Table 3.
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 |
Et ethanol; Ac acetic acid; Pr propionic acid; Ip isopropanol; Fo formic acid; Bu butyric acid; La lactic acid
aFor details, refer “Methods” section
bIn total, 18,817 16S rRNA gene sequences
cIn total, 532,381 16S rRNA sequences
dNot analyzed
eFormation of acetic acid in medium DSMZ 1328 [104] with 0.5 % (w/v) glucose
fMinimal medium (modified DSMZ 287 [36]) containing alanine, threonine, serine, glutamic acid, cysteine and methionine