Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil

Isolation and identification of a new Bacillus glycinifermentans strain from date palm rhizosphere and its effect on barley seeds under heavy metal stress

Soil contamination by heavy metals is one of the major problems that adversely decrease plant growth and biomass production. Inoculation with the plant growth-promoting rhizobacteria (PGPR) can attenuate the toxicity of heavy metals and enhancing the plant growth. In this study, we evaluated the potential of a novel extremotolerant strain (IS-2 T) isolated from date palm rhizosphere to improve barley seedling growth under heavy metal stress. The species-level identification was carried out using morphological and biochemical methods combined with whole genome sequencing. The bacterial strain was then used in vitro for inoculating Hordeum vulgare L. exposed to three different Cr, Zn, and Ni concentrations (0.5, 1, and 2 mM) in petri dishes and different morphological parameters were assessed. The strain was identified as Bacillus glycinifermentans species. This strain showed high tolerance to pH (6-11), salt stress (0.2-2 M), and heavy metals. Indeed, the minimum inhibitory concentrations at which bacterium was unable to grow were 4 mM for nickel, 3 mM for zinc, more than 8 mM for copper, and 40 mM for chromium, respectively. It was observed that inoculation of Hordeum vulgare L. under metal stress conditions with Bacillus glycinifermentans IS-2 T stain improved considerably the growth parameters. The capacity of the IS-2 T strain to withstand a range of abiotic stresses and improve barley seedling development under lab conditions makes it a promising candidate for use as a PGPR in zinc, nickel, copper, and chromium bioremediation.

The profile of the soil microbiota in the Cerrado is influenced by land use

Extensive areas of the Cerrado biome have been deforested by the rapid advance of agricultural frontiers, especially by agricultural monocultures, and cultivated pastures. The objective of this study was to characterize the soil microbial community of an environment without anthropogenic interference and to compare it with soybean soil and pasture areas. For that, metagenomic sequencing techniques of the 16S rRNA gene were employed. Consistent changes in the profiles of diversity and abundance were described between communities in relation to the type of soil. The soil microbiome of the native environment was influenced by the pH level and content of Al³⁺, whereas the soil microbiomes cultivated with soybean and pasture were associated with the levels of nutrients N and P and the ions Ca²⁺ and Mg²⁺, respectively. The analysis of bacterial communities in the soil of the native environment showed a high abundance of members of the Proteobacteria phylum, with emphasis on the Bradyrhizobium and Burkholderia genera. In addition, significant levels of species of the Bacillus genus, and Dyella ginsengisoli, and Edaphobacter aggregans of the Acidobacteria phylum were detected. In the soil community with soybean cultivation, there was a predominance of Proteobacteria, mainly of the Sphingobium and Sphingomonas genera. In the pasture, the soil microbiota was dominated by the Firmicutes, which was almost entirely represented by the Bacillus genus. These results suggest an adaptation of the bacterial community to the soybean and pasture cultivations and will support understanding how environmental and anthropogenic factors shape the soil microbial community. KEY POINTS: • The Cerrado soil microbiota is sensitive to impacts on the biome. • Microbial communities have been altered at all taxonomic levels.

Beneficial Plant-Associated Microorganisms From Semiarid Regions and Seasonally Dry Environments: A Review

Semiarid regions are apparently low biodiversity environments; however, these environments may host a phylogenetically diverse microbial community associated with plants. Their microbial inhabitants are often recruited to withstand stressful settings and improve plant growth under harsh conditions. Thus, plant-associated microorganisms isolated from semiarid and seasonally dry environments will be detailed in the present review, focusing on plant growth promotion potential and the microbial ability to alleviate plant abiotic stress. Initially, we explored the role of microbes from dry environments around the world, and then, we focused on seasonally dry Brazilian biomes, the Caatinga and the Cerrado. Cultivable bacteria from semiarid and seasonally dry environments have demonstrated great plant growth promotion traits such as plant hormone production, mobilization of insoluble nutrients, and mechanisms related to plant abiotic stress alleviation. Several of these isolates were able to improve plant growth under stressful conditions commonly present in typical semiarid regions, such as high salinity and drought. Additionally, we highlight the potential of plants highly adapted to seasonal climates from the Caatinga and Cerrado biomes as a suitable pool of microbial inoculants to maintain plant growth under abiotic stress conditions. In general, we point out the potential for the exploitation of new microbial inoculants from plants growing in dry environments to ensure a sustainable increase in agricultural productivity in a future climate change scenario.

Genetic and metabolic diversities of rhizobacteria isolated from degraded soil of Ethiopia

Genetic and metabolic diversities of rhizobacteria are the fundamental sources for their adaptation to cope with abiotic and biotic stresses in order to enhance growth and health of plants in the soil. Thus, this study was initiated to assess the genetic and metabolic diversities of rhizobacteria isolated from plants grown in degraded soil through BOX-PCR and partial sequencing of 16S rRNA genes. A total of eighty isolates were recovered and subjected to phenotypic profiling of carbohydrate and amino acid utilization, BOX PCR and 16S rRNA profiling. The phenotypic profiling showed remarkable metabolic versatility with Ochrobactrum spp, Pseudomonas spp and Klebsiella spp, and BOX-PCR showed greater discriminatory power for fingerprinting of rhizobacterial isolates with high degree of polymorphism. Bacillus spp showed the highest Simpson's diversity Index. The 16S rRNA genes sequence assigned the rhizobacteria to phyla Proteobacteria with Gammaproteobacteria and Alphaproteobacteria classes and Firmicutes with Bacilli class. The data also showed that the most dominant species were Pseudomonas and Ochrobactrum. Genetic and metabolic diversities of the rhizobacterial isolates reveal the potential of these microbes for plant growth improvement under water deficient soil after testing other inoculant traits.

Ecosystem Functions of Microbial Consortia in Sustainable Agriculture

Knowledge of the agricultural soil microbiota, of the microbial consortia that comprise it, and the promotion of agricultural practices that maintain and encourage them, is a promising way to improve soil quality for sustainable agriculture and to provide food security. Although numerous studies have demonstrated the positive effects of beneficial soil microorganisms on crop yields and quality, the use of microbial consortia in agriculture remains low. Microbial consortia have more properties than an individual microbial inoculum, due to the synergy of the microorganisms that populate them. This review describes the main characteristics, ecosystem functions, crop benefits, and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi (AMF), plant growth-promoting rhizobacteria (PGPR), and Actinobacteria, to promote the restoration of agricultural soils and, consequently, the quality and health of agricultural crops. The aim is to provide knowledge that will contribute to the development of sustainable and sufficiently productive agriculture, which will adapt in a good way to the pace of the growing human population and to climate change.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.