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.     

Weed and invertebrate community compositions in arable farmland

A large proportion of the land surface area of Great Britain (GB) is used for arable agriculture. Due to changes in farm management practices over the last 50 years, there have been marked declines in the abundance of arable wildlife groups of conservation importance, including weeds, invertebrates and birds. Here we ask whether changes in weed species composition, driven by changes in management, such as a change in crop or a modification in herbicide regime, might be expected to lead to changes in the species compositions of other wildlife groups, including invertebrates. Using multivariate analyses, on data from eight crop and herbicide management groups sampled across 266 arable fields, we show that the weed composition changes with the crop and herbicide management adopted and the invertebrate composition changes with the crop grown. We conclude that each conventional crop sampled had a unique composition of weeds and invertebrates, and expect this to be true for all conventional arable crops. Changes in weed species composition, driven by changes in crop or herbicide management, will lead to changes in the compositions of invertebrates, and possibly other wildlife groups. However, these changes will probably be buffered by the effect of functional redundancy, the crop and dispersal. Handling editor: Gimme Walter.     

Farmland bird invertebrate food provision in arable crops

Invertebrates are an essential food source for most farmland birds yet their relative abundance and biomass in the most commonly grown arable crops are poorly understood. Dvac suction sampling was used to determine the abundance, biomass and community composition of those invertebrate groups considered important in the diet of farmland birds for the commonest arable crops. Approximately 40 fields were sampled at the edge and mid‐field over 2 years in three different locations in England. In cereals, the fauna was primarily comprised of Araneae (10%), Coleoptera (30%) and Hemiptera (58%), whereas the oilseed rape fauna was dominated by Coleoptera (65%) and peas and potatoes by Hemiptera (89%). Beans contained a high proportion of Coleoptera (39%) and Hemiptera (49%). Aphididae were the most abundant family (20–86% of total), although in oilseed rape and beans, Chrysomelidae, Curculionidae and Nitidulidae formed ca 20% of the fauna. Aphids only formed a small proportion (7%) of the total biomass, except in peas (32%). Instead, Araneae, Carabidae, Heteroptera, Homoptera and Tipulidae formed much larger and more equal proportions. The highest abundance and biomass of invertebrates were recorded in cereals and least in potatoes. The Grey Partridge chick‐food index in all crops was only a half or less of the level required to ensure that chick survival is sufficient to maintain numbers of this red‐listed species. The total number of invertebrates, their biomass, diversity and the Grey Partridge chick‐food index were higher at the crop edge compared to mid‐field. Conservation measures are needed to help reverse the long‐term declines of invertebrates on farmland, which should include developing further invertebrate‐rich, agri‐environment scheme options and management techniques to encourage invertebrates considered important as bird food within arable crops.     

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     

Long‐term patterns of invertebrate abundance and relationships to environmental factors in arid Australia

Resource pulses are a key feature of semi‐arid and arid ecosystems and are generally triggered by rainfall. While rainfall is an acknowledged driver of the abundance and distribution of larger animals, little is known about how invertebrate communities respond to rain events or to vegetative productivity. Here we investigate Ordinal‐level patterns and drivers of ground‐dwelling invertebrate abundance across 6 years of sampling in the Simpson Desert, central Australia. Between February 1999 and February 2005, a total of 174 381 invertebrates were sampled from 32 Orders. Ants were the most abundant taxon, comprising 83% of all invertebrates captured, while Collembola at 10.3% of total captures were a distant second over this period. Temporal patterns of the six invertebrate taxa specifically analysed (Acarina, ants, Araneae, Coleoptera, Collembola and Thysanura) were dynamic over the sampling period, and patterns of abundance were taxon‐specific. Analyses indicate that all six taxa showed a positive relationship with the cover of non‐Triodia vegetation. Other indicators of vegetative productivity (seeding and flowering) also showed positive relationships with certain taxa. Although the influence of rainfall was taxon‐dependent, no taxon was affected by short‐term rainfall (up to 18 days prior to survey). The abundance of Acarina, ants, and Coleoptera increased with greater long‐term rainfall (up to 18 months prior to survey), whilst Araneae showed the opposite effect. Temperature and dune zone (dune crest vs. swale) also had taxon‐specific effects. These results show that invertebrates in arid ecosystems are influenced by a variety of abiotic factors, at multiple scales, and that responses to rainfall are not as strong or as predictable as those seen for other taxa. Our results highlight the diversity of invertebrates in our study region and emphasize the need for targeted long‐term sampling to enhance our understanding of the ecology of these taxa and the role they play in arid ecosystems.     

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.     

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/     

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.     

Removal of secondary compounds increases invertebrate abundance in lichens

We investigated how lichen carbon-based secondary compounds (CBSCs) affect abundance of invertebrates in five lichen species growing on the forest floor (Cladonia rangiferina, Cladonia stellaris) or on tree trunks (Evernia prunastri, Hypogymnia physodes, Pseudevernia furfuracea). To do this, CBSCs were removed by rinsing lichen thalli in acetone (which has no adverse effects on the lichens) and the lichens were re-transplanted in their natural habitat. After 4 months there was higher abundance of mites, springtails and spiders in the three epiphytic lichens that had their CBSC concentrations reduced. The increase in predatory spiders following CBSC reduction suggests that the compounds have multitrophic consequences. The acetone treatment reduced the number of nematodes in four of the lichen species. Given that lichens serve as important habitats for a diverse range of invertebrates, increased knowledge of how lichen CBSCs may regulate their abundance helps us to better understand the role that lichens and their defence compounds play in structuring forest food webs.     

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.     

Spatial sampling to detect slug abundance in an arable field

Overuse of molluscicides by farmers in arable systems can lead to environmental and product contamination. Here we assess a simple and inexpensive surface trapping method for monitoring populations of slugs (Deroceras reticulatum and Arion intermedius). This method was biased against small slugs, and against A. intermedius, when compared to direct soil sampling. Regression was used to model the relationship between the results of surface trapping and soil sampling methods. Spatial Analysis by Distance IndicEs (SADIE) algorithms were used to describe the spatial relationships between the two sets of samples. Using both traditional statistical methods and spatial statistics, the spatial information collected from surface traps was sufficient to identify patches and gaps in slug numbers and possibly to allow the spot application of slug control, and thus provide land managers who experience slug damage with a way of reducing molluscicides use, whilst maintaining slug control. Further improvements and applications of the model are discussed.     

Ecological assembly rules in plant communities—approaches,patterns and prospects

Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co‐occur randomly but are restricted in their co‐occurrence by interspecific competition. This concept can be redefined in a more general framework where the co‐occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta‐analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co‐occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta‐analyses suggest that non‐random co‐occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non‐random aspect of assembly in plant communities.     

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.     

亚高寒草甸不同生境植物群落物种多度分布格局的拟合

物种多度分布是群落生态学研究的核心内容。通过对青藏高原东部亚高寒草甸3种不同生境草本植物群落的抽样调查,结合16个物种多度分布模型的两种曲线拟合优度检验得出如下结果：多种不同模型可以拟合同一生境的物种多度分布。相比于其他可拟合模型,几何级数模型在3种生境中两种拟合优度检验方法下的平均拟合效果是最好的,拟合优度值均在最优拟合优度值10左右波动。次优模型鉴于不同生境不同的检验方法表现不一。除了几何级数模型外,Sugihara分数模型在最小二乘法的拟合方法下,也可以拟合3种生境的物种多度分布。研究结果表明,仅用拟合优度检验区分产生不同物种分布格局的模型和机制是不可靠的,需要做进一步的检验性实验研究。