Membrane Lipids Augment Cell Envelope Stress Signaling via the MadRS System to Defend Against Antimicrobial Peptides and Antibiotics in Enterococcus faecalis.

Enterococci have evolved resistance mechanisms to protect their cell envelopes against bacteriocins and host cationic antimicrobial peptides (CAMPs) produced in the gastrointestinal environment. Activation of the membrane stress response has also been tied to resistance to the lipopeptide antibiotic daptomycin. However, the actual effectors mediating resistance have not been elucidated. Here, we show that the MadRS (formerly YxdJK) membrane antimicrobial peptide defense system controls a network of genes, including a previously uncharacterized three gene operon (madEFG) that protects the E. faecalis cell envelope from antimicrobial peptides. Constitutive activation of the system confers protection against CAMPs and daptomycin in the absence of a functional LiaFSR system and leads to persistence of cardiac microlesions in vivo. Moreover, changes in the lipid cell membrane environment alter CAMP susceptibility and expression of the MadRS system. Thus, we provide a framework supporting a multilayered envelope defense mechanism for resistance and survival coupled to virulence.

Enabling food system innovation: accelerators for change.

It is widely accepted that current food systems are not on a trajectory for achieving the Sustainable Development Goals by the end of the decade. Technological innovation will have a considerable role to play in different parts of the food system; many promising options exist or are in the pipeline, some of which may be highly disruptive to existing value chains. Scaling up the innovations required, at the same time as protecting those who may lose out in the short term, will require a strong enabling environment. Here we apply an existing framework of eight change accelerators to six case studies of historical agricultural innovation. We estimated the degree to which each accelerator had been addressed at some stage in the innovation process, as a measure of the gap between what was needed and what was achieved. For the innovations that are being taken to scale and widely utilized, these accelerator gaps are small. Uptake of other innovations is stalled, and for these we found large gaps for one or more of the eight accelerators. Impactful innovation processes address all eight change accelerators at some point, with different phasing of the accelerators depending on the nature of the technology and on the impact pathway being pursued. This simple framework, when used in combination with narratives of uptake based on theories of change and impact pathways, may provide an effective means of screening future innovation processes to help prioritize and guide investment that can lead to more resilient, sustainable and equitable food systems.

A global clustering of terrestrial food production systems.

Food production is at the heart of global sustainability challenges, with unsustainable practices being a major driver of biodiversity loss, emissions and land degradation. The concept of foodscapes, defined as the characteristics of food production along biophysical and socio-economic gradients, could be a way addressing those challenges. By identifying homologues foodscapes classes possible interventions and leverage points for more sustainable agriculture could be identified. Here we provide a globally consistent approximation of the world's foodscape classes. We integrate global data on biophysical and socio-economic factors to identify a minimum set of emergent clusters and evaluate their characteristics, vulnerabilities and risks with regards to global change factors. Overall, we find food production globally to be highly concentrated in a few areas. Worryingly, we find particularly intensively cultivated or irrigated foodscape classes to be under considerable climatic and degradation risks. Our work can serve as baseline for global-scale zoning and gap analyses, while also revealing homologous areas for possible agricultural interventions.

Climate change and land-use change impacts on future availability of forage grass species for Ethiopian dairy systems.

Forage grasses are central feed resources for livestock globally. In Ethiopian dairy systems, they serve as feed sources during both wet and dry seasons, yet escalating climate change could threaten forage supply. Here, we investigate projected climate change impacts on three forage grasses currently recommended for Ethiopian dairy systems. We determine areas of geographical suitability for each species using three climate projections generated by General Circulation Models (GCMs) and calculate their ability to meet predicted dry matter demand under four scenarios for livestock intensification and land availability. By 2050, Buffel grass (Cenchrus ciliaris) is likely to be negatively affected by climate change in regions such as Tigray, while Rhodes grass (Chloris gayana) and Napier grass (Cenchrus purpureus) may have improved suitability under future climates. Our findings suggest that feed demands could theoretically be met by production of these forage grasses under current and future climates. However, if land availability is reduced and herd composition shifts towards higher-productivity exotic breeds, forage resources will not meet cattle demand even with improved agronomic management.

Impacts of heat stress on global cattle production during the 21st century: a modelling study.

