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Pathway for pyruvate metabolism performed using the KEGG pathway in KEGG Orthology. EC numbers in green are the enzymes identified in AB1 microcosm
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Abstract
Background: The purpose of this study is to decipher the diverse carbohydrate metabolism pathways in a spent
engine oil-perturbed agricultural soil, enunciate the carbohydrate-active enzymes and genes involved in the
process, taxonomically classify the annotated enzymes and genes, and highlight the importance of the study for
ecological an...
Citations
... All samples were multiplexed and sequenced in a single lane on Miseq, using 2 × 300 bp paired-end sequencing which generates 20 Mb of data for each sample. Sequence reads were generated in less than 65 h, and image analysis and base calling were performed directly on Miseq (Salam 2018;Salam and Idris 2019) Pre-processing of raw reads, quality control, assembly, taxonomic classification, and statistical analysis ...
Ologe Lagoon, in Lagos State Nigeria, is one of the freshwaters exposed to chemical and hydrocarbon pollution. The impacts of anthropogenic pollution on lagoon microbial communities were assessed. Three sampling points were identified, namely Ologe industrial contaminated water (OLICW), Ologe human activity water (OLHAW), and relatively undisturbed water (OLPW). The microbial community structure of samples was determined via Illumina shotgun next-generation sequencing, while taxonomic classification was done by centrifuge. Acidic pH of (3.8 ± 0.02; 4.6 ± 0.01; and 6.5 ± 0.04) were observed for OLHAW, OLICW and OLPW. The heavy metals nickel and lead showed increase at OLICW > OLPW > OLHAW with their values higher than the WHO permissible limit. The gas chromatography flame ionization detector (GC-FID) fingerprints of the samples showed presence of aliphatic (nC1-nC17) and aromatic hydrocarbons like pyrene, anthracene, phenanthraquinone, and phenanthridine which is evidence of pollution. Structurally, the water metagenomes comprised of 40, 43, and 42 phyla, 67, 74, and 72 classes, 666, 982, and 920 genera from OLHAW, OLICW, and OLPW metagenomes. Dominant phyla across the three sites were Proteobacteria (37.1–64.1%), Actinobacteria (6.1–21.6%), Cyanobacteria (5.3–14.0%), Planctomycetes (6.6%), Firmicutes (6.6–5.7%). Archaea phyla like Euryarchaeota and Creanarchaeota were encountered. Principal component ordination (PCO) showed that OLHAW prokaryotic community had total variance of 88.2% PCO1 separating it from OLICW and OLPW, also OLICW and OLPW were separated by PCO2 accounting for 11.8% variation but clustered showing 60% similarity. The study showed abundance of Cyanobacteria, Nitrospira and Clostridia which are biological indicator of pollution and their presence signify eutrophication.
... Shotgun metagenomics of the extracted DNA was prepared using the Illumina Nextera XT sample processing kit and sequenced on an Illumina MiSeq platform. The methods for preparing total DNA for Illumina shotgun sequencing were as previously described (Salam 2018;Salam and Ishaq 2019). Fastp (v 0.23.2), an ultra-fast FASTQ preprocessor, was used to preprocess fastq raw reads for quality profiling, read filtering, adaptor trimming, quality filtering, polyG/ polyX tail trimming, and per-read quality pruning (Chen et al. 2018). ...
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.
... The microbial metabolites of the central precursor's acetyl-CoA, pyruvate, and succinate are used in the biosynthesis of cell biomass. Moreover, gluconeogenesis produces the saccharides required for various biosynthesis and growth of microorganisms, and therefore, a specific enzyme system is capable of O&G degradation [29]. For biodegradation of O&G, microorganisms should have the ability of adhering to the substances. ...
... Among the most significant and promising aerobic treatment processes for wastewater is the activated sludge process which removes thin layers of fat from the surface of the aeration tank to allow oxygen transport [113]. Lipases derived from Candida rugosa, Pseudomonas, Bacillus, Production of methane gas from oil sands tailings [29] Altererythrobacter sp. N1 enzymes Pyrene is degraded via the salicylate and phthalate pathways [30] Acinetobacter, and other bacteria [114] can easily digest the impurities in skimmed fat-rich milk. ...
