Root associated bacteria are critical for plant growth and health. Understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. Here we analyzed the root-associated microbiomes of soybean and wheat under agricultural field conditions. We took samples from 11 different production fields across a large geographic area. We used 16S rRNA pyrosequencing to explore root microbial communities and also obtained 2,007 bacterial isolates from rhizospheres, which were tested for the presence of plant growth promoting (PGP) traits in-vitro. We observed that pH and nitrate content correlated with beta diversity variability of rhizospheric bacterial communities despite the variable field conditions. We described the dominant bacterial groups associated to roots from both crops at a large geographic scale and we found that a high proportion of them (60–70%) showed more than 97% similarity to bacteria from the isolated collection. Moreover, we observed that 55% of the screened isolates presented PGP activities in vitro. These results are a significant step forward in understanding crop-associated microbiomes and suggest that new directions can be taken to promote crop growth and health by modulating root microbiomes.

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Yeasts have been involved in bread making since ancient times and have thus played an important role in the history and nutrition of humans. Bakery-associated yeasts have only recently attracted the attention of researchers outside of the bread industry. More than 30 yeast species are involved in bread making, and significant progress has been achieved in describing these species. Here, we present a review of bread-making processes and history, and we describe the diversity of yeast species and the genetic diversity of Saccharomyces cerevisiae isolated from bakeries. We then describe the metabolic functioning and diversity of these yeasts and their relevance to improvements in bread quality. Finally, we examine yeast and bacterial interactions in sourdoughs. The purpose of this review is to show that bakery yeast species are interesting models for studying domestication and other evolutionary and ecological processes. Studying these yeasts can contribute much to our fundamental understanding of speciation, evolutionary dynamics, and community assembly, and this knowledge could ultimately be used to adjust, modify, and improve the production of bread and the conservation of microbial diversity.