Bacterial and Archaeal Communities Change With Intensity of Vegetation Coverage in Arenized Soils From the Pampa Biome

Arenization occurs in regions that present sandy soils with normal rainfall levels. Predatory use of environmental sources, the dissolution of arenitic rocks and reworking of non-consolidated surface sands intensify this degradation scenario. Thus, this work aimed to evaluate the impact of the arenization process in the Brazilian Pampa Biome and how this phenomenon affects the soil microbial and plant communities. For this purpose, three arenized areas in Southern Brazil (Pampa Biome) were selected and, in each one, three sampling points were studied: arenized (ARA), arenized to grassland transition (AGT), and grassland (GRA) areas. In the three sampling points, soils presented low levels of nutrients, organic matter, mud and pH acidic in all regions but, the presence of vegetation coverage in AGT and GRA areas preserved the topsoil structure. Our study related ARA with bacterial families Alcaligenaceae, Pseudomonadaceae, and Xanthomonadaceae. AGT with bacterial families Bacillaceae and Burkholderiaceae, and plant species Melinis repens (Willd.) Zizka and Paspalum stellatum Humb. and Bonpl. ex Flüggé, and GRA with bacterial families Koribacteraceae, Hyphomicrobiaceae, and Chthoniobacteraceae, and plant species Croton subpannosus Müll.Arg. ex Griseb., Piptochaetium montevidense (Spreng.) Parodi and Elyonurus sp. The three studied areas (as well as sampling points) present soils extremely poor in nutrients with sandy texture, and the bacterial and plant composition well known to be resistant to environmental stresses were dominant. The vulnerability of these areas causes a degradation scenario, which is worsened by agricultural activities. However, in general, this phenomenon is a natural process that occurs mainly due to soil characteristics (poor soils) and climatic variations

Screening of plant growth promoting bacteria associated with barley plants (Hordeum vulgare L.) cultivated in South Brazil

The occurrence of associations between bacteria and plant roots may be beneficial, neutral or detrimental. Plant growth promoting (PGP) bacteria form a heterogeneous group of beneficial microorganisms that can be found in the rhizosphere, the root surfaces or in association with host plant. The aim of this study was to isolate and characterize PGP bacteria associated to barley plants (Hordeum vulgare L.) aiming a future application as agricultural inoculant. One hundred and sixty bacterial strains were isolated from roots or rhizospheric soil of barley based on their growth in nitrogen-free selective media. They were evaluated for their ability to produce indolic compounds (ICs) and siderophores, and to solubilize tricalcium phosphate in in vitro assays. Most of them (74%) were able to synthesize ICs in the presence of the precursor L-tryptophan, while 57% of the isolates produced siderophores in Fe-limited liquid medium, and 17% were able to solubilize tricalcium phosphate. Thirty-two isolates possessing different PGP characteristics were identified by partial sequencing of their 16S rRNA gene. Strains belonging to Cedecea and Microbacterium genera promoted the growth of barley plants in insoluble phosphate conditions, indicating that these bacteria could be used as bioinoculants contributing to decrease the amount of fertilizers applied in barley crops

Genetic diversity and symbiotic compatibility among rhizobial strains and Desmodium incanum and Lotus spp. plants

This work aimed to evaluate the symbiotic compatibility and nodulation efficiency of rhizobia isolated from Desmodium incanum, Lotus corniculatus, L. subbiflorus, L. uliginosus and L. glaber plants by cross-inoculation. Twelve reference strains and 21 native isolates of rhizobia were genetically analyzed by the BOX-PCR technique, which showed a high genetic diversity among the rhizobia studied. The isolates were also characterized based on their production of indolic compounds and siderophores, as well as on their tolerance to salinity. Fifteen of the 33 rhizobia analyzed were able to produce indolic compounds, whereas 13 produced siderophores. All the tested rhizobia were sensitive to high salinity, although some were able to grow in solutions of up to 2% NaCl. Most of the native rhizobia isolated from L. uliginosus were able to induce nodulation in all plant species studied. In a greenhouse experiment using both D. incanum and L. corniculatus plants, the rhizobia isolate UFRGS Lu2 promoted the greatest plant growth. The results demonstrate that there are native rhizobia in the soils of southern Brazil that have low host specificity and are able to induce nodulation and form active nodules in several plant species

The genomes of three Bradyrhizobium sp. isolated from root nodules of Lupinus albescens grown in extremely poor soils display important genes for resistance to environmental stress

Abstract Lupinus albescens is a resistant cover plant that establishes symbiotic relationships with bacteria belonging to the Bradyrhizobium genus. This symbiosis helps the development of these plants in adverse environmental conditions, such as the ones found in arenized areas of Southern Brazil. This work studied three Bradyrhizobium sp. (AS23, NAS80 and NAS96) isolated from L. albescens plants that grow in extremely poor soils (arenized areas and adjacent grasslands). The genomes of these three strains were sequenced in the Ion Torrent platform using the IonXpress library preparation kit, and presented a total number of bases of 1,230,460,823 for AS23, 1,320,104,022 for NAS80, and 1,236,105,093 for NAS96. The genome comparison with closest strains Bradyrhizobium japonicum USDA6 and Bradyrhizobium diazoefficiens USDA110 showed important variable regions (with less than 80% of similarity). Genes encoding for factors for resistance/tolerance to heavy metal, flagellar motility, response to osmotic and oxidative stresses, heat shock proteins (present only in the three sequenced genomes) could be responsible for the ability of these microorganisms to survive in inhospitable environments. Knowledge about these genomes will provide a foundation for future development of an inoculant bioproduct that should optimize the recovery of degraded soils using cover crops

A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates

<div><p>Plant growth-promoting bacteria can greatly assist sustainable farming by improving plant health and biomass while reducing fertilizer use. The plant-microorganism-environment interaction is an open and complex system, and despite the active research in the area, patterns in root ecology are elusive. Here, we simultaneously analyzed the plant growth-promoting bacteria datasets from seven independent studies that shared a methodology for bioprospection and phenotype screening. The soil richness of the isolate's origin was classified by a Principal Component Analysis. A Categorical Principal Component Analysis was used to classify the soil richness according to isolate's indolic compound production, siderophores production and phosphate solubilization abilities, and bacterial genera composition. Multiple patterns and relationships were found and verified with nonparametric hypothesis testing. Including niche colonization in the analysis, we proposed a model to explain the expression of bacterial plant growth-promoting traits according to the soil nutritional status. Our model shows that plants favor interaction with growth hormone producers under rich nutrient conditions but favor nutrient solubilizers under poor conditions. We also performed several comparisons among the different genera, highlighting interesting ecological interactions and limitations. Our model could be used to direct plant growth-promoting bacteria bioprospection and metagenomic sampling.</p></div

A model to explain the distribution of bacteria displaying different plant growth promotion traits.

<p>In soils with fewer nutrients, plants leave the best growth hormone producers in the rhizosphere, while both endophytic and rhizospheric bacteria are good nutrient solubilizers. In soils with more nutrients, the best growth hormone producers are found inside plant roots, but the endophytic bacteria are poor nutrient solubilizers, with the best solubilizers found in the rhizosphere. In addition, genera diversity and growth hormone producers are more abundant in soils with more nutrients, while phosphate solubilizers and siderophores producers are more abundant in soils with fewer nutrients. Siderophores producers and phosphate solubilizers seem to co-occur, while indolic compound producers are clearly opposed to phosphate solubilizers. Plants seem to select bacterial PGP traits according to their nutritional needs: nutrient solubilizers under poor conditions and growth hormone producers under rich conditions.</p

Heat map associations of bacterial genera and PGP traits (left), soil richness (middle), and occurrence of putative endophytic (Root) and rhizospheric (Soil) bacteria under each soil richness condition (right).

<p>Phos  =  TCP solubilization, Sid  =  siderophores production, with 1 =  no halo, 2 =  small or average halo, and 3 =  large halo. ICs  =  Indolic compounds production, with 1 =  low (0–10 µg of ICs ml⁻¹), 2 =  average (11–80 µg of ICs ml⁻¹) and 3 =  high (80 or> µg of ICs ml⁻¹). The red cells  =  less isolates than expected under those conditions, the green cells  =  excessive number of isolates under those conditions, and the yellow cells  =  no significant differences between the observed and expected values. “–”  =  an association could not be calculated due to the lack of cases (no expected total marginal values). Percentages and residuals are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116020#pone.0116020.s004" target="_blank">S4 Fig</a>. Sample sizes and p values are presented on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116020#pone.0116020.s009" target="_blank">S3 Table</a>.</p