Optimality of codon usage in Escherichia coli due to load minimization

The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, an ability which in term is designated "load minimization". One parameter involved in calculating the load minimizing property of the genetic code is codon usage. In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference. It has been shown that the codon preference is correlated with the composition of the tRNA pool. Selection for translational efficiency and translational accuracy both result in such a correlation. In this work, it is shown that codon usage bias in Escherichia coli works so as to minimize the consequences of translational errors, i.e. optimized for load minimization.     

On multiple-nutrient-limited growth of microorganisms,with special reference to dual limitation by carbon and nitrogen substrates

Simultaneous limitation of microbial growth by two or more nutrients is discussed for dual carbon/nitrogen-limited growth in continuous culture. The boundaries of the zone where double-limited growth occurs can be clearly defined from both cultivation data and cellular composition and they can be also predicted from growth yield data measured under single-substrate-limited conditions. It is demonstrated that for the two nutrients carbon and nitrogen the zone of double nutrient limitation is dependent on both the C:N ratio of the growth medium and the growth (dilution) rate. The concept on double-(carbon/nitrogen)-limited growth presented here can be extended to other binary and multiple combinations of nutrients.     

Plankton and hydrochemistry of Lake Futalaufquen (Patagonia,Argentina) during the growing season

Plankton communities and hydrochemistry of an oligotrophic lake occupying a glacial valley in Argentinian Patagonia (42 °49S; 71 °43W) were studied. Monthly samples at three stations integrated from 0 to 50 m and stratified samples at the site of maximum depth, were taken during the growing season. Transparency was always controlled by glacial silt, and not by phytoplankton. Lake water belongs to the calcium-bicarbonate type, with low conductivity (24 µS cm^–1), and poor buffering capacity. Forty-five phytoplankton taxa were found. Mean phytoplankton density was 49 cells ml^–1 and mean biomass 69 µg l^–1. N:P relationships, inorganic nitrogen exhaustion in the photic layer, and correlations between nutrients and phytoplankton density suggests nitrogen as the main limiting factor. Fifteen zooplankton species were found. Mean zooplankton density was 12.2 ind. l^–1 and mean biomass 22.9 µg l^–1. Diatoms and Boeckellidae were the dominant planktonic groups. Morphometry and hydrological factors were responsible for horizontal heterogeneity in phytoplankton and chemical variables.     

The ontogeny and cost of migration in Drosophila subobscura Collin

The ontogeny of migratory potential of male and female Drosophila subobscura has been quantified using tethered flight in the laboratory. In both sexes there is an increase in the few days immediately after eclosion, and a decline before the flies cease reproductive activity. There is an intervening peak in the potential of males, which may result from an increased rejection-rate by inseminated females. The migratory potential generally appears greater than that usually utilized in the field. Such extended migration extracts a significant cost from female flies in terms of reduced fecundity.     

The presence of nitrogen fixing legumes in terrestrial communities: Evolutionary vs ecological considerations

Nitrogen is often a limiting factor to net primary productivity (NPP) and other processes in terrestrial ecosystems. In most temperate freshwater ecosystems, when nitrogen becomes limiting to NPP, populations of N-fixing cyanobacteria experience a competitive advantage, and begin to grow and fix nitrogen until the next most limiting resource is encountered; typically phosphorus or light. Why is it that N-fixing plants do not generally function to overcome N limitation in terrestrial ecosystems in the same way that cyanobacteria function in aquatic ecosystems? To address this question in a particular ecosystem, one must first know whether the flora includes a potential set of nitrogen fixers. I suggest that the presence or absence of N-fixing plant symbioses is foremost an evolutionary consideration, determined to a large extent by constraints on the geographical radiation of woody members of the family Fabaceae. Ecological factors such as competition, nutrient deficiencies, grazing and fire are useful to explain the success of N-fixing plants only when considered against the geographical distribution of potential N-fixers.     

Iron limitation in the marine cyanobacterium Trichodesmium reveals new insights into regulation of photosynthesis and nitrogen fixation

* As iron (Fe) deficiency is a main limiting factor of ocean productivity, its effects were investigated on interactions between photosynthesis and nitrogen fixation in the marine nonheterocystous diazotrophic cyanobacterium Trichodesmium IMS101. * Biophysical methods such as fluorescence kinetic microscopy, fast repetition rate (FRR) fluorimetry, and in vivo and in vitro spectroscopy of pigment composition were used, and nitrogenase activity and the abundance of key proteins were measured. * Fe limitation caused a fast down-regulation of nitrogenase activity and protein levels. By contrast, the abundance of Fe-requiring photosystem I (PSI) components remained constant. Total levels of phycobiliproteins remained unchanged according to single-cell in vivo spectra. However, the regular 16-kDa phycoerythrin band decreased and finally disappeared 16-20 d after initiation of Fe limitation, concomitant with the accumulation of a 20-kDa protein cross-reacting with the phycoerythrin antibody. Concurrently, nitrogenase expression and activity increased. Fe limitation dampened the daily cycle of photosystem II (PSII) activity characteristic of diazotrophic Trichodesmium cells. Further, it increased the number and prolonged the time period of occurrence of cells with elevated basic fluorescence (F(0)). Additionally, it increased the effective cross-section of PSII, probably as a result of enhanced coupling of phycobilisomes to PSII, and led to up-regulation of the Fe stress protein IsiA. * Trichodesmium survives short-term Fe limitation by selectively down-regulating nitrogen fixation while maintaining but re-arranging the photosynthetic apparatus.     

The influence of nitrogen availability on carbon and nitrogen storage in the biennial Cirsium vulgare (Savi) Ten. II. The cost of nitrogen storage

The cost of nitrogen storage to current growth was examined in relation to N availability in the biennial Cirsium vulgare. Plants were grown outdoors, in sand culture, with continuous diel drip irrigation of fertilization medium containing one of five different N concentrations. Plants grown at the highest N concentration stored twice as much N in their tap roots as did plants grown at the lowest N concentration. In high-N-grown plants, the storage of N reserves occurred during the period of maximum growth, at the same time as tap-root production. At the time of maximum biomass, stored N was also at a maximum. During the period following maximum biomass, no additional storage of N occurred. This pattern was observed despite frequent late-season leaf senescence which resulted in a large pool of potentially mobile N which could have been stored at no cost to growth. In low-N-grown plants, the production of tap-root storage tissue and the filling of that tissue with stored N were staggered. Tap-root production and growth occurred during the period of maximum growth, as in the high-N-grown plants. However, filling of the storage tissue with N occurred late in the growing season, when the pool of mobile N from senescent leaves was large. The utilization of this late-season N source occurred with little or no cost to growth, and this N is labelled, according to previous definitions, as ‘accumulated’. The costs of storing N in plants of the different N treatments were calculated using two models based on different growth constraints. In one model, the cost of N storage was represented as lost growth due to allocation of N to storage, rather than to the photosynthetic shoot (i.e. growth was assumed to be limited by carbon acquisition). In the second model, the storage cost was calculated as lost growth due to allocation of N to storage, rather than to the nitrogen-acquiring fine-root system (i.e. growth was assumed to be limited by nitrogen acquisition). In both models, the total cost of N storage was predicted to decrease as N availability decreased due to smaller storage pool sizes in plants of the low-N treatments. The cost of filling the tap root with stored N as a percentage of the total storage cost was also reduced as N availability decreased due to the occurrence of late-season accumulation. By relying, at least in part, on late-season accumulation, plants grown at the lowest three levels of N availability reduced total storage costs by 15 to 22%. The results demonstrate that plants are capable of adjusting their storage patterns in response to low nitrogen availability such that the costs of storage are reduced.     

The influence of a dissolved inorganic nitrogen gradient on phytoplankton community dynamics in a chain of lakes

In a chain of lakes along which nutrient availability varies in a gradient, we performed factorial nutrient enrichment experiments to determine if nitrogen limitation was the principal factor controlling the differences in phytoplankton biomass, photosynthetic productivity, diversity, and species composition among two of the lakes in the chain. In the least productive lake, East Graham Lake, P and C enrichments (in the absence of N enrichment) had no effect on biomass and diversity, whereas within two weeks the N enrichments (alone or in any combination with P and/or C) increased the biomass and decreased the diversity of East Graham Lake phytoplankton to levels similar or identical to those in more productive Shoe Lake. Short-term ¹⁴C photosynthetic rates in East Graham Lake water also responded only to N in the third week. However, photosynthesis was stimulated by P in the first week, and a few species did increase in numbers with P enrichment, suggesting that some degree of P limitation remains in addition to the strong N limitation in East Graham Lake. A number of species responded individually to the enrichments in a manner similar to that of the overall community, and a strong overlapping of discriminant analysis scores for N-enriched East Graham Lake with those of Shoe Lake was consistent with our prediction that the community structure of N-enriched East Graham Lake water would shift toward that of Shoe Lake. However, many species did not respond consistently with these results, and the nutrients tested were clearly not a major factor in the differences in abundance of those species among the two lakes. The results support the argument that overall biomass production and diversity of the phytoplankton community in a lake can be a relatively simple function of a single most-limiting nutrient. However, many of the species responses also confirm that, while nutrient availability is an important factor in the control of the species composition of the community, other factors are likely to prevent reliable predictions of all species effects on the basis of nutrient availability alone.     

The cost of floral longevity in Clarkia tembloriensis: An experimental investigation

The hypothesis that flower maintenance requires resources that would be used to support other plant functions (i.e. a cost of floral maintenance) was tested by experimentally manipulating floral longevity. Plants of Clarkia tembloriensis, a species with pollination-induced flower senescence, received either early or late pollinations (long and short longevities, respectively). We examined the effect of this manipulation on (1) per-flower allocation to nectar production and (2) flower, fruit and seed production per plant under two levels of resource availability. The direct costs of floral longevity measured in terms of nectar sugar were high: flowers that were maintained 35% longer invested proportionately more in nectar sugar (30%). At the whole-plant level, a cost of floral longevity was manifested as reduced seed production, but the magnitude of this cost varied with resource level. While plants with longer-lived flowers showed a 12% reduction in seed production, those that experienced reduced resource levels via partial defoliation, showed a decrement in seed production that was almost three times larger (34%). These differences were not brought about by changes in the number of flowers and fruits, but by significant alterations in their sizes. A model that expresses the cost of flower maintenance as a trade-off between floral longevity and seed production shows that an optimal flower longevity is determined by both the rate of fitness accrual and the cost of floral maintenance.     

The importance of nitrogen in Pyramid Lake (Nevada,USA), a saline,desert lake

The increase in human development in the downstream portion of the Pyramid Lake drainage basin has resulted in increased nutrient loading to the lake. Since this is a deep, terminal lake, concern over nutrient build up and change in trophic status exists. On the basis of lake chemistry which shows consistently high concentrations of total reactive-P (mean = 55 µg P l^–1) relative to dissolved inorganic-N (DIN) (mean = 15 µg N 1^–1), it has been hypothesized that Pyramid is N-limited. However, no systematic study of nutrient limitation had been undertaken. Nutrient enrichment bioassays conducted throughout an entire year clearly showed that additions of DIN resulted in a 350–600% stimulation of chlorophyll production. Phosphate, when added singly or in combination with DIN, had no effect. This positive response to N-addition was significant at all times of the year except, (1) immediately after complete lake mixing in February when a large pool of hypolimnetic nitrate was injected into the euphotic zone, and (2) during a fall bloom of the nitrogen fixing species Nodularia spumigena. The positive response to N-addition in the bioassay experiments was strong between March and November. However, the seston exhibited only a gradual depletion of nitrogen relative to carbon over this same period. PN:PC ratios suggested no N-deficiency in phytoplankton biomass in February, March and April, moderate N-deficiency in May, June and July and, severe N-deficiency from August until winter turnover. The appearance of nitrogen fixing blue-green algae in September supports the hypothesis of N-limitation in the summer-autumn. In evaluating the nutrient status of a lake, the concepts of nutrient stimulation versus nutrient deficiency versus nutrient limitation must clearly be defined.This paper is dedicated to G. Evelyn Hutchinson who first visited Pyramid Lake in 1933.     

