Lateef Babatunde Salam

This chapter examines the role of airborne microorganisms in the degradation of volatile organic compounds (VOCs) and atmospheric pollutants. It discusses the sources, diversity, and ecological functions of bioaerosols, including bacteria, fungi, archaea, and viruses, and highlights microbial survival strategies such as pigmentation, dormancy, DNA repair, and particle aggregation. Major pollutants, including NOx, SO2, PAHs, ozone, and particulate matter, are reviewed alongside their environmental and health impacts. The chapter emphasizes microbial metabolic pathways involved in aerobic and anaerobic VOC degradation, including oxygenase-mediated oxidation, reductive dehalogenation, fumarate addition, and cometabolism. It also explores the role of airborne microbes in atmospheric chemistry, cloud formation, pollutant cycling, and climate regulation. Emerging biotechnologies such as biofiltration, engineered consortia, CRISPR-based optimization, and bioelectrochemical systems are highlighted as sustainable strategies for air-pollution control.

Background: Aquaculture environments are increasingly recognized as reservoirs for antimicrobial-resistant bacteria due to the routine use of antibiotics such as tetracyclines. Members of the family Enterobacteriaceae readily acquire and disseminate resistance determinants, posing risks to food safety and public health. In Nigeria, molecular data on tetracycline resistance in aquaculture systems remain limited. This study investigated the occurrence and molecular basis of tetracycline resistance among Enterobacteriaceae isolated from earthen catfish ponds in Akure, Nigeria.Methodology: Composite samples were collected from five different locations within each of two randomly selected commercial-scale earthen catfish ponds and pooled for analysis. The resulting samples were cultured on selective media. Antibiotic susceptibility of four representative isolates was performed by the Kirby–Bauer disc diffusion method against ampicillin, cefuroxime, ciprofloxacin and tetracycline. The isolate exhibiting phenotypic tetracycline resistance was further characterized by 16S rRNA gene sequencing and phylogenetic analysis. Polymerase chain reaction (PCR) assay was used to detect tetracycline resistance genes (tetA and tetM) in the isolate.Results: All four representative isolates were fully resistant to ampicillin and cefuroxime but susceptible to ciprofloxacin. One isolate (EP9) displayed complete resistance to tetracycline. Molecular identification revealed EP9 as Escherichia albertii, confirmed by phylogenetic clustering within a distinct E. albertii clade. PCR analysis detected the presence of the tetA gene (210 bp) in EP9, while tetM was not detected.Conclusion: This study provides molecular evidence that earthen catfish ponds in Akure harbour tetracyclineresistant Escherichia albertii. The detection of the plasmid-mediated tetA gene underscores the role of aquaculture systems as reservoirs and dissemination hubs for clinically relevant antimicrobial resistance genes, highlighting the need for strengthened antibiotic stewardship and routine AMR surveillance in aquaculture.

The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate–gut–frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa’s circular bioeconomy.

The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobacteria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary.

The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.