Belowground carbon flux links biogeochemical cycles and resource‐use efficiency at the global scale

Nutrient limitation is pervasive in the terrestrial biosphere, although the relationship between global carbon (C) nitrogen (N) and phosphorus (P) cycles remains uncertain. Using meta‐analysis we show that gross primary production (GPP) partitioning belowground is inversely related to soil‐available N : P, increasing with latitude from tropical to boreal forests. N‐use efficiency is highest in boreal forests, and P‐use efficiency in tropical forests. High C partitioning belowground in boreal forests reflects a 13‐fold greater C cost of N acquisition compared to the tropics. By contrast, the C cost of P acquisition varies only 2‐fold among biomes. This analysis suggests a new hypothesis that the primary limitation on productivity in forested ecosystems transitions from belowground resources at high latitudes to aboveground resources at low latitudes as C‐intensive root‐ and mycorrhizal‐mediated nutrient capture is progressively replaced by rapidly cycling, enzyme‐derived nutrient fluxes when temperatures approach the thermal optimum for biogeochemical transformations.     

Seasonal and within‐canopy variation in shoot‐scale resource‐use efficiency trade‐offs in a Norway spruce stand

Previous leaf‐scale studies of carbon assimilation describe short‐term resource‐use efficiency (RUE) trade‐offs where high use efficiency of one resource requires low RUE of another. However, varying resource availabilities may cause long‐term RUE trade‐offs to differ from the short‐term patterns. This may have important implications for understanding canopy‐scale resource use and allocation. We used continuous gas exchange measurements collected at five levels within a Norway spruce, Picea abies (L.) karst., canopy over 3 years to assess seasonal differences in the interactions between shoot‐scale resource availability (light, water and nitrogen), net photosynthesis (A_n) and the use efficiencies of light (LUE), water (WUE) and nitrogen (NUE) for carbon assimilation. The continuous data set was used to develop and evaluate multiple regression models for predicting monthly shoot‐scale A_n. These models showed that shoot‐scale A_n was strongly dependent on light availability and was generally well described with simple one‐ or two‐parameter models. WUE peaked in spring, NUE in summer and LUE in autumn. However, the relative importance of LUE for carbon assimilation increased with canopy depth at all times. Our results suggest that accounting for seasonal and within‐canopy trade‐offs may be important for RUE‐based modelling of canopy carbon uptake.     

Effect of Bursaphelenchus xylophilus infection on leaf photosynthetic characteristics and resource‐use efficiency of Pinus massoniana

Pine wilt disease (PWD ) is considered as the most destructive forest‐invasive alien species in China. We measured gas exchange parameters and foliar carbon isotope ratios (δ¹³C) of different infection phases of Masson pine in order to investigate the effect of Bursaphelenchus xylophilus infection on photosynthetic responses and resource‐use efficiency. The results showed that net photosynthetic rate (P _n), transpiration rate (T ), stomatal conductance (g _s), and internal CO ₂ concentrations (C _i) decreased in the infested trees at photosynthetic photon flux density (PPFD ) levels from 0 to 2,000 μmol m^?2 s^?1 compared with controls. The maximum net photosynthetic rate (P _max) was significantly declined in the infected trees than in controls (p  <  .05). There also exist significant differences in dark respiration rate (R _d) among different infection phases (p  <  .05), but the value is highest in the middle infection phase, followed by the control and then the terminal infection phase. This indicates that Pinus massoniana plants need to consume more photosynthetic products during the middle infection phase in order to defend against pine sawyer beetle feeding and PWD infection. Isotopic analysis revealed a significant decrease of the foliar δ¹³C (p  <  .05), as much as 2.5‰ lower in the infected trees. The mean leaf N content was about 12.94% less in the middle infection phase and 27.06% less in the terminal infection phase, causing a significant increase of the foliar C:N ratio in infested trees. Both of the net photosynthetic rates and foliar δ¹³C were linearly correlated with the foliar N content. We also found a significant decrease (p  <  .05) of resource‐use efficiency in PWD ‐induced P. massoniana plants, which can be attributed to the closure of stomatal pores and the inactivation or loss of both Rubisco and other key Calvin cycle enzymes. This study highlights the impact of photosynthetic characteristics, foliar carbon isotope ratios, and resource‐use efficiency of PWD ‐induced trees, which can help identify PWD infestations at the photosynthetic and physiological levels so as to better facilitate management actions.     

