Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change

The impact of the diurnal cycle on the microbial transcriptome in the rhizosphere of barley.

While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods

Effect of plant nitrogen ultilizing efficiencies on Rhizospheric proteolytic bacterial communities of two maize inbred lines

Effect of two maize lines with different N uptake efficienc

Modeling Normal and Dysbiotic Subgingival Microbiomes: Effect of Nutrients

Screening for microbiome modulators requires availability of a high-throughput in vitro model that replicates subgingival dysbiosis and normobiosis, with a tool to measure microbial dysbiosis. Here, we tested various formulations to grow health- and periodontitis-associated subgingival microbiomes in parallel, and we describe a new subgingival dysbiosis index. Subgingival plaque samples pooled from 5 healthy subjects and, separately, 5 subjects with periodontitis were used to inoculate a Calgary Biofilm Device containing saliva-conditioned, hydroxyapatite-coated pegs. Microbiomes were grown for 7 d on either nutrient-rich media—including a modification of SHI medium, brain-heart infusion (BHI) supplemented with hemin and vitamin K, and a blend of SHI and BHI, each at 3 sucrose concentrations (0%, 0.05% and 0.1%)—or nutrient-limited media (saliva with 5%, 10%, or 20% inactivated human serum). The microbiomes were assessed for biomass, viability, and 16S rRNA profiles. In addition to richness and diversity, a dysbiosis index was calculated as the ratio of the sum of relative abundances of disease-associated species to that of health-associated species. The supplemented BHI and blend of SHI and BHI resulted in the highest biomass, whereas saliva-serum maximized viability. Distinct groups of bacteria were enriched in the different media. Regardless of medium type, the periodontitis-derived microbiomes showed higher species richness and alpha diversity and clustered with their inoculum separate from the health-derived microbiomes. Microbiomes grown in saliva-serum showed the highest species richness and the highest similarity to the clinical inocula in both health and disease. However, inclusion of serum reduced alpha diversity and increased dysbiosis in healthy microbiomes in a dose-dependent manner, mainly due to overenrichment of Porphyromonas species. The modification of SHI stood second in terms of species richness and diversity but resulted in low biomass and viability and significantly worsened dysbiosis in the periodontitis-derived microbiomes. Overall, saliva with 5% human serum was optimal for replicating subgingival microbiomes from health and disease

Microbial community structure and proteolytic activity in the rhizosphere of maize plants differing in nitrogen use efficiency

The rhizosphere, the thin soil layer influenced by the presence of plant roots has different physico-chemical properties from the bulk soil because of the active or passive rhizodepositions, which sustain larger and more active microbial populations in the rhizosphere than in bulk soil, and this plays a key role in soil organic matter decomposition and nutrient solubilization. The rhizosphere is chemically complex and dynamic microenvironment and this makes it difficult to study. Progresses in the study of the rhizosphere can be achieved by using rhizoboxes allowing the plant growth and precise sampling of rhizosphere. Plants select microbial bacterial and fungal populations in the rhizosphere during the plant growth, and while plant mechanisms involved in increased N uptake efficiency have been clarified, the importance of the rhizosphere microbial communities in nutrient availability to plants are still poorly understood. Nitrogen is the main nutrient limiting the plant growth and the crop yields and today, the nitrogen use efficiency (NUE) of crops at field scale is still relatively low, with detrimental effects on groundwater quality and atmosphere due to NO3- leaching and NH3 and nitrous oxide emissions caused be excessive fertilization, and large efforts have been carried out to increase the NUE to enhance the crop production and reduce the environmental impact of agriculture, especially through plant breeding and preparation of fertilizers with slow N release. We evaluated the changes in the biochemical activity and microbial community structure induced by the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE using rhizobox experiments. The adopted experimental approach allowed to describe the relative plant induced changes on the different rhizosphere chemical and microbiological components and provide information to improve the crop NUE. In this work we studied the changes in the biochemical activity and microbial community structure in the rhizosphere of the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE, repectively, using rhizobox experiments. Because of the importance of the proteolytic activity in soil N mineralization, the proteolytic activity in the rhizosphere of the two maize lines was also studied by the assessment of the diversity and abundance of the apr and npr genes coding for coding for alkaline protease and neutral metalloprotease, respectively, and determination of the protease activity. The results showed that the Lo5 plant, having the higher NUE, induced the greater modification in the rhizosphere chemical properties, induced significantly faster depletion of inorganic N, higher bacteria diversity, proteolytic populations and protease activity. The importance of the plant activity in modifying microbial community structure, protease functions and rhizosphere biochemical activity will be presented

Effect of nitrogen utilizing efficiencies on rhizospheric proteolytic bacterial communities of two maize inbred lines

Rhizospheric microbial composition plays an important role in plant growth and nutrient metabolism. Under the effect of root exudates, soil in rhizosphere is different from bulk soil in its microbial composition and functions from bulk soil. Effect of root exudates on microbial communities had been investigated by various researchers, still leaving a gap in study of effect on functions related to soil. One such important soil function is proteolysis. Proteases and peptidases are important enzymes that bring about N mineralization and in turn N uptake to facilitate plant growth and development. Understanding of the relationship between soil microbial communities expressing protease activity and nitrogen in the rhizosphere is still a challenge, due to the difficulties of sampling the rhizosphere microenvironment. This study investigated the interplay of plant nitrogen utilizing efficiency with N mineralization brought about by proteolysis with special focus on bacterial extracellular soil proteases. We studied changes in the biochemical activity and microbial community structure in the rhizosphere of the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low Nitrogen utilizing effeciencies (NUE) using rhizobox experiments. Plants were regularly regularly monitored for the inorganic N (NH4+-N and NO3--N) concentration in the rhizosphere by ion selective electrodes (ISE). At the stage of N depletion soil was sampled from rhizosphere and bulk compartments. Cellular biomass was estimated as a measure of ATP and protease activity was assayed as a measure on caseinate hydrolysis. Soil DNA was extracted and was used for molecular studies. Two bacterial genes coding for alkaline proteases (apr) and neutral protease (npr) were selected for studies. Bacterial gene abundance was measured using qPCR. To study diversity of these genes, amplicons were sequenced by Illumina high-throughput technology. Plant L05 with higher NUE, had shown a significant difference in the rhizospheric and bulk cellular biomass, whereas plant T250 with lower NUE showed no significant differences in the biomass content in rhizosphere and bulk soil. Proteolytic soil potential of plant L05 was found to be higher than that of T250. Furthermore abundance of genes apr and npr and their diversities, as indicated by qPCR and sequencing results respectively were favored by the higher NUE of L05 maize line. Analyses of several million apr and npr amplicons revealed a high diversity of proteases genes in soil and rhizosphere, with many sequences that are still unknown according to current sequences database information