BACKGROUND: Heat stress in animals is one of the major climate change impacts on domesticated livestock raised in both intensive and extensive production systems. At temperatures higher than an animal's thermoneutral zone, heat stress can affect liveweight gain, milk yield, and fertility. Animal welfare may also be negatively affected by heat stress even in the absence of effects on productivity, at least in the short term. METHODS: We estimated the comparative statics change in the value of cattle milk and meat production from heat stress-induced losses at the global level, using climate scenario outputs for the middle (2045) and end of the century (2085). The loss estimates are based on bioenergetic equations that relate changes in dry matter intake (DMI) to both cold and hot, humid weather. DMI changes were estimated using CMIP6 climate data and linked to a global dataset containing information on livestock production systems, animal numbers, and region-specific and system-specific animal diets. Changes in DMI were converted to changes in milk and meat production and valued using early 20th century world prices (ie, constant 2005 US dollars). FINDINGS: For a high greenhouse-gas emission scenario (SSP5-8.5), production losses from heat stress were estimated to amount to $39·94 billion (95% CI 34·39-45·49 billion) per year by the end of the century, or 9·8% of the value of production of meat and milk from cattle in 2005. For a low emission scenario (SSP1-2.6), the value of production losses was $14·89 billion (12·62-16·95 billion) per year, or 3·7% of 2005 value. In both scenarios, losses in most tropical regions were projected to be far greater than they were in temperate regions. INTERPRETATION: Our results highlight the potential magnitude and extent of the adaptation efforts that will be necessary to combat the effects of increasing heat stress on cattle production during this century if food security challenges are to be minimised. Adaptations include switching to more heat-tolerant breeds and provision of shade, ventilation, and cooling systems. FUNDING: CGIAR Trust Fund and bilateral donors.

Increases in extreme heat stress in domesticated livestock species during the twenty-first century.

Anthropogenic climate change is expected to have major impacts on domesticated livestock, including increased heat stress in animals in both intensive and extensive livestock systems. We estimate the changes in the number of extreme heat stress days per year for animals raised outdoors that can be expected in the major domesticated animal species (cattle, sheep, goats, poultry, and pigs) across the globe during this century. We used the temperature humidity index as a proxy for heat stress, calculated using temperature and relative humidity data collated from an ensemble of CMIP6 climate model output for mid and end century. We estimate changes in the proportions of different livestock species that may be at increased risk of extreme heat stress under two contrasting greenhouse gas emission scenarios. Results are discussed in relation to changes in the suitability of different climate conditions for domesticated livestock during the current century. We find that by end century, extreme heat stress risk is projected to increase for all livestock species in many parts of the tropics and some of the temperate zones, and to become climatically more widespread, compared to 2000. Although adaptation options exist for both intensive and extensive livestock production systems, the increasing pervasiveness of extreme heat stress risk in the future will seriously challenge the viability of outdoor livestock keeping, particularly in the lower latitudes in lower and middle-income countries where the costs of adaptation may be challenging to address.

In pursuit of a better world: crop improvement and the CGIAR.

The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.

Articulating the effect of food systems innovation on the Sustainable Development Goals.

Food system innovations will be instrumental to achieving multiple Sustainable Development Goals (SDGs). However, major innovation breakthroughs can trigger profound and disruptive changes, leading to simultaneous and interlinked reconfigurations of multiple parts of the global food system. The emergence of new technologies or social solutions, therefore, have very different impact profiles, with favourable consequences for some SDGs and unintended adverse side-effects for others. Stand-alone innovations seldom achieve positive outcomes over multiple sustainability dimensions. Instead, they should be embedded as part of systemic changes that facilitate the implementation of the SDGs. Emerging trade-offs need to be intentionally addressed to achieve true sustainability, particularly those involving social aspects like inequality in its many forms, social justice, and strong institutions, which remain challenging. Trade-offs with undesirable consequences are manageable through the development of well planned transition pathways, careful monitoring of key indicators, and through the implementation of transparent science targets at the local level.

Multiple cropping systems of the world and the potential for increasing cropping intensity.

Multiple cropping, defined as harvesting more than once a year, is a widespread land management strategy in tropical and subtropical agriculture. It is a way of intensifying agricultural production and diversifying the crop mix for economic and environmental benefits. Here we present the first global gridded data set of multiple cropping systems and quantify the physical area of more than 200 systems, the global multiple cropping area and the potential for increasing cropping intensity. We use national and sub-national data on monthly crop-specific growing areas around the year 2000 (1998-2002) for 26 crop groups, global cropland extent and crop harvested areas to identify sequential cropping systems of two or three crops with non-overlapping growing seasons. We find multiple cropping systems on 135 million hectares (12% of global cropland) with 85 million hectares in irrigated agriculture. 34%, 13% and 10% of the rice, wheat and maize area, respectively are under multiple cropping, demonstrating the importance of such cropping systems for cereal production. Harvesting currently single cropped areas a second time could increase global harvested areas by 87-395 million hectares, which is about 45% lower than previous estimates. Some scenarios of intensification indicate that it could be enough land to avoid expanding physical cropland into other land uses but attainable intensification will depend on the local context and the crop yields attainable in the second cycle and its related environmental costs.

Perspective article: Actions to reconfigure food systems.

There is broad agreement that current food systems are not on a sustainable trajectory that will enable us to reach the Sustainable Development Goals by 2030, particularly in the face of anthropogenic climate change. Guided by a consideration of some food system reconfigurations in the past, we outline an agenda of work around four action areas: rerouting old systems into new trajectories; reducing risks; minimising the environmental footprint of food systems; and realigning the enablers of change needed to make new food systems function. Here we highlight food systems levers that, along with activities within these four action areas, may shift food systems towards more sustainable, inclusive, healthy and climate-resilient futures. These actions, summarised here, are presented in extended form in a report of an international initiative involving hundreds of stakeholders for reconfiguring food systems.

