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We describe an innovative forecast presentation that aims to overcome obstacles to using seasonal climate forecasts for decision making, trace factors that influenced how seasonal forecast conventions have evolved, and describe a workshop process for training and supporting farmers in sub-Saharan Africa to use probabilistic seasonal forecasts. Mainstreaming seasonal climate forecasts through Regional Climate Outlook Forums (RCOFs) was an important milestone in the development of climate services. Most RCOFs and National Meteorological Services (NMS) adopted a subjective process to arrive at a consensus among different sources of prediction, and express the forecast as probabilities that rainfall in the upcoming season will fall in “below-normal,” “normal” or “above-normal” historical tercile categories. The Flexible Forecast is an online presentation that rectifies the main criticisms of the tercile convention by presenting downscaled forecasts as full probability distributions in probability-of-exceedance format along with the historical climate distribution. A map view provides seasonal forecast quantities, anomalies, or probabilities of experiencing above or below a user-selected threshold in amount or percentile, at the spatial resolution of the underlying gridded data (typically 4 to 5 km). We discuss factors that contributed to the persistence of the tercile convention, and milestones that paved the way to adopting seasonal forecast methods and formats that better align with user needs. The experience of adopting the new flexible forecast presentation regionally and at a national level in Eastern Africa illustrates the challenges and how they can be overcome. We also describe a seasonal forecast training and planning workshop process that has been piloted with smallholder farmers in several African countries. Beginning with participants' collective memory of past seasonal climate variations, the process leads them incrementally to understand the forecast presented in probability-of-exceedance format, and apply it to their seasonal planning decisions.

Ester-linked hydroxycinnamic acids ferulic acid (FA) and para-coumaric acid (p-CA) play important roles in crosslinking within cell wall arabinoxylans (AX) and between AX and lignin in grass cell walls. The addition of hydroxycinnamates to AX, is mediated by the Mitchell clade of BAHD acyl-coenzyme A-utilizing transferases. Overexpression of OsAT10 (a Mitchell clade BAHD acyl transferase) in rice, has previously been shown to increase p-CA content in AX in leaves and stems, leading to increased cell wall digestibility, potentially associated with a concomitant decrease in FA content. To investigate the physiological role of OsAT10 we established CRISPR/Cas9 rice knock-out mutants devoid of OsAT10. Our analysis of hydroxycinnamic acid content in wild type plants revealed that AX associated p-CA is found almost exclusively in rice husks, with very little found in other tissues. Mutant plants were essentially devoid of ester-linked p-CA associated with AX, indicating that OsAT10 represents the major enzyme responsible for the addition of p-CA to arabinoxylan in rice plants. We found no change in the digestibility of rice husk lacking AX-associated p-CA, suggesting that the changes in digestibility seen in OsAT10 overexpressing plants were solely due to compensatory decreases in AX-associated FA.

Background Citric acid is typically produced industrially by Aspergillus niger-mediated fermentation of a sucrose-based feedstock, such as molasses. The fungus Aspergillus niger has the potential to utilise lignocellulosic biomass, such as bagasse, for industrial-scale citric acid production, but realising this potential requires strain optimisation. Systems biology can accelerate strain engineering by systematic target identification, facilitated by methods for the integration of omics data into a high-quality metabolic model. In this work, we perform transcriptomic analysis to determine the temporal expression changes during fermentation of bagasse hydrolysate and develop an evolutionary algorithm to integrate the transcriptomic data with the available metabolic model to identify potential targets for strain engineering. Results The novel integrated procedure matures our understanding of suboptimal citric acid production and reveals potential targets for strain engineering, including targets consistent with the literature such as the up-regulation of citrate export and pyruvate carboxylase as well as novel targets such as the down-regulation of inorganic diphosphatase. Conclusions In this study, we demonstrate the production of citric acid from lignocellulosic hydrolysate and show how transcriptomic data across multiple timepoints can be coupled with evolutionary and metabolic modelling to identify potential targets for further engineering to maximise productivity from a chosen feedstock. The in silico strategies employed in this study can be applied to other biotechnological goals, assisting efforts to harness the potential of microorganisms for bio-based production of valuable chemicals.

