ALBERT

Notes: Abstract  Monitoring biodiversity presents the challenge of informing complex aspects of biological systems with consistent, repeatable, data-based indicators. The present paper does not address directly the selection of indicators for rangeland biodiversity, but rather presents essential aspects and examples of monitoring systems that address natural resource questions at comparable scales. In general, concepts of landscape quality, such as range condition, conservation value, health and biodiversity, are descriptive rather than quantitative and are either ill-defined or multiply defined. Assessment of the status of such indicators involves value systems, as well as process understanding at a range of scales for which data are often unavailable. Effective monitoring systems, in contrast, require repeated quantitative data at suitable temporal density and spatial scale, as well as appropriate methods and a conceptual framework to simplify and interpret these data. In recent years, broad-scale operational monitoring systems for land and vegetation have been developed in Australia based on sequences of satellite data, digital elevation models, ground information and appropriate statistical methods. These same datasets have been used to inform landscape qualities over broad areas; examples are given of the production of salinity risk maps and conservation management zones based on fragmentation patterns. These results have been achieved as a partnership between ecologists, resource scientists and statisticians and illustrate how surrogates for integrated concepts such as biodiversity can be derived from available data.

Notes: Abstract  Because grazing by livestock is one of the primary threats to rangeland biodiversity, but is unevenly distributed in space, rangeland monitoring programmes need to take account of the distribution of grazing pressure in order to distinguish between grazing-induced change, seasonal fluctuations and changes that are a result of other threats. Livestock watering places are one of the major influences that give spatial expression to gradations in grazing activity. Using research results from the goldfields of Western Australia, we show how distance from water can be incorporated in spatial models to predict cumulative grazing pressure at different sites within paddocks. Two surrogates of grazing activity are illustrated: one relying on a commercially available model, and one developed from measures of track density. Factors other than distance from water can also have profound effects on the distribution of grazing pressure and its impacts at landscape and regional scales, and we review some of these briefly. Finally, we outline key spatial implications for the design of rangeland monitoring programmes.

Notes: Abstract  We explored the key issues that are most likely to influence any set of guiding principles for developing biodiversity monitoring programmes in Australia's rangelands. We defined the Australian rangelands and came up with an overview of their climate extremes, land-use pressures and biodiversity loss, and then focussed on issues underpinning the design phase of any monitoring programme. Using Noss's 1990 framework of compositional, structural and functional attributes of biodiversity and its new revisions by others, we showed how the elusive, abstract concept of biodiversity can be used to identify many measurable attributes that can form a minimum and necessary set of indicators for any biodiversity monitoring task. We then described the steps in the monitoring process, with a particular focus on the reasons for monitoring biodiversity as they strongly influence the selection of indicators. We concluded by compiling a table of key issues as background information for developing guiding principles (Table 4). The list is by no means an exhaustive list for the design phase but it does indicate that considerable attention needs to be given to this phase when developing monitoring programmes. We have intentionally not addressed the equally important issues associated with the planning and delivery phases of developing a monitoring programme, as Wallace et al. and Watson and Novelly cover these in their papers in the present issue of Austral Ecology.

Notes: Abstract  Monitoring the biodiversity of Australian rangelands has been identified as a means of informing policy and supporting funding decisions in relation to the conservation of biodiversity. Australian rangelands are subject to invasion by alien plants that have the potential to have major impacts on ecosystem function and biodiversity, although there has been little quantitative documentation of these effects. Research is needed to improve our understanding of how and to what extent alien plants affect biodiversity in Australian rangelands so that this relationship can be considered when developing and implementing programmes to monitor biodiversity. It is also important to consolidate existing efforts to quantify the extent of alien plant invasions and monitor their progress, thus documenting a process that threatens biodiversity. Information on the presence and abundance of alien plant species should be considered for inclusion as a component of biodiversity monitoring programmes that are undertaken. Monitoring components of biodiversity can itself provide a basis for evaluating weed management strategies.

Notes: Odours in waters used for various purposes, especially musty odours, is a worldwide problem. To establish an early warning system, the nuisance odour in an aquatic environment, the causative microorganisms and compounds, and the mechanism of odour in Lake Kasumigaura, the second biggest lake in Japan, were examined using in situ studies. In this study, the mechanism for the occurrence of musty odours was determined, and the level of musty odour was discriminated, based on 32 months of phytoplankton data from three sampling stations. The results indicate that the cell numbers of Phormidium tenue, Synedra and Ankistrodesmus were significantly related to the occurrence of 2-methlisoborneol (MIB) and geosmin. Furthermore, the odour occurrence for both MIB and geosmin was effectively predicted and validated using environmental factors as explanatory variables, using multiple linear regression and artificial neural network technology.

Notes: During the 1970s−1990s, considerable emphasis was placed on minimizing the inputs of polychlorinated biphenyls (PCBs) from active sources. In addition, between 1993 and 2001, ≈ $US130 × 106 was spent for sediment remediation within the western Lake Erie – Detroit River basin. In general, although PCB contamination of the Detroit River and Lake Erie declined significantly between the 1970s and mid-1990s, it has remained fairly stable over the past 10 years. Control of PCBs and other contaminants at their source remains a primary imperative for action. Remediation of contaminated sediments is growing in importance, however, as greater levels of source control are achieved. From a sediment management perspective, it is estimated that between 1993 and 2001 a substantially higher mass of PCBs (over two orders of magnitude higher) was removed as a result of contaminated sediment remediation, as compared to navigational dredging of shipping channels. In addition, there is a strong and compelling rationale for moving expeditiously to remediate severely contaminated sediment while it is still relatively contained in a small geographical area. The cost of not acting in a timely manner might be to exacerbate environmental problems including increased deformities and reproductive problems in wildlife, delayed ecosystem recovery and increased costs, or even preclusion of future sediment remediation. Based on discussions at a United States of America–Canada workshop held in 2002, key management advice includes continued emphasis to be placed on remediating contaminated sediment hot spots (including evaluating the effectiveness of projects), integrated monitoring efforts to be focused on beneficial use restoration and a high priority to be placed on sustaining and building upon modelling efforts, in order to be able to accurately predict and evaluate ecosystem responses to remedial and preventive actions.

Notes: Lake Rodó (Montevideo, Uruguay) is a small, urban, hypertrophic lake undergoing restoration. In this study, we evaluated the nutrient removal efficiency and water quality improvement attributable to a water recirculation system, consisting of the lake and three connected pools converted to artificial wetlands dominated by free-floating hydrophytes. Eichhornia crassipes and Spirodela intermedia dominated the hydrophyte community during summer and winter, respectively, with the biomass production being maintained throughout the year. The maximum production values of E. crassipes were 11.3 and 5.6 g DW m−2 d−1 in the summers of 1998 and 2000, respectively, while those of S. intermedia were 2.7 and 0.8 g DW m−2 d−1 in the summers of 1999 and 2000, respectively. The aquatic plant community reduced the concentration of nutrients in the water column but did not significantly affect the sediment concentrations. Harvesting the hydrophytes removed the equivalent of 58–88% and 39–78% of the nitrogen (N) and phosphorus (P) load associated with the water column, respectively. In contrast, the harvests accounted for only 1–2% of the N and P load associated with the sediments. In the pools, the combination of water recirculation and hydrophytes generally diminished the algal biomass and the associated N and P, compared to that observed for the lake. The combined use of adequate aquatic plant harvests and hydraulic management increased the efficiency of the system and, therefore, seems to be a useful tool for restoring small, shallow lakes in tropical and subtropical regions.

Notes: Lake Yogo is a small, eutrophic lake located 1.3 km north of Lake Biwa, Japan. The lake, which was originally a natural, closed lake, has a unique water management system. It is replenished with water pumped from Lake Biwa and supplies irrigation water to ≈ 5 km2 of agricultural fields. As a result, Lake Yogo functions as a water storage dam and is artificially controlled. As seen in most stratified lakes in temperate regions, large amounts of phosphate (PO4) are released from the sediment in the hypolimnetic water layer during the summer stratification period. In order to reduce the impacts of internal phosphorus (P) loading, a destratification aeration system was installed in the lake. Although the stratification was weakened concomitant with a temperature increase in the hypolimnetic layers, anoxic conditions were still observed because of the small scale of the aeration system, with cyanobacterial blooms continuing to occur during the summer and autumn of every year. Although the internal P load at the autumn turnover is probably immediately scavenged by its incorporation into ferric oxyhydroxide colloids, the phytoplankton present at that time would doubtless benefit from the temporary, increased PO4 supply because of their rapid uptake rates. Although the PO4 transported continually from the hypolimnetic to the epilimnetic layers by the destratification aeration system should be scavenged as ferric oxyhydroxide colloids, a portion of the PO4 is probably incorporated into the phytoplankton biomass. As a result, an insufficient level of artificial destratification might support phytoplankton growth during the period of thermal stratification in the lake.

Notes: Abstract  In the present paper, we have provided an initial assessment of the current and future threats to biodiversity posed by introduced mammals (predators and herbivores) inhabiting the Australian rangelands, exploring trends in populations and options for management. Notably, rabbits have declined in recent years in the wake of rabbit haemorrhagic disease, populations of feral camels have increased dramatically and foxes appear to have moved northwards, thereby threatening native fauna within an expanded range. Following on, we developed a framework for monitoring the impacts of introduced mammals in the Australian rangelands. In doing so, we considered the key issues that needed to be considered in designing a monitoring programme for this purpose and critically evaluated the role of monitoring in pest animal management. Finally we have provided a brief inventory of current best-practice methods of estimating the abundance of introduced mammal populations in the Australian rangelands with some comments on new approaches and their potential applications.

Notes: Abstract  Taken literally, the aim of biodiversity monitoring is to track changes in the biological integrity of ecosystems. Given the overwhelmingly dominant contribution of invertebrates to biodiversity, no biodiversity monitoring programme can be considered credible if invertebrates are not addressed effectively. Here we review the use of terrestrial invertebrates, with a particular focus on ants, as bioindicators in Australia in the context of monitoring biodiversity in Australia's rangelands. Ant monitoring systems in Australia were initially developed for assessing restoration success following mining, and have since been applied to a wide range of other land-use situations, including grazing impacts in rangelands. The use of ants as bioindicators in Australia is supported by an extensive portfolio of studies of the responses of ant communities to disturbance, as well as by a global model of ant community dynamics based on functional groups in relation to environmental stress and disturbance. Available data from mining studies suggest that ants reflect changes in other invertebrate groups, but this remains largely undocumented in rangelands. The feasibility of using ants as indicators in land management remains a key issue, given the large numbers of taxonomically challenging specimens in samples, and a lack of invertebrate expertise within most land-management agencies. However, recent work has shown that major efficiencies can be achieved by simplifying the ant sorting process, and such efficiencies can actually enhance rather than compromise indicator performance.

Notes: The potential impacts of introducing barramundi (Lates calcarifer) for the purpose of recreational fishing into Lake Kununurra, a tropical impoundment in the Kimberley region of Western Australia, are predicted by dietary comparisons with the resident fishes of the lake. Classification of the pooled dietary data identified five major feeding groups based on similarities in food items consumed. There was no significant dietary overlap between L. calcarifer and all species within the lake. The current study demonstrates that adult L. calcarifer fed primarily on teleosts and decopods, and are known to prey on the majority of the fish species found in Lake Kununurra. Although the introduction of L. calcarifer to Lake Kununurra has the potential to influence the resident fish community through competition (for food and habitat) and predation, it is likely that its effects will be minor. However, the lack of any data that would allow estimation of the likely survival of stocked L. calcarifer fry and fingerlings in the reservoir needs to be addressed. Such data are mandatory if a successful fishery is to be developed in the reservoir.

Notes: In the outskirts of metropolitan areas of Japan, there is an increasing tendency for residential and commercial facilities to be located in close proximity to transportation networks, particularly around railway stations. The resulting sprawl, involving residential development and industrial estates, perpetuates land use distortions in the semi-urban areas, as well as in agricultural and forestry lands. Lake Biwa, the largest lake in Japan, provides water to a population of 14 million people in Shiga, Osaka, Kyoto and Hyogo Prefectures. The Lake Biwa watershed has undergone dramatic land use transformations resulting from the migration of the downstream population and industries attracted by the provision of necessary, basic infrastructure via the Lake Biwa Comprehensive Development Plan (1972–1997). The purposes of this study are to provide a quantitative analysis of land use transformations within the Lake Biwa watershed, with particular reference to urbanization, examine watershed land use controls by analysis of deviation of actual land uses from the land use control targets, assess the flaws in the present land use controls and to discuss the implications of the results within the context of the Lake Biwa Comprehensive Conservation Plan (1999–), using a geographic information system to illustrate the results. The major findings of this study are that the continued existence of farmland and forests, in conjunction with urban sprawl, in the Urbanization Promotion Areas and the Use Districts, has resulted in serious land use problems which are seriously aggravated in the south-eastern and north-eastern parts of the watershed, and the expansion of urban areas in the Urbanization Control Areas and the White Areas has resulted in land use control becoming more problematic, especially in the eastern part of the watershed.

Notes: Abstract  There is strong demand for information about the status of, and trends in, Australia's biodiversity. Almost inevitably, this demand for information has led to demand for a broad-scale monitoring system. However, the decision to embark on a monitoring system should only be made once it has been established that a monitoring system is the optimal way to inform management. We stress the need to invest resources in assessing whether a monitoring system is necessary before committing resources to the design and implementation of the system. Current debate associated with the design of a biodiversity monitoring system has similarities to the debate within the range management profession in the early 1970s. The experience with range monitoring shows that large-scale monitoring systems such as those being proposed will require considerable resources, recurrently expended into the distant future, but with only a limited ability to adapt to new demands. Those involved in any biodiversity monitoring system will need to understand the implications of investing in a long-term monitoring programme. Monitoring sustainability will only be possible if the monitoring system is itself sustainable. We discuss a number of issues that need to be addressed before the system is at all sustainable. These attributes are a mix of biophysical, social and institutional attributes and highlight the view that monitoring systems of the type being suggested comprise an unusual mixture of attributes not found in typical scientific activity. The present paper is not a technical manual, but rather considers some of the design issues associated with designing and implementing large-scale monitoring systems.

