Use of PCR-DGGE Based Molecular Methods to Analyse Microbial Community Diversity and Stability during the Thermophilic Stages of an ATAD Wastewater Sludge Treatment Process as an Aid to Performance Monitoring

Impact of whole grain highland hull-less barley on the denaturing gradient gel electrophoresis profiles of gut microbial communities in rats fed high-fat diets

Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague-Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of Lactobacillus gasseri, Uncultured Prevotella sp., and Clostridium sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species.

IMPORTANCE

While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.

Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant

High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically evaluated the fitness of different frequently used reference databases (i.e. SILVA 138 SSU, GTDB bact120_r207, Greengenes 13_5 and MiDAS 4.8) and primers of 16S rRNA gene in microbiota profiling of anaerobic digestion and activated sludge collected from a full-scale swine wastewater treatment plant (WWTP). The comparative results showed that MiDAS 4.8 achieved the highest levels of taxonomic diversity and species-level assignment rate. For whichever sample groups, microbiota richness captured by different primers decreased in the following order: V4 > V4-V5 > V3-V4 > V6-V8/V1-V3. Using primer-bias-free metagenomic data results as the judging standard, V4 region also best characterized microbiota structure and well represented typical functional guilds (e.g. methanogens, ammonium oxidizers and denitrifiers), while V6-V8 regions largely overestimated the archaeal methanogens (mainly Methanosarcina) by over 30 times. Therefore, MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure of the examined swine WWTP.

Removal of Hydrogen Sulfide from Swine-Waste Biogas on a Pilot Scale Using Immobilized Paracoccus versutus CM1

Hydrogen sulfide (H2S) is a toxic and corrosive component that commonly occurs in biogas. In this study, H2S removal from swine-waste biogas using sulfur-oxidizing Paracoccus versutus CM1 immobilized in porous glass (PG) and polyurethane foam (PUF) biofilters was investigated. Bacterial compositions in the biofilters were also determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The biofilters were first tested on a laboratory scale under three space velocities (SV): 20, 30, and 40 h−1. Within 24 h, at an SV of 20 h−1, PG and PUF biofilters immobilized with P. versutus CM1 removed 99.5% and 99.7% of H2S, respectively, corresponding to the elimination capacities (EC) of 83.5 and 86.2 gm−3 h−1. On a pilot scale, with the horizontal PG-P. versutus CM1 biofilter operated at an SV of 30 h−1, a removal efficiency of 99.7% and a maximum EC of 113.7 gm−3 h−1 were achieved. No reduction in methane content in the outlet biogas was observed under these conditions. The PCR-DGGE analysis revealed that Paracoccus, Acidithiobacillus, and Thiomonas were the predominant bacterial genera in the biofilters, which might play important roles in H2S removal. This PG−P. versutus CM1 biofiltration system is highly efficient for H2S removal from swine-waste biogas.

Why the importance of geo-origin tracing of edible bird nests is arising?

Edible bird's nest (EBN) swiftlet existed naturally 48,000 years ago in caves as their natural dwellings. Nowadays, edible bird's nest has become a very important industry due to its high nutritional, medicinal and economic value. Additionally, edible bird's nest has a long quality guarantee period. Obviously, the nutritional components and medicinal functions vary depending on geographical origins. Recently, the global demand for edible bird's nest has markedly increased, accompanied by the increasing attention of all key players of the global food trade system, i.e., producers, consumers, traders and the authorities to obtain safe and high-quality edible bird's nest. Hence, this target can be accomplished via the enforcement of an efficient and universal geo-tracing technique. Current methods of the geo-tracking of edible bird's nest, i.e., automation, physical and analytical techniques have several limitations and all of them fail to discriminate different quality grades of edible bird's nest. Meanwhile, in many studies and applications, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) has proven to be a "cutting edge" technique for greatly enhance food traceability from field to fork through its ability in distinguishing the food products in terms of their quality and safety. This article provides an overview of (1) edible bird's nest as a multiuse strategic food product, (2) quality issues associated with edible bird's nest including implications that the site of acquisition of the edible bird's nest has food safety implications, (3) current regulations and geo-tracking approaches to ensure the safety and quality of edible bird's nest with the special focus on polymerase chain reaction-denaturing gradient gel electrophoresis technique as a vigorous and universal geo-tracing tool to be suggested for edible bird's nest geo-traceability.

The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling

Gastrointestinal (GIT) diseases have risen globally in recent years, and early detection of the host’s gut microbiota, typically through fecal material, has become a crucial component for rapid diagnosis of such diseases. Human fecal material is a complex substance composed of undigested macromolecules and particles, and the processing of such matter is a challenge due to the unstable nature of its products and the complexity of the matrix. The identification of these products can be used as an indication for present and future diseases; however, many researchers focus on one variable or marker looking for specific biomarkers of disease. Therefore, the combination of genomics, transcriptomics, proteomics and metabonomics can give a detailed and complete insight into the gut environment. The proper sample collection, sample preparation and accurate analytical methods play a crucial role in generating precise microbial data and hypotheses in gut microbiome research, as well as multivariate data analysis in determining the gut microbiome functionality in regard to diseases. This review summarizes fecal sample protocols involved in profiling coeliac disease.

Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing

Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.

Computational analysis of successional changes in the microbial population and community diversity of the immobilized marine nitrifying bacterial consortium in a nitrifying packed bed bioreactor

Nitrifying bioreactor (NBR) connected to the recirculating aquaculture system (RAS), has a greater emphasis on the biological treatment of wastewater. Nitrifying bacterial consortium (NBC) formed bio-film on the substratum activating the NBR, and it was observed with high nitrification potential in shrimp maturation systems. Scanning Electron Microscopy (SEM) revealed the integrity of the biofilm substantiated with biomineralization. The fate of the matured bio-film population on subsequent operation under RAS, and the aggregated population at different points of RAS, including the rearing water were determined using fingerprints of Denaturing Gradient Gel Electrophoresis (DGGE). Altogether, 38 OTUs of biofilm sample and 35 OTUs of water samples represented the bacterial communities; the shared and unique OTUs indicated the diversity of the population at different time intervals in the operation of the NBR. The mathematical (range-weighted richness) and statistical (diversity indices) interpretation unveiled the OTUs based high bacterial diversity in the biofilm supporting the compositional changes and determined the distance between the community cluster. Ordination analyses indicated the population shift and stability of the activated bio-film till the matured biofilm community got established in the RAS. The DGGE with mathematical and statistical analysis revealed microbial diversity (high Shannon index, species richness and evenness), abundance (relative intensity), consecutive change in the population composition (OTUs, Rr index), and the dynamics (Δt) in the system during the operation.

Autothermal Thermophilic Aerobic Digestion (ATAD) for Heat, Gas, and Production of a Class A Biosolids with Fertilizer Potential

Autothermal thermophilic aerobic digestion (ATAD) is a microbial fermentation process characterized as a tertiary treatment of waste material carried out in jacketed reactors. The process can be carried out on a variety of waste sludge ranging from human, animal, food, or pharmaceutical waste where the addition of air initiates aerobic digestion of the secondary treated sludge material. Digestion of the sludge substrates generates heat, which is retained within the reactor resulting in elevation of the reactor temperature to 70-75 °C. During the process, deamination of proteinaceous materials also occurs resulting in liberation of ammonia and elevation of pH to typically pH 8.4. These conditions result in a unique microbial consortium, which undergoes considerable dynamic change during the heat-up and holding phases. The change in pH and substrate as digestion occurs also contributes to this dynamic change. Because the large reactors are not optimized for aeration, and because low oxygen solubility at elevated temperatures occurs, there are considerable numbers of anaerobes recovered which also contributes to the overall digestion. As the reactors are operated in a semi-continuous mode, the reactors are rarely washed, resulting in considerable biofilm formation. Equally, because of the fibrous nature of the sludge, fiber adhering organisms are frequently found which play a major role in the overall digestion process. Here, we review molecular tools needed to examine the ATAD sludge consortia, what has been determined through phylogenetic analysis of the consortia and the nature of the dynamics occurring within this unique fermentation environment.

A Unique Autothermal Thermophilic Aerobic Digestion Process Showing a Dynamic Transition of Physicochemical and Bacterial Characteristics from the Mesophilic to the Thermophilic Phase

A unique autothermal thermophilic aerobic digestion (ATAD) process has been used to convert human excreta to liquid fertilizer in Japan. This study investigated the changes in physicochemical and bacterial community characteristics during the full-scale ATAD process operated for approximately 3 weeks in 2 different years. After initiating simultaneous aeration and mixing using an air-inducing circulator (aerator), the temperature autothermally increased rapidly in the first 1 to 2 days with exhaustive oxygen consumption, leading to a drastic decrease and gradual increase in oxidation-reduction potential in the first 2 days, reached >50°C in the middle 4 to 6 days, and remained steady in the final phase. Volatile fatty acids were rapidly consumed and diminished in the first 2 days, whereas the ammonia nitrogen concentration was relatively stable during the process, despite a gradual pH increase to 9.3. Principal-coordinate analysis of 16S rRNA gene amplicons using next-generation sequencing divided the bacterial community structures into distinct clusters corresponding to three phases, and they were similar in the final phase in both years despite different transitions in the middle phase. The predominant phyla (closest species, dominancy) in the initial, middle, and final phases were Proteobacteria (Arcobacter trophiarum, 19 to 43%; Acinetobacter towneri, 6.3 to 30%), Bacteroidetes (Moheibacter sediminis, 43 to 54%), and Firmicutes (Thermaerobacter composti, 11 to 28%; Heliorestis baculata, 2.1 to 16%), respectively. Two predominant operational taxonomic units (OTUs) in the final phase showed very low similarities to the closest species, indicating that the process is unique compared with previously published ones. This unique process with three distinctive phases would be caused by the aerator with complete aeration.IMPORTANCE Although the autothermal thermophilic aerobic digestion (ATAD) process has several advantages, such as a high degradation capacity, a short treatment period, and inactivation of pathogens, one of the factors limiting its broad application is the high electric power consumption for aerators with a full-scale bioreactor. We elucidated the dynamics of the bacterial community structures, as well as the physicochemical characteristics, in the ATAD process with a full-scale bioreactor from human excreta for 3 weeks. Our results indicated that this unique process can be divided into three distinguishable phases by an aerator with complete aeration and showed a possibility of shortening the digestion period to approximately 10 days. This research not only helps to identify which bacteria play significant roles and how the process can be improved and controlled but also demonstrates an efficient ATAD process with less electric power consumption for worldwide application.

