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Table 1 Functional composition of the metatranscriptome. Metatranscriptome genes annotated to InterPro2GO and KEGG databases with significantly different abundances between control conditions and nanosilver-exposed (100 mg kg−1 soil) conditions in maize rhizosphere soil. Taxonomic origin of the genes is given at a general level, as well as the lowest possible level

From: Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis

  Database reference Database entry Taxonomic origin Lowest level taxonomic assignment Log2 fold change Base level: mean number of reads
Archaea Bacteria Maize Fungi Other
Higher incidence in AgNP-conditions IPR021604 Copper resistance protein K   x     Burkholderiales − 3.59 34.7
IPR027256 P-type ATPase, subfamily IB x x     Actinobacteria, Proteobacteria, Bacteroidetes, Thaumarchaeota, Euryarchaeota − 1.30 122.4
IPR004763 Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA   x     Bacteroidetes, Proteobacteria, Acidobacteria − 2.53 29.3
IPR006376 Copper-resistance protein CopA   x     Sphingomonadales, Xanthomonadales − 2.26 5.3
K07787 Cu(I)/Ag(I) efflux system membrane protein CusA/SilA   x     Bacteroidetes, Proteobacteria, Acidobacteria − 2.53 29.0
K07798 Membrane fusion protein, Cu(I)/Ag(I) efflux system   x     Proteobacteria, Acidobacteria, Nitrospira, Planctomycetes − 1.81 9.3
K17686 Cu+-exporting ATPase x x     Proteobacteria, Actinobacteria, Thaumarchaeota − 1.25 83.5
IPR001806 Small GTPase superfamily   x     Xanthomonadales − 0.64 171.1
IPR005294 ATPase, F1 complex, alpha subunit   x     Bacteria general − 1.23 76.2
GO:0005634 Nucleus    x x x Eukaryote general − 0.73 52.0
ko04121 Ubiquitin system    x x x Eukaryote general − 0.59 218.9
ko04144 Endocytosis    x x x Eukaryote general − 0.62 126.7
ko01009 Protein phosphatase and associated proteins    x x x Eukaryote general − 0.42 229.1
IPR005093 RNA-directed RNA polymerase beta-chain      x Leviviridae (Bacteriophage) − 3.12 113.8
K09872 aquaporin PIP    x    NA − 1.13 1.8
ko04075 Plant hormone signal transduction    x    NA − 2.37 12.1
ko00940 Phenylpropanoid biosynthesis    x    NA − 1.26 49.7
IPR005922 Phenylalanine ammonia-lyase    x    NA − 2.98 3.1
K01188 Beta-glucosidase    x    NA − 2.15 6.2
IPR015655 Protein phosphatase 2C family    x    NA − 1.27 17.4
IPR001246 Lipoxygenase, plant    x    NA − 2.57 2.8
K04733 Interleukin-1 receptor-associated kinase 4    x    NA − 1.77 6.2
IPR000864 Proteinase inhibitor I13, potato inhibitor I    x    NA − 1.89 1.7
IPR001929 Germin    x    NA − 2.21 3.2
ko00480 Glutathione metabolism   x x    Proteobacteria, Actinobacteria − 0.48 119.1
IPR003855 Potassium transporter    x    NA − 1.89 4.7
IPR009716 Ferroporti-1    x    NA − 1.77 1.3
K08176 MFS transporter, PHS family, inorganic phosphate transporter    x    NA − 1.50 2.5
K00695 Sucrose synthase    x    NA − 1.90 5.2
K10592 E3 ubiquitin-protein ligase HUWE1    x    NA − 1.58 4.0
IPR005150 Cellulose synthase    x    NA − 1.93 3.6
IPR016461 O-methyltransferase COMT-type    x    NA − 1.63 7.9
IPR018167 S-adenosylmethionine decarboxylase subgroup    x    NA − 2.09 2.2
K02132 F-type H+-transporting ATPase subunit alpha   x x x   Streptomyces, Leotiomyceta − 1.38 22.5
K02262 Cytochrome c oxidase subunit 3   x x x   Streptomyces, Leotiomyceta − 1.78 11.8
K03936 NADH dehydrogenase (ubiquinone) Fe-S protein 3   x x x   Streptomyces, Leotiomyceta − 1.56 2.9
IPR001128 Cytochrome P450   x x x   Streptomyces, Leotiomyceta − 0.84 36.5
GO:0005739 Mitochondrion    x x   Sordariomycetes − 1.76 6.2
ko04110 Cell cycle    x x   Leotiomyceta − 0.95 44.0
IPR012220 Glutamate synthase, eukaryotic    x x   Sordariomycetes − 1.85 5.4
ko00199 Cytochrome P450   x x    Streptomyces − 1.39 8.7
GO:0004872 Receptor activity   x x    Streptomyces − 1.52 19.5
IPR00136 Glycoside hydrolase, family 1   x x    Streptomyces, Sphingomonadales − 2.00 13.2
K00066 GDP-mannose 6-dehydrogenase   x     Pseudomonadales − 1.63 7.6
IPR031148 Plexin family   x     Streptomyces − 2.47 7.8
IPR001795 RNA-directed RNA polymerase, luteovirus      x Luteoviridae − 1.92 13.5
Lower incidence in AgNP-conditions IPR010946 Geranylgeranylglyceryl phosphate synthase x      Nitrosphaeraceae 2.07 24.2
IPR005938 AAA ATPase, CDC48 family x      Nitrosphaeraceae 0.85 49.4
IPR002386 Amicyanin/Pseudoazurin x      Nitrosphaeraceae 1.38 20.5
IPR005848 Urease, alpha subunit x      Nitrosphaeraceae 1.55 34.2
IPR000812 Transcription factor TFIIB x      Nitrosphaeraceae 1.54 29.7
IPR024656 Ammonia monooxygenase, subunit A, archaeal x      Archaea general 1.69 42.7
K04080 molecular chaperone IbpA   x     Rhizobiales 1.09 47.2
IPR026042 Stress response protein YjbJ   x     Alpha- & Gammaproteo, Bacteroidetes 1.17 183.5
IPR031107 Small heat shock protein HSP20   x     Rhizobiales, Chloroflexi, Actinobacteria 0.80 284.3
IPR001189 Manganese/iron superoxide dismutase   x     Bacteria general 0.61 75.2
IPR001287 Nitrite reductase, copper-type x      Nitrosphaeraceae 1.21 29.2
K02518 Translation initiation factor IF-1   x     Actinobacteria 1.01 50.8
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Microbiome

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