A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion.

Microbial communities are key drivers of ecosystem processes, but their behavior in disturbed environments is difficult to measure. How microbial community composition and function respond disturbances is a common challenge in biomedical, environmental, agricultural, and bioenergy research. A novel way to solve this problem is to use a systems-level perspective and describe microbial communities as networks. Based on a mesophilic anaerobic digestion system of swine manure as a tool, we propose a simple framework to investigate changes in microbial communities via compositions, metabolic pathways, genomic properties and interspecies relationships in response to a long-term temperature disturbance. After temperature disturbance, microbial communities tend towards a competitive interaction network with higher GC content and larger genome size. Based on microbial interaction networks, communities responded to the disturbance by showing a transition from acetotrophic (Methanotrichaceae and Methanosarcinaceae) to methylotrophic methanogens (Methanomassiliicoccaceae and Methanobacteriaceae) and a fluctuation in rare biosphere taxa. To conclude, this study may be important for exploring the dynamic relationships between disturbance and microbial communities as a whole, as well as for providing researchers with a better understanding of how changes in microbial communities relate to ecological processes.

Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience.

While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000mg/L with free ammonia (FA) 2000mg/L compared to 16,000mg/L (FA1500mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gVSin in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.

Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field.

A novel methane-producing archaeon, designated strain HASU(T), was isolated from a lotus field. Cells were Gram-negative, non-motile, irregular cocci, 2-3 mum in diameter, and occurred singly. Growth was observed at 15-40 degrees C (optimum, 37 degrees C) and pH 6.5-7.5 (optimum, pH 7.0). The G+C content of the genomic DNA was 60.9 mol%. Strain HASU(T) utilized ethanol, 1-propanol, 1-butanol, hydrogen and formate for growth and methane production. It converted ethanol to methane and acetate. Based on comparative 16S rRNA gene sequence analysis, strain HASU(T) was shown to be affiliated with the genus Methanofollis. It was related most closely to the type strain of Methanofollis liminatans (96.1 % 16S rRNA gene sequence similarity). Based on phylogenetic analysis and phenotypic characteristics, strain HASU(T) is considered to represent a novel species of the genus Methanofollis, for which the name Methanofollis ethanolicus sp. nov. is proposed. The type strain is HASU(T) (=NBRC 104120(T)=JCM 15103(T)=DSM 21041(T)).

Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China.

Three strictly anaerobic, thermophilic methanogens (ZC-2T, ZC-3 and ZC-6) were isolated from Shengli oil field, China. The 16S rRNA gene sequences of the three strains were nearly identical, possessing > 99.8% sequence similarity. They also possessed high sequence similarity, 97.4%, to Methanoculleus palmolei strain INSLUZ(T) (97.4% and 97.5%, respectively), indicating that they represented a novel species within the genus Methanoculleus. Cells of strain ZC-2T were nonmotile cocci, 0.8-1.7 microm in diameter, and always occurred singly or in pairs. The three strains used H2/CO2 or sodium formate as substrates for methanogenesis but not sodium acetate, trimethylamine, monomethylamine, ethanol, dimethyl sulfide, isopropanol, isobutanol, butan-2-ol or H2/CO. Optimum growth of strain ZC-2T occurred in the presence of 0.2 M NaCl, pH 7.5-7.8 and temperature 50-55 degrees C with a specific growth rate of 0.084 h(-1). The mol% G+C content of the genomic DNA was 55.2 mol%. Based on these phenotypic and phylogenetic characteristics, strains ZC-2T, ZC-3 and ZC-6 are proposed to represent a novel species in the genus Methanoculleus and named Methanoculleus receptaculi sp. nov. The type strain is ZC-2T (CGMCC 1.5087T=DSM 18860T).

Methanogenium frittonii Harris et al. 1996 is a later synonym of Methanoculleus thermophilus (Rivard and Smith 1982) Maestrojuan et al. 1990.

The 16S rRNA gene sequence of [Methanogenium] frittonii DSM 2832(T) was determined and was found to be 99.9 % similar to the sequence of Methanoculleus thermophilus DSM 2373(T). DNA-DNA hybridizations between both strains revealed 86 % DNA-DNA binding, indicating that both strains belong to the same species. The determination of the DNA G + C content of both type strains, DSM 2832(T) and DSM 2373(T), revealed values of 56.1 and 59.1 mol%, respectively. Based on the phenotypic and genotypic characteristics, it is proposed to unite the species [Methanogenium] frittonii and Methanoculleus thermophilus under the name Methanoculleus thermophilus, which is the earlier synonym and hence has priority. Emended descriptions of the species Methanoculleus thermophilus and the genus Methanogenium are also given.

Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species.

A strictly anaerobic, irregularly coccoid, methanogenic archaeon, strain MG62T (= JCM 10825T = DSM 13459T), was isolated from paddy field soil in Chikugo, Fukuoka, Japan. The cells stained gram-negative, were 1.0-2.0 microm in diameter, were lysed by SDS and hypotonic solutions and were flagellated. Motility was not observed. The strain was able to use H2/CO2, 2-propanol/CO2, formate, 2-butanol/CO2 and cyclopentanol/CO2 as substrates for methanogenesis, but did not utilize acetate, ethanol, methanol or methylamines. The optimum temperature and pH were 25-30 degrees C and 6.7-7.2. Analysis of lipid component parts (core lipids, phospholipid polar head groups and glycolipid sugar moieties) showed the characteristic pattern of members of the family Methanomicrobiaceae except for the absence of glucose as a glycolipid sugar moiety. The G+C content of the DNA was 62.2 mol %. Sequence analysis of the 16S rDNA revealed that the strain belonged to the genus Methanoculleus. The strain had DNA-DNA hybridization values of less than 50% with type strains of Methanoculleus species. On the basis of phenotypic, genotypic and phylogenetic characteristics, the name Methanoculleus chikugoensis sp. nov. is proposed for strain MG62T (= JCM 10825T = DSM 13459T). The DNA hybridization study also revealed the close relationships of three species, Methanoculleus olentangyi, Methanoculleus bourgensis and Methanoculleus oldenburgensis, among Methanoculleus species.

Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site.

A mesophilic hydrogenotrophic methanogen, strain MHT-1T, was isolated from the leachate of a sea-based site for solid waste disposal (the port of Osaka, Japan). Strain MHT-1T was found to be an irregular coccus and was able to use H2/CO2 and formate as energy sources. Acetate was required for growth. The optimum temperature and pH for growth were 35 degrees C and 6.5-7.5, respectively. Strain MHT-1T was resistant to high concentrations of several heavy metals such as CdCl2 and CuSO4. The G+C content of the DNA was 51.9 mol%. Analysis of the 16S rRNA gene revealed that the isolate was a member of the genus Methanocalculus but distinct from its nearest neighbour, Methanocalculus halotolerans, there being a sequence similarity of 98.9%. DNA-DNA hybridization analysis revealed 51% relatedness with the DNA of M. halotolerans strain SEBR 4845T. The optimum NaCl concentration was 1.0%, whereas the optimum in M. halotolerans was 5.0%. A new species, Methanocalculus pumilus, is proposed for strain MHT-1T. The type strain is MHT-1T (= DSM 12632T = JCM 10627T).