Microbial Ecology

ATP-grasp enzymes are involved in many different biological processes of primary and secondary metabolism and catalyze the production of many physiological or medicinally valuable peptides. Here, we report an ATP-grasp enzyme Alb28, from Streptomyces albogriseolus MGR072, which exhibits broad substrate promiscuity and strict stereoselectivity, thereby capable of producing at least 55 structurally diversified dipeptides, greatly expanding the existing dipeptide library. By combining crystallographic studies, molecular dynamics simulations, and mutagenesis assays, we identified the critical residues in Alb28 responsible for regulating the substrate recognition and enzymatic catalysis. Particularly, two structural motifs in Alb28 are involved in dictating the entry of substrate into the active-site via the opening/closing motions. Our work potentiates the future applications of Alb28 in generating structurally diversified dipeptides for therapeutic usages.

In the Arctic, the spatiotemporal variation of net methane uptake in upland soils depends on unresolved interactive controls between edaphic and microbial factors not yet included in current models, underpinning the uncertainty of upscaling the Arctic methane budget. Here we show that upland soils in Greenland are consistent methane sinks (−1.83 ± 0.19 nmol methane g−1 dw d−1) across a N-S (64–83 °N) pedoclimatic transect. We demonstrate that methane oxidizers abundance, soil pH, and available soil copper are important controls on the spatial variation in methane oxidation. We revised a soil biogeochemical model with a high-resolution land classification and meteorological data for Greenland and tested it against our methane uptake measurements. The model simulated well the magnitudes of observed methane uptake but not the spatial variation across all sites. This work provides novel insights into the controls of methane uptake, which are critical for the accuracy of methane budgets.

A new endophytic ascomycete, described herein as Fusarium endophyticum, was isolated from leaves of Camellia sinensis var. assamica collected from Nan Province, northern Thailand. This species is described using morphological characteristics and molecular multi-gene analyses. Multi-gene phylogenetic analyses of a combination of internal transcribed spacer region of the rDNA (ITS), translation-elongation factor 1 alpha (tef-1), RNA polymerase II second largest subunit (rpb2), and RNA polymerase II largest subunit (rpb1) genes revealed that F. endophyticum belonged to the Fusarium lateritium species complex (FLSC) and was distinct from all other known species. A full description, illustrations and a phylogenetic tree showing the position of F. endophyticum are provided.

PurposeAlthough past studies have found well-constrained soil carbon (C)/nutrient ratios, the effects of increased nitrogen (N) and water inputs on these ratios across soil depths have rarely been assessed in semi-arid grasslands.MethodsIn this study, we evaluated the contents of total C, N, phosphorus (P), sulfur (S), and their stoichiometric ratios in a 0–80 cm soil profile following 13 years of successive N (at rates of 5 and 15 g m−2 yearr−1) and water addition (180 mm per growing season) in a semi-arid grassland of the Mongolian Plateau.ResultsIn the 0–10 cm soil layer, long-term N addition tended to increase total C and N contents but decreased soil total P and S contents compared to the control. The effects of N addition, as observed in 0–10 cm soil, however, were not consistent with that in the deep 10–80 cm soil layers. Water addition increased the total C, N, and P contents across the entire soil profile but increased total S content only in 0–40 cm soil. Moreover, the combined addition of N and water generally had stronger effects on the four elements across the whole soil profile. For the stoichiometry of the four elements, a low rate of N addition (5 g m−2 year−1) increased soil C:N ratios and decreased soil P:S ratios in the 0–80 cm soils, but a high rate of N addition (15 g m−2 year−1) produced the opposite effect. Both N addition rates resulted in an increase in the soil C:P, C:S, N:P, and N:S ratios. Similarly, in plots that received water, water addition alone decreased the soil C:N ratios, while N addition caused higher fluctuations in these six elemental ratios. However, there was no consistent pattern of change in any one ratio, independent of the addition of water, when taking into account N addition rates and soil depths.ConclusionOur findings showed that the effects of N addition on soil total C, N, P, and S contents and their stoichiometric ratios were highly influenced by the rate of N addition and the depth of soil, and that these effects could be modulated by increasing precipitation. These results need to be carefully considered while managing the ecological environment in semi-arid steppes.

Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana’s intraspecific variability that can be explored to address questions at the interface of genetics and ecology.

Abstract The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.HighlightFormation of the rhizosheath, a layer of soil adhering to the root, is under complex genetic control in pearl millet and is mainly regulated by root exudation.

A synthetic biology platform for the production of plant volatile terpenoids (rose oil) was established, which provides a promising approach for a sustainable source of important plant natural products.

The survival of both African rhinoceros species is under threat due to large-scale poaching. The pressure that poaching currently exerts on rhino populations is too large to solely wait for long-term conservation strategies, e.g., demand and corruption reduction campaigns, to take effect. Consequently, protection efforts aimed at the short-term survival of the rhino species seem to be urgently needed. Unfortunately, current rhino protection efforts fail to prevent large rhino population declines as conservation officers often fail to localize poachers before they can kill a rhino. Therefore I aimed to develop a poacher early warning system that provides conservation officers with more situational awareness, which can therefore decrease the risk of shootouts between poachers and conservation officers.