Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future

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The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown.

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Anaerobic microbes are used in a variety of industrial applications.

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In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments.

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Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.

The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.

Monitoring of seven industrial anaerobic digesters supplied with biochar

BACKGROUND

Recent research articles indicate that direct interspecies electron transfer (DIET) is an alternative metabolic route for methanogenic archaea that improves microbial methane productivity. It has been shown that multiple conductive materials such as biochar can be supplemented to anaerobic digesters to increase the rate of DIET. However, the industrial applicability, as well as the impact of such supplements on taxonomic profiles, has not been sufficiently assessed to date.

RESULTS

Seven industrial biogas plants were upgraded with a shock charge of 1.8 kg biochar per ton of reactor content and then 1.8 kg per ton were added to the substrate for one year. A joint analysis for all seven systems showed a decreasing trend for the concentration of acetic acid (p < 0.0001), propionic acid (p < 0.0001) and butyric acid (p = 0.0022), which was significant in all cases. Quantification of the cofactor F420 using fluorescence microscopy showed a reduction in methanogenic archaea by up to a power of ten. Methanogenic archaea could grow within the biochar, even if the number of cells was 4 times less than in the surrounding sludge. 16S-rRNA gene amplicon sequencing showed a higher microbial diversity in the biochar particles than in the sludge, as well as an accumulation of secondary fermenters and halotolerant bacteria. Taxonomic profiles indicate microbial electroactivity, and show the frequent occurrence of Methanoculleus, which has not been described in this context before.

CONCLUSIONS

Our results shed light on the interplay between biochar particles and microbial communities in anaerobic digesters. Both the microbial diversity and the absolute frequency of the microorganisms involved were significantly changed between sludge samples and biochar particles. This is particularly important against the background of microbial process monitoring. In addition, it could be shown that biochar is suitable for reducing the content of inhibitory, volatile acids on an industrial scale.

A lab in the field: applications of real-time, in situ metagenomic sequencing

High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.

Assembly methods for nanopore-based metagenomic sequencing: a comparative study

Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility

Anaerobic digestion is a technology known for its potential in terms of methane production. During the digestion process, multiple metabolites of high value are synthesized. However, recent works have demonstrated the high robustness and resilience of the involved microbiomes; these attributes make it difficult to manipulate them in such a way that a specific metabolite is predominantly produced. Therefore, an exact understanding of the manipulability of anaerobic microbiomes may open up a treasure box for bio-based industries. In the present work, the effect of nalidixic acid, γ-aminobutyric acid (GABA), and sodium phosphate on the microbiome of digested sewage sludge from a water treatment plant fed with glucose was investigated. Despite of the induced process perturbations, high stability was observed at the phylum level. However, strong variations were observed at the genus level, especially for the genera Trichococcus, Candidatus Caldatribacterium, and Phascolarctobacterium. Ecological interactions were analyzed based on the Lotka–Volterra model for Trichococcus, Rikenellaceae DMER64, Sedimentibacter, Candidatus Cloacimonas, Smithella, Cloacimonadaceae W5 and Longilinea. These genera dynamically shifted among positive, negative or no correlation, depending on the applied stressor, which indicates a surprisingly dynamic behavior. Globally, the presented work suggests a massive resilience and stability of the methanogenic communities coupled with a surprising flexibility of the particular microbial key players involved in the process.

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput sequencing technologies. An additional innovation introduced by these technologies was the need of developing new strategies to manage and investigate the massive amount of sequencing data generated. This situation stimulated the rapid expansion of the field of bioinformatics with the release of new tools to be applied to the downstream analysis and interpretation of sequencing data mainly generated using Illumina technology. In recent years, a third generation of sequencing technologies has been developed and have been applied in parallel and complementarily to the former sequencing strategies. In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists. Nanopore technology offers a low price, portability and fast sequencing throughput. This powerful technology has been recently tested for 16S rRNA analyses showing promising results. However, compared with previous technologies, there is a scarcity of bioinformatic tools and protocols designed specifically for the analysis of Nanopore 16S sequences. Due its notable characteristics, researchers have recently started performing assessments regarding the suitability MinION on 16S rRNA sequencing studies, and have obtained remarkable results. Here we present a review of the state-of-the-art of MinION technology applied to microbiome studies, the current possible application and main challenges for its use on 16S rRNA metabarcoding.

Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production

Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out photoautotrophic metabolism when grown under anaerobic conditions. The results suggested that this bacterium, which is able to fix carbon dioxide, could be considered for use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH₄:CO₂ ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study characterising the phototrophic biofilm associated with illuminated bioreactors.