High-resolution and bias-corrected CMIP5 projections for climate change impact assessments.

Projections of climate change are available at coarse scales (70-400 km). But agricultural and species models typically require finer scale climate data to model climate change impacts. Here, we present a global database of future climates developed by applying the delta method -a method for climate model bias correction. We performed a technical evaluation of the bias-correction method using a 'perfect sibling' framework and show that it reduces climate model bias by 50-70%. The data include monthly maximum and minimum temperatures and monthly total precipitation, and a set of bioclimatic indices, and can be used for assessing impacts of climate change on agriculture and biodiversity. The data are publicly available in the World Data Center for Climate (WDCC; cera-www.dkrz.de), as well as in the CCAFS-Climate data portal (http://ccafs-climate.org). The database has been used up to date in more than 350 studies of ecosystem and agricultural impact assessment.

Climate change and variability impacts on grazing herds: Insights from a system dynamics approach for semi-arid Australian rangelands.

Grazing livestock are an important source of food and income for millions of people worldwide. Changes in mean climate and increasing climate variability are affecting grasslands' carrying capacity, thus threatening the livelihood of millions of people as well as the health of grassland ecosystems. Compared with cropping systems, relatively little is known about the impact of such climatic changes on grasslands and livestock productivity and the adaptation responses available to farmers. In this study, we analysed the relationship between changes in mean precipitation, precipitation variability, farming practices and grazing cattle using a system dynamics approach for a semi-arid Australian rangeland system. We found that forage production and animal stocking rates were significantly affected by drought intensities and durations as well as by long-term climate trends. After a drought event, herd size recovery times ranged from years to decades in the absence of proactive restocking through animal purchases. Decreases in the annual precipitation means or increases in the interannual (year-to-year) and intra-annual (month-to-month) precipitation variability, all reduced herd sizes. The contribution of farming practices versus climate effect on herd dynamics varied depending on the herd characteristics considered. Climate contributed the most to the variance in stocking rates, followed by forage productivity levels and feeding supplementation practices (with or without urea and molasses). While intensification strategies and favourable climates increased long-term herd sizes, they also resulted in larger reductions in animal numbers during droughts and raised total enteric methane emissions. In the face of future climate trends, the grazing sector will need to increase its adaptability. Understanding which farming strategies can be beneficial, where, and when, as well as the enabling mechanisms required to implement them, will be critical for effectively improving rangelands and the livelihoods of pastoralists worldwide.

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments.

Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.

Agricultural diversification as an important strategy for achieving food security in Africa.

Farmers in Africa have long adapted to climatic and other risks by diversifying their farming activities. Using a multi-scale approach, we explore the relationship between farming diversity and food security and the diversification potential of African agriculture and its limits on the household and continental scale. On the household scale, we use agricultural surveys from more than 28,000 households located in 18 African countries. In a next step, we use the relationship between rainfall, rainfall variability, and farming diversity to determine the available diversification options for farmers on the continental scale. On the household scale, we show that households with greater farming diversity are more successful in meeting their consumption needs, but only up to a certain level of diversity per ha cropland and more often if food can be purchased from off-farm income or income from farm sales. More diverse farming systems can contribute to household food security; however, the relationship is influenced by other factors, for example, the market orientation of a household, livestock ownership, nonagricultural employment opportunities, and available land resources. On the continental scale, the greatest opportunities for diversification of food crops, cash crops, and livestock are located in areas with 500-1,000 mm annual rainfall and 17%-22% rainfall variability. Forty-three percent of the African cropland lacks these opportunities at present which may hamper the ability of agricultural systems to respond to climate change. While sustainable intensification practices that increase yields have received most attention to date, our study suggests that a shift in the research and policy paradigm toward agricultural diversification options may be necessary.

Oxygen and RNA in stress-induced mutation.

Mechanisms of mutation upregulated by stress responses have been described in several organisms from bacteria to human. These mechanisms might accelerate genetic change specifically when cells are maladapted to their environment. Stress-induced mutation mechanisms differ in their genetic requirements from mutation in growing cells, occurring by different mechanisms in different assay systems, but having in common a requirement for the induction of stress-responses. Here, we review progress in two areas relevant to stress-response-dependent mutagenic DNA break repair mechanisms in Escherichia coli. First, we review evidence that relates mutation to transcription. This connection might allow mutagenesis in transcribed regions, including those relevant to any stress being experienced, opening the possibility that mutations could be targeted to regions where mutation might be advantageous under conditions of a specific stress. We review the mechanisms by which replication initiated by transcription can lead to mutation. Second, we review recent findings that, although stress-induced mutation does not require exogenous DNA-damaging agents, it does require the presence of damaged bases in DNA. For starved E. coli, endogenous oxygen radicals cause these altered bases. We postulate that damaged bases stall the replisome, which, we suggest, is required for DNA-polymerase exchange, allowing the action of low-fidelity DNA polymerases that promote mutation.