Heavy metal bioleaching and sludge stabilization in a single-stage reactor using indigenous acidophilic heterotrophs

Simultaneous sludge digestion and metal leaching (SSDML) have been reported at mesophilic temperature. It is generally perceived that while sludge stabilization is effected by heterotrophs at neutral pH, metal bioleaching is done by acidophilic autotrophs. However, little information is available on the microbial communities involved in the process. This study carried out SSDML in a single-stage reactor using sludge indigenous microorganisms and looked at the bacterial communities responsible for the process. Volatile suspended solids were reduced by more than 40%. The concentration of zinc, copper, chromium, cadmium and nickel decreased by more than 45% in the dry sludge. Acidophilic species of Alicyclobacillus genus were the dominant heterotrophs. A few heterotrophic bacteria were detected which can oxidize iron (Alicyclobacillus ferrooxydans, Alicyclobacillus ferripilum and Ferrimicrobium acidiphilum). Acidithiobacillus ferrooxidans (autotroph) was responsible for the oxidation of both iron and sulfur which lead to a change in the pH from neutral to acidic. The presence of acidophilic heterotrophs, which can oxidize either iron or sulfur, enhanced the efficiency of SSDML process with respect to sludge stabilization and metal leaching. This study shows that it is possible to carry out the SSDML in a single-stage reactor with indigenous microorganisms.

Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure

In situ biofilm sampling is a key step for the study of natural biofilms and using methodologies that reflect natural diversity is necessary to guarantee representative sampling. Here, we focalise on the impact of the type of substrata on which biofilms grow on bacterial and fungal communities’ structure. The indirect molecular approach, Denaturing Gel Gradient Electrophoresis (DGGE) of a gene fragment coding for either 16S rRNA or 28S rRNA, for bacteria or fungi respectively, was used to evaluate the variability of microbial community structures among different biofilm substrata: natural (pebbles, live plants, wood and sediment), or artificial (glass, Plexiglas^® and sterile wood), in a small river (the Loiret, France). Multivariate statistics, band richness and diversity indexes (Shannon and Simpson) were used to highlight variations in community structure between substrata. Results showed variations of bacterial and fungal diversity between different substrata according to substratum properties/origin (natural or artificial, organic or inorganic) but there was no optimal substratum for sampling, and artificial substrata were not significantly less applicable than natural substrata. Pooling 4 different substrata types allowed a higher bacterial and fungal biodiversity recovery. Point contact sampling may thus gain in robustness by increasing the number of substrata considered. Fungal species richness was similar to the bacterial one on most substrata which suggested they should be more frequently considered in riverine biofilm studies.

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about "methanogenic archaea composition" and "abundance" in the contrasting ecosystems like "landfill" and "marshland" may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations

As it is currently often not know how anaerobic bioreactors, e.g. for biogas production, react if the substrate is contaminated by toxic compounds like antibiotics. This study evaluated how anaerobic sequencing batch reactors were affected by amendments of different antibiotics and stepwise increasing concentrations. The compositions of microbial community were determined in the seed sludge using 16S rRNA gene clone libraries and PCR-DGGE analyses were used for the detection of microbial community changes upon antibiotics additions. According to PCR-DGGE results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors. Assessment of DGGE data is also useful for suggesting the potential to control ultimate microbial community structure, especially derived from Gram-negative bacteria, through bioaugmentation to successful for antibiotic biodegradation.

Extraction of polyhydroxyalkanoates from mixed microbial cultures: Impact on polymer quality and recovery

Polyhydroxyalkanoates (PHAs) can be extracted from mixed microbial cultures (MMCs) by means of dimethyl carbonate (DMC) or combination of DMC and sodium hypochlorite (NaClO). The protocol based on DMC, a green solvent never used before for the extraction of PHAs from MMC, allows an overall polymer recovery of 63%; also the purity and the molecular weight of the recovered polymers are good (98% and 1.2 MDa, respectively). The use of NaClO pretreatment before DMC extraction increases the overall PHA recovery (82%) but lowers the mean molecular weight to 0.6-0.2 MDa. A double extraction with DMC results to be the method of choice for the recovery of high quality PHAs from attractive but challenging MMCs.