Home About us Contact
|
Home About us Contact | ||
|
|
||
Archaeal Population (archaeal + population)
Selected AbstractsDenitrifying bacteria anaerobically oxidize methane in the absence of ArchaeaENVIRONMENTAL MICROBIOLOGY, Issue 11 2008Katharina F. Ettwig Summary Recently, a microbial consortium was shown to couple the anaerobic oxidation of methane to denitrification, predominantly in the form of nitrite reduction to dinitrogen gas. This consortium was dominated by bacteria of an as yet uncharacterized division and archaea of the order Methanosarcinales. The present manuscript reports on the upscaling of the enrichment culture, and addresses the role of the archaea in methane oxidation. The key gene of methanotrophic and methanogenic archaea, mcrA, was sequenced. The associated cofactor F430 was shown to have a mass of 905 Da, the same as for methanogens and different from the heavier form (951 Da) found in methanotrophic archaea. After prolonged enrichment (> 1 year), no inhibition of anaerobic methane oxidation was observed in the presence of 20 mM bromoethane sulfonate, a specific inhibitor of MCR. Optimization of the cultivation conditions led to higher rates of methane oxidation and to the decline of the archaeal population, as shown by fluorescence in situ hybridization and quantitative MALDI-TOF analysis of F430. Mass balancing showed that methane oxidation was still coupled to nitrite reduction in the total absence of oxygen. Together, our results show that bacteria can couple the anaerobic oxidation of methane to denitrification without the involvement of Archaea. [source] Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniquesFEMS MICROBIOLOGY ECOLOGY, Issue 2 2005Christoph Erkel Abstract We report first insights into a representative genome of rice cluster I (RC-I), a major group of as-yet uncultured methanogens. The starting point of our study was the methanogenic consortium MRE50 that had been stably maintained for 3 years by consecutive transfers to fresh medium and anaerobic incubation at 50 °C. Process-oriented measurements provided evidence for hydrogenotrophic CO2 -reducing methanogenesis. Assessment of the diversity of consortium MRE50 suggested members of the families Thermoanaerobacteriaceae and Clostridiaceae to constitute the major bacterial component, while the archaeal population was represented entirely by RC-I. The RC-I population amounted to more than 50% of total cells, as concluded from fluorescence in situ hybridization using specific probes for either Bacteria or Archaea. The high enrichment status of RC-I prompted construction of a large insert fosmid library from consortium MRE50. Comparative sequence analysis of internal transcribed spacer (ITS) regions revealed that three different RC-I rrn operon variants were present in the fosmid library. Three, approximately 40-kb genomic fragments, each representative for one of the three different rrn operon variants, were recovered and sequenced. Computational analysis of the sequence data resulted in two major findings: (i) consortium MRE50 most likely harbours only a single RC-I genotype, which is characterized by multiple rrn operon copies; (ii) seven genes were identified to possess a strong phylogenetic signal (eIF2a, dnaG, priA, pcrA, gatD, gatE, and a gene encoding a putative RNA-binding protein). Trees exemplarily computed for the deduced amino acid sequences of eIF2a, dnaG, and priA corroborated a specific phylogenetic association of RC-I with the Methanosarcinales. [source] Effects of high- and low-fiber diets on fecal fermentation and fecal microbial populations of captive chimpanzeesAMERICAN JOURNAL OF PRIMATOLOGY, Issue 7 2009Svetlana Ki, idayová Abstract We examined fiber fermentation capacity of captive chimpanzee fecal microflora from animals (n=2) eating low-fiber diets (LFDs; 14% neutral detergent fiber (NDF) and 5% of cellulose) and high-fiber diets (HFDs; 26% NDF and 15% of cellulose), using barley grain, meadow hay, wheat straw, and amorphous cellulose as substrates for in vitro gas production of feces. We also examined the effects of LFD or HFD on populations of eubacteria and archaea in chimpanzee feces. Fecal inoculum fermentation from the LFD animals resulted in a higher in vitro dry matter digestibility (IVDMD) and gas production than from the HFD animals. However, there was an interaction between different inocula and substrates on IVDMD, gas and methane production, and hydrogen recovery (P<0.001). On the other hand, HFD inoculum increased the production of total short-chain fatty acids (SCFAs), acetate, and propionate with all tested substrates. The effect of the interaction between the inoculum and substrate on total SCFAs was not observed. Changes in fermentation activities were associated with changes in bacterial populations. DGGE of bacterial DNA revealed shift in population of both archaeal and eubacterial communities. However, a much more complex eubacterial population structure represented by many bands was observed compared with the less variable archaeal population in both diets. Some archaeal bands were related to the uncultured archaea from gastrointestinal tracts of homeothermic animals. Genomic DNA in the dominant eubacterial band in the HFD inoculum was confirmed to be closely related to DNA from Eubacterium biforme. Interestingly, the predominant band in the LFD inoculum represented DNA of probably new or yet-to-be-sequenced species belonging to mycoplasms. Collectively, our results indicated that fecal microbial populations of the captive chimpanzees are not capable of extensive fiber fermentation; however, there was a positive effect of fiber content on SCFA production. Am. J. Primatol. 71:548,557, 2009. © 2009 Wiley-Liss, Inc. [source] Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 1 2001Lisa Y. Stein Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal-rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO2 using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese-oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal-oxidizing genera, Leptothrix of the ,-Proteobacteria and Hyphomicrobium of the ,-Proteobacteria, and a Fe(III)-reducing group related to the Magnetospirillum genus of the ,-Proteobacteria. Groups related to the metal-reducing ,-Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments. [source] Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewaterFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Changsoo Lee Abstract Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas -like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts. [source] The influence of urea feeding on the bacterial and archaeal community in the forestomach of collared peccary (Artiodactyla, Tayassuidae)JOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2009E.G. Oliveira Abstract Aims:, This study was carried out to test whether bacterial and archaeal populations, and products of fermentation in each compartment of collared peccary stomach, vary significantly with urea feeding. Bacteria and archaeal population variation among the four stomach compartments were also compared. Methods and Results:, Archaeal and bacterial communities in the forestomach of four individuals per treatment , peccaries fed diets with and without urea , were analysed at molecular level using PCR followed by denaturing gradient gel electrophoresis. Volatile fatty acids profiles in the three different compartments of the forestomach were also compared. The bacterial community composition varied considerably among each compartment and with urea provision, but no variation was observed between archaeal populations. Differences in bacterial communities between treatments , with and without urea , were greater than amongst stomach compartments. The acetate: propionate proportion decreased with urea provision in diet. Some differences in bacterial but not archaeal community composition were observed in each compartment of the collared peccary forestomach. Conclusions:, There are some differences in bacterial but not archaeal populations in each compartment of collared peccary stomach. Use of urea in the diet of peccary can substantially modify the profile of volatile fatty acids released in its forestomach, but does not influence the archaeal community composition. Urea has an important effect on bacterial population DGGE profile present in the peccary's forestomach. Significance and Impact of the Study:, These results demonstrate the ability of the collared peccary to use urea as source of nonprotein nitrogen, and confirm a hypothesis that the collared peccary has a digestive physiology more similar to ruminant than nonruminant animals. [source] | ||||||||||