Long-term detection of Hartmannibacter diazotrophicus on winter wheat and spring barley roots under field conditions revealed positive correlations on yield parameters with the bacterium abundance.

Monitoring of bioinoculants once released into the field remains largely unexplored; thus, more information is required about their survival and interactions after root colonization. Therefore, specific primers were used to perform a long-term tracking to elucidate the effect of Hartmannibacter diazotrophicus on wheat and barley production at two experimental organic agriculture field stations. Three factors were evaluated: organic fertilizer application (with and without), row spacing (15 and 50 cm), and bacterial inoculation (H. diazotrophicus and control without bacteria). Hartmannibacter diazotrophicus was detected by quantitative polymerase chain reaction on the roots (up to 5 × 105 copies g-1 dry weight) until advanced developmental stages under field conditions during two seasons, and mostly in one farm. Correlation analysis showed a significant effect of H. diazotrophicus copy numbers on the yield parameters straw yield (increase of 453 kg ha-1 in wheat compared to the mean) and crude grain protein concentration (increase of 0.30% in wheat and 0.80% in barley compared to the mean). Our findings showed an apparently constant presence of H. diazotrophicus on both wheat and barley roots until 273 and 119 days after seeding, respectively, and its addition and concentration in the roots are associated with higher yields in one crop.

Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens.

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.

Elevated atmospheric CO2 concentrations caused a shift of the metabolically active microbiome in vineyard soil.

BACKGROUND: Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS: Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS: The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.

Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2.

Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO2 (eCO2) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO2 directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO2 enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO2 with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N2O reductase, involved in the last step of the denitrification process, which explains the increase of N2O emissions in the Gi-FACE. Also, a shift in nitrate ( NO 3 - ) metabolism occurred, with an increase in transcript abundance for the dissimilatory NO 3 - reduction to ammonium ( NH 4 + ) (DNRA) pathway. S metabolism showed increased transcripts for sulfate ( SO 4 2 - ) assimilation under eCO2 conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO2 conditions. The results exhibited the effects of eCO2 on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO2 and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.

Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment.

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.

Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields.

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.