Enumeration of methanogens with a focus on fluorescence in situ hybridization

Cultureless enumeration of live bacteria in urinary tract infection by single-cell Raman spectroscopy

Urinary tract infections (UTIs) are the most common outpatient infections. Obtaining the concentration of live pathogens in the sample is crucial for the treatment. Still, the enumeration depends on urine culture and plate counting, which requires days of turn-around time (TAT). Single-cell Raman spectra combined with deuterium isotope probing (Raman-DIP) has been proven to identify the metabolic-active bacteria with high accuracy but is not able to reveal the number of live pathogens due to bacteria replication during the Raman-DIP process. In this study, we established a new approach of using sodium acetate to inhibit the replication of the pathogen and applying Raman-DIP to identify the active single cells. By combining microscopic image stitching and recognition, we could further improve the efficiency of the new method. Validation of the new method on nine artificial urine samples indicated that the exact number of live pathogens obtained with Raman-DIP is consistent with plate-counting while shortening the TAT from 18 h to within 3 h, and the potential of applying Raman-DIP for pathogen enumeration in clinics is promising.

The Fluorescence-Activating and Absorption-Shifting Tag (FAST) Enables Live-Cell Fluorescence Imaging of Methanococcus maripaludis

Live-cell fluorescence imaging of methanogenic archaea has been limited due to the strictly anoxic conditions required for growth and issues with autofluorescence associated with electron carriers in central metabolism. Here, we show that the fluorescence-activating and absorption-shifting tag (FAST) complexed with the fluorogenic ligand 4-hydroxy-3-methylbenzylidene-rhodanine (HMBR) overcomes these issues and displays robust fluorescence in Methanococcus maripaludis. We also describe a mechanism to visualize cells under anoxic conditions using a fluorescence microscope. Derivatives of FAST were successfully applied for protein abundance analysis, subcellular localization analysis, and determination of protein-protein interactions. FAST fusions to both formate dehydrogenase (Fdh) and F₄₂₀-reducing hydrogenase (Fru) displayed increased fluorescence in cells grown on formate-containing medium, consistent with previous studies suggesting the increased abundance of these proteins in the absence of H₂. Additionally, FAST fusions to both Fru and the ATPase associated with the archaellum (FlaI) showed a membrane localization in single cells observed using anoxic fluorescence microscopy. Finally, a split reporter translationally fused to the alpha and beta subunits of Fdh reconstituted a functionally fluorescent molecule in vivo via bimolecular fluorescence complementation. Together, these observations demonstrate the utility of FAST as a tool for studying members of the methanogenic archaea. IMPORTANCE Methanogenic archaea are important members of anaerobic microbial communities where they catalyze essential reactions in the degradation of organic matter. Developing additional tools for studying the cell biology of these organisms is essential to understanding them at a mechanistic level. Here, we show that FAST, in combination with the fluorogenic ligand HMBR, can be used to monitor protein dynamics in live cells of M. maripaludis. The application of FAST holds promise for future studies focused on the metabolism and physiology of methanogenic archaea.

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.

Chicken Gut Microbiota: Importance and Detection Technology

Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.

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.

Methylmercury production in soil in the water-level-fluctuating zone of the Three Gorges Reservoir, China: The key role of low-molecular-weight organic acids

As important parts of dissolved organic matter, low-molecular-weight organic acids (LMWOAs) typically play important roles in desorbing Hg(II) from the soil solid-phase, which may directly or indirectly impact methylmercury (MeHg) production. However, the mechanism of these processes remains unclear. To better understand the effects of LMWOAs on Hg methylation in the soil, a field study was conducted to investigate the distribution of LMWOAs and their relationship with soil MeHg in a seasonally inundated area in the Three Gorges Reservoir (TGR), China. Meanwhile, laboratory simulation experiments were performed to determine the potential mechanism of LMWOAs in Hg methylation. The field investigation detected considerable amounts of LMWOAs in soil, among which tartaric acid and oxalic acid were dominant components. Among which, tartaric acid and oxalic acid were dominant components. Also, a seasonally and spatially heterogeneous distribution of LMWOAs in soil was observed. Notably, a significant positive relationship was found between MeHg concentrations and LMWOA pools in soil (r = 0.969, p < .01), implying that LMWOAs could promote soil MeHg production. The simulation experiments confirmed that the MeHg levels in soil were largely elevated with the addition of LMWOAs, which occurred mainly in oxygen-deficient environment and was mediated by biotic factors. The soluble Hg-LMWOA complexes, which were formed by the enhanced desorption of Hg(II) from solid-phase, were mostly responsible for the elevated MeHg production in soil. Moreover, those LMWOAs with more carboxylic groups were believed to enhance the net production of MeHg. The generated MeHg in sediment could diffuse into the overlying water, which thus poses a potential threat to the aquatic food web. Therefore, the enhanced Hg methylation caused by LMWOAs should be given more attention, especially in a seasonally inundated ecosystem, where the MeHg exposure is usually related to fishery activities.

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

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.

Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids

Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.