Notes: Abstract  I investigated the relationship between species richness and composition of ant faunas, and sampling intensity in two regions with different long-term histories of grazing intensity in mulga (Acacia aneura) woodlands in northern New South Wales. There were two aims: (i) to examine the relationship between sampling intensity and species richness and composition; and (ii) to explore the differences in ant assemblages from two regions of markedly different grazing intensity when sampled at different intensities (i.e. when a higher proportion of the local ant fauna were collected). Ants were sampled in pit traps (120-mm diameter) at densities of two, four, six and nine pits per 100 m2. Each sampling-intensity treatment was replicated three times within each region. Pit traps filled with preservative were opened for 3 days. Species richness was higher with each successive increase in sampling intensity but was not different between regions for a given trapping intensity. There was no obvious asymptote of the curve relating trapping intensity to cumulative species richness suggesting that even greater trap densities than those used in the present study would be needed to collect most of the species of ants using a patch of ground over a few days. Spatial replication of a low-intensity sampling design did not capture as many species as one higher-intensity sampling array with the same total number of pit traps. This result can be explained by aggressive numerically dominant species of ants monopolizing access to a greater proportion of the traps in low-density arrays. Ordination reveals that regions and sampling-intensity treatments could be discriminated and that differences between regions with different grazing histories were less apparent with high-intensity sampling arrays than they were with low-intensity sampling arrays. This suggests that differences between locations in space (or potentially samples in time) could be exaggerated by incomplete sampling of the patch-scale fauna. Comparison of the present study with other studies suggests that most studies to date have used sampling intensities that would not give a thorough assessment of the patch-scale ground-dwelling fauna if sampled only by pit traps. The implications of the results for programmes of ant monitoring in rangelands are discussed.

Notes: Abstract  Functional integrity is the intactness of soil and native vegetation patterns and the processes that maintain these patterns. In Australia's rangelands, the integrity of these patterns and processes have been modified by clearing, grazing and fire. Intuitively, biodiversity should be strongly related to functional integrity; that is, landscapes with high functional integrity should maintain biodiversity, and altered, less functional landscapes may lose some biodiversity, defined here as the variety and abundance of the plants, animals and microorganisms of concern. Simple indicators of biodiversity and functional integrity are needed that can be monitored at a range of scales, from fine to coarse. In the present paper, we use examples, primarily from published work on Australia's rangeland, to document that at finer patch and hillslope scales several indicators of landscape functional integrity have been identified. These indicators, based on the quantity and quality of vegetation patches and interpatch zones, are related to biodiversity. For example, a decrease in the cover and width (quantity) and condition (quality) of vegetation patches, and an increase in bare soil (quantity of interpatch) near cattle watering points in a paddock are significantly related to declines in plant and grasshopper diversity. These vegetation patch-cover and bare-soil indicators have been monitored traditionally by field-based methods, but new high-resolution, remote-sensing imagery can be used in specific rangeland areas for this fine-scale monitoring. At intermediate paddock and small watershed scales, indicators that can be derived from medium-resolution remote-sensing are also needed for efficient monitoring of rangeland condition (i.e. functional integrity) and biodiversity. For example, 30–100-m-pixel Landsat imagery has been used to assess the condition of rangelands along grazing gradients extending from watering-points. The variety and abundance of key taxa have been related to these gradients (the Biograze project). At still larger region and catchment scales, indicators of rangeland functional integrity can also be monitored by coarse-resolution remote-sensing and related to biodiversity. For example, the extent and greenness (condition) of different regional landscapes have been monitored with 1-km-pixel satellite imagery. This regional information becomes more valuable when it indicates differences as a result of land management. Finally, we discuss potential future developments that could improve proposed indicators of landscape functional integrity and biodiversity, thereby improving our ability to monitor rangelands effectively.

Notes: Abstract  Birds have been widely regarded as a key element in monitoring biodiversity both in Australia and elsewhere. We believe that, although birds are unlikely to be an umbrella or indicator taxon for other biota (other vertebrates, invertebrates, plants, microorganisms), they do represent a taxon that can be monitored more easily and with less effort per datum than other biotic components. It has been shown by the great participation rate of lay observers (whom we call monitors) in several schemes (notably the Birds Australia Atlas programs) that there is a capacity to mobilize the public to undertake bird surveying. Although there are many limitations to acquiring high-quality information (scale, dynamism, mobility, irruptiveness, paucity of monitors over much of the rangelands), we think that these can be dealt with to allow the use of birds as a key component of biodiversity monitoring. We outline some of the possible options for statistically characterizing monitoring data for rangeland birds.

Notes: Abstract  As well as being important components of biodiversity in their own right, plants reflect the physical environment, are the primary target of many of the pressures acting on rangelands, and are relatively amenable to measurement. Hence, measurements based on plants have considerable potential to be efficient indicators of the response of rangeland biodiversity to land use. A recent report commissioned by the National Land and Water Resources Audit recommended a core set of 11 indicators, six of which relied on measurements of plants. These were trends in (i) the extent of clearing; (ii) the cover of native perennial ground-layer vegetation; (iii) the distribution and abundance of exotic plant species; (iv) the distribution and abundance of fire-sensitive species; (v) the distribution and abundance of grazing-sensitive species; and (vi) the distribution and abundance of listed threatened entities. Most indicated responses of plants to pressures acting on them. Only two (clearing and exotic plants) related to pressures. We recommend that the set be expanded to include two additional pressure indicators, one for grazing and another for fire, in recognition of their extent and potential influence on rangeland biodiversity. We also recommend that benchmark sites be included in all ground-based monitoring programmes to provide reference standards for those biotic indicators about which little is known. Assessments of the current state of knowledge about these indicators for two case-study regions, the Gascoyne–Murchison strategy area and Cape York Peninsula, have shown that it would be possible to monitor most of them directly at regional scales, but that current monitoring programmes fall short of achieving this.

Notes: Examination of 55 clinical isolates of uropathogenic Escherichia coli producing the CNF1 toxin demonstrated that the cnf1 gene is systematically associated with a hly operon via a highly conserved hlyD-cnf1 intergenic region (igs, 943 bp) as shown in the J96 UPEC strain. We examined if this association could reflect a co-regulation of the production of these toxins. Translation of cnf1 from an immediately upstream promoter has been shown to be controlled by means of an anti-Shine–Dalgarno sequence present in the cnf1 coding sequence [fold-back inhibition (cnf1 fbi)]. The cnf1 fbi was not regulated by elements present in the igs. An RNA covering the full hlyD sequence, the igs and extending on the cnf1 gene, was then detected in the J96 strain. This RNA could be part of a HlyCABD mRNA. Transcription of the haemolysin operon requires RfaH antitermination activity. Inactivation of rfaH in J96 resulted in a 100-fold reduction of the CNF1 content of bacteria. The production of CNF1 from a plasmidic igscnf1 DNA was not sensitive to RfaH, indicating that this factor acted on cnf1 transcription via the hly promoter. This way the cnf1 fbi mechanism might be overcome by transcription of cnf1 from the haemolysin promoter and antitermination by RfaH. This constitutes a novel system of bacterial virulence factors co-regulation.

Notes: The pathogenic fungus Candida albicans commonly causes mucosal surface infections. In immunocompromised patients, C. albicans may penetrate into deeper tissue, enter the bloodstream and disseminate within the host causing life-threatening systemic infections. In order to elucidate how C. albicans responds to the challenge of a blood environment, we analysed the transcription profile of C. albicans cells exposed to human blood using genomic arrays and a cDNA subtraction protocol. By combining data obtained with these two methods, we were able to identify unique sets of different fungal genes specifically expressed at different stages of this model that mimics bloodstream infections. By removing host cells and incubation in plasma, we were also able to identify several genes in which the expression level was significantly influenced by the presence of these cells. Differentially expressed genes included those that are involved in the general stress response, antioxidative response, glyoxylate cycle as well as putative virulence attributes. These data point to possible mechanisms by which C. albicans ensures survival in the hostile environment of the blood and how the fungus may escape the bloodstream as an essential step in its systemic dissemination.

Notes: Glycolysis is one of the best and widely conserved general metabolic pathways. Bacillus subtilis enzymes catalysing the central part of glycolysis, gathering the steps of interconversion of the triose phosphates from dihydroxyacetone-phosphate to phosphoenolpyruvate, are encoded by five genes, gapA, pgk, tpi, pgm and eno. They are transcribed in a hexacistronic operon together with cggR, the first cistron, encoding the repressor of this gapA operon. Using deletion analysis, we have localized the CggR operator between the promoter and the first gene of the operon. CggR was purified and used in gel mobility shift assays and DNase I footprinting experiments to delimit its target sequence. Site-directed mutagenesis and in vivo tests demonstrated that it consists of two direct-repeats (CGGGACN6TGTCN4CGGGACN6TG TC). Sequence analysis and transcriptome comparison of a wild-type and a cggR mutant strain strongly suggested that CggR regulates only the gapA operon. The presence of glycolytic carbon sources induces expression of the gapA operon. Genetic experiments allowed us to identify the metabolic steps required for the formation of the CggR effector. In vitro experiments with the suggested candidates allowed us to demonstrate that fructose-1,6-biphosphate (FBP) acts as an inhibitor of CggR DNA-binding activity (10 mM for full inhibition). FBP is thus the major signal for both CcpA-dependent catabolite repression (or activation) and activation of the central glycolytic genes. Genomic sequence comparisons suggest that these results can apply to numerous low-G+C, Gram-positive bacterial species.

Notes: We describe the isolation and characterization of ICL1 from the rice blast fungus Magnaporthe grisea, a gene that encodes isocitrate lyase, one of the principal enzymes of the glyoxylate cycle. ICL1 shows elevated expression during development of infection structures and cuticle penetration, and a targeted gene replacement showed that the gene is required for full virulence by M. grisea. In particular, we found that the prepenetration stage of development, before entry into plant tissue, is affected by loss of the glyoxylate cycle. There is a delay in germination, infection-related development and cuticle penetration in Δicl1 mutants. Recent reports have shown the importance of the glyoxylate cycle in the virulence of the human pathogenic fungus Candida albicans and the bacterial pathogen Mycobacterium tuberculosis. Our results indicate that the glyoxylate cycle is also important in this plant pathogenic fungus, demonstrating the widespread utility of the pathway in microbial pathogenesis.

Notes: Temporal variations in the stable carbon isotope composition (δ13C) of leaves and current-year stems were examined in beech trees over one year. The δ13C of both tissues were equal in the bud stage and started to diverge during growth, with values decreasing by 2·5 and 4·5‰ for stems and leaves, respectively. The dynamics of the δ13C and content of non-structural sugars were also assessed. The beginning of the growth period was characterized by a decrease in starch content and high starch δ13C values. Later in the season, the δ13C of leaf soluble sugars progressively decreased from the end of May and the δ13C of stem sucrose was at least 1·5‰ higher than that of leaves. The δ13C of CO2 respired by stem tissue increased during stem growth and exhibited large seasonal variations ( from −22·1 to −26·3‰). These values generally fell between those of starch and total organic matter. The results of the study showed that the δ13C of stems is altered by two apparent fractionation steps: one during sugar transfer from leaves to stems and one during stem respiration. These results may have implications for analysis of isotopic signals in tree rings and forest ecosystems.

Notes: The effect of prolonged water deficit on mRNA translation was quantitatively analysed in apical and basal leaves of whole tobacco (Nicotiana tabacum) plants. The level of large polysomes (six or more ribosomes per mRNA) was significantly higher in apical than basal leaves under well-watered conditions. In both young and old leaves, water deficit caused a progressive reduction in levels of polysomes with concomitant increases in 80S monosomes, indicative of reduced initiation of translation. Despite the global reduction in polysome formation over 144 h of water deficit, the water-deficit-induced putative lipid transfer protein (ltp) mRNA was associated with large polysomes and LTP content increased. Osmotin (osm) mRNA, another water-deficit-induced transcript, also remained associated with large polysomes during prolonged water deficit. In contrast, mRNAs encoding the non-stress proteins ribulose bisphosphate carboxylase/oxygenase small subunit (rbcS) and eukaryotic initiation factor 4A (eIF4A) decreased in abundance and shifted to small polysomes and non-polysomal complexes, indicating that initiation of translation of these mRNAs was impaired by water deficit. These results show that translational regulation is a component of the water-deficit response and the differential translation of individual mRNAs is distinct in leaves of different age.

Notes: Fluxes and concentrations of carbon dioxide and 13CO2 provide information about ecosystem physiological processes and their response to environmental variation. The biophysical model, CANOAK, was adapted to compute concentration profiles and fluxes of 13CO2 within and above a temperate deciduous forest (Walker Branch Watershed, Tennessee, USA). Modifications to the model are described and the ability of the new model (CANISOTOPE) to simulate concentration profiles of 13CO2, its flux density across the canopy–atmosphere interface and leaf-level photosynthetic discrimination against 13CO2 is demonstrated by comparison with field measurements. The model was used to investigate several aspects of carbon isotope exchange between a forest ecosystem and the atmosphere. During the 1998 growing season, the mean photosynthetic discrimination against 13CO2, by the deciduous forest canopy (Δcanopy), was computed to be 22·4‰, but it varied between 18 and 27‰. On a diurnal basis, the greatest discrimination occurred during the early morning and late afternoon. On a seasonal time scale, the greatest diurnal range in Δcanopy occurred early and late in the growing season. Diurnal and seasonal variations in Δcanopy resulted from a strong dependence of Δcanopy on photosynthetically active radiation and vapour pressure deficit of air. Model calculations also revealed that the relationship between canopy-scale water use efficiency (CO2 assimilation/transpiration) and Δcanopy was positive due to complex feedbacks among fluxes, leaf temperature and vapour pressure deficit, a finding that is counter to what is predicted for leaves exposed to well-mixed environments.

Notes: A combined model to simulate CO2 and H2O gas exchange at the leaf scale was parameterized using data obtained from in situ leaf-scale observations of diurnal and seasonal changes in the CO2 and H2O gas exchange of four temperate deciduous broad-leaved trees using a porometric method. The model consists of a Ball et al. type stomatal conductance submodel [Ball, Woodrow & Berry, pp. 221–224 in Progress in Photosynthesis Research (ed. I. Biggins), Martinus-Nijhoff Publishers, Dordrecht, The Netherlands, 1987] and a Farquhar et al. type biochemical submodel of photosynthesis (Farquhar, von Caemmerer & Berry, Planta 149, 78–90, 1980). In these submodels, several parameters were optimized for each tree species as representative of the quantitative characteristics related to gas exchange. The results show that the seasonal physiological changes of Vcmax25 in the biochemical model of photosynthesis should be used to estimate the long-term CO2 gas exchange. For Rd25 in the biochemical model of photosynthesis and m in the Ball et al. type stomatal conductance model, the difference should be counted during the leaf expansion period.

Notes: There is growing evidence that plant stomata have evolved physiological controls to satisfy the demand for CO2 by photosynthesis while regulating water losses by leaves in a manner that does not cause cavitation in the soil–root–xylem hydraulic system. Whether the hydraulic and biochemical properties of plants evolve independently or whether they are linked at a time scale relevant to plant stand development remains uncertain. To address this question, a steady-state analytical model was developed in which supply of CO2 via the stomata and biochemical demand for CO2 are constrained by the balance between loss of water vapour from the leaf to the atmosphere and supply of water from the soil to the leaf. The model predicts the intercellular CO2 concentration (Ci) for which the maximum demand for CO2 is in equilibrium with the maximum hydraulically permissible supply of water through the soil–root–xylem system. The model was then tested at two forest stands in which simultaneous hydraulic, ecophysiological, and long-term carbon isotope discrimination measurements were available. The model formulation reproduces analytically recent findings on the sensitivity of bulk stomatal conductance (gs) to vapour pressure deficit (D); namely, gs = gref(1 − m × lnD), where m is a sensitivity parameter and gref is a reference conductance defined at D = 1 kPa. An immediate outcome of the model is an explicit relationship between maximum carboxylation capacity (Vcmax) and soil–plant hydraulic properties. It is shown that this relationship is consistent with measurements reported for conifer and rain forest angiosperm species. The analytical model predicts a decline in Vcmax as the hydraulic capacity of the soil–root–xylem decreases with stand development or age.

Notes: The immunocytochemical localization of the plasma membrane H+-ATPase in epidermal cells of tomato roots was studied using a monoclonal antibody raised against purified maize P-type H+-ATPase. Plants subjected to iron starvation exhibited increased proton extrusion that was confined to the root elongation zones. Immunogold labelling of the H+-ATPase on the plasma membrane was considerably higher in rhizodermal cells within zones with intense proton extrusion than in non-acidifying areas of the roots. Transfer cells were formed in rhizodermal cells of Fe-deficient plants. Quantitative determination of immunolabelling revealed that the density of PM H+-ATPase in transfer cells was about twice that of ordinary epidermal cells. In transfer cells, H+-ATPase was most abundant on the plasma membrane lining the labyrinthine invaginations of the peripheral cell wall. While the number of immunologically detectable ATPase molecules in transfer cells was not spatially correlated with proton extrusion activity, the frequency of transfer cells was considerably higher in acidifying root areas relative to non-active segments. Split-root experiments indicated that both the steady-state level of plasma membrane H+-ATPase and proton extrusion activity are systemically regulated, indicating inter-organ regulation of rhizosphere acidification. Exogenous application of the auxin analog 2,4-dichlorophenoxyacetic acid and the ethylene precursor 1-aminocyclopropane-1-carboxlic acid caused the formation of transfer cells at a frequency similar to that observed in Fe-deficient roots. However, the number of proton pumps was not affected by the hormone treatment, suggesting that both responses are regulated independently. It is concluded that transfer cells in the rhizodermis may be important but not crucial for rhizosphere acidification.

Notes: Internal transport of gases is crucial for vascular plants inhabiting aquatic, wetland or flood-prone environments. Diffusivity of gases in water is approximately 10 000 times slower than in air; thus direct exchange of gases between submerged tissues and the environment is strongly impeded. Aerenchyma provides a low-resistance internal pathway for gas transport between shoot and root extremities. By this pathway, O2 is supplied to the roots and rhizosphere, while CO2, ethylene, and methane move from the soil to the shoots and atmosphere. Diffusion is the mechanism by which gases move within roots of all plant species, but significant pressurized through-flow occurs in stems and rhizomes of several emergent and floating-leaved wetland plants. Through-flows can raise O2 concentrations in the rhizomes close to ambient levels. In general, rates of flow are determined by plant characteristics such as capacity to generate positive pressures in shoot tissues, and resistance to flow in the aerenchyma, as well as environmental conditions affecting leaf-to-air gradients in humidity and temperature. O2 diffusion in roots is influenced by anatomical, morphological and physiological characteristics, and environmental conditions. Roots of many (but not all) wetland species contain large volumes of aerenchyma (e.g. root porosity can reach 55%), while a barrier impermeable to radial O2 loss (ROL) often occurs in basal zones. These traits act synergistically to enhance the amount of O2 diffusing to the root apex and enable the development of an aerobic rhizosphere around the root tip, which enhances root penetration into anaerobic substrates. The barrier to ROL in roots of some species is induced by growth in stagnant conditions, whereas it is constitutive in others. An inducible change in the resistance to O2 across the hypodermis/exodermis is hypothesized to be of adaptive significance to plants inhabiting transiently waterlogged soils. Knowledge on the anatomical basis of the barrier to ROL in various species is scant. Nevertheless, it has been suggested that the barrier may also impede influx of: (i) soil-derived gases, such as CO2, methane, and ethylene; (ii) potentially toxic substances (e.g. reduced metal ions) often present in waterlogged soils; and (iii) nutrients and water. Lateral roots, that remain permeable to O2, may be the main surface for exchange of substances between the roots and rhizosphere in wetland species. Further work is required to determine whether diversity in structure and function in roots of wetland species can be related to various niche habitats.

Notes: Many macroalgae have significant spatial differentiation involving higher rate resource use at a site than of acquisition of that resource from the environment at that site. Long-distance symplasmic transport of solutes occurs in some large green algae where the solutes are moved in streaming cytoplasm. In some large brown algae there is evidence of long-distance symplasmic transport of organic C and other solutes. Structural and physiological data suggest that while the transport in ‘sieve tubes’ of Macrocystis might be by a Munch pressure flow mechanism the transport in many other brown algae is less likely to be by this mechanism. Less is known of long-distance symplasmic transport in red algae. In terrestrial bryophytes transpiration occurs and in some liverworts and many mosses (but not in hornworts) there are files of dead cells in their tissues which may, and in some cases certainly, function in long-distance apoplasmic water transport. The hydraulic conductivity of these conduits is poorly characterized. Long-distance symplasmic transport in some mosses have been characterized both structurally and physiologically, but in other mosses and in liverworts the evidence is only structural. Most of these symplasmic transport pathways seem to have a high resistance to flow.

Notes: Plant cells exposed to photo-inhibitory conditions respond by accumulation of the early light-induced proteins (Elips) with a potential photoprotective function. Here we studied the expression of Elip in various pea cultivars grown under agricultural or climate-chamber conditions. We demonstrated that the expression of Elip in all cultivars was developmentally regulated and its level decreased during flowering and post-flowering periods. Surprisingly, significant amounts of Elip transcripts, but not proteins, accumulated in senescing leaves already under low light conditions and the exposure to light stress resulted in a 10-times higher induction of Elip transcripts. Furthermore, the expression pattern of Elip transcript and protein significantly differed under field and growth-chamber conditions. First, the expression level of Elip was much higher in field-grown than in chamber-grown cultivars. Second, substantial amounts of Elip transcripts and protein were detected during the night in field-grown plants in contrast to chamber-grown cultivars due to a synergistic effect of light stress occurring during the day and low temperature present during the following night. The expression of the PsbS protein related to Elips and involved in the photoprotection of the photosystem II was relatively constant under all conditions tested.

Notes: Colonization of the rhizosphere by micro-organisms results in modifications in plant growth and development. This review examines the mechanisms involved in growth promotion by plant growth-promoting rhizobacteria which are divided into indirect and direct effects. Direct effects include enhanced provision of nutrients and the production of phytohormones. Indirect effects involve aspects of biological control: the production of antibiotics and iron-chelating siderophores and the induction of plant resistance mechanisms. The study of the molecular basis of growth promotion demonstrated the important role of bacterial traits (motility, adhesion and growth rate) for colonization. New research areas emerge from the discovery that molecular signalling occurs through plant perception of eubacterial flagellins. Recent perspectives in the molecular genetics of cross-talking mechanisms governing plant–rhizobacteria interactions are also discussed.

Notes: The photosynthetic rates under saturating CO2 conditions per unit of leaf-N content were higher in wheat than in rice. This suggested that ribulose-1,5-bisphosphate (RuBP) regeneration capacity is greater in wheat. Therefore, the biochemical factor(s) for this difference were examined between rice and wheat. Soluble protein-N, insoluble-N, and trichloroacetic acid (TCA) soluble-N contents were found not to differ between the two species. The activities of several Calvin cycle enzymes such as RuBP carboxylase, NADP-glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and chloroplastic fructose-1,6-bisphosphatase (cpFBPase) activities per unit of leaf-N content were all higher in wheat than in rice. Among them, cpFBPase activity was most highly correlated with CO2-saturated photosynthesis. The Vmax activity of sucrose-phosphate synthase (SPS) for UDP-glucose was almost the same between the two species and its Km value was a little lower in rice. Chlorophyll content and its a/b ratio did not differ. Cytochrome (Cyt) f content was greater in wheat, whereas coupling factor 1 content was greater in rice. Cyt f content was highly correlated with CO2-saturated photosynthesis, irrespective of the two species. The results thus suggested that higher RuBP regeneration capacity in wheat leaves is most closely related to a greater Cyt f content and that another candidate is cpFBPase.

Notes: Mannitol, a sugar alcohol that may serve as a compatible solute to cope with salt stress, is synthesized via the action of a mannose-6-phosphate reductase (M6PR) in celery (Apium graveolens L). In contrast to previous approaches that have used a bacterial gene to engineer mannitol biosynthesis in plants and other organisms, Arabidopsis thaliana, a non-mannitol producer, was transformed with the celery leaf M6PR gene under control of the CaMV 35S promotor. In all independent Arabidopsis M6PR transformants, mannitol accumulated throughout the plants in amounts ranging from 0·5 to 6 µmol g−1 fresh weight. A novel compound, not found in either celery or Arabidopsis, 1-O-β-d-glucopyranosyl-d-mannitol, also accumulated in vegetative tissues of mature plants in amounts up to 4 µmol g−1 fresh weight, but not in flowers and seeds. In the absence of NaCl, all transformants were phenotypically the same as the wild type; however, in the presence of NaCl, mature transgenic plants showed a high level of salt tolerance, i.e. growing, completing normal development, flowering, and producing seeds in soil irrigated with 300 mm NaCl in the nutrient solution. These results demonstrate a major role in developing salt-tolerant plants by means of introducing mannitol biosynthesis using M6PR.

Notes: The present study was carried out to investigate whether the P concentration in the roots or the shoots controls the growth and citrate exudation of cluster roots in white lupin (Lupinus albus L). Foliar P application indicated that low P concentration in the shoots enhanced cluster-root growth and citrate-exudation rate more so than low P concentration in the roots. In the split-root study, the P concentration in the shoots increased with increased P supply (1, 25 or 75 mmol m−3 P), to the ‘privileged’ root halves. Roots ‘deprived’ of P invariably had the same low P concentrations, whereas those in the ‘privileged’ roots increased with increasing P supply (1, 25 or 75 mmol m−3 P). Nevertheless, the proportion of the total root mass allocated to cluster roots, and the citrate-exudation rates from the root halves were always similar on both root halves, irrespective of P supply, and decreased with increasing shoot P concentrations. Peak citrate exudation rates from developing cluster roots were significantly faster from cluster roots on the ‘deprived’ root halves when the ‘privileged’ half was exposed to 1 mmol m−3 P as compared with 25 or 75 mmol m−3 P. The possibility that changes in the concentrations of P fractions in the root halves influenced cluster-root growth and citrate exudation was discounted, because there were no significant differences in insoluble organic P, ester-P and inorganic P among all ‘deprived’ root halves. The results indicate that cluster-root proportions and citrate exudation rates were regulated systemically by the P status of the shoot, and that P concentrations in the roots had little influence on growth and citrate exudation of cluster roots in L. albus.

Notes: This review deals with aspects of the cellular and molecular biology of the sieve element/companion cell complex, the functional unit of sieve tubes in angiosperms. It includes the following issues: (a) evolution of the sieve elements; (b) the specific structural outfit of sieve elements and its functional significance; (c) modes of cellular and molecular interaction between sieve element and companion cell; (d) plasmodesmal trafficking between sieve element and companion cell as the basis for macromolecular long-distance signalling in the phloem; (e) diversity of sieve element/companion cell complexes in the respective phloem zones (collection phloem, transport phloem, release phloem); (f) deployment of carriers, pumps and channels on the plasma membrane of sieve element/companion cell complexes in various phloem zones; and (g) implications of the molecular-cellular equipment of sieve element/companion cells complexes for mass flow of water and solutes in a whole-plant frame.

Notes: Recent advances in allometric theory have proposed a novel quantitative framework by which to view the evolution of plant form and function. This general theory has placed strong emphasis on the importance of long-distance transport in shaping the evolution of many attributes of plant form and function. Specifically, it is hypothesized that with the evolutionary increase in plant size natural selection has also resulted in vascular networks that minimize scaling of total hydrodynamic resistance associated with increasing transport distances. Herein the central features of this theory are reviewed and a broad sampling of supporting but yet preliminary empirical data are analysed. In particular, subtle attributes of the scaling of tracheid and vessel anatomy are hypothesized to be crucial for the evolution of increased plant size. Furthermore, the importance of minimizing hydrodynamic resistance associated with increased transport distances is also hypothesized to be reflected in an isometric scaling relationship between stem mass, MS and root mass, MR(i.e. MS ∝ MR). Preliminary data from multiple extant and fossil plant taxa provide tantalizing evidence supporting the predicted relationships. Together, these results suggest that selection for the minimization of the scaling of hydrodynamic resistance within plant vascular networks has in turn allowed for the enormous diversification in vascular plant size.

Notes: Plant hydraulic conductance, namely the rate of water flow inside plants per unit time and unit pressure difference, varies largely from plant to plant and under different environmental conditions. Herein the main factors affecting: (a) the scaling between whole-plant hydraulic conductance and leaf area; (b) the relationship between gas exchange at the leaf level and leaf-specific xylem hydraulic conductance; (c) the short-term physiological regulation of plant hydraulic conductance under conditions of ample soil water, and (d) the long-term structural acclimation of xylem hydraulic conductance to changes in environmental conditions are reviewed. It is shown that plant hydraulic conductance is a highly plastic character that varies as a result of multiple processes acting at several time scales. Across species ranging from coniferous and broad-leaved trees to shrubs, crop and herbaceous species, and desert subshrubs, hydraulic conductance scaled linearly with leaf area, as expected from first principles. Despite considerable convergence in the scaling of hydraulic properties, significant differences were apparent across life forms that underlie their different abilities to conduct gas exchange at the leaf level. A simple model of carbon allocation between leaves and support tissues explained the observed patterns and correctly predicted the inverse relationships with plant height. Therefore, stature appears as a fundamental factor affecting gas exchange across plant life forms. Both short-term physiological regulation and long-term structural acclimation can change the levels of hydraulic conductance significantly. Based on a meta-analysis of the existing literature, any change in environmental parameters that increases the availability of resources (either above- or below-ground) results in the long-term acclimation of a less efficient (per unit leaf area) hydraulic system.

Notes: The ability of juvenile Laurus nobilis and Acer negundo plants to refill embolized xylem vessels was tested under conditions of soil drought when xylem sap pressure was substantially negative, thus violating the expected condition that pressure must rise to near atmospheric for refilling. Intact potted plants were dried to a stem water potential (ΣW) corresponding with approximately 80% loss of hydraulic conductivity (PLC) in shoots. Then plants were re-watered and kept at a less negative target ΨW for 1–48 h. The ΨW was measured continuously with stem psychrometers. Rewatered L. nobilis held at the target ΨW for 1 h showed no evidence for refilling unless ΨW was within a few tenths of a MPa of zero. In contrast, re-watered L. nobilis held for 24 and 48 h at water potentials well below zero showed a significant reduction in PLC. The recovery was highly variable, being complete in some stem segments, and scarcely evident in others. Embolism repair was accompanied by a significant but moderate decrease in the osmotic potential (Ψ) of the bulk xylem sap (Ψ = −67 kPa in recovering plants versus −31 kPa in controls). In contrast, embolized and re-watered A. negundo plants held for 24 h at target ΨW of −0·9 and −0·3 MPa showed no embolism reversal. The mechanism allowing L. nobilis plants to refill under negative pressure is unknown, but does not appear to operate in A. negundo, and is slower to act for drought-induced embolism than when embolism was artificially induced by air injection as previously shown for L. nobilis.

Notes: Dark chilling inhibited photosynthesis in two soybean [Glycine max (L.) Merr.] cultivars (Fiskeby V and Maple Arrow). The inhibition of CO2 assimilation was characterized by a simultaneous decrease in stomatal conductance (Gs) and intercellular CO2 concentration (Ci) in Maple Arrow, whereas a similar decrease in Gs in Fiskeby V occurred without any change in Ci. Dark chilling had little effect on total ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) activity, Rubisco protein content or Rubisco activation state in the subsequent light period. Chilling reduced the abundance of the nocturnal Rubisco inhibitor, 2-carboxyarabinitol 1-phosphate, only in Fiskeby V. The abundance of Rubisco small subunit transcripts was enhanced in both cultivars as a result of dark chilling. Dark chilling decreased the maximal extractable activities and activation states of stromal fructose-1,6-bisphosphatase (FBPase) and NADP-malate dehydrogenase but had no effect on sucrose phosphate synthase or leaf sucrose and starch contents. It is concluded that dark chilling-induced limitations on CO2 assimilation are predominantly due to metabolic restrictions rather than to direct effects on electron transport reactions and that stromal FBPase is particularly susceptible to dark chilling.

Notes: A model recently proposed by Siddiqi & Glass (Plant, Cell, and Environment 25, 1211–1217, 2002) attempts to reconcile discrepancies in the measurement of cytosolic nitrate concentrations ([NO3–]cyt) in plant root cells, specifically between low (∼ 4 mm) homeostatic values reported in studies using ion-specific microelectrodes on the one hand, and wide fluctuations in [NO3–]cyt reported in other studies, especially those using compartmental analysis by tracer efflux (CATE). Although Siddiqi & Glass concede that cytosolic NO3– homeostasis, as determined by microelectrodes, is at odds with certain experimental observations, they nevertheless promote a model that takes microelectrode readings at face value, and assert that the variations seen using CATE methodology are artefacts attributable to contributions from substantial, rapidly exchanging, and highly variable NO3– pools putatively residing in organelles such as plastids and the endoplasmic reticulum. We show here that such a model is not tenable, drawing upon experimental evidence from previous studies, and from a more comprehensive model that examines the characteristics and consequences of subcompartmented cytoplasmic exchange in root cells.

Notes: Stomatal function mediates physiological trade-offs associated with maintaining a favourable H2O balance in leaf tissues while acquiring CO2 as a photosynthetic substrate. The C3 and C4 species appear to have different patterns of stomatal response to changing light conditions, and variation in this behaviour may have played a role in the functional diversification of the different photosynthetic pathways. In the current study, we used gain analysis theory to characterize the stomatal conductance response to light intensity in nine different C3, C4 and C3-C4 intermediate species Flaveria species. The response of stomatal conductance (gs) to a change in light intensity represents both a direct (related to a change in incident light intensity, I) and indirect (related to a change in intercellular CO2 concentration, Ci) response. The slope of the line relating the change in gs to Ci was steeper in C4 species, compared with C3 species, with C3-C4 species having an intermediate response. This response reflects the greater relative contribution of the indirect versus direct component of the gs versus I response in the C4 species. The C3-C4 species, Flaveria floridana, exhibited a C4-like response whereas the C3-C4 species, Flaveria sonorensis and Flaveria chloraefolia, exhibited C3-like responses, similar to their hypothesized position along the evolutionary trajectory of the development of C4 photosynthesis. There was a positive correlation between the relative contribution of the indirect component of the gs versus I response and water use efficiency when evaluated across all species. Assuming that the C3-C4 intermediate species reflect an evolutionary progression from fully expressed C3 ancestors, the results of the current study demonstrate an increase in the contribution of the indirect component of the gs versus I response as taxa evolve toward the C4 extreme. The greater relative contribution of the indirect component of the stomatal response occurs through both increases in the indirect stomatal components and through decreases in the direct. Increases in the magnitude of the indirect component may be related to the maintenance of higher water use efficiencies in the intermediate evolutionary stages, before the appearance of fully integrated C4 photosynthesis.

Notes: The first objective of the present study was to quantify the effects of tree age and stem position on specific conductivity (ks), vulnerability to embolism and water storage capacity (capacitance) in trunks of young, mature and old-growth ponderosa pine. The second objective was to determine relationships between hydraulic characteristics and radial and height growth rates to increase the understanding of possible tradeoffs. Within sapwood at all heights and in all ages of trees, outer sapwood had 25–60% higher ks than inner sapwood. The water potential at which embolism started (air entry point) was 1.3 MPa lower in inner sapwood than outer sapwood within the mature trees, but there was no difference in the other trees. There was no significant difference in capacitances between the tops of the old growth trees, the mature trees and the young trees. Taking all data together, the capacitances increased sharply with an increase in ks and an increase in vulnerability to embolism. The hydraulic characteristics of the three age classes were correlated with the height growth rate but not with the diameter growth rate. Within these age classes, high ks was associated with the slowest yearly increase in sapwood area and with a low percentage of latewood, whereas high vulnerability to embolism and high capacitance were more closely associated with high height growth rates.

Notes: The mobility of Cd in potato plants (Solanum tuberosum) was examined using both short-term radioisotopic labelling with 109Cd and long-term growth experiments in soil supplemented with Cd, with an emphasis on the pathways through which Cd is taken up by tubers. Split-pot experiments showed that tubers and their associated stolons and stolon roots contribute only a minor fraction to the overall Cd absorption by the plant. Most of the Cd was absorbed by the basal roots. 109Cd absorbed from the soil was rapidly exported to other parts of the plant, especially the stem, with significant amounts appearing in the tubers within 30 h. Application of 109Cd to leaves showed that Cd can be rapidly distributed via the phloem to all tissues. The results suggest that unlike Ca, Cd has high mobility in plants in both xylem and phloem, and that stems may have an important role in transfer between these two pathways.

Notes: The distributing of materials throughout a symplastic domain must involve at least two classes of transport steps: plasmodesmatal and cytoplasmic. To underpin the latter, the most obvious candidate mechanisms are cytoplasmic streaming and diffusion. The thesis will be here advanced that, although both candidates clearly do transport cytoplasmic entities, the cytoplasmic streaming per se is not of primary importance in symplastic transport but that its underlying molecular motor activity (of which the streaming is a readily visible consequence) is. Following brief tutorials on low Reynolds number flow, diffusion, and targeted intracytoplasmic transport, the hypothesis is broached that macromolecular and vesicular transport along actin trackways is both the cause of visible streaming and the essential metabolically driven cytoplasmic step in symplastic transport. The concluding discussion highlights four underdeveloped aspects of the active cytoplasmic step: (i) visualization of the real-time transport of messages and metabolites; (ii) enumeration of the entities trafficked; (iii) elucidation of the routing of the messages and metabolites within the cytoplasm; and (iv) transference of the trafficked entities from cytoplasm into plasmodesmata.

Notes: In terrestrial higher plants, phloem transport delivers most nutrients required for growth and storage processes. Some 90% of plant biomass, transported as sugars and amino nitrogen (N) compounds in a bulk flow of solution, is propelled though the phloem by osmotically generated hydrostatic pressure differences between source (net nutrient export) and sink (net nutrient import) ends of phloem paths. Source loading and sink unloading of sugars, amino N compounds and potassium largely account for phloem sap osmotic concentrations and hence pressure differences. A symplasmic component is characteristic of most loading and unloading pathways which, in some circumstances, may be interrupted by an apoplasmic step. Raffinose series sugars appear to be loaded symplasmically. However, sucrose, and probably certain amino acids, are loaded into minor veins from source leaf apoplasms by proton symporters localized to plasma membranes of their sieve element/companion cell (se/cc) complexes. Sucrose transporters, with complementary kinetic properties, are conceived to function as membrane transporter complexes that respond to alterations in source/sink balance. In contrast, symplasmic unloading is common for many sink types. Intervention of an apoplasmic step, distal from importing phloem, is reserved for special situations. Effluxers that release sucrose and amino acids to the surrounding apoplasm in phloem loading and unloading are yet to be cloned. The physiological behaviour of effluxers is consistent with facilitated membrane transport that can be energy coupled. Roles of sucrose and amino acid transporters in phloem unloading remain to be discovered along with mechanisms regulating symplasmic transport. The latter is hypothesized to exert significant control over phloem unloading and, in some circumstances, phloem loading.

Notes: The architecture of the presumed water-conducting cells of the major lineages of early tracheophytes recorded in Silurian and Devonian rocks is reviewed, together with descriptions of further diverse types whose derivation remains uncertain. Evidence has been obtained from a wide gamut of fossils including coalified compressions, silicified, pyritized and calcium carbonate perimineralizations. Most of the cells, only a few having been unequivocally demonstrated to be tracheidal, have walls with two layers, the inner sometimes broadly similar to annular, spiral and scalariform secondary thickenings of extant xylem. There are, however, very few cases of identical construction and the fossil representatives show greater complexity and variety. Their walls are presumed to have been lignified, but the polymer has not yet been directly identified in the fossils. The implications of these wall architectures on the functioning of the cells in water conduction are briefly considered, as is their relevance to hypotheses on inter-relationships of early tracheophytes and on tracheid ontogeny.

Notes: The xylem is a long-distance transport system that is unique to higher plants. It evolved into a very sophisticated plumbing system ensuring controlled loading/unloading of ions and water and their effective translocation to the required sinks. The focus of this overview will be the intrinsic inter-relations between structural and functional features of the xylem. Taken together the xylem is designed to prevent cavitation (entry of air bubbles), induced by negative pressures under transpiration and to repair the cavitated vessels. Half-bordered pits between xylem parenchyma cells and xylem vessels are on the one hand the gates to the vessels but on the other hand a serious ‘bottle-neck’ for transport. Hence it becomes evident that special transport systems exist at the interface between the cells and vessels, which allow intensive fluxes of ions and water to and out of the xylem. The molecular identification and biophysical/biochemical characterization of these transporters has just started. Paradigms for the sophisticated mechanism of controlled xylem transport under changing environmental conditions are SKOR, a Shaker-like channel involved in K+-loading and SOS1, a Na+/H+ antiporter with a proposed dual function in Na+ transport. In view of the importance of plant water relations it is not surprising to find that water channels dominate the gate of access to xylem. Future studies will focus on the mechanism(s) that regulate water channels and ion transporters and on their physiological role in, for example, the repair of embolism. Clearly, progress in this specific field of research will greatly benefit from an integration of molecular and biophysical techniques aimed to understand ‘whole-plant’ behaviour under the ever-changing environmental conditions in the daily life of all plants.

Notes: Rice cultivation areas in East, Southeast and South Asia account for 89% of the world total, and field measurements of methane (CH4) emission from rice cultivation have been widely performed in this area. In this paper, we assembled most of the measurements and developed region-specific CH4 emission factors. Efforts were made in order to regionalize rice fields by climate and soil properties, and to incorporate the effect of organic input and water regime on emission. Data on rice cultivation areas of 1995 were collected at subdivision level (province, state, prefecture, etc.). Total emission from these areas was estimated at 25.1 Tg CH4 year−1, of which 7.67 Tg was emitted from China and 5.88 Tg from India. Irrigated and rainfed rice fields contributed 70.4 and 27.5% to the total emission, respectively. Deepwater rice fields had a very small share. A high-resolution and quality emission distribution map was constructed as the emission was directly estimated at province level and below that, a 30-second land-use dataset was used in order to translate the emission to grid format. As the rice cultivation area in the study region accounts for 89% of the world total, extrapolating the estimate to the global scale indicates a global emission of 28.2 Tg CH4 year−1.The estimate was compared with country reports made by local scientists. For some countries – such as Indonesia, Myanmar, Thailand, Vietnam, Japan, South Korea, Pakistan and the Philippines – the results of this estimate agree reasonably well with their country reports (CV 〈 15%). For some other countries – such as China, India and Bangladesh – there is relatively large disagreement between our estimate and their country reports. The reasons for the discrepancies were discussed.

Notes: Nitrogen-fixing plant species growing in elevated atmospheric carbon dioxide concentration ([CO2]) should be able to maintain a high nutrient supply and thus grow better than other species. This could in turn engender changes in internal storage of nitrogen (N) and remobilisation during periods of growth. In order to investigate this one-year-old-seedlings of Alnus glutinosa (L.) Gaertn and Pinus sylvestris (L.) were exposed to ambient [CO2] (350 µmol mol−1) and elevated [CO2] (700 µmol mol−1) in open top chambers (OTCs). This constituted a main comparison between a nitrogen-fixing tree and a nonfixer, but also between an evergreen and a deciduous species. The trees were supplied with a full nutrient solution and in July 1994, the trees were given a pulse of 15N-labelled fertiliser. The allocation of labelled N to different tissues (root, leaves, shoots) was followed from September 1994 to June 1995. While N allocation in P. sylvestris (Scots pine) showed no response to elevated [CO2], A. glutinosa (common alder) responded in several ways. During the main nutrient uptake period of June–August, trees grown in elevated [CO2] had a higher percentage of N derived from labelled fertiliser than trees grown in ambient [CO2]. Remobilisation of labelled N for spring growth was significantly higher in A. glutinosa grown in elevated [CO2] (9.09% contribution in ambient vs. 29.93% in elevated [CO2] leaves). Exposure to elevated [CO2] increased N allocation to shoots in the winter of 1994–1995 (12.66 mg in ambient vs. 43.42 mg in elevated 1993 shoots; 4.81 mg in ambient vs. 40.00 mg in elevated 1994 shoots). Subsequently significantly more labelled N was found in new leaves in April 1995. These significant increases in movement of labelled N between tissues could not be explained by associated increases in tissue biomass, and there was a significant shift in C-biomass allocation away from the leaves towards the shoots (all above-ground material except leaves) in A. glutinosa. This experiment provides the first evidence that not only are shifts in C allocation affected by elevated [CO2], but also internal N resource utilisation in an N2-fixing tree.

Notes: High evaporative demand and periodic drought characterize the growing season in midwestern grasslands relative to deciduous forests of the eastern US, and predicted climatic changes suggest that these climatic extremes may be exacerbated. Despite this less than optimal environment for tree seedling establishment, deciduous trees have expanded into adjacent tallgrass prairie within the last century leading to a dramatic land cover change. In order to determine the role of light and temperature on seedling establishment, we assessed carbon and water relations and aboveground growth of first-year Quercus macrocarpa seedlings exposed to one of three conditions: (1) intact tallgrass prairie communities (control), (2) aboveground herbaceous biomass removed (grass removal), and (3) shade plus biomass removal to reduce light (PFD) to levels typical of the grassland-forest ecotone (shade). In the 2000 growing season, precipitation was 35% below the long-term average, which had a significant negative effect on oak seedling carbon gain at midseason (photosynthesis declined to 10% of maximum rates). However, net photosynthesis and stomatal conductance in the shade treatment was ca. 2.5 and 1.5 times greater, respectively, than in control treatment seedlings during this drought. During this period, leaf and air temperatures in control seedlings were similar whereas leaf temperatures in the shade treatment remained below air temperature. A late-season recovery period, coincident with decreased air temperatures, resulted in increased net photosynthesis for all seedlings. Increased photosynthetic rates and water relations in shaded seedlings compared to seedlings in full sun suggest that, at least in dry years, high light and temperature may negatively impact oak seedling performance. However, high survival rates for all seedlings indicate that Q. macrocarpa seedlings are capable of tolerating both present-day and future climatic extremes. Unless historic fire regimes are restored, forest expansion and land cover change are likely to continue.

Notes: Nitric oxide emissions from a typical rice–wheat rotation system in southeastern China were continuously measured with an automatic system in 1996–1997. The seasonal pattern of the NO emissions was characterized for the non-waterlogged period of a rotation cycle. Nitric oxide emissions during the period from March through June were 3.9–6.3 folds for the fertilized plots and 1.6 folds for the unfertilized plot larger than those from November through December. Nitric oxide emissions were not detectable during the winter period from January through February. Amendment of synthetic fertilizer N significantly enhanced the NO emission by a factor of 6.5, but the enhancement was significantly mitigated by 25% through substituting ca. 16% of the synthetic fertilizer N with organic N from fermented crop residues or by 21% through deep tillage. The NO–N emission factor, defined as the amount of NO–N released per unit of synthetic fertilizer N input, was determined to be 0.025 kg NO–N kg−1 of N applied for the non-waterlogged period, which was reduced by 32% through substituting part of the synthetic N fertilizer with fermented crop residues or by 24% through deep tillage. In addition, the NO emission factor, defined as the amount of NO–N emitted from unit unfertilized area per day, was observed to be ca. 3.8 g N ha−1 d−1. Approximately 0.55 Tg N yr−1 was likely released as NO from Chinese cultivated lands.

Notes: Forest soils, rather than woody biomass, are the dominant long-term sink for N in forest fertilization studies and, by inference, for N from atmospheric deposition. Recent evidence of significant abiotic immobilization of inorganic-N in forest humus layers challenges a previously widely held view that microbial processes are the dominant pathways for N immobilization in soil. Understanding the plant, microbial, and abiotic mechanisms of N immobilization in forest soils has important implications for understanding current and future carbon budgets. Abiotic immobilization of nitrate is particularly perplexing because the thermodynamics of nitrate reduction in soils are not generally favorable under oxic conditions. Here we present preliminary evidence for a testable hypothesis that explains abiotic immobilization of nitrate in forest soils. Because iron (and perhaps manganese) plays a key role as a catalyst, with Fe(II) reducing nitrate and reduced forms of carbon then regenerating Fe(II), we call this ‘the ferrous wheel hypothesis’. After nitrate is reduced to nitrite, we hypothesize that nitrite reacts with dissolved organic matter through nitration and nitrosation of aromatic ring structures, thus producing dissolved organic nitrogen (DON). In addition to ignorance about mechanisms of DON production, little is known about DON dynamics in soil and its fate within ecosystems. Evidence from leaching and watershed studies suggests that DON production and consumption may be largely uncoupled from seasonal biological processes, although biological processes ultimately produce the DOC and reducing power that affect DON formation and the entire N cycle. The ferrous wheel hypothesis includes both biological and abiological processes, but the reducing power of plant-derived organic matter may build up over seasons and years while the abiotic reduction of nitrate and reaction of organic matter with nitrite may occur in a matter of seconds after nitrate enters the soil solution.

Notes: Estimates of the role of the European terrestrial biosphere in the global carbon cycle still vary by a factor 10. This is due to differences in methods and assumptions employed, but also due to difference in reference periods of the studies. The magnitude of the sink varies between years because of inter-annual variation of short-term climate, but also due to long-term trends in development of the vegetation and its management. For this purpose, we present the results of an application of a carbon bookkeeping model to the forest sector of the European forests from 1950 to 1999. The analysis includes the compartments trees, soils, and wood products. The model uses statistics on European (30 countries excl. CIS) stemwood volume increment, forest area change, fellings, wood products and their international trade, and natural disturbances, supplemented with conversion coefficients, soil parameters and information on management.An (almost uninterrupted) increasing sink (Net Biome Production) in the European forest sector was found, increasing from 0.03 Pg C year−1 in the 1950s to 0.14 Pg C year−1 in the 1990s (for resp. 132 million hectares and 140 million hectares of forest). The sink in the tree and the soil compartment were approximately of the same size until 1970. After the 1970s the size of the sink in the tree biomass increases quickly, causing the tree biomass to account for some two thirds of the total sink in the 1990s. The results as presented here have to be regarded with caution especially with regard to the early decades of the analysis and with regard to the soil compartment.

Notes: Climate change treatments – winter warming, summer drought and increased summer precipitation – have been imposed on an upland grassland continuously for 7 years. The vegetation was surveyed yearly. In the seventh year, soil samples were collected on four occasions through the growing season in order to assess mycorrhizal fungal abundance. Mycorrhizal fungal colonisation of roots and extraradical mycorrhizal hyphal (EMH) density in the soil were both affected by the climatic manipulations, especially by summer drought. Both winter warming and summer drought increased the proportion of root length colonised (RLC) and decreased the density of external mycorrhizal hyphal. Much of the response of mycorrhizal fungi to climate change could be attributed to climate-induced changes in the vegetation, especially plant species relative abundance. However, it is possible that some of the mycorrhizal response to the climatic manipulations was direct – for example, the response of the EMH density to the drought treatment. Future work should address the likely change in mycorrhizal functioning under warmer and drier conditions.

Notes: Measurements were made of nitrous oxide (N2O) emissions from N-fertilised ungrazed grassland and arable land at sites widely distributed across Great Britain during 1999–2001. The closed static chamber method was used throughout. Emissions varied widely throughout the year at each site, and between sites. Daily fluxes up to 1200 g N2O–N ha−1 d−1 were recorded. The highest annual flux was 27.6 kg N2O–N ha−1 at a grassland site in Wales, whereas the lowest, 1.7 kg N2O–N ha−1, occurred on a soil overlying chalk in southern England. The key factors affecting N2O emissions from agricultural soil were soil WFPS, temperature and soil NO3––N content. On grassland, rainfall (particularly around the time of N application), with its consequent effect on water-filled pore space (WFPS), was the main driving factor during the growing season. Annual emission factors (EFs), uncorrected for background emission, varied from 0.4 to 6.5% of the nitrogen (N) applied, covering a similar range for grassland to that found previously for sites restricted to Scotland. Continued monitoring at a grassland reference site near Edinburgh showed that annual EFs vary greatly from year to year, even with similar management, and that several years' data are required to produce a robust mean EF. The overall distribution of EFs in this and previous studies was log-normal. The EFs for small-grain cereals (and oilseed rape) peaked at a much lower value than those for grassland, whereas the values for leafy vegetables and potato crops fitted well into the grassland distribution. These differences in EF between various types of crop should be taken into account when compiling regional or national N2O emission inventories.

Notes: Year-round eddy covariance flux measurements were made in a native tallgrass prairie in north-central Oklahoma, USA during 1997–2000 to quantify carbon exchange and its interannual variability. This prairie is dominated by warm season C4 grasses. The soil is a relatively shallow silty clay loam underlined with a heavy clay layer and a limestone bedrock. During the study period, the prairie was burned in the spring of each year, and was not grazed. In 1997 there was adequate soil moisture through the growing season, but 1998 had two extended periods of substantially low soil moisture (with concurrent high air temperatures and vapor pressure deficits), one early and one later in the growing season. There was also moisture stress in 1999, but it was less severe and occurred later in the season. The annual net ecosystem CO2 exchange, NEE (before including carbon loss during the burn) was 274, 46 and 124 g C m−2 yr−1 in 1997, 1998, and 1999, respectively (flux toward the surface is positive), and the associated variation seemed to mirror the severity of moisture stress. We also examined integrated values of NEE during different periods (e.g. day/night; growing season/senescence). Annually integrated carbon dioxide uptake during the daytime showed the greatest variability from year to year, and was primarily linked to the severity of moisture stress. Carbon loss during nighttime was a significant part of the annual daytime NEE, and was fairly stable from year to year. When carbon loss during the burn (estimated from pre- and post-burn biomass samples) was incorporated in the annual NEE, the prairie was found to be approximately carbon neutral (i.e. net carbon uptake/release was near zero) in years with no moisture stress (1997) or with some stress late in the season (1999). During a year with severe moisture stress early in the season (1998), the prairie was a net source of carbon. It appears that moisture stress (severity as well as timing of occurrence) was a dominating factor regulating the annual carbon exchange of the prairie.

Notes: Teleconnection patterns are large-scale atmospheric circulation systems and variation in them is often associated with impacts on climate and weather over broad areas. Arctia caja L. is a well-known, widespread and charismatic tiger moth. In recent decades, the abundance of A. caja in UK has fallen abruptly. The annual abundance of A. caja in UK is known to be affected adversely by wet winter weather and warm spring temperatures. We examined A. caja population dynamics from 1968 to 1999 for weather and climatological effects. Population growth rate displayed endogenous effects of abundance in the previous two seasons. Accounting for this, growth rate in the present season was still affected significantly by winter precipitation and spring temperature. Annual abundance of A. caja was inversely related to winter East Atlantic teleconnection pattern (winter EA index) and annual population growth rate was inversely related to winter EA in the present and previous two seasons. An index of the North Atlantic Oscillation (NAO), commonly used as an indicator of winter climate in northern Europe, did not show a significant relationship with growth rate. We noted, for the first time, that the winter EA index has increased steadily over the past five decades. The model presented here therefore implies a further decline of A. caja population growth rates and abundance in the future. This is the first demonstration of a relationship between EA and population dynamics and indicates the EA and other lesser-known teleconnection patterns may prove useful in modeling the ecological effects of climate change.

Notes: Uncertainty about the amounts of the greenhouse gas nitrous oxide (N2O), which arise from N leaching from agricultural soils, predominantly as nitrate (NO3–), is large. To date, the bulk of studies of N2O in aquatic systems have relied upon measurement of dissolved N2O concentrations at wide spatial intervals (of the order of km) down a stream, river or estuary. When we combined a fine-scale (m) assessment of N2O concentrations in agricultural drainage water with novel measurement of net N2O emission from the same drainage system, we found that dissolved N2O in agricultural drainage water was very rapidly lost to the atmosphere, while dissolved NO3– in the same water was conserved. Consequently, the N2O emission factor (as a proportion of the nitrate-N present, the IPCC's ‘EF5’) fell by a factor of more than 5 within only 100 m. Direct measurement of N2O emission from the drainage water confirmed the disappearance of N2O as being due to emission from water to the atmosphere, rather than in situ consumption by denitrification. Our findings indicate that making widely spaced measurements of dissolved N2O concentration and/or emissions from the water surface will not take account of this much more dynamic behaviour over short distances. Realistic assessment of the ‘indirect’ agricultural emissions of N2O from leached N will necessitate much more intensive sampling of the whole drainage system, from ditch to stream to river to estuary, accompanied by measurements of in-stream production. The quantities of N2O actually released in the ditches gave values for EF5-g (the IPCC's emission factor for N2O from surface drainage and groundwaters) of between 0.02 and 0.03%, compared with the IPCC value of 1.5%. For the latter to be realistic, the quantity of N2O required to be formed after the initial entry of water into the drainage system would need to exceed the initial load by the order of 50-fold.

Notes: Elevated atmospheric carbon dioxide (CO2) and ozone (O3) concentrations have both been shown to affect plant tissue quality, which in turn could affect litter decomposition and carbon (C) and nutrient cycling. In order to evaluate effects of climate change on litter chemistry, needle litter was collected from Scots pine (Pinus sylvestris L.) saplings exposed to elevated CO2 or O3 concentration and their combination over three growing seasons in open-top chambers. The decomposition of needle litter was followed for 19 months in a pine forest. During decomposition, needle samples for secondary compound analysis were collected and the mass loss of needles was followed. Main nutrients and total phenolics were analysed from litter in the beginning and at the end of the experiment. After 19-month decomposition, the accumulated mass loss was about 34%; however, no significant differences were found in decomposition rates of needle litter between various treatments. Concentrations of total monoterpenes were about 4%, total resin acids 21% and total phenolics 14% of the initial concentrations in litter after 19-month decomposition. In the beginning of litter decomposition, concentrations of individual monoterpenes –α-pinene and β-pinene – were significantly higher in needle litter grown under elevated CO2. However, concentrations of total monoterpenes during the whole decomposition period were not significantly affected by CO2 or O3 treatments. Concentrations of some individual and total resin acids were higher in needle litter grown under elevated CO2 or O3 than under ambient air. There were no significant differences in concentrations of total phenolics as well as nitrogen (N) and the main nutrient concentrations between treatments during decomposition. High concentrations of monoterpenes and resin acids in needles might slightly delay C recycling in forest soils. It is concluded that elevated CO2 and O3 concentrations do not have remarkable impacts on litter decomposition processes in Scots pine forests.

Notes: Boreal peatlands may be particularly vulnerable to climate change, because temperature regimes that currently constrain biological activity in these regions are predicted to increase substantially within the next century. Changes in peatland plant community composition in response to climate change may alter nutrient availability, energy budgets, trace gas fluxes, and carbon storage. We investigated plant community response to warming and drying in a field mesocosm experiment in northern Minnesota, USA. Large intact soil monoliths removed from a bog and a fen received three infrared warming treatments crossed with three water-table treatments (n = 3) for five years. Foliar cover of each species was estimated annually.In the bog, increases in soil temperature and decreases in water-table elevation increased cover of shrubs by 50% and decreased cover of graminoids by 50%. The response of shrubs to warming was distinctly species-specific, and ranged from increases (for Andromeda glaucophylla) to decreases (for Kalmia polifolia). In the fens, changes in plant cover were driven primarily by changes in water-table elevation, and responses were species- and lifeform-specific: increases in water-table elevation increased cover of graminoids – in particular Carex lasiocarpa and Carex livida– as well as mosses. In contrast, decreases in water-table elevation increased cover of shrubs, in particular A. glaucophylla and Chamaedaphne calyculata. The differential and sometimes opposite response of species and lifeforms to the treatments suggest that the structure and function of both bog and fen plant communities will change – in different directions or at different magnitudes – in response to warming and/or changes in water-table elevation that may accompany regional or global climate change.

Notes: It has been suggested that desert vegetation will show the strongest response to rising atmospheric carbon dioxide due to strong water limitations in these systems that may be ameliorated by both photosynthetic enhancements and reductions in stomatal conductance. Here, we report the long-term effect of 55 Pa atmospheric CO2 on photosynthesis and stomatal conductance for three Mojave Desert shrubs of differing leaf phenology (Ambrosia dumosa—drought-deciduous, Krameria erecta—winter-deciduous, Larrea tridentata—evergreen). The shrubs were growing in an undisturbed ecosystem fumigated using FACE technology and were measured over a four-year period that included both above and below-average precipitation. Daily integrated photosynthesis (Aday) was significantly enhanced by elevated CO2 for all three species, although Krameria erecta showed the greatest enhancements (63% vs. 32% for the other species) enhancements were constant throughout the entire measurement period. Only one species, Larrea tridentata, decreased stomatal conductance by 25–50% in response to elevated CO2, and then only at the onset of the summer dry season and following late summer convective precipitation. Similarly, reductions in the maximum carboxylation rate of Rubisco were limited to Larrea during spring. These results suggest that the elevated CO2 response of desert vegetation is a function of complex interactions between species functional types and prevailing environmental conditions. Elevated CO2 did not extend the active growing season into the summer dry season because of overall negligible stomatal conductance responses that did not result in significant water conservation. Overall, we expect the greatest response of desert vegetation during years with above-average precipitation when the active growing season is not limited to ∼2 months and, consequently, the effects of increased photosynthesis can accumulate over a biologically significant time period.

Notes: Production of Atlantic salmon Salmo salar L. utilizes feeds with high fat concentrations to give low feed:gain. However, increased dietary fat content inevitably leads to increased body fat deposition, and salmon with very high fat concentrations in the muscle (fillet) are regarded as being of inferior quality. Adiposity is thought to participate in the regulation of feed intake by means of negative feedback control. Thus, elevated adiposity is predicted to result in lower feed consumption, and thereby possibly impair growth. We tested the hypothesis that high body fat content in salmon would lead to reduced feed intake and growth. Salmon (740 g) were preconditioned with high- or low-fat feed (38.8 and 27.8% dietary fat content) for 10 weeks to establish differences in body fat storage (build-up phase). Thereafter, fat and lean fish (19.4% and 16.7% body fat content) were fed the high- and low-fat feeds for an additional 7 weeks (Phase Two). During Phase Two, the fat fish consumed 30% less feed than lean fish, which resulted in corresponding differences in growth. The differences in adiposity seen at the end of the build-up phase were still evident at trial end. Groups of fish, which were preconditioned with the same feed during the build-up phase, had similar feed consumption and growth to each other during Phase Two, indicating that body fat was playing an important role in the regulation of feed intake.

Notes: Because European sea bass (Dicentrarchus labrax L.) has strictly carnivorous feeding habits, protein and fat are the most important dietary components. In this paper we study the effect of restricted availability of protein and fat on the feeding behaviour and macronutrient selection. To this end, five groups of 20 sea bass with a body weight of 100.0 ± 20.1 g (mean ± SD) were raised in five circular 450-L tanks. Each group could choose among three self-feeders (experiment 1 and 2), each containing a different, incomplete, diet: P + CH (55.4% protein, 18.5% carbohydrate, DM diet), P + F (55.4% protein, 18.5% fat) or F + CH (36.9% fat, 36.9% carbohydrate) or between two self-feeders (experiment 3), each containing protein (100%) or carbohydrate–fat (52.7% and 47.3% respectively). In experiments 1 and 2, sea bass selected a diet consisting of 65.3% digestible energy (DE) protein, 26.2% DE fat and 8.4% DE carbohydrate. The composition of the self-selected diet did not differ when sea bass selected between the two diets in experiment 3. When fish were deprived of protein for two weeks, or deprived of fat for three weeks, they were unable to sustain their previous energy intake. This phenomenon was particularly evident during protein fasting, with the intake of fat and carbohydrate being negligible. During the first 2–3 days, after each fasting period, sea bass showed hyperphagic behaviour, but restricted availability of specific nutrients did not trigger any subsequent increased intake of these specific macronutrients. In conclusion, although sea bass were able to self-compose a nutritionally balanced diet from three or two incomplete diets, no specific hunger was elicited after two weeks of protein fasting or three weeks of fat fasting.

Notes: As reference diets for bivalve molluscs are missing, this study first evaluated the best mixed algal diet (Tetraselmis suecica Butch/Phaeodactylum tricornutum Bohlin) concentration for 4-mm-length Tapes decussatus (L.) clams. It also assessed the performance of an industrial by-product (cheese whey) as a single diet or supplement for the best algal ration previously determined. Growth, survival, condition index and filtration rate were used to compare the different diets. Implications of rations tested on rearing water quality were also investigated, especially ammonium and heterotrophic bacteria levels. With a food concentration as algal dry weight per total seed live weight of 0.7% day−1, seed for grow-out (7 mm) could be obtained within 1 month. A mixture of 25% algal ration and 75% cheese whey gave the best performances. Artificial diets resulted in lower growth rates than live food (20 % to 40% of the best algal ration), but could be considered good maintenance rations in energetic terms. Using cheese whey, and without any algae, hatchery produced seed can be kept economically indoors for at least 30 days without loss in condition.

Notes: Tissue (fillet, viscera and carcass) distributions of fat were examined in Atlantic salmon, Salmo salar L. (≈740→≈1400→≈2000 g) to test the hypothesis that the fillet becomes increasingly important as a fat depot when fish increase in size. The salmon were fed for 11 weeks on either a high-fat feed (H: ≈39% fat) or a low-fat feed (L: ≈28% fat), and half of the fish were then subjected to a dietary switch to create four feed treatments (HH, HL, LL and LH). Fillet fat concentration increased with the passage of time, and the fillet also represented an increasing percentage of the body mass (≈48.5→≈55→≈58.5%) as the fish increased in size. As a consequence, the fillet became increasingly important as a fat depot, containing ≈30% of the body fat in the small fish at the start of the experiment, and ≈50% in the fish sampled at the end of the trial. The proportion of fat localised in the viscera was little influenced by either fish size or feeding treatment, and was within the range of 19–25%, whereas the carcass held a decreasing percentage of the body fat stores as fish size increased. There was a highly significant negative correlation between the percentages of body fat found within the carcass (C) and fillet (F): F = 73.589–0.9285C (R2 = 0.973; n = 13). Although the fillet became more important as a fat depot as fish increased in size, the percentage of the body fat reserves found within this tissue appeared to plateau at 50–55%.

Notes: Chemical characteristics and P-fractionation of sediments from the Deroua fish culture farm (Beni Mellal, Morocco) were analysed in 1998 and 1999. The high concentrations of organic N and organic C in the sediments reflect the high productivity of phytoplankton in the lined ponds. Despite the fact that these ponds were not frequently fertilized, inorganic P was more important in the sediments. The P released from CaCO3≈P was the principal source of P for phytoplankton. The mineralization rate of organic C during the drying period was about 87 µg g−1 day−1 in the sediments. The mineralization rate of organic N seems to be less, compared with organic C. The experimental results indicate that the C:N ratio and texture of sediments could explain the immobilization of organic N. All forms of P remained almost unchanged after the drying period except for Fe(OOH)≈P. The ferric (oxy) hydroxides protect NaOHext-P from the bacterial lyses and stabilize therefore their concentration. The inorganic P represented about 88% of Total P in the sediments and may influence the mineralization rate of organic P. The growth of silver carp were reduced in presence of high concentrations of organic C in sediments (〉 30 mg/g). Compounds toxic to fish such as Fe2+, Mn2+, H2S and CH4 were then released in the water column.

Notes: Recent efforts have been made to culture marine shrimp in systems operating under low or zero-water exchange and with decreased water salinity. The aim of this study was to investigate the impact of various salinity levels on qualitative and quantitative characteristics of the natural community and, more particularly, ciliated protozoa, and compare this information with shrimp growth and survival. Tanks with 9‰ salinity were characterized by a higher pH, but also by a significantly higher concentration of chlorophyll a (Chl a) per weight of suspended matter (1.93 ± 0.72 µg Chl a/mg TSS) than tanks with 18‰ (1.29 ± 0.68 µg Chl a/mg TSS) or 36‰ (1.37 ± 0.61 µg Chl a/mg TSS) salinity. Concentrations of ciliates (max 6000 cells mL−1) showed considerable fluctuations over the sampling period, reflecting the impact of water salinity, dynamic interactions between ciliates and their diverse roles within the shrimp production system. There was no significant difference between survival rates of shrimp reared at 9‰, 18‰ or 36‰, but decreasing salinity from 36‰ to 9‰ led to a significant decrease in final shrimp body weight (from 13.40 ± 0.26 g to 10.23 ± 2.72 g). Future work should address the potential of ciliates as an indicator of aquaculture water quality, as is currently being done in the wastewater industry, and the contribution of ciliates as food sources.

Notes: Weaning success of pond-cultured pikeperch and wild-caught perch (mean length 51 and 48 mm respectively) was evaluated using different weaning techniques and different formulated feeds. Juveniles that were fed formulated feed grew as well as or better than juveniles that were weaned successively using zooplankton or yolk. Four different formulated feeds (agglomerated marine larvae feed, marine larvae feed, trout feed and a semi-moist feed) were evaluated regarding specific growth rate (SGR), condition factor and a subjective stomach fullness estimate. The agglomerated marine larvae feed gave significantly better weaning performance than the other feeds regarding all parameters (SGR = 7.3% day−1 and 3.4% day−1 for pikeperch and perch respectively).

Notes: The effects of tank bottom substrates and presence of shelter on growth, survival and condition of cheliped in the juvenile (stage 2) signal crayfish, Pacifastacus leniusculus (Dana), with an initial stocking density of 200 individuals m−2 were investigated. In the first trial, three different tank bottom substrates with or without shelter were used. The three bottom types were loose gravel, glued gravel and bare bottom. The fastest growth both in terms of wet weight and carapace length was observed on loose gravel bottom. Also survival (range 30.1% to 49.8%) was affected by bottom type being higher on gravel bottoms than on bare bottom. Shelter improved survival only on loose gravel bottom. Bottom type influenced also the number of animals with cheliped injuries. The highest proportion of animals with no injuries (59.5%) was found on bare bottom and the proportion was about 12% and 13% units less on loose gravel and on glued gravel bottom. The presence of shelter had a marginal probability in increasing the number of animals without injuries. In the second trial, the substitution of ordinary gravel as tank bottom substrate with crushed limestone was studied. The mean final wet weights were 0.517 g on ordinary gravel bottom and 0.481 g on limestone bottom. The survivals were about 74% and 80% respectively. Limestone bottom decreased marginally final wet weight, and increased survival but did not affect the final carapace length that had a mean value of 13.6 mm. We conclude from the present experiments that the type of tanks and the rearing system used supported good growth of juvenile signal crayfish. The best growth results could be obtained by using loose gravel (or loose limestone) on the bottom of the tanks with a sufficient quantity of hiding places. However, there appears to be an increased risk for cheliped injuries on bottoms with loose materials.

Notes: The subtilin gene cluster (spa) of Bacillus subtilis ATCC 6633 is organized in transcriptional units spaBTC, spaS, spaIFEG and spaRK. Specific binding of the response regulator protein SpaR to spaB, spaS and spaI DNA promoter fragments was shown by means of electromobility shift assays. A repeated pentanucleotide sequence spaced by six nucleotides was identified as SpaR binding motif (spa-box). Saturating mutational analysis of the spa-box by single- and multiple-base-pair substitutions revealed the consensus motif (A/T)TGAT for optimal SpaR binding with the second, third and fifth position being absolutely conservative. Variations in the spacer size between the two pentanucleotide repeats revealed a strong conservation of their relative location. Only DNA with a proximal arrangement of two pentanucleotide repeats showed affinity to SpaR. A 2:1 stoichiometry between SpaR and DNA was obtained by optical biosensor analyses, which corresponds to the binding of two SpaR proteins per spa-box.

Notes: A collagen-binding adhesin of Enterococcus faecium, Acm, was identified. Acm shows 62% similarity to the Staphylococcus aureus collagen adhesin Cna over the entire protein and is more similar to Cna (60% and 75% similarity with Cna A and B domains respectively) than to the Enterococcus faecalis collagen-binding adhesin, Ace, which shares homology with Acm only in the A domain. Despite the detection of acm in 32 out of 32 E. faecium isolates, only 11 of these (all clinical isolates, including four vancomycin-resistant endocarditis isolates and seven other isolates) exhibited binding to collagen type I (CI). Although acm from three CI-binding vancomycin-resistant E. faecium clinical isolates showed 100% identity, analysis of acm genes and their promoter regions from six non-CI-binding strains identified deletions or mutations that introduced stop codons and/or IS elements within the gene or the promoter region in five out of six strains, suggesting that the presence of an intact functional acm gene is necessary for binding of E. faecium strains to CI. Recombinant Acm A domain showed specific and concentration-dependent binding to collagen, and this protein competed with E. faecium binding to immobilized CI. Consistent with the adherence phenotype and sequence data, probing with Acm-specific IgGs purified from anti-recombinant Acm A polyclonal rabbit serum confirmed the surface expression of Acm in three out of three collagen-binding clinical isolates of E. faecium tested, but in none of the strains with a non-functional pseudo acm gene. Introduction of a functional acm gene into two non-CI-binding natural acm mutant strains conferred a CI-binding phenotype, further confirming that native Acm is sufficient for the binding of E. faecium to CI. These results demonstrate that acm, which encodes a potential virulence factor, is functional only in certain infection-derived clinical isolates of E. faecium, and suggest that Acm is the primary adhesin responsible for the ability of E. faecium to bind collagen.

Notes: Abstract –  The interaction between brown trout (Salmo trutta; fork length (FL) range 255–390 mm) and inanga (Galaxias maculatus; FL range 55–115 mm) was tested during summer through autumn in an artificial stream consisting of a single run-riffle-pool sequence with a natural food supply. Each experimental trial lasted for 15 days, and consisted of two brown trout and 50 inanga collected fresh from a nearby stream, with each species given prior residence in four replicate tests, totalling eight trials in all. In addition, two control trials (each 10 days), with 50 inanga in each, were run. Brown trout almost exclusively occupied the pool, whereas inanga occupied all habitat types, although in different proportions, when tested with and without brown trout. The proportion of inanga in the pool was appreciably lower in the experimental trials with brown trout than in the control trials with no brown trout; prior residence had no significant effect on inanga habitat use. Mortality of inanga attributable to predation by brown trout ranged from 0 to 40% with a mean of 14.5 ± 4.7%. The results suggest that habitat use and survival of inanga populations in small streams can be adversely affected by brown trout.

Notes: Abstract –  Our study assesses swimming capacity (speed and stamina) and possible morphometric determinants of locomotor performance of juvenile brown trout (Salmo trutta L.). We addressed these issues at the individual level to have an approach of the functional significance of intraspecific variation in morphological design. Both swimming speed and endurance time showed significant positive relationships with fish length. Size-corrected values of speed and endurance time were negatively correlated suggesting a phenotypic trade-off between burst and prolonged swimming. Size was also highly correlated with all the morphological variables measured. Therefore, we used the residuals of the regressions of those variables on fish length to remove the effect of body size. A principal components analysis (PCA) summarised the 12 morphological variables into two factors, which accounted for 44.3% of the variance. PC1 combined several measures of body depth and width, whereas PC2 represented mainly postanal length relative to abdomen length. Relationships between the scores of the two factors and size-corrected values of maximum swimming speed and endurance time were weak. PC2 showed a significant positive relationship with endurance time; that is, individuals with longer caudal regions were able to swim against water flow for longer periods of time. Stoutness (PC1) showed a marginally significant negative correlation with endurance time. The lack of stronger relationships could be because of the low morphometric variability among the test individuals, all proceeding from the same population, reared in a common environment, and measured at the same ontogenetic stage.

Notes: Abstract –  Habitat suitability criteria (HSC) for depth, mean velocity, nose velocity, substrate, embeddedness, and cover were developed for brown trout ≥170 mm (Salmo trutta Linnaeus) on the West Branch Farmington River, CT, USA. Microhabitat data was collected by underwater observation using an equal effort habitat sampling design; HSC were constructed using nonparametric tolerance limits. Transferability of previously published HSC to the West Branch Farmington River was poor; only 1 of 13 HSC tested was considered transferable. The HSC developed for the West Branch Farmington River were tested for transferability to the East Branch Westfield River, Massachusetts. First, a composite suitability index (SI) score was calculated using the source HSC for each occupied and unoccupied location in the Westfield River. Then, χ2-tests were used to determine if optimal or suitable locations were occupied in greater proportion than usable or unsuitable locations. Composite SI scores based on total depth, mean velocity, and cover were not transferable, but composite SI scores based only on total depth and mean velocity were. A multivariate profile analysis was also used to test for transferability. In each test, only total depth, fish depth, and mean velocity HSC were successfully transferred. Transferability of depth and velocity HSC between rivers shows promise for applications to similar systems where brown trout occur.

Notes: Abstract –  Modelling-governing patterns of European eel (Anguilla anguilla L.) distribution of four eel size classes (〈150, 150–300, 300–450 and 〉450 mm) in the Frémur basin (northwest France) was done using artificial neural network (ANN) techniques and ecological profiles. Our results demonstrate the high predictive power of the ANN models. Some macro- and microscale factors, such as distance from the sea, depth and flow velocity, have the most significant influence on the models. Influence of distance from the sea appears to be very different from the spatial organisation usually described in river systems. In fact, the general tendencies of total eel densities according to the distance from the sea showed that densities increase weakly upstream. Another outcome was the variations in habitat preference according to the eel size, even if this species is spread over practically every type of microhabitat. Small eels were mainly found in shallow habitats with strong abundance of aquatic vegetation, whereas large eels tend to be found in intermediate to high depth with small to intermediate abundance of aquatic vegetation. Finally, we hypothesise that European eels change behaviour and microhabitat characteristic preference around a size of 300 mm.

Notes: Abstract –  The zooplanktivorous cichlid Haplochromis pyrrhocephalus, which was one of the most common haplochromine species in the Mwanza Gulf of Lake Victoria, had almost completely disappeared after the Nile perch upsurge in the 1980s. In the second half of the 1990s, this species suddenly reappeared in the strongly changed ecosystem. Gut content investigation revealed a change in diet. Currently, H. pyrrhocephalus eats large prey more frequently than in the past. These large prey comprise fish, shrimps and molluscs. The latter two were never encountered in specimens from the past. Particularly feeding on molluscs was unexpected, as it had been suggested that, because of anatomical constraints, molluscivory and zooplanktivory are incompatible in cichlid fish. Our observations provide a new example of the extreme versatility in feeding behaviour in haplochromine cichlids.

Notes: Abstract  – The aim of this study was to explain the growth differences of the two sympatric sparsely rakered whitefish (Coregonus lavaretus (L.)) forms in the subarctic Lake Muddusjärvi by comparing their habitat and food selection to available benthic food resources. The average number of gillrakers was 22.9 for large sparsely rakered whitefish (LSR) and 16.8 for small sparsely rakered whitefish (SSR). LSR dwelled primarily in the littoral zone at depths 〈 10 m, whereas SSR used mostly profundal habitats in depths 〉 10 m. LSR and SSR consumed mainly benthic macroinvertebrates, their abundance, biomass and diversity was highest in the littoral, decreasing towards the profundal. As the individual size of fish increased, LSR was able to shift to larger food items, which were available in the littoral. Possibility of SSR to ontogenetic food shift was scarce in the profundal, where availability of larger benthic macroinvertebrates was low. Because of abundant food resources in the littoral, growth rate of LSR was faster than that of SSR.

Notes: Abstract  – Movements of adult Atlantic salmon were tracked through a series of four fish passes and an impoundment on the River Conon system, Northern Scotland. Proportions of fish passing individual obstructions ranged from 63 to 100%. The cumulative effect was that only 4 of the 54 tagged fish reached the spawning areas. The fish were delayed for 1–41 days at a pool-and-overfall ladder and 1–52 days at a Borland fish lift. The fish swam through a 10 km long reservoir at 0.21–1.16 km·h−1. A total of 13 fish negotiated a 2.5 km long, 3 m diameter diversion tunnel through a mountain to their home river. High levels of electromyogram (EMG) activity were recorded during ascent of a pool-and-overfall fish ladder, indicating that high energy demanding burst swimming was required.

Notes: Abstract  – Seasonal pattern of energy content was determined in a population of Arctic char, Salvelinus alpinus (L.), living in an ultraoligotrophic alpine lake (altitude 1100 m) located in central Norway (62°5′N). Specific somatic energy content varied between 4.3 and 6.1 kJ · g−1 in spawners and between 4.8 and 6.6 kJ · g−1 in immatures. Corresponding values for specific somatic lipid energy were 0.5–1.6 kJ · g−1 for spawners and 0.7–2.1 kJ · g−1 for immatures. The temporal pattern in storage energy residuals (deviation from mean storage energy, all sampling periods pooled) indicated that total, protein and lipid energy accumulated in the autumn and early winter. This increase was followed by a winter decrease in somatic energy (January to April). A new increase in total somatic energy and somatic lipid energy occurred during late winter (March/April to June), while the lake was still ice covered and water temperatures ranged between 0.5 and 2.5 °C. The observed seasonal pattern of specific energy storage and lipid deposition demonstrated a considerable potential for energy accumulation in Arctic char at low temperatures. It is discussed whether freshwater lakes at high altitudes or latitudes represent a temperature-stabilised and predictable environment in contrast to the variable temperature experienced in the corresponding terrestrial system.