Negative density dependence is stronger in resource‐rich environments and diversifies communities when stronger for common but not rare species

Conspecific negative density dependence is thought to maintain diversity by limiting abundances of common species. Yet the extent to which this mechanism can explain patterns of species diversity across environmental gradients is largely unknown. We examined density‐dependent recruitment of seedlings and saplings and changes in local species diversity across a soil‐resource gradient for 38 woody‐plant species in a temperate forest. At both life stages, the strength of negative density dependence increased with resource availability, becoming relatively stronger for rare species during seedling recruitment, but stronger for common species during sapling recruitment. Moreover, negative density dependence appeared to reduce diversity when stronger for rare than common species, but increase diversity when stronger for common species. Our results suggest that negative density dependence is stronger in resource‐rich environments and can either decrease or maintain diversity depending on its relative strength among common and rare species.     

Advantages and disadvantages of cytidine deamination

Cytidine deamination of nucleic acids underlies diversification of Ig genes and inhibition of retroviral infection, and thus, it would appear to be vital to host defense. The host defense properties of cytidine deamination require two distinct but homologous cytidine deaminases-activation-induced cytidine deaminase and apolipoprotein B-editing cytidine deaminase, subunit 3G. Although cytidine deamination has clear benefits, it might well have biological costs. Uncontrolled cytidine deamination might generate misfolded polypeptides, dominant-negative proteins, or mutations in tumor suppressor genes, and thus contribute to tumor formation. How cytidine deaminases target a given nucleic acid substrate at specific sequences is not understood, and what protects cells from uncontrolled mutagenesis is not known. In this paper, I shall review the functions and regulation of activation-induced cytidine deaminase and apolipoprotein B-editing cytidine deaminase, subunit 3G, and speculate about the basis for site specificity vis-à-vis generalized mutagenesis.     

Causes and consequences of variation in competitive ability in plant communities

Abstract. Several factors may define the cause and pattern of variation in competitive ability among individuals within a plant community. Variation may be a consequence of genetic or environmental variability. These two sources of variation may vary in their relative magnitudes. The relevant scale of genetic variation may occur at the individual genotype level or at the species level. The relevant scale of environmental variation may occur at the individual plant level or at the neighbourhood (or community) level. Relative competitive abilities may be effected by genotype-environment interaction or by genotype-genotype (or species-species) interaction. The complex relationship among these factors reveals the mechanistic basis for establishing a clear distinction among five specific hypotheses for species coexistence and diversity that are all variations of the general hypothesis that competitive abilities do not differ sufficiently among coexisting species to cause any competitive exclusion at the community level. These hypotheses are compared in terms of the degree to which they are restricted by assumptions and supported by existing data, and in the extent to which they involve evolutionary consequences of competition.     

Molecular ecology ofFrankia: Advantages and disadvantages of the use of DNA probes

Ecological studies on the actinomyceteFrankia are often influenced by the difficulty to isolate and identify this microorganism. The application of molecular biological techniques offers possibilities to detect microbes without isolation and cultivation.Nif genes or whole plasmids can serve as targets for the design of specific probes. Alternatively, ribosomal RNA (rRNA), commonly used in modern phylogenetic studies, can be used as a target molecule in ecological studies. This paper gives an overview of new developments on the use of 16S rRNA as a target molecule for oligonucleotide probes. Group-specific sequences in the 16S rRNA ofFrankia can be used as targets for oligonucleotide probes that a) recognize ineffectiveFrankia strains onAlnus, b) recognize effective strains onAlnus, c) recognize allFrankia strains tested so far. The present paper summarizes the essential steps needed for the use of these probes for the detection ofFrankia strains in soil without isolation and cultivation.     

Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modelling metabolic pathways.

It is now widely accepted that mathematical models are needed to predict the behaviour of complex metabolic networks in the cell, in order to have a rational basis for planning metabolic engineering with biotechnological or therapeutical purposes. The great complexity of metabolic networks makes it crucial to simplify them for analysis, but without violating key principles of stoichiometry or thermodynamics. We show here, however, that models for branched complex systems are sometimes obtained that violate the stoichiometry of fluxes at branch points and as a result give unrealistic metabolite concentrations at the steady state. This problem is especially important when models are constructed with the S-system form of biochemical systems theory. However, the same violation of stoichiometry can occur in metabolic control analysis if control coefficients are assumed to be constant when trying to predict the effects of large changes. We derive the appropriate matrix equations to analyse this type of problem systematically and to assess its extent in any given model.     

