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

Sillen, Wouter M. A.; Thijs, Sofie; Abbamondi, Gennaro Roberto; De La Torre Roche, Roberto; Weyens, Nele; White, Jason C.; Vangronsveld, Jaco

doi:10.1186/s40168-020-00904-y

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
	Database reference	Database entry	Archaea	Bacteria	Maize	Fungi	Other	Lowest level taxonomic assignment	Log2 fold change	Base level: mean number of reads
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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