Abstract:Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG-RAST, Actinomycetales (9.8%) … Show more
“…Actinobacteria (14%), Bacteroidetes (4%) and Firmicutes (4%) were also highly represented. This community makeup is similar to that previously reported in metagenomic studies of contaminated soils [ 25 ]. Fig.…”
Section: Resultssupporting
confidence: 88%
“…For PAH degradation, bacterial dioxygenase enzymes are considered the principal means of ring fission [ 26 , 143 ] (although cytochrome p450 monooxygenase are common), whereas alpha-ketoglutarate-dependent dioxygenases ( alkB ) are one of the most recognised enzymes driving degradation of aliphatic hydrocarbons [ 25 ] (not to be confused with alkane monooxygenase, alkB ). The contig c596278_g1_i5 was upregulated here (containing yojIalkBadaapbEmqo ), functionally comprising an ABC transporter ATP-binding protein ( yojI ), alpha-ketoglutarate-dependent dioxygenase ( alkB ), regulatory protein ( ada ), thiamine biosynthesis lipoprotein ( apbE ) and malate:quinone oxidoreductase ( mqo ) (Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Additionally to this, a number of genes well characterised as accompanying toluene tolerance [ 144 , 145 ] were DE, including a putative operon which contained the toluene transporter subunits mlaCDEF and kdsCDlptACkdsCD encoding a lipopolysaccharide export system. Degradation of alkanesulphonates, previously identified as involved in crude oil degradation by metagenomic study [ 25 ], occurs through desulfonation and relies on expression of the operon ssuABCDE [ 146 , 147 ] comprising an alkanesulfonate transporter subunit, a putative alkanesulfonate transporter subunit, an FMNH(2)-dependent alkanesulfonate monooxygenase, putative aliphatic sulfonate binding protein and NAD(P)H-dependent FMN reductase. Here, the entirety of the ssuABCDE operon was assembled and DE in higher abundance in contaminated conditions (two similar contigs c595976_g1_i2 and c595976_g1_i9).…”
Section: Resultsmentioning
confidence: 99%
“…The peril of confounding bacterial community assessment by culturing methodology alone is also widely acknowledged, but the progression of contemporary sequencing techniques and extensive research advancement driven by fields relating to the human microbiome has led to an understanding of the ubiquitous, exceedingly diverse, presence and involvement of bacteria in eukaryotic biology. The importance of bacteria to mycorrhizal fungi and/or plant health has been established even in conditions less challenging than anthropogenic soil contamination [ 25 – 28 ]. Bacteria whose presence and function is beneficial to mycorrhizal fungi and/or plants are often termed mycorrhizal helper bacteria MHB [ 29 , 30 ] or plant growth-promoting bacteria (PGPB), such as the recently identified Enterobacter sp.…”
BackgroundOne method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.MethodsHere, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. ‘Fish Creek’ roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.ResultsThe 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.ConclusionsFungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0432-5) contains supplementary material, which is available to authorized users.
“…Actinobacteria (14%), Bacteroidetes (4%) and Firmicutes (4%) were also highly represented. This community makeup is similar to that previously reported in metagenomic studies of contaminated soils [ 25 ]. Fig.…”
Section: Resultssupporting
confidence: 88%
“…For PAH degradation, bacterial dioxygenase enzymes are considered the principal means of ring fission [ 26 , 143 ] (although cytochrome p450 monooxygenase are common), whereas alpha-ketoglutarate-dependent dioxygenases ( alkB ) are one of the most recognised enzymes driving degradation of aliphatic hydrocarbons [ 25 ] (not to be confused with alkane monooxygenase, alkB ). The contig c596278_g1_i5 was upregulated here (containing yojIalkBadaapbEmqo ), functionally comprising an ABC transporter ATP-binding protein ( yojI ), alpha-ketoglutarate-dependent dioxygenase ( alkB ), regulatory protein ( ada ), thiamine biosynthesis lipoprotein ( apbE ) and malate:quinone oxidoreductase ( mqo ) (Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Additionally to this, a number of genes well characterised as accompanying toluene tolerance [ 144 , 145 ] were DE, including a putative operon which contained the toluene transporter subunits mlaCDEF and kdsCDlptACkdsCD encoding a lipopolysaccharide export system. Degradation of alkanesulphonates, previously identified as involved in crude oil degradation by metagenomic study [ 25 ], occurs through desulfonation and relies on expression of the operon ssuABCDE [ 146 , 147 ] comprising an alkanesulfonate transporter subunit, a putative alkanesulfonate transporter subunit, an FMNH(2)-dependent alkanesulfonate monooxygenase, putative aliphatic sulfonate binding protein and NAD(P)H-dependent FMN reductase. Here, the entirety of the ssuABCDE operon was assembled and DE in higher abundance in contaminated conditions (two similar contigs c595976_g1_i2 and c595976_g1_i9).…”
Section: Resultsmentioning
confidence: 99%
“…The peril of confounding bacterial community assessment by culturing methodology alone is also widely acknowledged, but the progression of contemporary sequencing techniques and extensive research advancement driven by fields relating to the human microbiome has led to an understanding of the ubiquitous, exceedingly diverse, presence and involvement of bacteria in eukaryotic biology. The importance of bacteria to mycorrhizal fungi and/or plant health has been established even in conditions less challenging than anthropogenic soil contamination [ 25 – 28 ]. Bacteria whose presence and function is beneficial to mycorrhizal fungi and/or plants are often termed mycorrhizal helper bacteria MHB [ 29 , 30 ] or plant growth-promoting bacteria (PGPB), such as the recently identified Enterobacter sp.…”
BackgroundOne method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.MethodsHere, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. ‘Fish Creek’ roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.ResultsThe 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.ConclusionsFungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0432-5) contains supplementary material, which is available to authorized users.
“…4 ). Members of the class Sphingobacteria that have been recovered in polluted soil 41 are reported to be involved in the degradation of aromatic and aliphatic hydrocarbons 42 .…”
Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called “Terra dei Fuochi”. The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.
Ultisols are peculiar soils generally known for their poor nutrient status. When contaminated, remediation of ultisols present the additional challenge of nutrient and ecological restoration. In this study, we report the distribution of total petroleum hydrocarbons (TPHs) in a simulated crude oil-contaminated ultisol amended with biochar (BC)/humus sediment (HS) slurry. We also investigated the microbial abundance, diversity, and enzyme expression in the treatment medium that gave the optimum remediation results. We recorded lowest TPH levels in remediant amendments with BC produced at 700°C. Majority of the OTUs (27.96%) found in the remediated ultisol belonged to Firmicutes (27.96%), Proteobacteria (25.88%), and Gemmatimonadetes (23.32%) while enzymes (AlkM, alkB, AlmA, PRM, cP450, MMO/AMO subunits A, B, and C, and Genes ssuD, ssuC, dszC, dszA, and dszB) encountered in this study were expressed mainly by bacteria belonging to the order Actinomycetales and Bulkhoderiales.
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