Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Maus, Irena; Bremges, Andreas; Stolze, Yvonne; Hahnke, Sarah; Cibis, Katharina G.; Koeck, Daniela E.; Kim, Yong S.; Kreubel, Jana; Hassa, Julia; Wibberg, Daniel; Weimann, Aaron; Off, Sandra; Stantscheff, Robbin; Zverlov, Vladimir V.; Schwarz, Wolfgang H.; König, Helmut; Liebl, Wolfgang; Scherer, Paul; McHardy, Alice C.; Sczyrba, Alexander; Klocke, Michael; Pühler, Alfred; Schlüter, Andreas

doi:10.1186/s13068-017-0947-1

Biotechnology for Biofuels and Bioproducts

Table 1 Summary of 22 bacterial and archaeal strains used in this study

From: Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Species and strain	Family	Origin					Reference for the isolation strategy or strain origin	Closest related NCBI GenBank entry with a validly published taxonomic affiliation	Similarity of 16S rRNA gene between isolate and GenBank entry (%)	NCBI GenBank entry of closest relative
		Location of BGP		Type of reactor	Fed substrate	T (°C) of reactor
		Latitude	Longitude	Type of reactor	Fed substrate	T (°C) of reactor
Bacteria
Clostridium cellulosi DG5	Clostridiaceae	51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[18]^b	Clostridium cellulosi AS1.1777	98.8	LN881577
Clostridium sp. N3C		51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[18]^c	Clostridium putrefaciens DSM 1291^T	93.0	NR113324
Clostridium bornimense M2/40^T		52.3871	13.0993	Lab-scale UASS/wet fermentation	Maize silage, wheat straw	37	[20]	Clostridium bornimense M2/40^T	100	JQ388596
Clostridium thermocellum BC1		48.135125	11.581981	Bio-waste compost treatment site close to BGP		60	[18]^d	Clostridium thermocellum DSM 1237^T	99.0	NR074629
Proteiniborus sp. DW1	Clostridiales incertae sedis	49.512893	7.083068	CSTR, wet fermentation	Maize silage, grass, cattle manure	39	[21]	Proteiniborus ethanoligenes GW^T	96.0	NR044093
Sporanaerobacter sp. PP17-6a	Clostridiales incertae sedis	51.255499	6.396524	Lab-scale CSTR/wet fermentation	Maize silage, pig manure, cattle manure	37	This study	Sporanaerobacter acetigenes Lup33	91.0	NR025151
Herbinix hemicellulosilytica T3/55^T	Lachnospiraceae	51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[18, 54]^b	Herbinix hemicellulosilytica T3/55^T	100	LN626355
Herbinix luporum SD1D^T	Lachnospiraceae	51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[18, 55]^b	Herbinix luporum SD1D^T	100	LN626359
Peptoniphilaceae bacterium str. ING2-D1G	Peptoniphilaceae	51.255499	6.396524	Lab-scale CSTR/wet fermentation	Maize silage, pig manure, cattle manure	37	[22]	Peptoniphilus indolicus DSM 20464^T	90.6	AY153431
Propionispora sp. 2/2-37	Veillonellaceae	48.3924	11.7569	CSTR, wet fermentation	Maize silage, grass	38	[18]^e	Propionispora hippei KS^T	95.0	NR036875
Bacillus thermoamylovorans 1A1	Bacillaceae	48.3924	11.7569	CSTR, wet fermentation	Maize silage, pig manure	52	[18]^f	Bacillus thermoamylovorans DKP^T	99.0	NR029151
Proteiniphilum saccharofermentans M3/6^T	Porphyromonadaceae	52.3871	13.0993	Lab-scale UASS/wet fermentation	Maize silage, wheat straw	37	[26]	Proteiniphilum saccharofermentans M3/6^T	100	KP233809
Fermentimonas caenicola ING2-E5B^T		51.255499	6.396524	Lab-scale CSTR/wet fermentation	Maize silage, pig manure, cattle manure	37		Fermentimonas caenicola ING2-E5B^T	100	KP233810
Petrimonas mucosa ING2-E5A^T		51.255499	6.396524	Lab-scale CSTR/wet fermentation	Maize silage, pig manure, cattle manure	37		Petrimonas mucosa ING2-E5A^T	100	KP233808
Defluviitoga tunisiensis L3	Petrotogaceae	51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[27]	Defluviitoga tunisiensis SulfLac1^T	99.9	NR122085
Archaea
Methanobacterium formicicum MF^T	Methanobacteriaceae	DSMZ^a				37	[50]	Methanobacterium formicicum MF^T	100	NR115168
Methanobacterium formicicum Mb9		49.878359	6.481390	CSTR, wet fermentation	Maize silage, grass, cattle manure	40	[21]	Methanobacterium formicicum MF^T	100	NR115168
Methanobacterium sp. Mb1		49.512893	7.083068	CSTR, wet fermentation	Maize silage, grass, cattle manure	39	[21]	Methanobacterium formicicum MF^T	98.0	NR115168
Methanobacterium congolense Buetzberg		53.736687	10.083949	CSTR, dry fermentation	Household garbage	37	[18]^g	Methanobacterium congolense C^T	99.0	NR028175
Methanothermobacter wolfeii SIV6		51.255499	6.396524	Liquid pump/wet fermentation	Maize, pig manure, grass	54	[18]^h	Methanothermobacter wolfeii VKM B-1829^T	100	NR040964.1
Methanoculleus bourgensis MS2^T	Methanomicrobiaceae	DSMZ				37	[49]	Methanoculleus bourgensis MS2^T	100	NR042786
Methanoculleus chikugoensis L21-II-0	Methanomicrobiaceae	51.255499	6.396524	Lab-scale CSTR/wet fermentation	Maize silage, pig manure, cattle manure	37	This study	Methanoculleus chikugoensis MG62^T	99.0	NR028152

CSTR, continuously stirred tank reactor; UASS, upflow anaerobic solid-state reactor
^aDSMZ, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
^bIsolation strategy number four described in more detail by [18]
^cIsolation strategy number eight (a) published in [18]
^dIsolation strategy number five published in [18]
^eIsolation strategy number seven published in [18]
^fIsolation strategy number two published in [18]
^gIsolation strategy number ten published in [18]
^hIsolation strategy number eleven published in [18]

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ISSN: 2731-3654

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