GC chromatograms and photos of extracts

GC chromatograms and photos of extracts

Globally, 2.01 billion tonnes of municipal solid waste (MSW) were generated in 2016, about 37% of which was disposed of into landfills. This study evaluates the environmental and financial viability of producing ethanol from autoclaved MSW via fermentation. Experimental screening of four different microorganisms (i.e., S. cerevisiae, Z. mobilis, E. coli, and S. pombe) and process modelling indicate that MSW-derived ethanol can significantly reduce greenhouse gas emissions relative to gasoline (84% reduction following EU Renewable Energy Directive accounting methodology, and by 156–231% reduction following the US Energy Independence and Security Act methodology). Utilisation of wastes for biofuel production in the UK benefits from policy support and financial support for renewable fuels (Renewable Transport Fuel Certificates). Financial analysis highlights that microorganisms achieving higher ethanol yield and productivity (S. cerevisiae and Z. mobilis) can achieve financial viability with higher cumulative net present value than E. coli, S. pombe. However, the positive net present value can be achieved primarily due to the benefit of gate fees received by diverting wastes to autoclave and ethanol production (64% of total revenues), rather than from revenues from ethanol sales (7% of total revenues). Key process improvements must be achieved to improve the financial viability of ethanol production from MSW and deliver a clear advantage over waste incineration, specifically improving hydrolysis yield, reducing enzyme loading rate and, to a lesser extent, increasing solid loading rate. The results provide significant insights into the role of policy and technology development to achieve viable waste-to-biofuel systems.

Additional file 12: Fig. S7. Characterisation of the recombinant bacterial CAZymes encoded by the endosymbionts. DNS reducing sugars assays showing activities on a number of substrates for LpsGH5_8, LpsGH11, LpsGH134a and LpsGH134b. CMC = carboxymethyl cellulose, LBG = locust bean gum. The nanomoles of sugars released by the different proteins cannot be compared quantitatively as different amounts were used for the assay. File format .DOCX.

Additional file 8: Table S2. CAZy families. List of the CAZy families mentioned in the results, with the description of the activities that have been recorded for enzymes listed in each family. The information has been gathered from the CAZy database ( http://www.cazy.org ). File format .DOCX.

Additional file 1: Figure S1. Experiment location. Figure S2. Coverage estimates for each 16S rRNA amplicon library for all biological replicates across each time point. Figure S3. CAZyme families identified within the metatranscriptomic databases presented as transcripts per million. Figure S4. CAZyme producing genera and their respective CAZyme contributions. Figure S5. Productivity index for CAZyme producing taxa at family level resolution. Figure S6. Phylogenetic distribution of CAZyme classes at class resolution for week one. Figure S7. Phylogenetic distribution of CAZyme classes at class resolution for week three. Figure S8. Phylogenetic distribution of CAZyme classes at class resolution for week five. Figure S9. Phylogenetic distribution of CAZyme classes at class resolution for week ten. Figure S10. Functional classification of proteins within the metasecretome. Figure S11. Fungal profiles and OTU richness elucidated from internal transcribed spacer region 2 amplicon sequencing across the 16-week time course. Figure S12. Nutrient acquisition strategy of fungi profile across the 16-week time course. Figure S13. Bacteria profiles elucidated from 16S rRNA sequence homology. Figure S14. Bacteria profiles elucidated from 16S rRNA sequence homology. Table S1. Transect position of the five biological replicates in Welwick salt marsh. Table S2. Sequence reads throughout RNA sequence processing and assembly. Table S3. Commands for the replication of the 16S rRNA amplicon database processing pipeline.

Additional file 14: Table S6. Primers used for the cloning of the bacterial proteins LpsGH5_8, LpsGH11, LpsGH134a and LpsGH134b. LpsAA10A could not be amplified from the cDNA and therefore a synthetic version of the gene was codon-optimised for E-coli expression. File format .DOCX.

Additional file 2: Fig. S2. Searching for the opening of the duct of Deshayes in the shipworm digestive system. Left, transverse sections through the shell valve, from the anterior to posterior adductor muscle (A-E). Right, 3D rendered model of the whole shipworm, with the green highlighted region showing the position of the transverse cross section displayed on the left. File format .DOCX.

Additional file 10: Table S4. Details of the proteins for which heterologous recombinant expression from symbionts cDNA was successful. The annotation was performed against the NCBI non-redundant database, the signal peptides were identified with the Signal P4.1 server and the CAZy domains were searched using dbCAN. Dis. bonds = disulfide bonds. File format .DOCX.

