Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Irena Maus; Michael Klocke; Jaqueline Derenkó; Yvonne Stolze; Michael Beckstette; Carsten Jost; Daniel Wibberg; Jochen Blom; Christian Henke; Katharina Willenbücher; Madis Rumming; Antje Rademacher; Alfred Pühler; Alexander Sczyrba; Andreas Schlüter

doi:10.1186/s40793-020-00354-x

Environmental Microbiome

Table 2 Most actively transcribed genes for enzymes involved in carbohydrate or protein utilization of selected HR biofilm MAGs

From: Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Metagenome assembled genome (MAG)¹	Assumed taxonomic affiliation	Analyzed HR² biofilm sample	Gene transcripts involved in carbohydrate or protein utilization							Predicted functional role in AD⁴
Metagenome assembled genome (MAG)¹	Assumed taxonomic affiliation	Analyzed HR² biofilm sample	GenID	Gene length	Putative gene product	Gene	EC number	Transcripts mapped	Normalized number of transcripts [TPM]³	Predicted functional role in AD⁴
17	Bacteroidales (Prevotella sp.)	T1_OLR1500	Bin_17_01477	366	Deoxyguanosinetriphosphate triphosphohydrolase	dgt	3.1.5.1	141	3.9	n/s
			Bin_17_01805	171	Hypothetical protein	n/s	n/s	28	3.4
			Bin_17_00602	177	50S ribosomal protein	rpmD	n/s	10	1.5
			Bin_17_00172	651				75	0.8
			Bin_17_00603	519	50S ribosomal protein	rpsE	n/s	53	0.8
			Bin_17_00862	1041	L-3,5-diaminohexanoate dehydrogenase	kdd	1.4.1.11	92	0.6
			Bin_17_00014	579	N-acetylhexosamine 1-kinase	nahK	2.7.1.162	38	0.5
18	Clostridiales (Acetivibrio sp.)	M1_OLR1500	Bin_18_02374	207	Small; acid-soluble spore protein C2	sspC		4876	619	Hydrolysis
			Bin_18_01750	144	Hypothetical protein	n/s	n/s	462	145
			Bin_18_01164	192	Hypothetical protein	n/s	n/s	384	58
			Bin_18_00189	786	Sulfurtransferase	tusA	2.8.1.-	3938	53
			Bin_18_01827	108	Hypothetical protein	n/s	n/s	74	46
			Bin_18_02918	711	Glycerol uptake facilitator protein	glpF	n/s	573	9
			Bin_18_01829	912	Lactose transport system permease protein	lacF	n/s	760	9
			Bin_18_01831	1377	Beta-glucosidase A	bglA	3.2.1.21	798	6
			Bin_18_01301	1272	Peptidoglycan binding domain protein		n/s	678	5
			Bin_18_01830	858	L-arabinose transport system permease protein	araQ	n/s	413	5
			Bin_18_01016	1119	D-galactose-binding periplasmic protein precursor	mglB	n/s	309	3
40	Lachnospirales (Herbinix sp.)	M1_OLR1500	Bin_40_01523	225	Acid-soluble spore protein C2	sspC_1	n/s	42,076	2942	Hydrolysis
			Bin_40_01017	114	Manganese containing catalase	n/s	n/s	5156	1711
			Bin_40_00454	147	Hypothetical protein	n/s	n/s	5508	1017
			Bin_40_00073	246	Hypothetical protein	n/s	n/s	17,299	1006
			Bin_40_01138	228	Acid-soluble spore protein C2	sspC_2	n/s	14,627	994
			Bin_40_00033	1770	Oligopeptide-binding protein	oppA	n/s	14,445	50
			Bin_40_00081	819	Maritimacin	n/s	n/s	4915	42
			Bin_40_00131	681	Thiamine transporter	thiT	n/s	3522	38
			Bin_40_00519	1116	Trehalose import ATP-binding protein	sugC	n/s	6385	37
