Software Management Environment (SME) release 9.4 user reference material

This document contains user reference material for the Software Management Environment (SME) prototype, developed for the Systems Development Branch (Code 552) of the Flight Dynamics Division (FDD) of Goddard Space Flight Center (GSFC). The SME provides an integrated set of management tools that can be used by software development managers in their day-to-day management and planning activities. This document provides an overview of the SME, a description of all functions, and detailed instructions concerning the software's installation and use

Understanding and Enhancing Soil Biological Health: The Solution for Reversing Soil Degradation

Our objective is to provide an optimistic strategy for reversing soil degradation by increasing public and private research efforts to understand the role of soil biology, particularly microbiology, on the health of our world’s soils. We begin by defining soil quality/soil health (which we consider to be interchangeable terms), characterizing healthy soil resources, and relating the significance of soil health to agroecosystems and their functions. We examine how soil biology influences soil health and how biological properties and processes contribute to sustainability of agriculture and ecosystem services. We continue by examining what can be done to manipulate soil biology to: (i) increase nutrient availability for production of high yielding, high quality crops; (ii) protect crops from pests, pathogens, weeds; and (iii) manage other factors limiting production, provision of ecosystem services, and resilience to stresses like droughts. Next we look to the future by asking what needs to be known about soil biology that is not currently recognized or fully understood and how these needs could be addressed using emerging research tools. We conclude, based on our perceptions of how new knowledge regarding soil biology will help make agriculture more sustainable and productive, by recommending research emphases that should receive first priority through enhanced public and private research in order to reverse the trajectory toward global soil degradation

Phosphorus recycling in photorespiration maintains high photosynthetic capacity in woody species

Leaf photosynthetic CO2 responses can provide insight into how major nutrients, such as phosphorus (P), constrain leaf CO2 assimilation rates (Anet). However, triose-phosphate limitations are rarely employed in the classic photosynthesis model and it is uncertain as to what extent these limitations occur in field situations. In contrast to predictions from biochemical theory of photosynthesis, we found consistent evidence in the field of lower Anet in high [CO2] and low [O2] than at ambient [O2]. For 10 species of trees and shrubs across a range of soil P availability in Australia, none of them showed a positive response of Anet at saturating [CO2] (i.e. Amax) to 2 kPa O2. Three species showed >20% reductions in Amax in low [O2], a phenomenon potentially explained by orthophosphate (Pi) savings during photorespiration. These species, with largest photosynthetic capacity and Pi > 2 mmol P m−2, rely the most on additional Pi made available from photorespiration rather than species growing in P-impoverished soils. The results suggest that rarely used adjustments to a biochemical photosynthesis model are useful for predicting Amax and give insight into the biochemical limitations of photosynthesis rates at a range of leaf P concentrations. Phosphate limitations to photosynthetic capacity are likely more common in the field than previously considered

Contrasting effects of long term versus short-term nitrogen addition on photosynthesis and respiration in the Arctic

We examined the effects of short (<1–4 years) and long-term (22 years) nitrogen (N) and/or phosphorus (P) addition on the foliar CO2 exchange parameters of the Arctic species Betula nana and Eriophorum vaginatum in northern Alaska. Measured variables included: the carboxylation efficiency of Rubisco (Vcmax), electron transport capacity (Jmax), dark respiration (Rd), chlorophyll a and b content (Chl), and total foliar N (N). For both B. nana and E. vaginatum, foliar N increased by 20–50 % as a consequence of 1–22 years of fertilisation, respectively, and for B. nana foliar N increase was consistent throughout the whole canopy. However, despite this large increase in foliar N, no significant changes in Vcmax and Jmax were observed. In contrast, Rd was significantly higher (>25 %) in both species after 22 years of N addition, but not in the shorter-term treatments. Surprisingly, Chl only increased in both species the first year of fertilisation (i.e. the first season of nutrients applied), but not in the longer-term treatments. These results imply that: (1) under current (low) N availability, these Arctic species either already optimize their photosynthetic capacity per leaf area, or are limited by other nutrients; (2) observed increases in Arctic NEE and GPP with increased nutrient availability are caused by structural changes like increased leaf area index, rather than increased foliar photosynthetic capacity and (3) short-term effects (1–4 years) of nutrient addition cannot always be extrapolated to a larger time scale, which emphasizes the importance of long-term ecological experiments