Additional file 1: Fig. S1. Scanning electron microscopic images of the gills and food groove of L. pedicellatus. A) Close up of the gills lamellae to show the numerous cilia that capture food and draw it to the food groove. B) Close up of the food groove to show the numerous cilia (most of the mucus is lost during critical point drying). File format .DOCX.

Additional file 6: Fig. S6. Immunogold labelling of LpsGH5_8 in L. pedicellatus using pre-immune serum (negative control). A) SEM image illustrating the anatomical position of the gills, food groove, caecum and mouth in the shipworm body. B-D) Immunogold labelling of the lumen of the food groove (B), lumen of the caecum (C), and the gills (D) performed with pre-immune serum. No gold particles are observed in any of the samples. B = bacteria. File format .DOCX.

Additional file 11: Table S5. The amino acid sequences of the bacterial proteins LpsGH5_8, LpsGH11, LpsGH134a, LpsGH134b and LpsAA10A. Text in red represents the signal peptide. File format .DOCX.

Additional file 7: Table S1. Details of the proteins identified through proteomic analysis of the crystalline style. The annotation was performed against the NCBI non-redundant database, the signal peptides were identified with the Signal P4.1 server and the CAZy domains were searched using dbCAN. Many of the contigs were out of frame or not full length (particularly the bacterial ones) and therefore the identification of the signal peptide was not possible. File format .DOCX.

Additional file 1: Table S1. The functional annotations of proteins identified in the proteome of PfMig188. Table S2. The distribution of upregulated proteins across the different secretomes containing sugarcane bagasse.

Additional file 4: Fig. S4. Bacterial symbionts in L. pedicellatus. A) TEM image of a gill bacteriocyte. Arrows indicate the numerous rod-shaped bacteria in the cell. B) Close-up view of gill bacteria (TEM). C) Detailed TEM showing a cross section of a gill bacterium and some of its features (periplasmic space and membranes). File format .DOCX.

Additional file 5: Fig. S5. SDS-PAGE and nitrocellulose western blot obtained by loading 0.6 ��g of the recombinant purified bacterial LpsGH5_8 (without the appended CBM). A) Coomassie Brilliant Blue stained SDS-PAGE gel of the purified protein. B) Western blot detection performed with the purified pre-immune serum. C) Western blot detection performed with the purified anti-protein serum. File format .DOCX.

Additional file 3: Fig. S3. Scanning electron microscopy of L. pedicellatus. A dissected specimen with the mantle removed, showing the food groove connecting the gills to the mouth. File format .DOCX.

Additional file 13: Fig. S8. MALDI-TOF MS analysis of in vitro activity assays with purified LpsAA10A under the same experimental conditions as in Fig. 5 C. Panels from a to d show spectra of products obtained after incubation of the enzyme with 4 mg mL-1 Avicel (a), 4 mg mL-1 Avicel plus 4 mM gallic acid (b), 4 mg mL-1 Avicel plus 2 ��M LPMO (c) and 4 mg mL-1 Avicel plus 2 ��M LPMO and 4 mM gallic acid (d). In panels a to d, 100% relative intensity represents 1.3 �� 104 arbitrary units (a.u.). The panels from e to g show spectra of products obtained after incubation of 4 mg mL-1 PASC (e), 4 mg mL-1 PASC plus 4 mM gallic acid (f) and 4 mg mL-1 PASC plus 2 ��M LPMO (g). In panels e to g, 100% relative intensity represents 1.0 �� 104 arbitrary units. File format .DOCX.

Additional file 9: Table S3. CAZy families of the caecum. Table showing the relative abundance (calculated from the emPAI score) of eukaryotic and prokaryotic CAZy families identified in the proteomic analysis of the caecum content of L. pedicellatus. File format .DOCX.

Additional file 1. Containing Q-Q plots of GWAS

There is growing awareness among governments, businesses, and the general public of risks arising from changes to our climate on time scales from months through to decades. Some climatic changes could be unprecedented in their harmful socioeconomic impacts, while others with adequate forewarning and planning could offer benefits. There is therefore a pressing need for decision-makers, including policy-makers, to have access to and to use high-quality, accessible, relevant, and credible climate information about the past, present, and future to help make better-informed decisions and policies. We refer to the provision and use of such information as climate services. Established programs of research and operational activities are improving observations and climate monitoring, our understanding of climate processes, climate variability and change, and predictions and projections of the future climate. Delivering climate information (including data and knowledge) in a way that is usable and useful for decision-makers has had less attention, and society has yet to optimally benefit from the available information. While weather services routinely help weather-sensitive decision-making, similar services for decisions on longer time scales are less well established. Many organizations are now actively developing climate services, and a growing number of decision-makers are keen to benefit from such services. This article describes progress made over the past decade developing, delivering, and using climate services, in particular from the worldwide effort galvanizing around the Global Framework for Climate Services under the coordination of UN agencies. The article highlights challenges in making further progress and proposes potential new directions to address such challenges.

