Draft genome sequence of Bacillus velezensis strains AOA1 and AKS2, the potential plant growth-promoting rhizobacteria.

This report describes the draft genome sequence of Bacillus velezensis strains AOA1 and AKS2 isolated from maize rhizosphere soil in South Africa. Bacillus velezensis plays important biological roles as plant growth promoting rhizobacterium (PGPR). Bacillus velezensis strains also exhibit numerous biotechnological application potentials in agriculture and diverse industrial settings.

Draft genome sequence of Acinetobacter sp. AYS6, a potential plant growth-promoting endophyte.

Here, we report the draft genome sequence of Acinetobacter sp. AYS6, an endophyte isolated from the roots of maize plant in Mafikeng, South Africa. The genome was 7,072,605 bp and exhibited a GC content of 45.6% and 3,654 genes with 3,539 coding sequences, 64 rRNA, 60 tRNAs, and 2 CRISPR.

Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture.

Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots and their associated microbes interact to bring about crop growth and yield is limited. Here, we presented (i) the communication strategies between plant roots and root-associated microbes and (ii) the applications of plant root-associated microbes in enhancing plant growth and yield. This review has been divided into three main sections: communications between root microbiome and plant root; the mechanism employed by root-associated microbes; and the chemical communication mechanisms between plants and microbes and their application in plant growth and yield. Understanding how plant root and root-associated microbes communicate is vital in designing ecofriendly strategies for targeted disease suppression and improved plant growth that will help in sustainable agriculture. Ensuring that plants become healthy and productive entails keeping plants under surveillance around the roots to recognize disease-causing microbes and similarly exploit the services of beneficial microorganisms in nutrient acquisition, stress mitigation, and growth promotion.

Bambara Nut Root-Nodules Bacteria from a Semi-Arid Region of South Africa and Their Plant Growth-Promoting Traits.

Rhizobial nitrogen-fixing bacteria are the main inhabitants of the root nodules of legume plants. Studying the bacterial community of legume nodules is important in understanding plant growth and nutrient requirements. Culture-based technique was used to examine the bacterial community of these underground organs from Vigna subterranea L. Verdc (Bambara nut), an underutilized legume in Africa, for plant growth-promoting traits. In this study, Bambara nuts were planted to trap root-nodule bacteria, and the bacteria were morphologically, biochemically, and molecularly characterized. Five selected isolates were screened in vitro for their plant growth-promoting traits and exhibited differences in their phenotypic traits. The polymerase chain reaction (PCR) products were subjected to partial 16S rRNA gene sequencing for phylogenetic analysis. Based on 16S rRNA gene sequence, the isolates were identified as BA1 (Stenotrophomonas maltophilia), BA2 (Chryseobacterium sp.), BA3 (Pseudomonas alcaligenes), BA4 (Pseudomonas plecoglossicida), and BA5 (Pseudomonas hibiscicola). Results showed that four of the five isolates could produce IAA. The capability to solubilize phosphate in Pikovskaya's agar plates was positively shown by four isolates (BA2, BA3, BA4, and BA5). Three isolates could produce hydrogen cyanide while isolates BA1, BA3, BA4, and BA5 were found to have ammonia-production traits. The results suggest that these plant growth-promoting isolates can be used as inoculants for plant growth and productivity.

Shotgun metagenomics dataset of Striga hermonthica-infested maize (Zea mays L.) rhizospheric soil microbiome.

This dataset includes shotgun metagenomics sequencing of the rhizosphere microbiome of maize infested with Striga hermonthica from Mbuzini, South Africa, and Eruwa, Nigeria. The sequences were used for microbial taxonomic classification and functional categories in the infested maize rhizosphere. High throughput sequencing of the complete microbial community's DNA was performed using the Illumina NovaSeq 6000 technology. The average base pair count of the sequences were 5,353,206 bp with G+C content of 67%. The raw sequence data used for analysis is available in NCBI under the BioProject accession numbers PRJNA888840 and PRJNA889583. The taxonomic analysis was performed using Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST). Bacteria had the highest taxonomic representation (98.8%), followed by eukaryotes (0.56%), and archaea (0.45%). This metagenome dataset provide valuable information on microbial communities associated with Striga-infested maize rhizosphere and their functionality. It can also be used for further studies on application of microbial resources for sustainable crop production in this region.

Corrigendum to "Shotgun metagenomics dataset of Striga hermonthica-infested maize (Zea mays L.) rhizospheric soil microbiome" [Data in Brief, volume 48 (2023) 1-5/109132].

[This corrects the article DOI: 10.1016/j.dib.2023.109132.].

