Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia

Clostridium thailandense sp. nov., a novel CO2-reducing acetogenic bacterium isolated from peatland soil

Some species of the genus Clostridium are efficient acetate producers and have been deemed useful for upgrading industrial biogas. An acetogenic, strictly anaerobic, Gram-stain-positive, subterminal endospore-forming bacterium designated strain PL3T was isolated from peatland soil enrichments with H2 and CO2. Cells of strain PL3T were 0.8–1.0×4.0–10.0 µm in size and rod-shaped. Growth of strain PL3T occurred at pH 6.0–7.5 (optimum, pH 7.0), at 20–40 °C (optimum, 30 °C) and with 0–1.5 % (w/v) NaCl (optimum, 0.5%). Biochemical analyses revealed that strain PL3T metabolized lactose, maltose, raffinose, rhamnose, lactic acid, sorbitol, arabinose and glycerol. Acetic acid was the predominant metabolite under anaerobic respiration with H2/CO2. The major cellular fatty acids were C16 : 0, C16 : 1 cis 9 and C17 : 0 cyc. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminolipid and aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PL3T belongs to the genus Clostridium with the highest sequence similarity to Clostridium aciditolerans DSM 17425T (98.6 %) followed by Clostridium nitrophenolicum (97.8 %). The genomic DNA G+C content of strain PL3T was 31.1 mol%.The genomic in silico DNA–DNA hybridization value between strain PL3T and C. aciditolerans DSM 17425T was 25.1 %, with an average nucleotide identity of 80.2 %. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PL3T was suggested to represent a novel species of the genus Clostridium , for which the name Clostridium thailandense sp. nov. is proposed. The type strain is PL3T (=DSM 111812T=TISTR 2984T).

Integrated process for the production of fermentable sugar and methane from rubber wood

Pretreatment is required for the enhancement of the bioconversion of lignocellulosic biomass. This study aimed to develop an integrated process producing efficient biochemical conversion of rubber wood waste (RW) into co-biofuels, fermentable sugar and methane. The glucan conversion was enhanced to 93.8% with temperature (210 °C) and delignification by organosolv pretreatment (OS). Thereafter, anaerobic digestion of the residue left after enzymatic hydrolysis was conducted which further improved the methane yield (205.5 LCH₄/kg VS) by 33% over hydrothermal pretreatment (154.3 LCH₄/kg VS). Delignification during OS plays a key role in improving the degradability of RW resulting in efficient energy recovery (11.23 MJ/kg pretreated RW) which was clearly higher than an integrated process based on hydrothermal (HT) or HT plus process water. Scaled up to a biorefinery, the integrated process based on OS would economically produce fermentable sugar while other value-added chemicals might be produced from the process water.

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment

Microcystis biomass remineralization after blooming represents a hotspot of nutrient recycling in eutrophic lakes. Because Microcystis blooms are massively deposited on lake sediments, resulting in anoxic conditions, it is important to understand the response and role of benthic microbial communities during the anoxic decomposition of Microcystis in freshwater lakes. In the present study, we employed a microcosm method, combined with high-throughput sequencing, functional prediction, and network analysis, to investigate microbial succession during the short-term (30 days) anaerobic decomposition of Microcystis in a eutrophic sediment. Continuous accumulation of CH4 and CO2 and increasing relative abundance of methanogens were observed during the incubation. The microbial community composition (MCC) significantly changed after addition of Microcystis biomass, with a shift in the community from a stochastic to a functional, deterministic succession. Families, including Clostridiaceae, Rhodocyclaceae, Rikenellaceae, Peptostreptococcaceae, Syntrophomonadaceae, Lachnospiraceae, and Methanosarcinaceae, were predominantly enriched and formed diverse substitution patterns, suggesting a synergistic action of these family members in the decomposition of Microcystis biomass. Importantly, intense species-to-species interactions and weak resistance to disturbance were observed in the microbial community after Microcystis biomass addition. Collectively, these results suggest that the addition of Microcystis induce phylogenetic clustering and structure instability in the sediment microbial community and the synergistic interactions among saprotrophic bacteria play a key role in Microcystis biomass remineralization.