Additional file 7. Full derivation of the fitness function used for in silico evolution of organic acid production.

Producing probabilistic subseasonal forecasts of extreme events up to six weeks in advance is crucial for many economic sectors. In agribusiness, this time scale is particularly critical because it allows for mitigation strategies to be adopted for counteracting weather hazards and taking advantage of opportunities. For example, spring frosts are detrimental for many nut trees, resulting in dramatic losses at harvest time. To explore subseasonal forecast quality in boreal spring, identified as one of the most sensitive times of the year by agribusiness end users, we build a multisystem ensemble using four models involved in the Subseasonal to Seasonal Prediction project (S2S). Two-meter temperature forecasts are used to analyze cold spell predictions in the coastal Black Sea region, an area that is a global leader in the production of hazelnuts. When analyzed at the global scale, the multisystem ensemble probabilistic forecasts for near-surface temperature are better than climatological values for several regions, especially the tropics, even many weeks in advance; however, in the coastal Black Sea, skill is low after the second forecast week. When cold spells are predicted instead of near-surface temperatures, skill improves for the region, and the forecasts prove to contain potentially useful information to stakeholders willing to put mitigation plans into effect. Using a cost–loss model approach for the first time in this context, we show that there is added value of having such a forecast system instead of a business-as-usual strategy, not only for predictions released 1–2 weeks ahead of the extreme event, but also at longer lead times.

Additional file 4. Detailed calculation for estimated gains of using a marker in breeding

Little has been documented about the benefits and impacts of the recent growth in climate services, despite a growing call to justify their value and stimulate investment. Regional Climate Outlook Forums (RCOFs), an integral part of the public and private enterprise of climate services, have been implemented over the last 20 years with the objectives of producing and disseminating seasonal climate forecasts to inform improved climate risk management and adaptation. In proposing guidance on how to measure the success of RCOFs, we offer three broad evaluative categories that are based on the primary stated goals of the RCOFs: 1) quality of the climate information used and developed at RCOFs; 2) legitimacy of RCOF processes focused on consensus forecasts, broad user engagement, and capacity building; and 3) usability of the climate information produced at RCOFs. Evaluating the quality of information relies largely on quantitative measures and statistical techniques that are standardized and transferrable, but assessing the RCOF processes and perceived usability of RCOF products will necessitate a combination of quantitative and qualitative social science methods that are sensitive to highly variable regional contexts. As RCOFs have taken up different formats and procedures to adapt to diverse institutional and political settings and varied technical and scientific capacities, objective evaluation methods adopted should align with the goals and intent of the evaluation and be performed in a participatory, coproduction manner where producers and users of climate services together design the evaluation metrics and processes. To fully capture the potential benefits of the RCOFs, it may be necessary to adjust or recalibrate the goals of these forums to better fit the evolving landscape of climate services development, needs, and provision.

Additional file 5: Table S15. Index numbers of mutations and corresponding reactions and mutation effects.

Additional file 1. The file provides the Additional Tables S1–S14.

Additional file 7. Field trial GPS coordinates

Additional file 9. Containing a report of Genotyping by Sequencing (GBS) – Reference Pipeline

Additional file 7. Field trial GPS coordinates

Additional file 7. Full derivation of the fitness function used for in silico evolution of organic acid production.

Additional file 6. The file provides the additional Figures S1–S15.

Additional file 9. Containing a report of Genotyping by Sequencing (GBS) – Reference Pipeline

Additional file 4. Detailed calculation for estimated gains of using a marker in breeding

Additional file 5: Table S15. Index numbers of mutations and corresponding reactions and mutation effects.

Additional file 1. The file provides the Additional Tables S1–S14.

Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining., Marine woodborers can digest woody biomass without the help of gut microbiota but the mechanism has remained unclear. Here, the authors provide evidence that the woodborer’s respiratory protein hemocyanin plays a central role in wood digestion and may offer a route toward biorefining of woody plant biomass.