Grain yield and kernel weight of two maize genotypes differing in nitrogen use efficiency at various levels of nitrogen and carbohydrate availability during flowering and grain filling

Grain yield per plant (GYP) and mean kernel weight (KW) of maize (Zea mays L.) are sensitive to changes in the environment during the lag phase of kernel growth (the time after pollination in which the potential kernel size is determined), and during the phase of linear kernel growth. The aim of this study was to assess genotypic differences in the response to environmental stresses associated with N and/or carbohydrate shortage at different phases during plant development. The rate and timing of N and carbohydrate supply were modified by application of fertilizer, shading, and varying the plant density at sowing, at silking or at 14 d after silking. The effects of these treatments on the photosynthetic capacity, grain yield and mean kernel weight were investigated in two hybrids differing in N use efficiency. The total above-ground biomass and grain yield per plant of the efficient hybrid responded little to altered environmental conditions such as suboptimal N supply, enhanced inter-plant competition, and shading for 14 d during flowering, when compared to the less efficient genotype. We conclude that grain yields in the efficient genotype are less sensitive not only to N stress, but also to carbohydrate shortage before grain filling. Shading of N deficient plants from 14 d after silking to maturity did not significantly reduce grain yield in the non-efficient genotype, indicating complete sink limitation of grain yield during grain filling. In the efficient genotype, in contrast, grain yield of N-deficient plants was significantly reduced by shading during grain filling. The rate of photosynthesis declined with decreasing foliar N content. No genotypic differences in photosynthesis were observed at high or low foliar N contents. However, at high plant density and low N supply, the leaf chlorophyll content after flowering in the efficient genotype was higher than that in the non-efficient genotype. Obviously, the higher source capacity of the efficient genotype was not due to higher photosynthetic N use efficiency but due to maintenance of high chlorophyll contents under stressful conditions. In the efficient genotype, the harvest index was not significantly affected by N fertilization, plant density, or shading before the grain filling period. In contrast, in the non-efficient genotype the harvest index was diminished by N deficiency and shading during flowering. We conclude that the high yielding ability of the efficient genotype under stressful conditions was associated with formation of a high sink capacity of the grains under conditions of low carbohydrate and N availability during flowering and with maintenance of high source strength during grain filling under conditions of high plant density and low N availability.     

Construction cost of loblolly and ponderosa pine leaves grown with varying carbon and nitrogen availability

We grew loblolly and ponderosa pine seedlings in a factorial experiment with two CO₂ partial pressures (35 and 70 Pa), and two nitrogen treatments (1.0 and 3.5 mol m^?3 NH₄⁺), for one growing season to examine the effects of carbon and nitrogen availability on leaf construction cost. Growth in elevated CO₂ reduced leaf nitrogen concentrations by 17 to 40%, and increased C:N by 22 to 68%. Elevated N availability increased leaf N concentrations and decreased C:N. Non-structural carbohydrates increased in high-CO₂-grown loblolly seedlings, except in fascicles from low N, and in ponderosa primary and fascicle leaves grown in high N. In loblolly, increases in starch were nearly 2-fold greater than the increases in soluble sugars. In ponderosa, only the soluble sugars were affected by CO₂. Leaf construction cost (g glucose g^?1 dm) varied by 9.3% across all treatments. All of the variation in loblolly leaf construction cost could be explained by changes in non-structural carbohydrates. A model of the response of construction cost to changes in the mass of different biochemical fractions suggests that the remainder of the variation in ponderosa, not explained by non-structural carbohydrates, is probably attributable to changes in lignin, phenolic or protein concentrations.     

