Focus on Metabolism: Changes in Whole-Plant Metabolism during the Grain-Filling Stage in Sorghum Grown under Elevated CO2 and Drought

Projections indicate an elevation of the atmospheric CO₂ concentration ([CO₂]) concomitant with an intensification of drought for this century, increasing the challenges to food security. On the one hand, drought is a main environmental factor responsible for decreasing crop productivity and grain quality, especially when occurring during the grain-filling stage. On the other hand, elevated [CO₂] is predicted to mitigate some of the negative effects of drought. Sorghum (Sorghum bicolor) is a C₄ grass that has important economical and nutritional values in many parts of the world. Although the impact of elevated [CO₂] and drought in photosynthesis and growth has been well documented for sorghum, the effects of the combination of these two environmental factors on plant metabolism have yet to be determined. To address this question, sorghum plants (cv BRS 330) were grown and monitored at ambient (400 µmol mol⁻¹) or elevated (800 µmol mol⁻¹) [CO₂] for 120 d and subjected to drought during the grain-filling stage. Leaf photosynthesis, respiration, and stomatal conductance were measured at 90 and 120 d after planting, and plant organs (leaves, culm, roots, prop roots, and grains) were harvested. Finally, biochemical composition and intracellular metabolites were assessed for each organ. As expected, elevated [CO₂] reduced the stomatal conductance, which preserved soil moisture and plant fitness under drought. Interestingly, the whole-plant metabolism was adjusted and protein content in grains was improved by 60% in sorghum grown under elevated [CO₂].Global food demand is projected to increase up to 110% by the middle of this century (Tilman et al., 2011; Alexandratos and Bruinsma, 2012), particularly due to a rise in world population that is likely to plateau at about 9 billion people (Godfray et al., 2010). Additionally, the average concentration of atmospheric CO₂ ([CO₂]) has increased 1.75 µmol mol⁻¹ per year between 1975 and today, reaching 400 µmol mol⁻¹ in April 2015 (NOAA, 2015). According to the A2 emission scenario from the U.S. Environmental Protection Agency, in the absence of explicit climate change policy, atmospheric CO₂ concentrations will reach 800 µmol mol⁻¹ by the end of this century. The increasing atmospheric [CO₂] is resulting in global climate changes, such as reduction in water availability and elevation in temperature. These factors are expected to heavily influence food production in the next years (Godfray and Garnett, 2014; Magrin et al., 2014).Sorghum (Sorghum bicolor) is a C₄ grass, considered a staple food grain for millions of the poorest and most food-insecure people in the semiarid tropics of Africa, Asia, and Central America, serving as an important source of energy, proteins, vitamins, and minerals (Taylor et al., 2006). Moreover, this crop is used for animal feed and as industrial raw material in developed countries such as the United States, which is the main world producer (FAO, 2015). With a fully sequenced genome (Paterson et al., 2009) and over 45,000 accessions representing a large geographic and genetic diversity, sorghum is a good model system in which to study the impact of global climate changes in C₄ grasses.The increase in [CO₂] in the atmosphere, which is the main driver of global climate changes (Meehl et al., 2007), is predicted to boost photosynthesis rates and productivity in a series of C₃ legumes and cereals, mainly due to a decrease in the photorespiration process (Grashoff et al., 1995; Long et al., 2006). On the contrary, due to their capacity to concentrate CO₂ in bundle sheath cells and reduce photorespiration to virtually zero, C₄ plants are unlikely to respond to the elevation of atmospheric [CO₂] (Leakey, 2009). However, even for C₄ plants, elevated [CO₂] can ameliorate the effects caused by drought, maintaining higher photosynthetic rates. This is due to an improvement in the efficiency of water use that is achieved by the reduction in stomatal conductance (Leakey et al., 2004; Markelz et al., 2011).The rate of photosynthesis as well as the redistribution of photoassimilates accumulated in different plant tissues during the day and/or during vegetative growth are crucial to grain development, and later, to its filling (Schnyder, 1993). Due to this relationship, any environmental stress such as drought occurring during the reproductive phase has the potential to result in poor grain filling and losses in yield (Blum et al., 1997). For instance, postanthesis drought can cause up to 30% decrease in yield (Borrell et al., 2000). It is also known that elevated [CO₂], drought, high temperature, and any combinations of these stresses can lead to significant changes in grain composition (Taub et al., 2008; Da Matta et al., 2010; Uprety et al., 2010; Madan et al., 2012), suggesting diverse metabolic alterations and/or adaptations that occur in the plant when it is cultivated in such conditions.Although the impacts of elevated [CO₂] and drought on photosynthesis and the growth of sorghum have been well documented (Conley et al., 2001; Ottman et al., 2001; Wall et al., 2001), no attention has been given to the impact of the combination of these two environmental changes on plant metabolism and composition. Regarding physiology, studies on the growth of sorghum under elevated [CO₂] and drought showed an increase of the net assimilation rate of 23% due to a decrease of 32% in stomatal conductance (Wall et al., 2001). This resulted in sorghum’s ability to use water 17% more efficiently (Conley et al., 2001). An improvement in the final overall biomass under elevated [CO₂] and drought has also been described (Ottman et al., 2001), but without a significant effect in grain yield (Wall et al., 2001).Few studies have been monitoring metabolic pathways in plants under elevated [CO₂] (Li et al., 2008; Aranjuelo et al., 2013) and drought (Silvente et al., 2012; Nam et al., 2015; Wenzel et al., 2015). Furthermore, to our knowledge, there are only two reports in which metabolite profiles or metabolic pathways were investigated under the combination of these two environmental conditions (Sicher and Barnaby, 2012; Zinta et al., 2014). Although it is widely accepted that whole-plant metabolism and composition can impact grain filling and yield, metabolic studies conducted so far have focused on a specific plant organ. For instance, Sicher and Barnaby (2012) analyzed the metabolite profile of leaves from maize (Zea mays) plants that were grown under elevated [CO₂] and drought, but they did not show how those environmental changes could have affected the metabolism of other tissues (e.g. culm and roots) or how they might have influenced the biomass or grain composition.In order to address how the combination of elevated [CO₂] and drought can modify whole-plant metabolism as well as biomass composition in sorghum, this study aimed to (1) evaluate photosynthesis, growth, and yield; (2) underline the differences in biomass composition and primary metabolite profiles among leaves, culm, roots, prop roots, and grains; and (3) determine the effect of elevated [CO₂] and drought on the primary metabolism of each organ.     

