Three novel, facultatively anaerobic bacteria of the family
(phylum
) were isolated from mesophilic laboratory-scale biogas reactors. The strains were Gram-negative rods. Optimal growth occurred ...between 35 and 45 °C and at pH 7.1-7.8. The main fermentation products were acetic and propionic acids. The predominant fatty acid in all strains was anteiso-C
, and the only respiratory quinone detected was menaquinone MK-8. 16S rRNA gene sequence comparison indicated that strains M3/6
and ING2-E5B
were most closely related to the type strain of
, with sequence similarities of 97.3 and 94.5 %. Strain ING2-E5A
showed the closest affiliation to the type strain of
, with 97 % sequence identity. DNA-DNA hybridization of strain M3/6
and ING2-E5A
with the most closely related type strains showed 43.3-45.6 and 23.8-25.7 % relatedness, respectively, which supports the conclusion that both isolates represent novel species. Phylogenetic analysis and comparison of cellular fatty acid patterns indicated that strain ING2-E5B
cannot be classified as a member of any previously described genus. Therefore, because of the physiological, genotypic and chemotaxonomic differences, it is proposed to designate novel species within the genera
and
,
sp. nov. (type strain M3/6
= DSM 28694
= CECT 8610
= LMG 28299
) and
sp. nov. (type strain ING2-E5A
= DSM 28695
= CECT 8611
), and a novel species of a new genus,
gen. nov., sp. nov. (type strain of
is ING2-E5B
= DSM 28696
= CECT 8609
= LMG 28429
). In addition, an emended description of the genus
is provided.
Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. ...We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydrogenase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. This unique gene arrangement would allow a metabolic flexibility beyond known sulfur-oxidizing pathways. We confirmed the presence of dsrA by geneFISH in closely related RCB from an enrichment culture. Our results show that RCB are an integral part of the microbial community in marine sediments, where they possibly oxidize inorganic and organic sulfur compounds in oxic and suboxic sediment layers.
Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in ...order to optimize the performance of the process and the biogas output. Previously,
Lachnospiraceae
species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative
Lachnospiraceae
strain,
Anaeropeptidivorans aminofermentans
M3/9
T
was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9
T
possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9
T
was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9
T
and closely related
Anaerotignum
type strains, genome sequence comparisons were performed. M3/9
T
harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9
T
in other environments, large-scale fragment recruitments with the M3/9
T
genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.
A new
bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome ...sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family
outside recently described genera.
•P. saccharofermentans str. M3/6T harbors several carbohydrate active enzymes.•The strain encodes 64 polysaccharide utilization loci (PULs).•Several PULs are associated with genes encoding ...carbohydrate active enzymes.•P. saccharofermentans M3/6T harbors two CRISPR-cas systems.
Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.
A new
isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the ...bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism.
A novel strictly anaerobic bacterium, designated strain BA2-13
, was isolated from a thermophilic industrial-scale biogas plant. Cells were rod-shaped and Gram-stain-positive. Growth occurred at ...temperatures of 25 to 50 °C and between pH 6.3 and 9.5. Strain BA2-13
produced indole. Cell growth was stimulated by yeast extract, peptone, meat extract, a mixture of 20 amino acids, glucose, pyruvate and ribose. When grown on peptone and yeast extract, the main fermentation products were acetic acid, H2 and CO2. The predominant cellular fatty acids were iso-C15 : 0 and iso-C14 : 0 3-OH. Major polar lipids were diphosphatidylglycerol, glycolipids, phospholipids and phosphatidylgycerol. Phylogenetic analysis based on 16S rRNA gene nucleotide sequence analysis placed strain BA2-13
within the order Clostridiales showing closest affiliation with Proteiniborusethanoligenes with 95.9 % sequence identity. Physiological, genotypic and chemotaxonomic differences of strain BA2-13
from P. ethanoligenes support the description of a new species within the genus Proteiniborus for which we suggest the name Proteiniborusindolifex sp. nov. (type strain BA2-13
=DSM 103060
=LMG 29818
).
One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation ...of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.
The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis.
Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.
A Gram-negative, aerobic, pink-pigmented, and bacteriochlorophyll a -containing bacterial strain, designated B14 T , was isolated from the macroalga Fucus spiralis sampled from the southern North ...Sea, Germany. Based on 16S rRNA gene sequences, species of the genera Roseobacter and Sulfitobacter were most closely related to strain B14 T with sequence identities ranging from 98.15 % ( Roseobacter denitrificans Och 114 T ) to 99.11 % ( Roseobacter litoralis Och 149 T ), whereas Sulfitobacter mediterraneus CH-B427 T exhibited 98.52 % sequence identity. Digital DNA–DNA hybridization and average nucleotide identity values between the genome of the novel strain and that of closely related Roseobacter and Sulfitobacter type strains were <20 % and <77 %, respectively. The novel strain contained ubiquinone-10 as the only respiratory quinone and C 18 : 1 ω7 c , C 16 : 0 , C 18 : 0 , C 12 : 1 ω7 c , C 18 : 2 ω7,13 c , and C 10 : 0 3-OH as the major cellular fatty acids. The predominant polar lipids of strain B14 T were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genome of strain B14 T comprises a chromosome with a size of 4.5 Mbp, one chromid, and four plasmids. The genome contains the complete gene cluster for aerobic anoxygenic photosynthesis required for a photoheterotrophic lifestyle. The results of this study indicate that strain B14 T (=DSM 116946 T =LMG 33352 T ) represents a novel species of the genus Roseobacter for which the name Roseobacter fucihabitans sp. nov. is proposed.
Phylogenetic studies were performed on a group of novel Gram-stain-positive, anaerobic, non-sporulating rod-shaped bacteria isolated from a thermophilic biogas plant. The novel organisms were able to ...degrade crystalline cellulose. 16S rRNA gene sequence comparison indicated that the isolates SD1DT, SD1G, SD1I and RK1P share 100 % sequence identity, and are most closely related to Herbinix hemicellulosilytica T3/55T with which they share a 16S rRNA gene sequence similarity of 96.4 %. As a representative of the whole group of isolates, strain SD1DT was further characterized. Strain SD1DT was catalase-negative, indole-negative, and produced acetate, ethanol, butyric acid and hydrogen as major end-products during fermentative cellobiose utilization. Cells are rod-shaped, growing optimally at 40-65 °C and pH 6.5-8.5. The major cellular fatty acids (>10 %) were C19 : 0cyc 9,10 dimethyl acetal, C16 : 0 and C14 : 0. The DNA G+C content was 35.1 mol%. Due to the genetic and phenotypic differences to the most closely affiliated species, the isolates represent a novel species of the genus Herbinix within the family Lachnospiraceae, for which the name Herbinix luporum sp. nov. is proposed. The type strain is SD1DT(=DSM 100831T=CECT 8959T).
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