Clostridium bovifaecis sp. nov., a novel acetogenic bacterium isolated from cow manure

A strictly anaerobic, Gram-staining-positive, spore-forming rod-shaped bacterium, and designated BXX^T, was isolated from cow manure. Colonies on DSMZ medium 311c agar plates were cream, circular, opaque and lustrous. Growth occurred at 20-45 °C with a pH range of 5.0-10.0 and at NaCl concentrations of up to 2 % (w/v). The optimum temperature, pH and NaCl concentration for growth were 30 °C, pH 7 and 1 % (w/v), respectively. The major cellular fatty acids were C16 : 0 (26.8 %), C14 : 0 (22.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (16.4 %) and C16 : 1ω9c (10.7 %). The main polar lipids of BXX^T were diphosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Acetate was mainly produced from H2/CO2, H2/CO2/CO (4/3/3, v/v/v), formate, glycerol, 1,2-propanediol, pyruvate, d-fructose and 2-methoxyethanol. BXX^T is most closely related to Clostridium thermobutyricumDSM 4928^T, Clostridiumhomopropionicum DSM 5847^T and Clostridium thermopalmarium DSM 5974^T with 16S rRNA gene sequence similarities of 96.9, 96.6 and 96.5 %, respectively. The DNA G+C content of BXX^T was 33.7 mol%, which was lower than that of C. thermobutyricum DSM 4928^T (37.0 mol%) and C. thermopalmarium DSM 5974^T (35.7 mol%). In addition, DSM 4928^T and DSM 5974^Tare thermophilic members of the genus Clostridium. The absence of C15 : 0 also distinguished BXX^T from Clostridium thermobutyricum. On the basis of phylogenetic, phenotypic and chemotaxonomic evidence, the novel isolate represents a novel species within the genus Clostridium, for which the name Clostridium bovifaecis sp. nov is proposed. The type strain of the type species is BXX^T (=JCM 32382^T=CGMCC 1.5228^T).

Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris

Earthworms are a dominant macrofauna in soil ecosystems and have determinative effects on soil fertility and plant growth. These invertebrates feed on ingested material, and gizzard-linked disruption of ingested fungal and bacterial cells is conceived to provide diverse biopolymers in the anoxic alimentary canals of earthworms. Fermentation in the gut is likely important to the utilization of ingested biopolymer-derived compounds by the earthworm. This study therefore examined the fermentative responses of gut content-associated microbes of the model earthworm Lumbricus terrestris to (i) microbial cell lysate (to simulate gizzard-disrupted cells) and (ii) dominant biopolymers of such biomass, protein, and RNA. The microbial cell lysate augmented the production of H₂, CO₂, and diverse fatty acids (e.g., formate, acetate, propionate, succinate, and butyrate) in anoxic gut content microcosms, indicating that the cell lysate triggered diverse fermentations. Protein and RNA also augmented diverse fermentations in anoxic microcosms of gut contents, each yielding a distinct product profile (e.g., RNA yielded H₂ and succinate, whereas protein did not). The combined product profile of protein and RNA treatments was similar to that of cell lysate treatments, and 16S rRNA-based analyses indicated that many taxa that responded to cell lysate were similar to taxa that responded to protein or RNA. In particular, protein stimulated Peptostreptococcaceae, Clostridiaceae, and Fusobacteriaceae, whereas RNA stimulated Aeromonadaceae. These findings demonstrate the capacity of gut-associated obligate anaerobes and facultative aerobes to catalyze biopolymer-driven fermentations and highlight the potential importance of protein and RNA as substrates linked to the overall turnover dynamics of organic carbon in the alimentary canal of the earthworm.

IMPORTANCE The subsurface lifestyle of earthworms makes them an unnoticed component of the terrestrial biosphere. However, the propensity of these invertebrates to consume their home, i.e., soil and litter, has long-term impacts on soil fertility, plant growth, and the cycling of elements. The alimentary canals of earthworms can contain up to 500 ml anoxic gut content per square meter of soil, and ingested soil may contain 10⁹ or more microbial cells per gram dry weight, considerations that illustrate that enormous numbers of soil microbes are subject to anoxia during gut passage. Feeding introduces diverse sources of biopolymers to the gut, and the gut fermentation of biopolymers could be important to the transformation of matter by the earthworm and its capacity to utilize fermentation-derived fatty acids. Thus, this study examined the capacity of microbes in earthworm gut contents to ferment protein and RNA, dominant biopolymers of cells that become disrupted during gut passage.