A large volume of traditional crude oil is still transported through the ocean from production sites to utilization areas around the world. Unconventional petroleum products also cross pelagic natural habitats: for example, diluted bitumen from Canada's oil sands is transported through the Pacific coast to the USA and Asia. Oil and grease (O&G) concentrations in industrial wastewaters and the environment have been reported as rising, with increasing negative effects on the environment. The primary sources of O&G contaminations in aquatic and terrestrial environments are use of O&G in high-demand oil-processed foods, establishment and expansion of oil refinery and petrochemical plants around the world, and spills of O&G into environment during transportation. In most cases, O&G may be cleaned up by the environment's natural processes (such as photooxidation, biodegradation, and evaporation). The bulk oil is removed by naturally existing bacterial populations via one of the several oil weathering methods, which is why bioremediation has gained a lot of attention. Thus, with an ongoing need to evaluate the toxicological effects of chronic and disastrous petroleum spills on marine wildlife, several microorganisms capable of degrading O&G have been identified and may be potential candidates for bioaugmentation products. Therefore, this review focuses on the potential of using microbial candidates as an effective solution to remove the presence of O&G in various wastewaters and soil environments. The review also summarizes the current understanding of the extent and effects of O&G as well as hydrocarbon spills in aquatic and terrestrial environments, the function of microorganisms on degradation of these O&G, and current gaps in knowledge.
Graphical Abstract
... Shotgun metagenomics of the four DNA samples were prepared using the Illumina Nextera XT sample processing kit and sequenced on a MiSeq. The protocols for total DNA preparation for Illumina shotgun sequencing were as reported previously [41,42]. ...
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.
... Shotgun metagenomics of SL7 and SL9 microcosms was prepared using the Illumina Nextera XT sample processing kit and sequenced on a MiSeq. The protocols for total DNA preparation for Illumina shotgun sequencing were as earlier reported (Salam 2018;Salam and Ishaq 2019). ...
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.
... CAZy enzymes perform the catabolism, anabolism, and modification of complex carbohydrates. 47,48 It obtains this information primarily from NCBI. 46,47 Xylanases may be placed in GH families, that is, 5, 7-12, 16, 26, 30, 43, 44, 51, and 62, as per CAZy database. ...
... 51 Finally, members of rest of the families, that is, 9,12,26,30, and 44, possess vestigial or secondary xylolytic action. The characteristics of enzymes belonging to 10 and 11 families have been abundantly studied, and therefore, xylanase enzymes have been predominantly placed in these two families (20,35,37,40,(48)(49)(50). However, rest of the families with sole catalytic domain, that is 5, 7, 8, and 43, have not been explored extensively. ...
Endo 1,4-β-d- xylanases (EC3.2.1.8) are one of the key lignocellulose hydrolyzing enzymes. Xylan, which is present in copious amounts on earth, forms the primary substrate of endo-xylanases which can unchain the constituent monosaccharides linked via β-1,4 glycosidic bonds from the xylan backbone. Researchers have shown keen interest in the xylanases belonging to glycoside hydrolase families 10 and 11 whereas those placed in other GH families are yet to be investigated. Various microbes such as bacteria and fungi harbor these enzymes for the metabolism of their lignocellulose fibers. These microbes can be used as miniature biofactories of xylanase enzymes for a plethora of environmentally benign applications in pulp and paper industry, biofuel production and for improving the quality of food in bread baking and fruit juice industry. This review highlights the potential of microbes in production of xylanase for industrial biotechnology. This article is protected by copyright. All rights reserved.
... The family of glycoside hydrolases (GHs) hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate [55]. In the present study GH18, GH47 and GH125 were the most prevalent in this family. ...
Chrysosporium is a polyphyletic genus belonging (mostly) to different families of the order Onygenales (Eurotiomycetes, Ascomycota). Certain species, such as Chrysosporium keratinophilum, are pathogenic for animals, including humans, but are also a source of proteolytic enzymes (mainly keratinases) potentially useful in bioremediation. However, only a few studies have been published regarding bioactive compounds, of which the production is mostly unpredictable due to the absence of high-quality genomic sequences. During the development of our study, the genome of the ex-type strain of Chrysosporium keratinophilum, CBS 104.66, was sequenced and assembled using a hybrid method. The results showed a high-quality genome of 25.4 Mbp in size spread across 25 contigs, with an N50 of 2.0 Mb, 34,824 coding sequences, 8002 protein sequences, 166 tRNAs, and 24 rRNAs. The functional annotation of the predicted proteins was performed using InterProScan, and the KEGG pathway mapping using BlastKOALA. The results identified a total of 3529 protein families and 856 superfamilies, which were classified into six levels and 23 KEGG categories. Subsequently, using DIAMOND, we identified 83 pathogen–host interactions (PHI) and 421 carbohydrate-active enzymes (CAZymes). Finally, the analysis using AntiSMASH showed that this strain has a total of 27 biosynthesis gene clusters (BGCs), suggesting that it has a great potential to produce a wide variety of secondary metabolites. This genomic information provides new knowledge that allows for a deeper understanding of the biology of C. keratinophilum, and offers valuable new information for further investigations of the Chrysosporium species and the order Onygenales.
