Shotgun metagenomics reveals the functional diversity of root-associated endophytic microbiomes in maize plant

In this study, we used shotgun metagenomics to analyze the whole DNA from maize root planted with different fertilization and without fertilization in a bid to profile the impact of fertilizer applications on the functional diversity of endophytic microbiomes. Complete DNA extraction from roots of maize plant grown on different farming sites such as organic (FK), inorganic (NK) and no fertilizer (CK) sites was carried out, and sequenced using a shotgun metagenomic approach. The raw sequenced data obtained were analyzed using an online database called MG-RAST. Through MG-RAST analysis, endophytic microbiome sequences were identified while sequences of maize origin were discarded. The prediction of the functions of the endophytic microbiomes was done using the SEED subsystem. Our results revealed that no significant difference (P > 0.05) exist in the relative abundance of the 28 functional groups identified within the endophytic microbiomes across the sites. Also, some functional groups and metabolic pathways associated with plant growth promotion such as carbohydrate, secondary metabolism, nitrogen metabolism, iron acquisition and metabolism alongside phosphorus metabolism were observed in the endophytes across the sites. Alpha diversity study revealed no significant difference exist among the functional groups of the endophytes across the sites, while beta diversity study indicated that there was a significant difference (P = 0.01) among the functional groups of the endophytes across the fertilizer sites. Going by the high abundance of functional groups observed in this study, especially in FK samples, it is evident that different farming practices influenced the functions of endophytic microbiomes. We recommend that further studies should explore the functional genes in endophytic microbiomes with the aim of assessing their usefulness in promoting sustainable agriculture

SCREENING FOR HEAVY MOLECULAR WEIGHT HYDROCARBON UTILIZING BACTERIA FROM OIL IMPACTED, NON OIL IMPACTED SOIL AND NATURAL DEPOSITS

Control and treatment of hazardous effects of heavy molecular weight oil (bitumen) pollution are essential in contaminated soil. This study involved the isolation and screening of microorganisms capable of utilizing heavy molecular weight hydrocarbon from oil impacted, non oil impacted soil and natural deposits of bitumen. Total heterotrophic bacterial counts in the samples ranged from 1.4 ªª? 105 CFU/g to 2.0 ªª? 106 CFU/g. Total oil utilizing bacterial counts varied from 1.5 ªª? 104 CFU/g to 3.6 ªª? 105 CFU/g. Isolates were identified using API 20E kit. They belong to the genera Burkholderia, Pseudomonas, and Serratia. Degradation efficiency of the isolates on Premium Motor Spirit (PMS), Dual Purpose Kerosene (DPK) and Low Pour Point Fuel Oil (LPFO) were carried out by a colorimetric rapid screen test using 2, 6-dichlorophenol indophenol (DCPIP) reduction test which was monitored by measuring absorbance at 600 nm at every 24 hrs for 120 hrs. Order of ability of the isolates to degrade PMS: P. aeruginosa > P. mendocina > P. borbori > S. rubidae > P. cichorii > B. cepacia while for DPK is P. cichorii > P. borbori > S. rubidae > P. mendocina > B. cepacia > P. aeruginosa. Ability to degrade LPFO: P. cichorii > P. borbori > P. aeruginosa > P. mendocina > B. cepacia > S. rubidae.ª¤

Shotgun Metagenomic Sequencing Data of Sunflower Rhizosphere Microbial Community in South Africa

This dataset presents shotgun metagenomic sequencing of sunflower rhizosphere microbiome in Bloemhof, South Africa. Data were collected to decipher the structure and function in the sunflower microbial community. Illumina HiSeq platform using next generation sequencing of the DNA was carried out. The metagenome comprised 8,991,566 sequences totaling 1,607,022,279 bp size and 66% GC content. The metagenome was deposited into the NCBI database and can be accessed with the SRA accession number SRR10418054. An online metagenome server (MG RAST) using the subsystem database revealed bacteria had the highest taxonomical representation with 98.47%, eukaryote at 1.23%, and archaea at 0.20%. The most abundant genera were the Conexibacter (17%), Nocardioides (8%), Streptomyces (7%), Geodermatophilus (6%), Methylobacterium (5%), and Burkholderia (4%). MG-RAST assisted analysis also revealed functional annotation based on subsystem, carbohydrates sequence had 13.74%, clustering based subsystem 12.93%, amino acids and derivatives 10.30% coupled with other useful functional traits needed for plant growth and health

Bacteriological pollution indicators in Ogun River flowing through Abeokuta Metropolis