The mechanistic basis for higher‐order interactions and non‐additivity in competitive communities

Motivated by both analytical tractability and empirical practicality, community ecologists have long treated the species pair as the fundamental unit of study. This notwithstanding, the challenge of understanding more complex systems has repeatedly generated interest in the role of so‐called higher‐order interactions (HOIs) imposed by species beyond the focal pair. Here we argue that HOIs – defined as non‐additive effects of density on per capita growth – are best interpreted as emergent properties of phenomenological models (e.g. Lotka–Volterra competition) rather than as distinct ‘ecological processes’ in their own right. Using simulations of consumer‐resource models, we explore the mechanisms and system properties that give rise to HOIs in observational data. We demonstrate that HOIs emerge under all but the most restrictive of assumptions, and that incorporating non‐additivity into phenomenological models improves the quantitative and qualitative accuracy of model predictions. Notably, we also observe that HOIs derive primarily from mechanisms and system properties that apply equally to single‐species or pairwise systems as they do to more diverse communities. Consequently, there exists a strong mandate for further recognition of non‐additive effects in both theoretical and empirical research.     

Balancing food and density‐dependence in the spatial distribution of an interference‐prone forager

Foraging distributions are thought to be density‐dependent, because animals not only select for a high availability and quality of resources, but also avoid conspecific interference. Since these processes are confounded, their relative importance in shaping foraging distributions remains poorly understood. Here we aimed to rank the contribution of density‐dependent and density‐independent effects on the spatio‐temporal foraging patterns of eurasian oystercatchers. In our intertidal study area, tides caused continuous variation in oystercatcher density, providing an opportunity to disentangle conspecific interference and density‐independent interactions with the food landscape. Spatial distributions were quantified using high‐resolution individual tracking of foraging activity and location. In a model environment that included a realistic reconstruction of both the tides and the benthic food, we tested a family of behaviour‐based optimality models against these tracking data. Density‐independent interactions affected spatial distributions much more strongly than conspecific interference, even in an interference‐prone species like oystercatchers. Spatial distributions were governed by avoidance of bill injury costs, selection for high interference‐free intake rates and a decreasing availability of benthic bivalve prey after their exposure. These density‐independent interactions outweighed interference competition in terms of effect size. We suggest that the bottleneck in our mechanistic understanding of foraging distributions may be primarily the role of density‐independent prey attributes unrelated to intake rates, like damage costs in the case of oystercatchers foraging on perilous prey. At a landscape scale, above the finest inter‐individual distances, effects of conspecific interaction on spatial distributions may have been overemphasised.     

Variation in the ability of Didemnum sp. to invade established communities

Over the past 30 years southern New England, USA has been invaded by several species of ascidians, including Botrylloides violaceus, Diplosoma listerianum, Styela clava, and Ascidiella aspersa. These species have become dominate in coastal embayments and marinas but are usually absent from more open water coastal areas. A colonial ascidian, Didemnum sp. has invaded southern New England during the past 10 years and we first observed this species in eastern Long Island Sound in 2000. It has become the dominant at several field sites while remaining in low abundance at others. We conducted an experiment at two places, a protected marina and an open coast site, to examine its ability to compete with the established fouling community. Small colonies of Didemnum were transplanted onto panels with communities that varied in age from one to four weeks old and these treatments along with controls with only Didemnum were exposed at both sites. In most treatments Didemnum became a dominant species in the communities at both sites but it reached higher abundances at the open coast site. Potential causes of the observed differences are predation on other species of ascidians at the open coast site reducing recruitment of these species and competition, lower tolerance for elevated temperatures at the marina site, or other environmental parameters that might affect growth rates.     

Biomass allocation, relative competitive ability and water use efficiency of two dominant species in semiarid Loess Plateau under water stress

A better understanding of the growth and interspecific competition of native dominant species under water stress should aid in prediction of succession in plant communities. In addition, such research would guide the selection of appropriate conservation and agricultural utilization of plants in semiarid environments that have not been very well characterized. Biomass production and allocation, relative competitive ability and water use efficiency of one C₄ herbaceous grass (Bothriochloa ischaemum) and one C₃ leguminous subshrub (Lespedeza davurica), both important species from the semiarid Loess Plateau of China, were investigated in a pot-cultivation experiment. The experiment was conducted using a replacement series design in which B. ischaemum and L. davurica were grown with twelve plants per pot, in seven combinations of the two species (12:0, 10:2, 8:4, 6:6, 4:8, 2:10, and 0:12). Three levels of water treatments included sufficient water supply (HW), moderate water stress (MW) and severe water stress (LW). These treatments were applied after seedling establishment and remained until the end of the experiment. Biomass production and its partitioning, and transpiration water use efficiency (TWUE) were determined at the end of the experiment. Interspecific competitive indices (competitive ratio (CR), aggressiveness (A) and relative yield total (RYT)) were calculated from the dry weight for shoots, roots and total biomass. Water stress decreased biomass production of both species in monoculture and mixture. The growth of L. davurica was restrained in their mixtures for each water treatment. L. davurica had significantly (P < 0.05) greater root:shoot allocation than B. ischaemum for each water treatment and proportion within the replacement series. Aggressiveness (A) values for B. ischaemum with respect to L. davurica were negative only at the proportions of B. ischaemum to L. davurica being 8:4 and 10:2 in LW treatment. B. ischaemum had a significantly (P < 0.05) higher CR value under each water treatment, and water stress considerably reduced its relative CR while increased that of L. davurica. RYT values of the two species indicated some degree of resource complimentarity under both water sufficient and deficit conditions. The results suggest that it is advantageous for growing the two species together to maximize biomass production, and the suggested ratio was 10:2 of B. ischaemum to L. davurica because of significantly higher (P < 0.05) RYT and TWUE under low water availability condition.     

Modified Papanicolaou staining protocol with minimum alcohol use: a cost‐cutting measure for resource‐limited settings

S. Gupta, K. L. Chachra, P. Bhadola and P. Sodhani
Modified Papanicolaou staining protocol with minimum alcohol use: a cost‐cutting measure for resource‐limited settings Objective: To devise a simple, cost‐effective protocol for Papanicolaou (Pap) staining of cervicovaginal smears. Methods: Five hundred coded paired cervical smears were collected from women as part of routine cervical cancer screening. One set of smears was stained by conventional Pap staining protocol (CP) and the other by a modified protocol (MP) in which alcohol was replaced by 1% acetic acid in all the steps except during fixation and prior to mounting; in addition, one alcohol‐based counterstain, OG, was omitted. The smears were examined blindly by the pathologists and then decoded. Each pair of smears was compared and the two protocols were analysed for staining quality and diagnoses by McNemar and chi‐square tests. Results: The staining quality in the MP was satisfactory. The nuclear and cytoplasmic features were comparable to the CP. Cytoplasmic transparency was maintained in the MP and the differential staining of blue/green and pink was acceptable to the pathologists and technicians. The diagnoses agreed in all cases and there was no compromise in interpreting the smears. With MP it took only 3–4 minutes to stain a batch of 50 slides. in contrast to the 20 minutes taken by CP. The MP used almost one‐seventh of the amount of alcohol compared with CP, which translated into a significant cost reduction per smear. Conclusions: The improvised Pap staining protocol with minimum alcohol use is a simple, cost‐effective and technician‐friendly procedure that can be easily adopted in high‐volume, resource‐limited laboratories for mass cervical cancer screening.     

Gas exchange and water‐use efficiency in plant canopies

In this review, I first address the basics of gas exchange, water‐use efficiency and carbon isotope discrimination in C₃ plant canopies. I then present a case study of water‐use efficiency in northern Australian tree species. In general, C₃ plants face a trade‐off whereby increasing stomatal conductance for a given set of conditions will result in a higher CO₂ assimilation rate, but a lower photosynthetic water‐use efficiency. A common garden experiment suggested that tree species which are able to establish and grow in drier parts of northern Australia have a capacity to use water rapidly when it is available through high stomatal conductance, but that they do so at the expense of low water‐use efficiency. This may explain why community‐level carbon isotope discrimination does not decrease as steeply with decreasing rainfall on the North Australian Tropical Transect as has been observed on some other precipitation gradients. Next, I discuss changes in water‐use efficiency that take place during leaf expansion in C₃ plant leaves. Leaf phenology has recently been recognised as a significant driver of canopy gas exchange in evergreen forest canopies, and leaf expansion involves changes in both photosynthetic capacity and water‐use efficiency. Following this, I discuss the role of woody tissue respiration in canopy gas exchange and how photosynthetic refixation of respired CO₂ can increase whole‐plant water‐use efficiency. Finally, I discuss the role of water‐use efficiency in driving terrestrial plant responses to global change, especially the rising concentration of atmospheric CO₂. In coming decades, increases in plant water‐use efficiency caused by rising CO₂ are likely to partially mitigate impacts on plants of drought stress caused by global warming.