... Shotgun metagenomic of the extracted DNA was prepared using the Illumina Nextera XT sample processing kit and sequenced on a MiSeq. The protocols for total DNA preparation for Illumina shotgun sequencing were as described previously (Salam 2018;Salam and Ishaq 2019). The sequence reads of 1S and AB1 metagenomes were deposited on the MG-RAST server with the IDs 4704688.3 and 4704689.3. ...
In hydrocarbon-impacted matrices, accessibility to iron, an essential micronutrient poses a significant challenge to microorganisms due to its complexation with hydrocarbon pollutants. This necessitates the elicitation of diverse adaptive responses to counteract the iron stress and achieve cellular iron homeostasis. In this study, putative genes responsible for iron acquisition, iron regulation, and iron storage in agricultural soil (1S) and agricultural soil amended with spent engine oil (AB1) were evaluated through functional annotation of their open reading frames (ORFs). Functional annotation was done using KEGG KofamKOALA and BacMet. Annotation revealed 110 genes in AB1 of which 96 (87.3%) were annotated for iron acquisition. The iron acquisition genes were responsible for Fe²⁺/Fe³⁺ transport and efflux, heme transport, vitamin B12/cobalamin transport, siderophore transport and biosynthesis. In IS metagenome, 28 genes were detected, of which 20 (71.4%) were annotated for iron acquisition. More genes involved in iron regulation and oxidative stress protection were detected in AB1 metagenome while significant differences observed in the iron metabolism genes recovered from 1S and AB1 metagenomes were statistically validated (p < 0.05). The study revealed that spent engine oil contamination of the agricultural soil imposed significant iron stress on the AB1 microbiome necessitating the expression of several genes encoding high affinity iron uptake systems (siderophores, ABC iron transporters), global iron regulators, and iron-induced oxidative stress protection proteins.
... The short Frontiers in Microbiology 08 frontiersin.org metabolizable oligosaccharides produced are fed into the core carbohydrate metabolic pathways, providing energy and precursor metabolites for other pathways (Salam, 2018). Among the components of lignocellulosic biomass, cellulose is the most prevalent biopolymer on the planet (Lakhundi et al., 2015). ...
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
... Soil microbes play a critical role in the decomposition and mineralization of plant residues (Gabhane et al. 2012;Berlemont et al. 2014;Zhong et al. 2018), which can decompose lignocellulose of plant residues by secreting carbohydrate-active enzymes (CAZymes) (Salam 2018;Ma et al. 2020). Lombard et al. (2014) have shown that CAZymes could be classified into auxiliary activities (AAs), polysaccharide lyase (PLs), carbohydrate esterase (CEs), glycosyl transferases (GT), carbohydrate-binding module (CBMs), and glycoside hydrolase (GHs), according to the similarity of amino acid sequences in protein domains. ...
... He found that GHs and GTs had the highest abundance in soil samples from Caatinga. GHs can cleave glycosides, glucans, and glycoside bonds in glycoconjugates (Salam 2018). have shown that GTs are involved in the synthesis of glycosidic bonds (Cantarel et al. 2009), have the specificity of degrading complex carbohydrate molecules, and are very abundant in the organic layer of soil rich in litter (Uroz et al. 2013). ...
Purpose
Reclamation of saline-alkali soils to grow cotton (Gossypium spp.) is very common in the arid Manas River Basin in Northwest China. However, little is known about the degradation potential of soil microbes in reclaimed saline-alkali soils.
Methods
Hence, in this study, the high-throughput metagenomic sequencing was used to assess the degradation potential of soil microbes over seven years after reclamation. Results The results showed that bacteria is the dominant microbial group, and Actinobacteria, Proteobacteria, Chloroflexi, and Firmicutes were dominant phyla in the soil samples collected in each year. Among them, Actinobacteria and Proteobacteria accounted for more than 60% of the total bacteria. Further, soil microbial diversity and abundance of carbohydrate-active enzymes (CAZymes) encoding genes increased after reclamation, as did the abundance of CAZyme encoding genes involved in the decomposition of cellulose, hemicellulose, chitin, and lignin. Deterministic and stochastic processes jointly dominated the succession of microbial communities in reclaimed soils. Redundancy analysis and permutational multivariate analysis of variance showed that soil EC, C/N ratio, and Na⁺ content significantly affected microbial community succession and the abundance of CAZyme encoding genes in reclaimed soils, and soil pH affected soil microbial community diversity.
Conclusions
In conclusion, the degradation potential of soil microbes significantly increased after reclamation. This study deepens our understanding of the degradation potential of soil microbes in the process of reclamation of abandoned saline-alkali soils.