Impact of migratory snow geese on nitrogen and phosphorus dynamics in a freshwater reservoir

1. We examined impacts of nutrient loading, particularly of nitrogen and phosphorus, from greater snow geese (Chen caerulescens atlantica) on a reservoir in south‐eastern Pennsylvania, U.S.A. Approximately 100 000 geese use the reservoir for 2–6 weeks prior to their spring migration northward. 2. We estimated the magnitude of nutrient loading by geese during their presence and compared that to surface input and output rates. We also conducted nutrient limitation bioassay experiments to examine patterns of algal nutrient limitation upstream and downstream of the reservoir. 3. During their presence from 1 February to 27 March 2001, snow geese contributed 85–93% of the phosphorus and 33–44% of the nitrogen loaded to the reservoir. Both nutrients were exported from the reservoir slowly rather than as a quick pulse. Consequently, phosphorus concentrations in the outflow were higher than in the inflow from February to the end of July. However, nitrogen concentrations were consistently lower in the outflow than the inflow. 4. Nutrient limitation bioassays conducted in June and July indicated that primary production in the outflow was limited by nitrogen whereas the inflow was co‐limited by nitrogen and phosphorus. Further downstream from the reservoir, primary production was consistently phosphorus limited. Therefore, nitrogen limitation persisted long after the geese had left, but was relatively localised.     

The marine nitrogen cycle: recent discoveries,uncertainties and the potential relevance of climate change

The ocean''s nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation, assimilation, nitrification, anammox and denitrification. Dinitrogen is the most abundant form of nitrogen in sea water but only accessible by nitrogen-fixing microbes. Denitrification and nitrification are both regulated by oxygen concentrations and potentially produce nitrous oxide (N₂O), a climate-relevant atmospheric trace gas. The world''s oceans, including the coastal areas and upwelling areas, contribute about 30 per cent to the atmospheric N₂O budget and are, therefore, a major source of this gas to the atmosphere. Human activities now add more nitrogen to the environment than is naturally fixed. More than half of the nitrogen reaches the coastal ocean via river input and atmospheric deposition, of which the latter affects even remote oceanic regions. A nitrogen budget for the coastal and open ocean, where inputs and outputs match rather well, is presented. Furthermore, predicted climate change will impact the expansion of the oceans'' oxygen minimum zones, the productivity of surface waters and presumably other microbial processes, with unpredictable consequences for the cycling of nitrogen. Nitrogen cycling is closely intertwined with that of carbon, phosphorous and other biologically important elements via biological stoichiometric requirements. This linkage implies that human alterations of nitrogen cycling are likely to have major consequences for other biogeochemical processes and ecosystem functions and services.     

Atmospheric nitrogen deposition has caused nitrogen enrichment and eutrophication of lakes in the northern hemisphere

We compiled chemical data and phytoplankton biomass (PB) data (chlorophyll a ) from unproductive lakes in 42 different regions in Europe and North America, and compared these data to inorganic nitrogen (N) deposition over these regions. We demonstrate that increased deposition of inorganic N over large areas of Europe and North America has caused elevated concentrations of inorganic N in lakes. In addition, the unproductive lakes in high N deposition areas had clearly higher PB relative to the total phosphorus (P) concentrations illustrating that the elevated inorganic N concentrations has resulted in eutrophication and increased biomass of phytoplankton. The eutrophication caused by inorganic N deposition indicates that PB yield in a majority of lakes in the northern hemisphere is (was) limited by N in their natural state. We, therefore, suggest that P limitation largely concerns lakes where the balance between N and P has been changed because of increased anthropogenic input of N.     

