Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.     

Smallholder farms have and can store more carbon than previously estimated

Increasing soil organic carbon (SOC) stocks is increasingly targeted as a key strategy in climate change mitigation and improved ecosystem resiliency. Agricultural land, a dominant global land use, provides substantial challenges and opportunities for global carbon sequestration. Despite this, global estimates of soil carbon sequestration potential often exclude agricultural land and estimates are coarse for regions in the Global South. To address these discrepancies and improve estimates, we develop a hybrid, data-augmented database approach to better estimate the magnitude of SOC sequestration potential of agricultural soils. With high-resolution (30 m) soil maps of Africa developed by the International Soils Database (iSDA) and Malawi as a case study, we create a national adjustment using site-specific soil data retrieved from 1160 agricultural fields. We use a benchmark approach to estimate the amount of SOC Malawian agricultural soils can sequester, accounting for edaphic and climatic conditions, and calculate the resulting carbon gap. Field measurements of SOC stocks and sequestration potentials were consistently larger than iSDA predictions, with an average carbon gap of 4.42 ± 0.23 Mg C ha⁻¹ to a depth of 20 cm, with some areas exceeding 10 Mg C ha⁻¹. Augmenting iSDA predictions with field data also improved sensitivity to identify areas with high SOC sequestration potential by 6%—areas that may benefit from improved management practices. Overall, we estimate that 6.8 million ha of surface soil suitable for agriculture in Malawi has the potential to store 274 ± 14 Tg SOC. Our approach illustrates how ground truthing efforts remain essential to reduce errors in continent-wide soil carbon predictions for local and regional use. This work begins efforts needed across regions to develop soil carbon benchmarks that inform policies and identify high-impact areas in the effort to increase SOC globally.     

Soil carbon stocks in stable tropical landforms are dominated by geochemical controls and not by land use

Soil organic carbon (SOC) dynamics depend on soil properties derived from the geoclimatic conditions under which soils develop and are in many cases modified by land conversion. However, SOC stabilization and the responses of SOC to land use change are not well constrained in deeply weathered tropical soils, which are dominated by less reactive minerals than those in temperate regions. Along a gradient of geochemically distinct soil parent materials, we investigated differences in SOC stocks and SOC (Δ¹⁴C) turnover time across soil profile depth between montane tropical forest and cropland situated on flat, non-erosive plateau landforms. We show that SOC stocks and soil Δ¹⁴C patterns do not differ significantly with land use, but that differences in SOC can be explained by the physicochemical properties of soils. More specifically, labile organo-mineral associations in combination with exchangeable base cations were identified as the dominating controls over soil C stocks and turnover. We argue that due to their long weathering history, the investigated tropical soils do not provide enough reactive minerals for the stabilization of C input in either high input (tropical forest) or low-input (cropland) systems. Since these soils exceeded their maximum potential for the mineral related stabilization of SOC, potential positive effects of reforestation on tropical SOC storage are most likely limited to minor differences in topsoil without major impacts on subsoil C stocks. Hence, in deeply weathered soils, increasing C inputs may lead to the accumulation of a larger readily available SOC pool, but does not contribute to long-term SOC stabilization.     

Ecological restoration in the age of apocalypse

Billions of dollars are spent annually on ecological restoration efforts around the world and yet successful attainment of restoration targets still falls short in many regions. Globally, ecosystem restoration is becoming increasingly challenged with changes in climate. Years with extreme climatic events that limit plant establishment, such as severe drought, heatwaves, and floods are projected to increase in frequency. A critical evaluation of current ecological restoration practices and changes to those practices are needed to attain global restoration targets. For plant restoration, many efforts globally focus on planting in a single year following disturbance. The odds of restoration efforts being conducted in a year that is inconducive to plant establishment may be calculated using climatic risk data. We propose a risk-mitigation approach to restoration wherein plantings are conducted across multiple years for projects in a bet-hedging strategy and evaluated through an adaptive management approach.     

Anne Barnard,her life and contribution to Curtis's Botanical Magazine

Anne Barnard (23 June 1833–19 January 1899), née Henslow, made around 125 illustrations for Curtis's Botanical Magazine, during the editorship of J.D. Hooker. Her life and botanical works are reviewed here, and examples of her original paintings are given.     

Integrating carbon stocks and landscape connectivity for nature-based climate solutions

Actions to protect against biodiversity loss and climate change will require a framework that addresses synergies between these interrelated issues. In this study, we present methods for identifying areas important for the implementation of nature-based climate solutions and biodiversity conservation by intersecting high-resolution spatial data for carbon storage and landscape connectivity. We explored the spatial congruence of carbon and connectivity in Ontario, Canada and examined effectiveness of current protected areas coverage. We found a weak positive relationship between carbon stocks and landscape connectivity; however, our maps revealed large hotspots, with high values of both indices, throughout the boreal forest and northern peatlands and smaller, isolated hotspots, in the settled landscapes of the south. Location of hotspots varied depending on whether we considered forest or soil carbon. Further, our results show that current protected and conserved areas in Ontario only cover 13% of landscapes with the highest values for both carbon storage and connectivity. Protection or restoration of areas that maximize the co-benefits of carbon storage and connectivity would make significant contributions toward ambitious national targets to reduce greenhouse gas emissions and conserve biodiversity.     

From dusk till dawn: camera traps reveal the diel patterns of flower feeding by hawkmoths

1. Diel rhythms of foraging activity by animal flower visitors can reflect niche partitioning and are considered an important component of selection on floral traits. However, it has been notoriously difficult to obtain objective information on the patterns of flower visitation by crepuscular and nocturnal insects. 2. Motion-activated cameras were used for field-based studies of hawkmoth foraging behaviour on six African plant species. 3. The results showed that short-tongued hawkmoth species forage mainly around dusk and then sporadically throughout the night, whereas long-tongued hawkmoth species feed consistently throughout the night, with a peak shortly before midnight. 4. These results provide the first quantitative estimates of diel patterns of interactions between multiple hawkmoth and plant species and, when combined with qualitative reports from other studies, suggest that differences in diel activity between the two main hawkmoth functional groups (short- and long-tongued) are consistent across the Old and New Worlds.     

Co‐occurrence of defensive traits in the potato aphid Macrosiphum euphorbiae

1. Insecticide usage selects strongly for resistance in aphid populations, but this could entail fitness costs in other resistance traits. The potato aphid Macrosiphum euphorbiae Thomas exhibits intraspecific variation in susceptibility to parasitism by braconid wasps and provides a suitable species to study the relation between the defensive traits of parasitism and insecticide resistance. 2. Clonal lines (23 in total) of M. euphorbiae were established from aphids collected in 2013 from geographically separate populations in the U.K. Clonal lines belonged to five aphid genotypes, but one genotype predominated (78% of samples), and the facultative endosymbiont Hamiltonella defensa was detected in c. 40% of lines. 3. Total esterase activity in aphid tissues varied significantly between aphid genotypes and collection areas, but there was no clear pattern in relation to H. defensa infection or between collection sites likely to differ in insecticide pressures. 4. Five clonal lines representing low to moderate levels of enzyme activity, which included different aphid genotypes and presence/absence of H. defensa infection, were assayed for their susceptibility to the parasitoid wasp Aphidius ervi Haliday. Aphid mummification varied significantly between aphid genotypes, with low values in one genotype of aphids irrespective of H. defensa presence. 5. The results revealed that aphid lines belonging to the parasitism‐resistant genotype exhibited moderate levels of total esterase activity, indicating a competitve advantage for this genotype of M. euphorbiae when exposed to chemical and biological control factors in agroecosystems.