Estimating Impact Forces of Tail Club Strikes by Ankylosaurid Dinosaurs

BACKGROUND: It has been assumed that the unusual tail club of ankylosaurid dinosaurs was used actively as a weapon, but the biological feasibility of this behaviour has not been examined in detail. Ankylosaurid tail clubs are composed of interlocking vertebrae, which form the handle, and large terminal osteoderms, which form the knob. METHODOLOGY/PRINCIPAL FINDINGS: Computed tomographic (CT) scans of several ankylosaurid tail clubs referred to Dyoplosaurus and Euoplocephalus, combined with measurements of free caudal vertebrae, provide information used to estimate the impact force of tail clubs of various sizes. Ankylosaurid tails are modeled as a series of segments for which mass, muscle cross-sectional area, torque, and angular acceleration are calculated. Free caudal vertebrae segments had limited vertical flexibility, but the tail could have swung through approximately 100 degrees laterally. Muscle scars on the pelvis record the presence of a large M. longissimus caudae, and ossified tendons alongside the handle represent M. spinalis. CT scans showed that knob osteoderms were predominantly cancellous, which would have lowered the rotational inertia of the tail club and made it easier to wield as a weapon. CONCLUSIONS/SIGNIFICANCE: Large knobs could generate sufficient force to break bone during impacts, but average and small knobs could not. Tail swinging behaviour is feasible in ankylosaurids, but it remains unknown whether the tail was used for interspecific defense, intraspecific combat, or both

A Naturally Associated Rhizobacterium of Arabidopsis thaliana Induces a Starvation-Like Transcriptional Response while Promoting Growth

Plant growth promotion by rhizobacteria is a known phenomenon but the underlying mechanisms are poorly understood. We searched for plant growth-promoting rhizobacteria that are naturally associated with Arabidopsis thaliana to investigate the molecular mechanisms that are involved in plant growth-promotion. We isolated a Pseudomonas bacterium (Pseudomonas sp. G62) from roots of field-grown Arabidopsis plants that has not been described previously and analyzed its effect on plant growth, gene expression and the level of sugars and amino acids in the host plant. Inoculation with Pseudomonas sp. G62 promoted plant growth under various growth conditions. Microarray analysis revealed rapid changes in transcript levels of genes annotated to energy-, sugar- and cell wall metabolism in plants 6 h after root inoculation with P. sp. G62. The expression of several of these genes remained stable over weeks, but appeared differentially regulated in roots and shoots. The global gene expression profile observed after inoculation with P. sp. G62 showed a striking resemblance with previously described carbohydrate starvation experiments, although plants were not depleted from soluble sugars, and even showed a slight increase of the sucrose level in roots 5 weeks after inoculation. We suggest that the starvation-like transcriptional phenotype - while steady state sucrose levels are not reduced - is induced by a yet unknown signal from the bacterium that simulates sugar starvation. We discuss the potential effects of the sugar starvation signal on plant growth promotion

Effects of Soil Water and Nitrogen on Growth and Photosynthetic Response of Manchurian Ash (Fraxinus mandshurica) Seedlings in Northeastern China

Soil water and nitrogen (N) are considered to be the main environmental factors limiting plant growth and photosynthetic capacity. However, less is known about the interactive effects of soil water and N on tree growth and photosynthetic response in the temperate ecosystem. seedlings. The seedlings were exposed to three water regimes including natural precipitation (CK), higher precipitation (HW) (CK +30%) and lower precipitation (LW) (CK −30%), and both with and without N addition for two growing seasons. We demonstrated that water and N supply led to a significant increase in the growth and biomass production of the seedlings. LW treatment significantly decreased biomass production and leaf N content, but they showed marked increases in N addition. N addition could enhance the photosynthetic capability under HW and CK conditions. Leaf chlorophyll content and the initial activity of Rubisco were dramatically increased by N addition regardless of soil water condition. The positive relationships were found between photosynthetic capacity, leaf N content, and SLA in response to water and N supply in the seedling. Rubisco expression was up-regulated by N addition with decreasing soil water content. Immunofluorescent staining showed that the labeling for Rubisco was relatively low in leaves of the seedlings under LW condition. The accumulation of Rubisco was increased in leaf tissues of LW by N addition. seedlings, which may provide novel insights on the potential responses of the forest ecosystem to climate change associated with increasing N deposition

Shake a tail feather: the evolution of the theropod tail into a stiff aerodynamic surface