Variable rates of phosphate uptake by shallow marine carbonate sediments: Mechanisms and ecological significance

We determined phosphate uptake by calcareous sediments at two locations within a shallow lagoon in Bermuda that varied in trophic status, with one site being mesotrophic and the other being more eutrophic. Phosphate adsorption over a six hour period was significantly faster in sediments from the mesotrophic site. Uptake at both sites was significantly less than that reported for a similar experiment on calcareous sediments in an oligotrophic lagoon in the Bahamas. The difference in phosphorus adsorption between our sites did not appear to be related to sediment characteristics often cited as important, such as differences in surface area (as inferred from grain size distributions), total organic matter content, or iron content. However, the sediment total phosphorus contents were inversely related to phosphorus uptake at our sites in Bermuda, and at the previously studied Bahamas site.We hypothesize that phosphate uptake in these calcareous sediments is a multi-step process, as previously described for fluvial sediments or pure calcium carbonate solids, with rapid initial surface chemisorption followed by a slower incorporation into the carbonate solid-phase matrix. Accordingly, sediments already richer in solid phase phosphorus take up additional phosphate more slowly since the slower incorporation of surface-adsorbed phosphate into the carbonate matrix limits the rate of renewal of surface-reactive adsorption sites.Although carbonate sediments are a sink for phosphate, and thereby reduce the availability of phosphorus for benthic macrophytes and phytoplankton in the shallow overlying water, phosphate uptake by these sediments appears to decrease along a gradient from oligotrophic to eutrophic sites. If our result is general, it implies a positive feedback in phosphorus availability, with a proportionately greater percentage of phosphorus loading being biologically available longer as phosphorus loading increases. This pattern is supported by the significantly higher tissue phosphorus content of the seagrass,Thalassia testudinum, collected from the eutrophic inner bay site. Over time, this effect may tend to cause a shift from phosphorus to nitrogen limitation in some calcareous marine environments.     

海洋微生物多样性的研究进展

海洋微生物多样性（marine microorganisms diversity)是指所有海洋微生物种类、种内遗传变异和它们的生存环境的总称。本文介绍了海洋微生物多样性方面的研究和利用进展,包括研究微生物多样性方法的改进,有价值的海洋微生物功能性产品的开发;关于海洋微生物抗肿瘤、抗病毒药物的研究等。     

The ecological significance of plasticity in root weight ratio in response to nitrogen: Opinion

We analyzed data on root weight ratio from a range of experimental studies documenting plant allocation changes in response to altered nitrogen availability. Our goal was to determine the degree to which plasticity in allocation between roots and shoots exists and to search for patterns in such plasticity among species. Our survey included 77 studies representing 206 cases and 129 species. As expected, we found that root weight ratio decreased with increased nitrogen availability in the majority of cases examined, and this response was most consistent when plants were grown individually or in intraspecific competition (versus interspecific competition). Surprisingly, however, we found no evidence to support existing hypotheses that fast-growing species adapted to high soil fertilities exhibit the highest levels of morphological plasticity, or that plasticity is positively associated with competitive ability. Rather, we found that average amounts of plasticity in root weight ratio in response to nitrogen availability were similar among species grouped by maximum relative growth rate and habitat fertility. Similar results were obtained for species categorized by life form, life history or root weight ratio itself, and plasticity in root weight ratio also had no consistent relationship with competitive ability. Numerous difficulties are associated with the attempt to search for pattern using independent studies, however our results lead to the conclusion that strong patterns in plasticity of root weight ratio in response to nitrogen availability among species do not exist. We discuss two reasons for this: (1) the costs of plasticity relative to its benefits are lower than previously predicted and (2) plasticity in traits other than root weight ratio is more important to plant foraging ability.