Table 3 Summary of pure isolates obtained from the thermophilic biogas plant applying different isolation strategies (1)–(11) assigned to characterized reference species by means of their 16S rRNA gene sequence similarity using the EzTaxon identification tool; metagenomic and metatranscriptomic sequences were mapped on a reference strain 16S rRNA gene sequence applying the gsMapper program
Closest related NCBI GenBank entry | Isolates from the thermophilic biogas plant | Number of metagenome sequences mapped on the 16S rRNAb | Number of metatranscriptome sequences mapped on the 16S rRNAc | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Class | Family | Species | Accession number | 16S rRNA identity (%) | Number of isolates and/or colony forming units (CFU) | Isolate designation | NCBI Genbank entry | Cellulose degrader | Main substrate | Fermentation products | Isolation strategya | ||
Cellulolytic Bacteria | |||||||||||||
Clostridia | Lachnospiraceae | Herbinix hemicellulosilytica | LN626355 | 100.0 | 1 isolate | T3/55T | LN626355 | Yes | Cellobiose | Et, Ac, Pr | 4 | 17 | 1552 |
96.4 | 8 isolates | SD1D | LN626359 | Yes | Cellobiose | Et, Ac, Pr | 4, 5 | 17 | 858 | ||||
Ruminococcaceae | Clostridium cellulosi | L09177 | 98.9 | 14 isolates | DG5 | LN881577 | Yes | Cellobiose | Et, Ac | 3, 4 | 0 | 1831 | |
Clostridium clariflavum | CP003065 | 100.0 | 34 isolates | K50/5 | LN881585 | Yes | Cellulose | NAd | 3, 4 | 862 | 9152 | ||
Clostridium stercorarium | CP004044 | 99.3 | 13 isolates | Neu14 | LN881576 | Yes | Cellobiose | NA | 3 | 28 | 12,099 | ||
Clostridium thermocellum | CP000568 | 99.9 | 27 isolates | HAW2/1 | HG917924 | Yes | Cellulose | Et, Ac, Ip | 3, 4, 5 | 1279 | 7814 | ||
Acidogenic/acetogenic Bacteria | |||||||||||||
Bacilli | Bacillaceae | Bacillus cereus | – | NA | 2 × 107 CFU g−1 | (No) | NA | NA | 1 | NA | NA | ||
Bacillus licheniformis | AE017333 | 99.9 | 5 × 107 CFU g−1, 9 isolates | L2C | KT351634 | (No) | NA | NA | 1, 8a, 8b, 9 | 2 | 2696 | ||
Bacillus oleronius | – | NA | 1 × 107 CFU g−1 | (No) | NA | NA | 2 | NA | NA | ||||
Bacillus thermoamylovorans | L27478 | 99.5 | 1 × 107 CFU g−1, 7 isolates | Neu19 | LN881587 | No | Starch | Et, Ac, Fo | 2, 3, 4, 8c, 8d | 1 | 5070 | ||
Bacillus coagulans | AB271752 | 99.6 | 2 isolates | M1A | KT351636 | NA | NA | NA | 8a | 3 | 2566 | ||
Bacillus infernus | U20385 | 99.9 | 3 isolates | E2C | KT351638 | NA | NA | NA | 8d | 3 | 3989 | ||
Geobacillus thermodenitrificans | CP000557 | 100.0 | 2 isolates | J2B | KT351633 | NA | NA | NA | 8a, 8b | 0 | 4181 | ||
Enterococcaceae | Enterococcus faecium | – | NA | <102 CFU g−1 | (No) | NA | NA | 2 | NA | NA | |||
Paenibacillaceae | Aneurinibacillus spp. | – | NA | <103 CFU g−1 | (No) | NA | NA | 2 | NA | NA | |||
Paenibacillus barengoltzii | AY167814 | 99.1 | 6 isolates | YP4-6A | KT351639 | NA | NA | NA | 8a | 0 | 1788 | ||
Planococcaceae | Ureibacillus thermosphaericus | AB101594 | 100.0 | 3 × 107 CFU g−1, 3 isolates | A6A | KT351635 | NA | NA | NA | 1, 9 | 2 | 4376 | |
Clostridia | Clostridiaceae | Clostridium isatidis | X98395 | 99.9 | 13 isolates | MV1 | LN881568 | No | Glucose | NA | 3, 4 | 738 | 2404 |
99.3 | 2 isolates | RX1 | LN881572 | No | Glucose | NA | 3 | 65 | 2027 | ||||
Clostridium perfringens | – | NA | <105 CFU g−1 | (No) | NA | NA | 1 | NA | NA | ||||
Clostridium putrefaciens | Y18177 | 94.2 | 7 isolates | Neu23 | LN881581 | No | Cellobiose | NA | 4, 8a | 286 | 4415 | ||