Theropod dinosaurs show striking morphological and functional tail variation; e.g., a long, robust, basal theropod tail used for counterbalance, or a short, modern avian tail used as an aerodynamic surface. We used a quantitative morphological and functional analysis to reconstruct intervertebral joint stiffness in the tail along the theropod lineage to extant birds. This provides new details of the tail's morphological transformation, and for the first time quantitatively evaluates its biomechanical consequences. We observe that both dorsoventral and lateral joint stiffness decreased along the non-avian theropod lineage (between nodes Theropoda and Paraves). Our results show how the tail structure of non-avian theropods was mechanically appropriate for holding itself up against gravity and maintaining passive balance. However, as dorsoventral and lateral joint stiffness decreased, the tail may have become more effective for dynamically maintaining balance. This supports our hypothesis of a reduction of dorsoventral and lateral joint stiffness in shorter tails. Along the avian theropod lineage (Avialae to crown group birds), dorsoventral and lateral joint stiffness increased overall, which appears to contradict our null expectation. We infer that this departure in joint stiffness is specific to the tail's aerodynamic role and the functional constraints imposed by it. Increased dorsoventral and lateral joint stiffness may have facilitated a gradually improved capacity to lift, depress, and swing the tail. The associated morphological changes should have resulted in a tail capable of producing larger muscular forces to utilise larger lift forces in flight. Improved joint mobility in neornithine birds potentially permitted an increase in the range of lift force vector orientations, which might have improved flight proficiency and manoeuvrability. The tail morphology of modern birds with tail fanning capabilities originated in early ornithuromorph birds. Hence, these capabilities should have been present in the early Cretaceous, with incipient tail-fanning capacity in the earliest pygostylian birds

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition

Soil aggregates are microhabitats for microorganisms, and directly influence microorganisms that live within and are influenced by microorganisms in return. Two methods are used to isolate soil aggregates by their size: dry sieving (sieving air-dried soil) and wet sieving (sieving soil in water). Wet-sieving methods are generally considered to represent separation of aggregate classes that are stable to physical disaggregation in water, a condition considered favorable for protecting soil structure over time. However, little is known about the effect of sieving methods on microbial abundance, diversity, and functions, hindering the understanding of the relationship between soil structure and soil aggregates as habitat and soil microorganisms. In this study, the effect of dry and wet sieving on bacterial diversity, and abundance of microorganisms involved in N fixation (nifH gene), nitrification (amoA bacteria and archaea), and denitrification (narG, nirS and nosZ genes), was determined for four sizes of soil aggregates from a cropland and grassland. Quantitative-PCR (Q-PCR) showed little differences in relative gene abundance between size fractions of soil aggregates, but wet-sieving method significantly increased gene abundance for amoA bacteria, nirS and nosZ genes. When the N functional genes were expressed as percentage of the bacterial 16S rRNA genes, the wet sieving resulted in significantly higher genes percentage for all the genes (except for narG gene), and significant differences between soil aggregate size fractions at the grassland site. The different sieving methods resulted in different bacterial community compositions, but only the wet-sieving method was able to reveal significant differences in bacterial community composition between soil fractions in grassland. The results demonstrate significantly different quantitative and qualitative interpretation of soil microbial community depending on whether aggregate samples were obtained from wet or dry sieving, highlighting the importance in the choice of the sieving method

A window into fungal endophytism in Salicornia europaea: deciphering fungal characteristics as plant growth promoting agents

Aim Plant-endophytic associations exist only when equilibrium is maintained between both partners. This study analyses the properties of endophytic fungi inhabiting a halophyte growing in high soil salinity and tests whether these fungi are beneficial or detrimental when non-host plants are inoculated. Method Fungi were isolated from Salicornia europaea collected from two sites differing in salinization history (anthropogenic and naturally saline) and analyzed for plant growth promoting abilities and non-host plant interactions. Results Most isolated fungi belonged to Ascomycota (96%) including dematiaceous fungi and commonly known plant pathogens and saprobes. The strains were metabolically active for siderophores, polyamines and indole-3-acetic acid (mainly Aureobasidium sp.) with very low activity for phosphatases. Many showed proteolytic, lipolytic, chitinolytic, cellulolytic and amylolytic activities but low pectolytic activity. Different activities between similar fungal species found in both sites were particularly seen for Epiccocum sp., Arthrinium sp. and Trichoderma sp. Inoculating the non-host Lolium perenne with selected fungi increased plant growth, mainly in the symbiont (Epichloë)-free variety. Arthrinium gamsii CR1-9 and Stereum gausapatum ISK3-11 were most effective for plant growth promotion. Conclusions This research suggests that host lifestyle and soil characteristics have a strong effect on endophytic fungi, and environmental stress could disturb the plant-fungi relations. In favourable conditions, these fungi may be effective in facilitating crop production in non-cultivable saline lands