Draft Genome Sequence of Citrobacter freundii AYS58, a Potential Plant Growth-Promoting Endophyte.

Here, we report the draft genome sequence of Citrobacter freundii AYS58, an endophyte isolated from the roots of a maize plant in Mafikeng, South Africa. The genome was 5,569,547 bp and exhibited a GC content of 50.5% and 5,904 genes, with 5,658 coding sequences, 3 rRNAs, 82 tRNAs, and 1 CRISPR.

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal.

The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.

Draft Genome Sequence of Enterobacter mori AYS9, a Potential Plant Growth-Promoting Rhizobacterium.

Here, we report the draft genome sequence of Enterobacter mori AYS9, a rhizobacterium isolated from the rhizosphere of sorghum plants in South Africa. The genome sequence comprised 4,852,175 bp and exhibited a GC content of 55.5% and 4,567 genes, with 4,453 coding sequences, 3 rRNAs, 64 tRNAs, and 1 CRISPR.

Draft Genome Sequences of Four Strains of Plant Growth-Promoting Bacteria Associated with Maize Rhizosphere.

This study presents the draft genome sequences of four strains of rhizobacteria, namely, Bacillus cereus ADO11, Stenotrophomonas maltophilia NAA11, Acinetobacter pittii LAM11, and Serratia marcescens NSA15, which were isolated from maize soils and have the ability to stimulate plant growth. The genome assembly sizes for the strains were 4,476,462 bp, 4,731,402 bp, 4,080,875 bp and 4,959,744 bp, respectively.

Microbiome of Soybean (Glycine max L.) Rhizosphere from Free State, South Africa.

Soybean develop a symbiotic relationship with the rhizospheric microbial communities. These organisms are important in maintaining soybean growth and health. Soil samples for this study were collected from Free State, South Africa. We present the microbiome of the soybean rhizosphere and its functional categories at level 1 of the SEED subsystem.

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa.

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal-Wallis test was used to test samples' diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.

Amplicon sequencing data profiling of bacterial community connected with the rhizospheric soil from sunflower plants.

This article presents dataset on the bacterial community structure associated with rhizospheric sunflower soils from Lichtenburg, South Africa. The Illumina Miseq sequencing of 16S rRNA gene amplicon unveiled the bacterial community diversities as well as generated metagenomic library from sunflower rhizospheric soils to understand the diversities and distribution. The metagenome contained a total of 41,471 sequences with 45,975 operational taxonomic units (OTUs). Metagenome sequence information is obtainable at NCBI under the Bioproject assigned accession number PRJNA782103. Taxonomic hits distribution from USEARCH analysis at phylum level classification of BN_E discovered predominantly Actinobacteria (33.89%), followed by Proteobacteria (35.45%), Firmicutes (6.45%), Planctomycetes (4.12%), Chloroflexi (4.28%) and Gemmatimonadetes (2.40%). Also, USEARCH assisted analysis of BN_F sample also detected the prevalence of Actinobacteria (45.92%), Proteobacteria (23.23%), Firmicutes (3.84%), Planctomycetes (6.46%), Chloroflexi (4.94%) and Gemmatimonadetes (1.99%), which take part in vital ecological functions and biogeochemical activities needed for plant growth and health.

Effects of soil properties and carbon substrates on bacterial diversity of two sunflower farms.

The sustainable production of sunflower (Helianthus annuus) is crucial and one way to accomplish this feat is to have an understanding of the beneficial bacteria of sunflower rhizosphere. Similarly, the respiratory response of these bacteria needs to be studied to understand their roles in the ecosystem. This study was therefore conceptualized to gain insights into the effects of soil properties and carbon substrate utilization on bacterial community diversity of sunflower rhizosphere grown in Ditsobottla and Kraaipan, North West Province, South Africa. Extracted DNA from sunflower rhizosphere and bulk soils was subjected to 16S amplicon sequencing. Significant differences were observed in the alpha and beta diversities of the soil bacterial communities (p < 0.05). At the order level, among all the bacterial taxa captured in the farms, Bacillales were the most dominant. The abundance of Lactobacillales, Bacillales, Rhizobiales, Enterobacteriales, Burkholderiales, Flavobacteriales, Sphingomonadales, Myxococcales, and Nitrosomonadales obtained from Ditsobottla rhizosphere soil (R1) was positively influenced by organic matter (OM), while the abundance of Planctomycetales, Cytophagales, Gemmatimonadales, Nitrospirales and Caulobacteriales from Kraaipan rhizosphere soil (R2) was positively influenced by total N and pH. Bacterial communities of all the soil samples utilized the different carbon substrates (three amino acids, six carbohydrates, and three carboxylic acids) as an energy source. Significant differences (p < 0.05) were only observed in tryptophan and methionine amended soils. Unclassified bacteria were also captured in this study, such bacteria can further be harnessed for sustainable production of sunflower and other agricultural crops.

Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere.

The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.

16S rRNA gene amplicon sequence data from sunflower endosphere bacterial community.

Insights into plant endosphere bacterial diversity and exploration of their bioincentives in the formulation of biofertilizers promise to avert ecological disturbances. Here, we presented the sequence dataset of the endophytic bacterial community from the roots and stems of sunflower obtained from farmlands in Itsoseng and Lichtenburg, North West Province of South Africa, using 16S rRNA gene amplicon sequencing. The climatic conditions of this region are characterized by an annual rainfall of about 600 mm and a temperature range of 3 to 21°C during winter and 22 to 34°C during summer. The genomic DNA was obtained from 1 g of each macerated sample using commercial DNA kits (DNeasy® Plant Mini kit, Qiagen, USA). The DNA was amplified through polymerase chain reaction at the V4 region using the specific forward and reverse primers. Amplicon sequencing was performed on the Miseq Illumina platform. Sequence read processing was performed using QIIME 1 16S-based pipeline implemented on Nephele microbial bioinformatics platform using default parameters. The sequence has been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned Bioproject accession numbers. The data reveals the endophytic bacterial community structure and functions in sunflower cultivated in organic and nonorganic soils at growing and flowering stages.

Comparative study of microbial structure and functional profile of sunflower rhizosphere grown in two fields.

BACKGROUND: Microbial communities inhabiting the rhizosphere play pivotal roles in determining plant health and yield. Manipulation of the rhizosphere microbial community is a promising means to enhance the productivity of economically viable and important agricultural crops such as sunflower (Helianthus annuus). This study was designed to gain insights into the taxonomic and functional structures of sunflower rhizosphere and bulk soil microbiome at two different locations (Sheila and Itsoseng) in South Africa. RESULTS: Microbial DNA extracted from the sunflower rhizosphere and bulk soils was subjected to next-generation sequencing using 16S amplicon sequencing technique. Firmicutes, Actnobacteria and Proteobacteria predominated sunflower rhizosphere soils. Firmicutes, Cyanobacteria, Deinococcus-Thermus and Fibrobacteres were positively influenced by Na+ and clay content, while Actinobacteria, Thaumarchaeota, Bacteroidetes, Planctomycetes, Aquificae and Chloroflexi were positively influenced by soil resistivity (Res) and Mg2+. The community-level physiological profiling (CLPP) analysis showed that the microbial communities in SHR and ITR used the amino acids tryptophan and malic acid efficiently. The metabolisms of these carbon substrates may be due to the dominant nature of some of the organisms, such as Actinobacteria in the soils. CONCLUSION: The CLPP measurements of soil from sunflower rhizosphere were different from those of the bulk soil and the degree of the variations were based on the type of carbon substrates and the soil microbial composition. This study has shown the presence of certain taxa of rhizobacteria in sunflower rhizosphere which were positively influenced by Na+ and Mg2+, and taxa obtained from SHR and ITR were able to effectively utilized tryptophan and malic acid. Many unclassified microbial groups were also discovered and it is therefore recommended that efforts should further be made to isolate, characterize and identify these unclassified microbial species, as it might be plausible to discover new microbial candidates that can further be harnessed for biotechnological purpose.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories.

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the ß diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Bacterial community structure of the sunflower (Helianthus annuus) endosphere.

Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits.

Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower in South Africa has not been studied. Therefore, we present whole-genome sequence of agriculturally important B. cereus strain T4S isolated from sunflower plants. The NextSeq Illumina sequencing yielded 7,255,762 bp sequence reads, 151 bp average read length, 5,945,881 bp genome size, 56 tRNA, 63 rRNA, and G + C content of 34.8%. The phylogeny analysis of strain T4S was similar to B. cereus NJ-W. Secondary metabolites, such as petrobactin, bacillibactin, bacitracin, molybdenum factor, zwittermicin, and fengycin underlining bacterial biocontrol efficacy against phytopathogens were found in the T4S genome. The predicted novel genes in the bacterial genome mediating the complex metabolic pathways can provide a genetic basis in understanding endosphere biology and their multiple functions thereof in crop improvement. Interestingly, seed and root inoculation with strain T4S contributed to sunflower yield under greenhouse experiments. Hence, the detection of notable genes specific for plant growth promotion as validated under in vitro screening, promisingly, suggests the relevance of strain T4S in agricultural biotechnology.