			Bin_40_00505	1008	Glyceraldehyde-3-phosphate dehydrogenase	gapN	1.2.1.12	4163	27
			Bin_40_01590	1329	Maltose/maltodextrin-binding protein precursor	malX	n/s	5638	27
107	Clostridiales (Clostridium sp.)	T2_OLR1500	Bin_107_01262	183	Small; acid-soluble spore protein C1	sspC1_1	n/s	29,669	3262	Hydrolysis
			Bin_107_01261	180	Small; acid-soluble spore protein C2	sspC2_2	n/s	24,756	2829
			Bin_107_01260	171	Small; acid-soluble spore protein C2	sspC2_1	n/s	16,600	2136
			Bin_107_00122	186	Small; acid-soluble spore protein C1	sspC1_2	n/s	9026	956
			Bin_107_00144	234	Glutaredoxin-3	grxC	n/s	7124	459
			Bin_107_01233	258	Peptidase domain protein	n/s	n/s	1245	65
			Bin_107_00711	99	Enolase	eno	4.2.1.11	87	37
			Bin_107_01338	1530	4-alpha-glucanotransferase	malQ	2.4.1.2	4863	20
			Bin_107_00018	114	L-cystine import ATP-binding protein	tcyN	n/s	58	19
			Bin_107_01344	678	Trehalose import ATP-binding protein	sugC	3.6.3.-	1732	19
			Bin_107_01340	894	Maltose transport system permease protein	malG	n/s	2415	19
			Bin_107_01038	531	PTS system, maltose-specific, EIICB component	malP	n/s	1017	16
			Bin_107_01656	1002	Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde-3-phosphate dehydrogenase	gapN	1.2.1.12	2090	14
			Bin_107_01134	627	Lysozym	acm	3.2.1.17	1086	13
			Bin_107_00091	1881	Amylopullulanase	apu	3.2.1.41	3989	13
			Bin_107_01040	1335	6-phospho-alpha-glucosidase	pagL	3.2.1.-	2015	10
			Bin_107_00188	624	Thiamine transporter	thiT	n/s	692	9
			Bin_107_01547	132	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	gap	1.2.1.9	158	8
108	Bacteroidales (unclassified genus)	T2_OLR1500	Bin_108_01400	213	Hypothetical protein	n/s	n/s	18	1.4	n/s
			Bin_108_00987	726	Alkyl hydroperoxide reductase	ahpC	1.11.1.15	85	0.8
			Bin_108_00986	183	Nitrite reductase [NAD(P)H]	nasD	1.7.1.4	4	0.4
			Bin_108_00047	1140	Hypothetical protein	n/s	n/s	60	0.3
			Bin_108_01184	441	50S ribosomal protein L15	rplO	n/s	14	0.2
134	Lachnospirales (Kineothrix sp.)	T2_OLR1500	Bin_134_02838	177	Transition state regulatory protein	abrB	n/s	1527	181	Hydrtolysis
			Bin_134_00038	555	Hypothetical protein	n/s	n/s	491	7
			Bin_134_00185	291	ATP-dependent Clp protease, proteolytic subunit	clpP	n/s	81	3
			Bin_134_00184	1278	ATP-dependent Clp protease, ATP-binding subunit	clpX	n/s	622	3
			Bin_134_00305	906	HTH-type transcriptional regulator	yofA	n/s	324	2
			Bin_134_02093	1110	Trehalose import ATP-binding protein	acm	3.2.1.17	234	1
			Bin_134_00012	570	Amylopullulanase	pulA	3.2.1.41	74	1
			Bin_134_00958	3558	Pyruvate-flavodoxin oxidoreductase	ydbK	1.2.7.1	623	1

1 The first five transcripts of each MAG represent the top transcripts of the corresponding MAG
2 Hydrolysis reactor
3 Transcripts per million averaged for datasets from two technical replicates
4 Anaerobic digestion
n/s Not specified

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