Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.

Effect of Storage Technologies on Postharvest Insect Pest Control and Seed Germination in Mexican Maize Landraces.

Smallholder farmers who grow maize landraces face important challenges to preserve their seed biodiversity from one season to another. This study was carried out in the central highlands of Mexico to compare the effectiveness of two seed storage practices-specifically, polypropylene woven bags (farmers' conventional practice) vs. hermetic containers-for minimizing seed losses and maintaining germination. Four Mexican landraces were stored for three and six months. Data on moisture content and kernel damage were collected at the beginning and the end of the storage period. Pest-free samples collected were also analyzed for seed germination. Moisture content was below 13% overall and was not significantly affected by storage technology or storage time. Samples from the polypropylene woven bags suffered significant damage from Sitophilus zeamais and Prostephanus truncatus, with the percentages of insect damage and weight loss reaching 61.4% and 23.4%, respectively. Losses were minimal in seed stored in hermetic containers, with a maximum insect damage of 4.1% and weight loss of 2.2%. Overall, the germination rate of samples stored in these airtight containers was greater than 90%. This study provides additional evidence on the effectiveness of hermetic containers at maintaining Mexican landraces' seed quantity and quality during storage in smallholder conditions in central Mexico.

Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study.

To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.

Dataset of historic and modern bread and durum wheat cultivar performance under conventional and reduced tillage with full and reduced irrigation.

Conservation agriculture (CA) is an agronomic management system based on zero tillage and residue retention. Due to its potential for climate change adaptation through the reduction of soil erosion and improved water availability, CA is becoming more important in many regions of the world. However, increased bulk density and large amounts of crop residues may be a constraint for early plant establishment. This holds especially true under irrigated production areas with high yield potential. Genotype × tillage effects on yield are not well understood and it is unclear whether tillage should be an evaluation factor in breeding programs. Fourteen CIMMYT bread (Triticum aestivum) and thirteen durum (Triticum turgidum) wheat genotypes, created between 1964 and 2011, were tested for yield and agronomic performance at CIMMYT's experimental station near Ciudad Obregon, Mexico, during nine seasons. The genotypes were subjected to different tillage and irrigation treatments which consisted of conventional and permanent raised beds with full and reduced irrigation. The dataset includes traits collected during the growing period (days to emergence, days to flowering, maturity, plant height, NDVI, days from flowering to maturity, grain production rate) and at harvest (yield, harvest index, thousand grain weight, spikes/m², grains/m², test weight) and weather data (daily minimum and maximum temperature, rainfall). Six years of data of 26 genotypes were published along with the Honsdorf et al. (2018) paper in Field Crops Research (DOI: s10.1016/j.fcr.2017.11.011). This updated dataset includes three additional seasons of data (harvest years 2016 to 2018) and an additional bread wheat genotype (Borlaug100).

Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices.

Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage. IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere.

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha-1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha-1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2- was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.

Multiyear Maize Management Dataset collected in Chiapas, Mexico.

For several decades, maize (Zea mays L.) management decisions in smallholder farming in tropical regions have been a puzzle. To best balance alternative management practices' environmental and economic outcomes, an extensive dataset was gathered through CIMMYT's knowledge hub in Chiapas, a state in southern Mexico. In a knowledge hub, farmers, with the support of farm advisors, compare conventional and improved agronomic practices side-by-side and install demonstration fields where they implement improved practices. In all these fields data on on-farm operations and results is collected. The dataset was assembled using field variables (yield, cultivars, fertilization and tillage practice), as well as environment variables from soil mapping (slope, elevation, soil texture, pH and organic matter concentration) and gridded weather datasets (precipitation, temperature, radiation and evapotranspiration). The dataset contains observations from 4585 fields and comprises a period of 7 years between 2012 and 2018. This dataset will facilitate analytical approaches to represent spatial and temporal variability of alternative crop management decisions based on observational data and explain model-generated predictions for maize in Chiapas, Mexico. In addition, this data can serve as an example for similar efforts in Big Data in Agriculture.

One CGIAR and the Integrated Agri-food Systems Initiative: From short-termism to transformation of the world's food systems.

Agri-food systems are besieged by malnutrition, yield gaps, and climate vulnerability, but integrated, research-based responses in public policy, agricultural, value chains, and finance are constrained by short-termism and zero sum thinking. As they respond to current and emerging agri-food system challenges, decision makers need new tools that steer toward multi-sector, evidence-based collaboration. To support national agri-food system policy processes, the Integrated Agri-food System Initiative (IASI) methodology was developed and validated through case studies in Mexico and Colombia. This holistic, multi-sector methodology builds on diverse existing data resources and leverages situation analysis, modeled predictions, and scenarios to synchronize public and private action at the national level toward sustainable, equitable, and inclusive agri-food systems. Culminating in collectively agreed strategies and multi-partner tactical plans, the IASI methodology enabled a multi-level systems approach by mobilizing design thinking to foster mindset shifts and stakeholder consensus on sustainable and scalable innovations that respond to real-time dynamics in complex agri-food systems. To build capacity for these types of integrated, context-specific approaches, greater investment is needed in supportive international institutions that function as trusted in-region 'innovation brokers.' This paper calls for a structured global network to advance adaptation and evolution of essential tools like the IASI methodology in support of the One CGIAR mandate and in service of positive agri-food systems transformation.

The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices.

Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.

Bacterial colonization of a fumigated alkaline saline soil.

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

Greenhouse gas emissions under conservation agriculture compared to traditional cultivation of maize in the central highlands of Mexico.

In 1991, the 'International Maize and Wheat Improvement Center' (CIMMYT) started a field experiment in the rain fed Mexican highlands to investigate conservation agriculture (CA) as a sustainable alternative for conventional maize production practices (CT). CT techniques, characterized by deep tillage, monoculture and crop residue removal, have deteriorated soil fertility and reduced yields. CA, which combines minimum tillage, crop rotations and residue retention, restores soil fertility and increases yields. Soil organic matter increases in CA compared to CT, but increases in greenhouse gas emissions (GHG) in CA might offset the gains obtained to mitigate global warming. Therefore, CO(2), CH(4) and N(2)O emissions, soil temperature, C and water content were monitored in CA and CT treatments in 2010-2011. The cumulative GHG emitted were similar for CA and CT in both years, but the C content in the 0-60 cm layer was higher in CA (117.7 Mg C ha(-1)) than in CT (69.7 Mg C ha(-1)). The net global warming potential (GWP) of CA (considering soil C sequestration, GHG emissions, fuel use, and fertilizer and seeds production) was -7729 kg CO(2) ha(-1) y(-1) in 2008-2009 and -7892 kg CO(2) ha(-1) y(-1) in 2010-2011, whereas that of CT was 1327 and 1156 kg CO(2) ha(-1) y(-1). It was found that the contribution of CA to GWP was small compared to that of CT.