewed, and future prospects for their potential role in crop improvement are highlighted.     

Changes in soil hyphal abundance and viability can alter the patterns of hydraulic redistribution by plant roots

Background and aims

We conducted a mesocosm study to investigate the extent to which the process of hydraulic redistribution of soil water by plant roots is affected by mycorrhizosphere disturbance.

Methods

We used deuterium-labeled water to track the transfer of hydraulically lifted water (HLW) from well-hydrated donor oaks (Quercus agrifolia Nee.) to drought-stressed receiver seedlings growing together in mycorrhizal or fungicide-treated mesocosms. We hypothesized that the transfer of HLW from donor to receiver plants would be enhanced in undisturbed (non-fungicide-treated) mesocosms where an intact mycorrhizal hyphal network was present.

Results

Contrary to expectations, both upper soil and receiver seedlings contained significantly greater proportions of HLW in mesocosms where the abundance of mycorrhizal hyphal links between donor and receiver roots had been sharply reduced by fungicide application. Reduced soil hyphal density and viability likely hampered soil moisture retention properties in fungicide-treated mesocosms, thus leading to faster soil water depletion in upper compartments. The resulting steeper soil water potential gradient between taproot and upper compartments enhanced hydraulic redistribution in fungicide-treated mesocosms.

Conclusions

Belowground disturbances that reduce soil hyphal density and viability in the mycorrhizosphere can alter the patterns of hydraulic redistribution by roots through effects on soil hydraulic properties.     

Clonal growth and plant species abundance

Background and Aims

Both regional and local plant abundances are driven by species'' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden.

Methods

Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates.

Key Results

After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level.

Conclusions

Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden performance parameters provide a practical approach to assessing the roles of clonal growth morphological traits (and LHS traits) for large sets of species.     

High-throughput approaches for plant epigenomic studies

In plant cells, DNA is packaged into chromatin by wrapping around histone octamers. Pathways that lead to cytosine DNA methylation, posttranslational histone modifications and certain components of the RNA interfering (RNAi) pathway are critically important in modulating chromatin structure, thereby affecting many molecular processes that take place in a cell. Recent advances in microarray and high-throughput sequencing technologies have made it possible to study these pathways on a genome-wide scale. Results from such epigenomic studies are broadening our understanding of plant genomes and are also providing important clues regarding the mechanisms and functions of these pathways that can be further tested using genetic and biochemical approaches. This review focuses on the high-throughput approaches that have been successfully applied in plant epigenomic studies.     

Environmental correlates of plant and invertebrate species richness in ponds

Ponds (lentic water bodies <2 ha) constitute a considerable biodiversity resource. Understanding the environmental factors that underlie this diversity is important in protecting and managing the habitat. We surveyed 425 ponds for biological and physical characteristics with 78 of those also surveyed for chemical characteristics. A total of 277 invertebrate species and 265 plant species were found. Species richness varied between 2 and 99 (mean 27.2 ± 0.6 SE) for invertebrates and 1 and 58 (mean 20.8 ± 0.4 SE) for plants. Generalised additive models were used to investigate variables that correlate with the species richness of plants and invertebrates, with additional models to investigate insect, Coleoptera, Odonata, Hemiptera, Trichoptera and Mollusca species richness. Models performed reasonably well for invertebrates in general (R ² = 30.3%) but varied between lower-order invertebrate taxa (12.7–34.7%). Ponds with lower levels of shading and no history of drying contained higher numbers of species of plants and all invertebrate groups. Aquatic plant coverage positively correlated with species richness in all invertebrate groups apart from Trichoptera and the presence of fish was associated with high invertebrate species richness in all groups apart from Coleoptera. The addition of chemistry variables suggested non-linear relationships between oxygen demand and phosphate concentration and higher-order richness. We demonstrate that the composition of biological communities varies along with their species richness and that less diverse ponds are more variable compared to more diverse ponds. Variables positively correlated with richness of one taxon may be negatively correlated with that of another, making comprehensive management recommendations difficult. Promoting a high landscape-level pond biodiversity will involve the management of a high diversity of pond types within that landscape.