94.2 | 17 isolates | N1F | KT351631 | NA | NA | NA | 8a, 8b | 281 | 4347 | ||||
Clostridium sporogenes | – | NA | <105 CFU g−1 | (No) | NA | NA | 1 | NA | NA | ||||
Clostridium thermopalmarium | X72869 | 99.5 | 1 isolate | Neu4 | LN881579 | No | Glucose | NA | 4 | 11 | 1180 | ||
Lutispora thermophila | AB186360 | 100.0 | 1 isolate | XV1 | LN881567 | No | Glucose | NA | 3 | 3 | 2000 | ||
Tepidimicrobium ferriphilum | AY656718 | 97.4 | 1 isolate | GRX2 | LN881569 | No | Glucose | NA | 3 | 9 | 6191 | ||
97.4 | 1 isolate | GRM1 | LN881570 | No | Glucose | NA | 3 | 10 | 6204 | ||||
97.5 | 1 isolate | Z2-16 | KT351637 | NA | NA | NA | 8a | 9 | 6123 | ||||
98.7 | 1 isolate | GRC5 | LN881575 | No | Glucose | NA | 3 | 20 | 5958 | ||||
96.2 | 1 isolate | D1 | KT274718 | NA | Glucosee | Ac | 6 | 5 | 6609 | ||||
94.4 | 1 isolate | GRC3 | LN890940 | No | Glucose | NA | 3 | 12 | 7329 | ||||
Tepidimicrobium xylanilyticum | EF522948 | 99.7 | 1 isolate | GRC4 | LN881574 | No | Glucose | NA | 3 | 27 | 4322 | ||
96.7 | 2 isolates | GRC1 | LN881571 | No | Glucose | NA | 3 | 13 | 8131 | ||||
96.3 | 1 isolate | XV2 | LN881586 | No | Glucose | NA | 3 | 22 | 5549 | ||||
Defluviitaleaceae | Defluviitalea saccharophila | HQ020487 | 96.5 | 1 isolate | GRX3 | LN881573 | No | Glucose | NA | 3 | 12 | 2923 | |
Peptococcaceae | Desulfotomaculum australicum | M96665 | 99.5 | 1 isolate | L14 | KT274713 | No | Lactic acid | Ac | 6 | 1 | 3784 | |
Ruminococcaceae | Clostridium straminisolvens | BAVR01000144 | 98.3 | 3 isolates | Neu18 | LN881580 | No | Cellobiose | NA | 4 | 37 | 9436 | |
Clostridium caenicola | AB221372 | 97.6 | 3 isolates | Neu21 | LN881582 | No | Glucose | NA | 3, 4 | 9 | 8238 | ||
Clostridium thermosuccinogenes | Y18180 | 99.8 | 14 isolates | Iso4/1b | LN881583 | No | Glucose | NA | 3, 4 | 7 | 6742 | ||
Thermoanaerobacteraceae | Tepidanaerobacter syntrophicus | AB106353 | 96.6 | 1 isolate | AS34 | KT274714 | NA | Amino acidsf | Ac, Pr | 6 | 23 | 8696 | |
96.2 | 1 isolate | AS46 | KT274715 | NA | Amino acidsf | Ac, Pr | 6 | 43 | 12,295 | ||||
Incertae sedis | Sporanaerobacter acetigenes | AF358114 | 98.7 | 1 isolate | XP2-13-3 | KT351640 | NA | NA | NA | 8b | 0 | 1715 | |
Thermoanaerobacterium thermosaccharolyticum | CP002171 | 99.2 | 24 isolates | Iso6/1b | LN881584 | No | Glucose | NA | 3 | 0 | 1838 | ||
99.9 | 1 isolate | Gluc2 | KT274716 | NA | Glucose | Ac, Bu, La | 7 | 0 | 3000 | ||||
99.9 | 1 isolate | Gluc4 | KT274717 | No | Glucose | Ac, Bu, La | 7 | 0 | 2881 | ||||
Tissierella creatinini | FR749955 | 96.2 | 1 isolate | DG3 | LN881578 | No | Glucose | NA | 3 | 1 | 2229 | ||
Unclassified | Proteiniborus ethanoligenes | EF116488 | 95.9 | 2 isolates | BA2-13 | KT351641 | NA | NA | NA | 8e | 0 | 1809 | |
Thermotogae | Petrotogaceae | Defluviitoga tunisiensis | FR850164 | 99.9 | 7 isolates | L3 | KT274706 | No | Lactic acid | Ac | 6 | 968 | 115,754 |
99.3 | 1 isolate | AS30 | KT274709 | NA | Amino acidsf | Ac | 6 | 201 | 39,551 | ||||
Methanogenic Archaea | |||||||||||||
Methanobacteria | Methanobacteriaceae | Methanothermobacter marburgensis | CP001710 | 99.7 | 1 isolate | Viersen-HAW | KU667127 | (No) | H2/CO2 | NA | 10 | 13 | 32 |
Methanothermobacter wolfeii | AB104858 | 100.0 | 1 isolate | SIV6 | KT368944 | (No) | H2/CO2 | NA | 11 | 39 | 60 | ||
Methanomicrobia | Methano-microbiaceae | Methanoculleus thermophilus | AB065297 | 100.0 | 3 isolates | V2.1 | KT368945 | (No) | H2/CO2 | NA | 11 | 389 | 35,733 |