Evolutionary history of aphid-plant associations and their role in aphid diversification

Aphids are intimately linked with their host plants that constitute their only food resource and habitat, and thus impose considerable selective pressure on their evolution. It is therefore commonly assumed that host plants have greatly influenced the diversification of aphids. Here, we review what is known about the role of host plant association on aphid speciation by examining both macroevolutionary and population-level studies. Phylogenetic studies conducted at different taxonomic levels show that, as in many phytophagous insect groups, the radiation of angiosperms has probably favoured the major Tertiary diversification of aphids. These studies also highlight many aphid lineages constrained to sets of related host plants, suggesting strong evolutionary commitment in aphids’ host plant choice, but they fail to document cospeciation events between aphid and host lineages. Instead, phylogenies of several aphid genera reveal that divergence events are often accompanied by host shifts, and suggest, without constituting a formal demonstration, that aphid speciation could be a consequence of adaptation to new hosts. Experimental and field studies below the species level support reproductive isolation between host races as partly due to divergent selection by their host plants. Selected traits are mainly feeding performances and life cycle adaptations to plant phenology. Combined with behavioural preference for favourable host species, these divergent adaptations can induce pre- and post-zygotic barriers between host-specialized aphid populations. However, the hypothesis of host-driven speciation is seldom tested formally and must be weighed against overlooked explanations involving geographic isolation and non-ecological reproductive barriers in the process of speciation.     

Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota

Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.     

RNA and DNA binding properties of HIV-1 Vif protein: a fluorescence study

The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Some "non-permissive" cell lines cannot sustain replication of Vif(-) HIV-1 virions. In these cells, Vif counteracts the natural antiretroviral activity of the DNA-editing enzymes APOBEC3G/3F. Moreover, Vif is packaged into viral particles through a strong interaction with genomic RNA in viral nucleoprotein complexes. To gain insights into determinants of this binding process, we performed the first characterization of Vif/nucleic acid interactions using Vif intrinsic fluorescence. We determined the affinity of Vif for RNA fragments corresponding to various regions of the HIV-1 genome. Our results demonstrated preferential and moderately cooperative binding for RNAs corresponding to the 5'-untranslated region of HIV-1 (5'-untranslated region) and gag (cooperativity parameter omega approximately 65-80, and K(d) = 45-55 nM). In addition, fluorescence spectroscopy allowed us to point out the TAR apical loop and a short region in gag as primary strong affinity binding sites (K(d) = 9.5-14 nM). Interestingly, beside its RNA binding properties, the Vif protein can also bind the corresponding DNA oligonucleotides and their complementary counterparts with an affinity similar to the one observed for the RNA sequences, while other DNA sequences displayed reduced affinity. Taken together, our results suggest that Vif binding to RNA and DNA offers several non-exclusive ways to counteract APOBEC3G/3F factors, in addition to the well documented Vif-induced degradation by the proteasome and to the Vif-mediated repression of translation of these antiviral factors.     

Gold mining in the Peruvian Amazon: global prices, deforestation, and mercury imports

Many factors such as poverty, ineffective institutions and environmental regulations may prevent developing countries from managing how natural resources are extracted to meet a strong market demand. Extraction for some resources has reached such proportions that evidence is measurable from space. We present recent evidence of the global demand for a single commodity and the ecosystem destruction resulting from commodity extraction, recorded by satellites for one of the most biodiverse areas of the world. We find that since 2003, recent mining deforestation in Madre de Dios, Peru is increasing nonlinearly alongside a constant annual rate of increase in international gold price (∼18%/yr). We detect that the new pattern of mining deforestation (1915 ha/year, 2006–2009) is outpacing that of nearby settlement deforestation. We show that gold price is linked with exponential increases in Peruvian national mercury imports over time (R² = 0.93, p = 0.04, 2003–2009). Given the past rates of increase we predict that mercury imports may more than double for 2011 (∼500 t/year). Virtually all of Peru''s mercury imports are used in artisanal gold mining. Much of the mining increase is unregulated/artisanal in nature, lacking environmental impact analysis or miner education. As a result, large quantities of mercury are being released into the atmosphere, sediments and waterways. Other developing countries endowed with gold deposits are likely experiencing similar environmental destruction in response to recent record high gold prices. The increasing availability of satellite imagery ought to evoke further studies linking economic variables with land use and cover changes on the ground.