Water resources are significant part of integrated community development policy and good health. Hence, the need to reduce the impact of natural and anthropogenic pollution causes so as to enhance water quality. The bacteriological quality of the Ogun River was investigated to determine the sanitary conditions of the water body between March and August, 2014. Total heterotrophic bacteria counts (THBC), total coliform counts (TCC) and total Escherichia coli counts (TEC) using standard plate count and Most Probable Number (MPN) techniques were determined. The isolates were identified using 16SrRNA gene. Total heterotrophic bacteria counts varied between 1.13 × 106 and 4.1 × 107 CFU/ml, TCC ranged between 2.5 × 105 and 2.33× 107 CFU/ml and TEC was between 5 × 104 and 1.3 × 106 CFU/ml. Most Probable Number of coliforms in all samples varied between 120 and 1600 MPN/100 ml. Isolated microorganisms include Escherichia coli strain SUS9EC, Escherichia coli O157:H7 strain SSI7, Escherichia coli strain BW25113, Escherichia coli strain C-X1B, and Klebsiella oxytoca strain KU-5. One-wayanalysis of variance showed significant difference within the samples at (P<0.05).The results revealed high bacteria counts which is higher than the recommended value of 1.2 × 102 for THBC, a zero E. coli count and not more than 10 coliforms per 100 ml by World Health Organization standards for drinking water.Keywords: Water, bacteria, Escherichia coli, pollutio

Sulfate-Reducing Bacteria as an Effective Tool for Sustainable Acid Mine Bioremediation

Mining industries produce vast waste streams that pose severe environmental pollution challenge. Conventional techniques of treatment are usually inefficient and unsustainable. Biological technique employing the use of microorganisms is a competitive alternative to treat mine wastes and recover toxic heavy metals. Microorganisms are used to detoxify, extract or sequester pollutants from mine waste. Sulfate-reducing microorganisms play a vital role in the control and treatment of mine waste, generating alkalinity and neutralizing the acidic waste. The design of engineered sulfate-reducing bacteria (SRB) consortia will be an effective tool in optimizing degradation of acid mine tailings waste in industrial processes. The understanding of the complex functions of SRB consortia vis-à-vis the metabolic and physiological properties in industrial applications and their roles in interspecies interactions are discussed

Trenchant microbiological-based approach for the control of Striga: Current practices and future prospects

Striga species are obligate parasitic weeds most of which are members of the Orobanchaceae family. They are commonly associated with staple crops and constitute threats to food security, especially in Sub-Saharan Africa. They pose deleterious impacts on staple cereal crops like maize and pearl millet, resulting in 7–10 billion dollars yield losses or, in extreme infestations, entire crop losses. Farmers' limited knowledge about the weed (genetics, ecology, nature of the damage caused, complex life cycle, interactions with its host and associated microbes) and their attitude toward its control have negatively affected its management and sustainability. With the present Striga management such as mechanical, chemicals, cultural and biological measures, it is extremely difficult to achieve its active management due to nature of the association between host plants and parasites, which requires highly selective herbicides. The use of soil microbes has not been well explored in the management of Striga infection in African countries. However, many soil microorganisms have been considered viable biological control techniques for fighting parasitic weeds, due to their vast action and roles they play in the early stage of host-Striga interaction. Their application for pest control is well perceived to be cost-effective and eco-friendly. In this review, we gave a comprehensive overview of major knowledge gaps and challenges of smallholders in Striga management and highlighted major potentials of microbial-based approach with respect to the mechanisms of host-Striga-microbe interactions, and the metagenomics roles on Striga management that include understanding the microbe and microbial systems of Striga-infested soil

A New Strategy for Heavy Metal Polluted Environments: A Review of Microbial Biosorbents

Persistent heavy metal pollution poses a major threat to all life forms in the environment due to its toxic effects. These metals are very reactive at low concentrations and can accumulate in the food web, causing severe public health concerns. Remediation using conventional physical and chemical methods is uneconomical and generates large volumes of chemical waste. Bioremediation of hazardous metals has received considerable and growing interest over the years. The use of microbial biosorbents is eco-friendly and cost effective; hence, it is an efficient alternative for the remediation of heavy metal contaminated environments. Microbes have various mechanisms of metal sequestration that hold greater metal biosorption capacities. The goal of microbial biosorption is to remove and/or recover metals and metalloids from solutions, using living or dead biomass and their components. This review discusses the sources of toxic heavy metals and describes the groups of microorganisms with biosorbent potential for heavy metal removal

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 β 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

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant’s rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO3 (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms