Search

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., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Elevated levels of atmospheric CO 2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO 2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO 2 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 CO 2 , 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 CO 2 (p = 0.002); increased atmospheric CO 2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO 2 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 CO 2 . The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO 2 increase of climate change will significantly shift the microbiome structure in the rhizosphere., (© 2021. The Author(s).)

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA , nirK , nirS , nosZ -I and nosZ -II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales ) , and a bulk soil cluster, dominated by Acidobacteria , Gemmatominadetes and " Latescibacteria " (hub taxa: Acidobacteria ). In the bulk soil, mineral N-fertilization reduced nirK , amoA , nosZ -I and nosZ -II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

A Gram-negative bacterium, designated E130 T , was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130 T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131 T (97.6 %), Ancylobacter defluvii CCUG 63806 T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507 T (97.4 %). The DNA G+C content of strain E130 T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130 T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130 T to A. rudongensis DSM 17131 T , A. defluvii CCUG 63806 T and A. dichloromethanicus DSM 21507 T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130 T (LMG 29367 T =DSM 102029 T ).

A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19(T) was distinct from other taxa within the class Alphaproteobacteria. Strain E19(T) showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera Rhizobium (≤93.5 %), Labrenzia (≤93.1 %), Stappia (≤93.1 %), Aureimonas (≤93.1 %) and Mesorhizobium (≤93.0 %) and was most closely related to Rhizobium rhizoryzae (93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19(T) was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19(T) ( = LMG 27460(T) = KACC 17263(T))., (© 2014 IUMS.)

Two motile, Gram-staining-negative, aerobic, rod-shaped bacteria designated strains E48(T) and E49(T) were isolated from the rhizosphere of Hordeum secalinum from a natural salt meadow near Münzenberg, Germany. 16S rRNA gene sequence similarity analysis revealed that strains E48(T) and E49(T) shared similarities of 97.6 % with Rheinheimera pacifica KMM 1406(T) and 98.5 % with Rheinheimera nanhaiensis E407-8(T), respectively. Major fatty acids of strain E48(T) were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 1ω8c, and of strain E49(T) were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The DNA G+C contents were 50.5 mol% (E48(T)) and 50.0 mol% (E49(T)). Strains E48(T) and E49(T) grew at 4-37 °C (optimum 28 °C) and with 0-6 % NaCl (optimum 0-3 %) and 0-5 % NaCl (optimum 0-3 %), respectively. The potential for nitrogen fixation by strains E48(T) and E49(T) was evaluated by molecular techniques and the acetylene reduction assay. The DNA-DNA hybridization, physiological and molecular data demonstrated that strains E48(T) and E49(T) represent two novel species of the genus Rheinheimera, and therefore the names Rheinheimera hassiensis sp. nov. (type strain E48(T) = LMG 27268(T) = KACC 17070(T)) and Rheinheimera muenzenbergensis sp. nov. (type strain E49(T) = LMG 27269(T) = KACC 17071(T)) are proposed.

Two Gram-reaction-negative, aerobic, nitrogen-fixing, rod-shaped bacteria, designated strains E20 and E50(T), were isolated from the rhizosphere of salt meadow plants Plantago winteri and Hordeum secalinum, respectively, near Münzenberg, Germany. Based on the 16S rRNA gene sequence analysis both strains E20 and E50(T) are affiliated with the genus Cellvibrio, sharing the highest similarity with Cellvibrio gandavensis LMG 18551(T) (96.4%) and (97.1%), respectively. Strains E20 and E50(T) were oxidase and catalase-positive, grew at a temperature range between 16 and 37 °C and in the presence of 0-5% NaCl (w/v). The DNA G+C contents were 52.1 mol% (E20) and 51.6 mol% (E50(T)). Major fatty acids of strains E20 and E50(T) were summed feature 3 (C16 : 1ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c, C(12 : 0), C(18 : 0) and C(12 : 0) 3-OH. The DNA-DNA relatedness of the strains to Cellvibrio gandavensis LMG 18551(T) was 39% for strain E20 and 58% for strain E50(T). The nitrogen fixation capability of strains E20 and E50(T) was confirmed by the acetylene reduction assay. On the basis of our polyphasic taxonomic study, strains E20 and E50(T) represent a novel species of the genus Cellvibrio, for which the name Cellvibrio diazotrophicus is proposed. The type strain of Cellvibrio diazotrophicus is E50(T) ( = LMG 27267(T) = KACC 17069(T)). An emended description of the genus Cellvibrio is proposed based on the capability of fixing nitrogen and growth in presence of up to 5% NaCl (w/v).