Quantification of methanogens by fluorescence in situ hybridization with oligonucleotide probe

Effects of phase separation on dewaterability promotion and heavy metal removal of sewage sludge during bioleaching

Bioleaching is of increasing interest because of its high efficiency in improving sludge dewaterability and removing heavy metals from sewage sludge. However, in traditional single-phase bioleaching, a high-efficiency level cannot be maintained continuously, wherein the microbial synergistic effect is disrupted at a low pH environment. Therefore, in this study, a series of multi-compartment-baffled flow trials were performed to assess the effects of phase separation on sludge bioleaching by comparing a two-phase trial with two single-phase trials. Energy substrate and part of the bioleached sludge were introduced separately into two compartments to form two phases, namely selection phase and bioleaching phase. The results show that phase separation apparently shortened the start-up duration of sludge bioleaching from 7 days in a single-phase bioleaching to 4 days in two-phase bioleaching. The dewaterability of bioleached sludge was also enhanced by phase separation with relative decreases of 25.0-33.3% for specific resistance to filtration and 14.2% for capillary suction time, which was attributed to lower pH values, zeta potential closer to zero, and less dissolved organic matter in bioleached sludge after two-phase bioleaching. Phase separation generally increased the removal ratios of heavy metals during sludge bioleaching by -0.79 to 2.60%, 11.06 to 15.04%, 4.45 to 11.03%, 17.98 to 23.46%, 7.20 to 9.28%, -9.22 to -2.46%, and -6.72 to -10.68% for As, Cd, Cr, Cu, Ni, Pb, and Zn, respectively. Phase separation also enriched the Acidithiobacillus spp. and reduced the inactivation of acid-tolerant fungi, which can be conducive to better synergistic effect, and therefore maintain long-term stable state in the bioleaching phase of the two-phase bioleaching process.

FISH analysis of microbial communities in a full-scale technology for biogas production

The anaerobic digestion is a biological process that consists of four stages. At the final step of the biodegradation of the organics the most sensitive to the ambient factors group of microorganisms - the methanogens, produces biogas with main component methane. Common problems of these technologies are low biogas yield, production of biogas with low quality or situations in which the plant gets out of exploitation. These problems are related to the lack of biological indicators of the process used in the practice and lack of understanding of the structure and functioning of the methanogenic consortium. Different fluorescent techniques have the potential to fulfill this gap and to contribute to the deep understanding of the structure of the microbial communities. In this study it was applied fluorescence in situ hybridization analysis for identifying and localization of microorganisms by the Archaea domain in digesters of wastewater treatment plant "Kubratovo". High negative correlation between the quantity of Archaea and the biogas and methane production has been registered. This method has the potential to be used as a tool for analyzing the structure of the microbial communities in the digesters and thus to allow the adaptation of the consortium and the optimization of the whole process.

Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem

Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.

A novel and efficient assay for identification and quantification of Acidithiobacillus ferrooxidans in bioleaching samples

Acidithiobacillus ferrooxidans is a Gram-negative, acidophilic, and chemolithotrophic bacterium that is active in bioleaching. The leaching efficacy is directly influenced by the biomass changes of this specie in bioleaching microbial community. In order to perform a simple and sensitive assay on A. ferrooxidans from mixed strains in this process, a novel assay was developed based on sandwich hybridization assay with the aid of S1 nuclease treatment and fluorescent labeling. In the work, a designed DNA probe complementary to the conservative region of its 16S rRNA was synthesized, which showed high accuracy for distinguishing homologous species with the exclusion of even-only two base pairs difference. The specificity of this assay was verified in different systems with mixed strains, and the quantitative result was proved by comparison of microscopic cell counting. The detection sensitivity was about 8 × 10(2) cells/ml and the inter-assay coefficient of variation of three independent assays was from 3.8 to 7.7 %, respectively. In addition, the cycle of assay was about 3-4 h when the cost estimated was less than $0.5 per sample. This assay method might be applied for identifying and monitoring any kind of bacterial strain from a mixed microbial flora in bioleaching or other areas.

Enumeration of methanogens with a focus on fluorescence in situ hybridization

Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

Rumen methanogens: a review

The Methanogens are a diverse group of organisms found in anaerobic environments such as anaerobic sludge digester, wet wood of trees, sewage, rumen, black mud, black sea sediments, etc which utilize carbon dioxide and hydrogen and produce methane. They are nutritionally fastidious anaerobes with the redox potential below -300 mV and usually grow at pH range of 6.0-8.0 [1]. Substrates utilized for growth and methane production include hydrogen, formate, methanol, methylamine, acetate, etc. They metabolize only restricted range of substrates and are poorly characterized with respect to other metabolic, biochemical and molecular properties.

Biogas production: current state and perspectives

Anaerobic digestion of energy crops, residues, and wastes is of increasing interest in order to reduce the greenhouse gas emissions and to facilitate a sustainable development of energy supply. Production of biogas provides a versatile carrier of renewable energy, as methane can be used for replacement of fossil fuels in both heat and power generation and as a vehicle fuel. For biogas production, various process types are applied which can be classified in wet and dry fermentation systems. Most often applied are wet digester systems using vertical stirred tank digester with different stirrer types dependent on the origin of the feedstock. Biogas is mainly utilized in engine-based combined heat and power plants, whereas microgas turbines and fuel cells are expensive alternatives which need further development work for reducing the costs and increasing their reliability. Gas upgrading and utilization as renewable vehicle fuel or injection into the natural gas grid is of increasing interest because the gas can be used in a more efficient way. The digestate from anaerobic fermentation is a valuable fertilizer due to the increased availability of nitrogen and the better short-term fertilization effect. Anaerobic treatment minimizes the survival of pathogens which is important for using the digested residue as fertilizer. This paper reviews the current state and perspectives of biogas production, including the biochemical parameters and feedstocks which influence the efficiency and reliability of the microbial conversion and gas yield.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.