Notes: Abstract  – To study the behaviour of silver eels (Anguilla anguilla L.) during their downstream migration, particularly near a hydroelectric power dam, we tagged nine eels with ultrasonic transmitters and tracked their paths in the River Mosel, Germany. The onset of migration coincided with the first flood event that followed the full moon but was independent of daytime, because migration and turbine passage occurred during both day and night. During migration eels swam actively downstream with a velocity of 0.3–1.2 m · s−1. When migrating eels arrived at the dam, they either passed through the turbines immediately or stayed upstream of the powerhouse for up to 8 days, showing a characteristic circling behaviour. Circling eels repeatedly approached the trashrack, sprinted upstream, and finally passed through the turbines with the next high water discharge. These observations are discussed with regard to the design of appropriate downstream passage facilities.

Notes: Abstract –  Minnow trapping was used to determine the distribution and abundance of two small, benthic species of fish, common bullies (Gobiomorphus cotidianus) and koaro (Galaxias brevipinnis), in five oligotrophic lakes varying in both turbidity and the extent of water-level variation. Koaro were 5–20 times more abundant in the large turbid lakes than in the clear ones, indicating that turbidity may reduce the extent of salmonid predation on koaro. However, the scarcity of koaro in the clear lakes was related mainly to the prevalence of brown trout (Salmo trutta) compared with rainbow trout (Oncorhynchus mykiss) as the former were more piscivorous and had a stronger inverse relationship with koaro. Common bullies were more abundant at sites 20 m or more away from the shoreline, and at depths of 9–12 m irrespective of season, year and turbidity level. However, the overall abundance of bullies was reduced by 70–90% in the turbid lakes. As bullies are relatively insensitive to the direct effects of increased turbidity, indirect effects such as reductions in macrophytes from reduced water clarity or smothering of benthic habitats by settled solids are thought to influence their abundance in the lakes affected by glacial turbidity. There was no relationship between the extent of water-level fluctuation and the abundance of koaro or common bullies in the lakes, but the depth distribution of bullies was shallowest in the lake with the least water-level fluctuation and was deepest in the lake with the greatest water-level fluctuation.

Notes: Abstract –  Mature male brown trout and Atlantic salmon parr were offered a choice of two fish pass entrances: a weir and an orifice. Peak velocities and turbulence were closely matched between the pass entrances. There was very strong selection for the orifice among both salmon (20 of 20) and trout (19 of 20). Combined with data in the literature, these results add to the impression that the main behavioural characteristics of salmonid fish migrating upstream through fish passes may largely be independent of size and life stage.

Notes: Abstract –  We used radio telemetry to measure the habitat use and movements of 20 tagged pikeperch (44–59 cm) in the hydropeaking Pyhäkoski Reservoir, Finland, during June 1999–2000. The hydrological conditions in the 8-km-long reservoir were measured and then modeled over eight discharge rates between 30 and 700 m3 · s−1. Pikeperch preferred relatively low water velocities and deep water depths especially during the winter. During the summer, pikeperch moved actively in different parts of the reservoir. No relationship was found between hydroelectric plant operations and distances moved by pikeperch during the summer. Movements peaked in autumn but decreased during the winter to a restricted area. After 1 year of monitoring, 4 out of 20 tagged pikeperch remained in the Pyhäkoski Reservoir, three had died when descending from hydroelectric dams, 10 had descended downstream to other reservoirs or sea, two were captured by local fishermen, and one fish's signal was lost for unknown reasons.

Notes: Abstract – Upstream passage of adult sea trout (Salmo trutta) in a nature-like bypass channel was investigated in the Tirsbæk brook, Denmark, in autumn and winter 1999/2000. Sea trout were caught by electrofishing up- and downstream of the weir at which the bypass was situated. Fish were tagged with passive integrated transponder (PIT) tags and released downstream of the weir. Automatic PIT-tag logging stations were positioned downstream, in the lower part, and at the upstream exit of the bypass to investigate the passage success of the fish. The bypass was neither size- nor sex-selective in the size ranges investigated. The majority (68%) of fish approached the bypass at night. Over 90% of tagged upstream-searching fish located and entered the bypass channel, but only about half of them passed through. The inefficiency is suggested to be because of a combination of the length of the bypass channel and inadequate flow in the bypass channel.

Notes: Abstract – The survival of brown trout and Atlantic salmon smolts during passage over small weirs was estimated in two small Danish rivers during the spring of 1998. Parallel groups of smolts were released upstream and downstream of the weirs and recaptured in traps further downstream. The results showed a smolt loss varying from 18 to 71% for trout and 53% for salmon. Furthermore, the surviving smolts from the upstream groups were delayed for up to 9 days compared to downstream groups. The study demonstrated that an increased proportion of total river discharge allocated to fish passage increased the smolt survival. Losses may be because of fish penetrating grids erected at fish farm inlets, predation and delays, which may lead to desmoltification. The low survival may seriously threat both the long-term viability of wild populations of anadromous salmonids and the outcome of the intensive stocking programme in Denmark.

Notes: Abstract - The possibility of using indices to quantitatively predict short-term growth rates of juvenile three-spined sticklebacks (Gasterosteus aculeatus L.) was assessed. A range of weight-specific growth rates (GW) was obtained in experiments with individual sticklebacks fed enchtraeid worms at different daily rations over 21 days. There was a strong, positive correlation between GW and the RNA : DNA ratio in white muscle (r2 = 0.90) and lipid concentration (as percentage dry weight) of the carcass (r2 = 0.92). There were smaller, but significant correlations between GW and the percentage of dry matter in the carcass (r2 = 0.67), and the residuals from the weight–length relationship (r2 = 0.49). Regressions relating growth to RNA : DNA ratio and lipid concentration offer a means of estimating short-term growth rates in natural populations. A test of such predictions using the results from a 56-day experiment on stickleback growth suggested that predictions from percentage lipid were biased and inefficient, while predictions from the RNA : DNA ratio were unbiased but inefficient. Predictions from percentage lipid were higher than from the RNA : DNA ratio.

Notes: Abstract –  Hemlock (Tsuga canadensis) forests of the eastern U.S. are in decline due to invasion by the exotic insect hemlock woolly adelgid (Adelges tsugae). Aquatic biodiversity in hemlock ecosystems has not been documented; thus the true impact of the infestation cannot be assessed. We compared ichthyofaunal assemblages and trophic structure of streams draining hemlock and hardwood forests by sampling first- and second-order streams draining 14 paired hemlock and hardwood stands during base flows in July 1997 at the Delaware Water Gap National Recreation Area of Pennsylvania and New Jersey. Over 1400 fish of 15 species and 7 families were collected, but hemlock and hardwood streams individually harbored only one to four species. Brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta) were two to three times as prevalent in hemlock than hardwood streams. Insectivorous fishes occurred in significantly higher proportion in streams of hardwood (0.90) than hemlock (0.46) stands, while piscivores occurred more often in hemlock (0.85) than hardwood (0.54) stands. Functional (trophic) diversity of fishes in hemlock and second-order streams was numerically greater than that of hardwood and first-order streams. Species composition also differed by stream order and terrain type. Biodiversity is threatened at several levels within hemlock ecosystems at risk to the hemlock woolly adelgid in eastern U.S. forests.

Notes: Abstract  – Among the species in the family Salmonidae, those represented by the genera Salmo, Salvelinus, and Oncorhynchus (subfamily Salmoninae) are the most studied. Here, various aspects of phenotypic and life-history variation of Atlantic salmon Salmo salar L., brown trout Salmo trutta L., and Arctic charr Salvelinus alpinus (L.) are reviewed. While many strategies and tactics are commonly used by these species, there are also differences in their ecology and population dynamics that result in a variety of interesting and diverse topics that are challenging for future research. Atlantic salmon display considerable phenotypic plasticity and variability in life-history characters ranging from fully freshwater resident forms, where females can mature at approximately 10 cm in length, to anadromous populations characterised by 3–5 sea-winter (5SW) salmon. Even within simple 1SW populations, 20 or more spawning life-history types can be identified. Juveniles in freshwater can use both fluvial and lacustrine habitats for rearing, and while most smolts migrate to sea during the spring, fall migrations occur in some populations. At sea, some salmon undertake extensive oceanic migrations while other populations stay within the geographical confines of areas such as the Baltic Sea. At the other extreme are those that reside in estuaries and return to freshwater to spawn after spending only a few months at sea. The review of information on the diversity of life-history forms is related to conservation aspects associated with Atlantic salmon populations and current trends in abundance and survival. Brown trout is indigenous to Europe, North Africa and western Asia, but was introduced into at least 24 countries outside Europe and now has a world-wide distribution. It exploits both fresh and salt waters for feeding and spawning (brackish), and populations are often partially migratory. One part of the population leaves and feeds elsewhere, while another part stays as residents. In large, complex systems, the species is polymorphic with different size morphs in the various parts of the habitat. Brown trout feed close to the surface and near shore, but large individuals may move far offshore. The species exhibits ontogenetic niche shifts partly related to size and partly to developmental rate. They switch when the amount of surplus energy available for growth becomes small with fast growers being younger and smaller fish than slow growers. Brown trout is an opportunistic carnivore, but individuals specialise at least temporarily on particular food items; insect larvae are important for the young in streams, while littoral epibenthos in lakes and fish are most important for large trout. The sexes differ in resource use and size. Females are more inclined than males to become migratory and feed in pelagic waters. Males exploit running water, near-shore and surface waters more than females. Therefore, females feed more on zooplankton and exhibit a more uniform phenotype than males. The Arctic charr is the northernmost freshwater fish on earth, with a circumpolar distribution in the Holarctic that matches the last glaciation. Recent mtDNA studies indicate that there are five phylogeographic lineages (Atlantic, Arctic, Bering, Siberian and Acadian) that may be of Pleistocene origin. Phenotypic expression and ecology are more variable in charr than in most fish. Weights at maturation range from 3 g to 12 kg. Population differences in morphology and coloration are large and can have some genetic basis. Charr live in streams, at sea and in all habitats of oligotrophic lakes, including very deep areas. Ontogenetic habitat shifts between lacustrine habitats are common. The charr feed on all major prey types of streams, lakes and near-shore marine habitats, but has high niche flexibility in competition. Cannibalism is expressed in several cases, and can be important for developing and maintaining bimodal size distributions. Anadromy is found in the northern part of its range and involves about 40, but sometimes more days in the sea. All charr overwinter in freshwater. Partial migration is common, but the degree of anadromy varies greatly among populations. The food at sea includes zooplankton and pelagic fish, but also epibenthos. Polymorphism and sympatric morphs are much studied. As a prominent fish of glaciated lakes, charr is an important species for studying ecological speciation by the combination of field studies and experiments, particularly in the fields of morphometric heterochrony and comparative behaviour.

Notes: Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei.

Notes: The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.

Notes: The pathogenic yeast Cryptococcus neoformans (Cn) var. gattii causes meningoencephalitis in healthy individuals, unlike the better known Cn varieties grubii and neoformans, which are common in immunocompromised individuals. The virulence determinants and mechanisms of host predilection are poorly defined for var. gattii. The present study focused on the characterization of a Cu,Zn superoxide dismutase (SOD1) gene knock-out mutant constructed by developing a DNA transformation system. The sod1 mutant was highly sensitive to the redox cycling agent menadione, and showed fragmentation of the large vacuole in the cytoplasm, but no other defects were seen in growth, capsule synthesis, mating, sporulation, stationary phase survival or auxotrophies for sulphur-containing amino acids. The sod1 mutant was markedly attenuated in virulence in a mouse model, and it was significantly susceptible to in vitro killing by human neutrophils (PMNs). The deletion of SOD1 also resulted in defects in the expression of a number of virulence factors, i.e. laccase, urease and phospholipase. Complementation of the sod1 mutant with SOD1 resulted in recovery of virulence factor expression and menadione resistance, and in restoration of virulence. Overall, these results suggest that the antioxidant function of Cu,Zn SOD is critical for the pathogenesis of the fungus, but is dispensable in its saprobic life. This report constitutes the first instance in which superoxide dismutase has been directly implicated in the virulence of a fungal pathogen.

Notes: SLP2 is a 50 kb linear plasmid in Streptomyces lividans that contains short (44 bp) terminal inverted repeats and covalently bound terminal proteins. The nucleotide sequence of SLP2 was determined. The  rightmost 15.4 kb sequence is identical to that of the host chromosome, including the Tn4811 sequence at the border, which is interrupted by an insertion sequence (IS) element in SLP2. Examination of the flanking target sequences of Tn4811 suggests a previous recombinational event there. The 43 putative protein coding sequences contained many involved in replication (including two terminal protein homologues), partitioning, conjugal transfer and intramycelial spread. The terminally located helicase-like gene ttrA was necessary for conjugal transfer. The two telomeres diverge significantly in primary sequence, while preserving similar secondary structures. Mini-linear plasmids containing these telomeres replicated in S. lividans using the chromosomally encoded terminal protein. In addition, two pseudotelomere sequences are present near the left telomere. The G+C content and GC or AT skew profiles exhibit complex distributions. These, plus the inferred recombination at the right arm, indicate that SLP2 has evolved through rounds of exchanges involving at least three replicons.

Notes: Environmental signals can be transduced into intracellular responses by the action of MAP kinase cascades. Sequential phosphorylation results in the transient activation of a MAP kinase, which in turn activates certain transcription factors and thus a set of pathway-specific genes. Many steps in this cascade are conserved, and homologues have been discovered from yeast to human. We have characterized the MAPKK kinase, SteC, a homologue of Saccharomyces cerevisiae Ste11, in the filamentous fungus Aspergillus nidulans. The 886-amino-acid-long protein shares the highest similarity to Neurospora crassa Nrc-1. Deletion of the gene in A. nidulans results in a slower growth rate, the formation of more branched hyphae, altered conidiophore morphology, an inhibition of heterokaryon formation and a block of cleistothecium development. The gene is transcriptionally activated during asexual development and controls the phosphorylation of two putative MAP kinases.