During the austral summer 2015/16, severe flooding displaced over 170 000 people on the Paraguay River system in Paraguay, Argentina, and southern Brazil. These floods were driven by repeated heavy rainfall events in the lower Paraguay River basin. Alternating sequences of enhanced moisture inflow from the South American low-level jet and local convergence associated with baroclinic systems were conducive to mesoscale convective activity and enhanced precipitation. These circulation patterns were favored by cross-time-scale interactions of a very strong El Niño event, an unusually persistent Madden–Julian oscillation in phases 4 and 5, and the presence of a dipole SST anomaly in the central southern Atlantic Ocean. The simultaneous use of seasonal and subseasonal heavy rainfall predictions could have provided decision-makers with useful information about the start of these flooding events from two to four weeks in advance. Probabilistic seasonal forecasts available at the beginning of November successfully indicated heightened probability of heavy rainfall (90th percentile) over southern Paraguay and Brazil for December–February. Raw subseasonal forecasts of heavy rainfall exhibited limited skill at lead times beyond the first two predicted weeks, but a model output statistics approach involving principal component regression substantially improved the spatial distribution of skill for week 3 relative to other methods tested, including extended logistic regressions. A continuous monitoring of climate drivers impacting rainfall in the region, and the use of statistically corrected heavy precipitation seasonal and subseasonal forecasts, may help improve flood preparedness in this and other regions.

Additional file 7: Figure S6. The Na+ Site on the TtAA10A Surface. The modelled sodium ion is shown as a grey sphere with the groups that coordinate it shown as sticks coloured by atom type. The 2Fobsâ Fcalc map is shown as a blue wire mesh contoured at 1Ď . The sodium ion is octahedrally coordinated with three main chain carbonyl groups and three water molecules. Sodium was assigned at this site based on the coordinating bond lengths and this was the ion that gave a B-factor following refinement closest to the surrounding protein atoms.

Additional file 4: Table S1. TtAA10A Data collection and refinement statistics.

Additional file 6: Figure S5. SEC-MALLS analysis of TtAA10A, where the solid red line indicates the refractive index, the dashed line is the light scattering (these are essentially identical so indistinguishable), dotted line the UV response at 280 nm. The central line inside the peak is representative of the molar mass (2.44 × 104 Da), indicating that TtAA10A forms a monomer in solution.

Additional file 3: Figure S3. EPR Cu titration reveals the presence of two distinct Cu sites. EPR copper titration experiment in which the protein was pre-treated with EDTA to remove the copper (as shown by the lack of EPR signal). Addition of 0.2 equivalents of Cu (to the concentration of protein) produced a single Cu species indicative of the histidine brace. Addition of a further 0.2 equivalents caused a change in the spectra with appearance of a second set of hyperfine peaks in the parallel region. The clearest change is seen after 0.6 equivalents of Cu have been added, where multiple peaks in the spectra indicate two Cu species. Loss of resolution in the last two spectra may be due to signal dilution.

East Africa experiences chronic food insecurity, with levels varying from year-to-year across the region. Given that much can be done to prevent this level of suffering before it happens, humanitarian agencies monitor early indicators of food insecurity to trigger early action. Forecasts of total seasonal rainfall are one tool used to monitor and anticipate food security outcomes. Factors beyond rainfall, such as conflict, are key determinants of whether lack of rainfall can become a problem. In this paper, we present a quantitative analysis that isolates the value of rainfall information in anticipating food security outcomes across livelihood groups in East Africa. Comparing observed rainfall and temperature with food security classifications, we quantify how much the chance of food insecurity increases when rainfall is low. Results differed dramatically among livelihood groups; pastoralists in East Africa more frequently experience food insecurity than do non-pastoralists, and 12 months of low rainfall greatly increases the chances of "crisis" and "emergency" food security in pastoralist regions. In non-pastoralist regions, the relationship with total rainfall is not as strong. Similar results were obtained for livelihood groups in Kenya and Ethiopia, with slightly differing results in Somalia. Given this, we evaluated the relevance of monitoring and forecasting seasonal total rainfall. Our quantitative results demonstrate that six months of rainfall observations can already indicate a heightened risk of food insecurity, a full six months before conditions deteriorate. Combining rainfall observations with seasonal forecasts can further change the range of possible outcomes to indicate higher or lower risk of food insecurity, but the added value of seasonal forecasts is noticeable only when they show a strong probability of below-normal rainfall.