Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis

Maus, Irena; Kim, Yong‐Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

doi:10.4014/jmb.1605.05083

Cited by 28 publications

(28 citation statements)

References 44 publications

(67 reference statements)

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“…On the contrary, Clostridia were higher in T1 hydrogen producing samples (see Figure 1 and Table S3) as reported in literature (Davila Vazquez et al, 2009;Cheng et al, 2011;Maus et al, 2017). Among the Clostridia, Family XIII, the C. Incertae Sedis was the most represented (6.5% in our trial), in particular in T1-Y, the quantity was twice as much as T1-N; in T2 trial we observed the opposite trend.…”

Section: Microbial Community Analysis and Compositionsupporting

confidence: 79%

“…Clostridium Senso Stricto 1 (1.7%), among Clostridiaceae_1, reported by Maus et al (2017) as the most represented, in our trial was the second more abundant genus and we observed higher quantity in T1-N than T1-Y, and lower quantity in T2-N than T2-Y.…”

Section: Microbial Community Analysis and Compositionsupporting

confidence: 47%

“…In AD of cattle manure and sludge, some authors (Rivière et al, 2009;St-Pierre and Wright, 2014;Campanaro et al, 2016) reported, as part of the core group, also Cloroflexi, which, on the contrary, we found at 0.03% only. Maus et al (2017) also reported Firmicutes, Bacteroidetes as the main bacteria phyla in mesophyllic conditions plants with cow manure as inoculum. The Firmicutes are important because they are implicated in several metabolic processes including carbohydrates degradation, fatty acids utilization, WoodLjungdahl pathway (WLP) (homoacetogenesis) or syntrophic acetate oxidation (SAO) as reported by Campanaro et al (2016).…”

Section: Microbial Community Analysis and Compositionmentioning

confidence: 81%

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Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

Chiariotti¹,

Crisà²

2018

Front. Sustain. Food Syst.

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Biogas production from agricultural and industrial wastes delivers two benefits: on one side, the treatment of organic residues prevents the environmental and economic impact of their disposal; on the other side, methane and/or hydrogen are generated. The aims of this study were both to produce bio-hydrogen from buffalo wastes and to investigate the relationship between biogas production and bacterial and archaeal community composition. Anaerobic codigestion of livestock by-products (buffalo sludge and low protein cheese whey-scotta), with buffalo rumen and buffalo sludge as inoculum, was performed. The microbial community was analyzed using next-generation sequencing of 16S rRNA gene amplicons. Codigestion showed to be positive because of both sludge buffering capability and highly degradable carbohydrates content in scotta. Rumen inoculum proved more efficient compared to sludge during fermentation. In fact, cumulated production was higher (120.8 vs. 65.4 ml H 2 g VS −1 respectively) and the average percentage of hydrogen in biogas was 48.1 (v/v) with maximum peak at 64.6. Moreover, rumen bacterial profile showed higher genera richness. Taxonomic classification showed that among the bacteria, Firmicutes, 23.3% of whom Clostridia; Bacteroidetes, and in particular Bacteroidia; Proteobacteria and Tenericutes, accounted for 88.2% of total sequences. Concerning the Clostridia Family XIII, the C. Incertae Sedis was the most represented (6.6%), and its quantity was twice as much in rumen inoculated hydrogen-producing samples than those non-producing. In the archaeal, community predominated the phylum Euryarcheota, with Methanobrevibacter the most represented, which was higher when hydrogen was produced with rumen inoculum. Studies on buffalo rumen as inoculum for hydrogen production are limited and this paper gives a first overview of microbial community composition by NGS in producing and non-producing samples.

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Section: Microbial Community Analysis and Compositionsupporting

confidence: 79%

Section: Microbial Community Analysis and Compositionsupporting

confidence: 47%

Section: Microbial Community Analysis and Compositionmentioning

confidence: 81%

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Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

Chiariotti¹,

Crisà²

2018

Front. Sustain. Food Syst.

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“…In order to determine the taxonomic complexity of the hologenome, high-throughput 16S rRNA gene amplicon sequencing was performed as described by Maus et al [46]. Primers Pro341F (5΄-CCTACGGGGNBGCASCAG-3΄) and Pro805R (5΄-GACTACNVGGGTATCTAATCC-3΄) [47] were used to amplify the hypervariable regions V3 and V4 of the 16S rRNA gene in Bacteria and Archaea as well as in single-celled algae and other eukaryotes.…”

Section: Methodsmentioning

confidence: 99%

“…Adapter and primer trimming were performed through an in-house pipeline [48]. For amplicon processing, a pipeline including FLASH v.1.2.11 [49], USEARCH v.8.1 [50], UPARSE v.10.0.240 [51], and the Ribosomal Database Project (RDP) classifier v.2.9 [52] was used as described recently [46, 53, 54]. All sequences that were not merged by FLASH using default settings were filtered out.…”

Section: Methodsmentioning

confidence: 99%

Binning enables efficient host genome reconstruction in cnidarian holobionts

et al. 2018

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BackgroundMany cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.ResultsOur results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.ConclusionsBinning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.

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Performance and microbial analysis during long‐term anaerobic digestion of olive mill wastewater in a packed‐bed biofilm reactor

Enaime

Nettmann

Berzio

et al. 2019

J of Chemical Tech & Biotech

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BACKGROUND: The treatment of olive mill wastewater (OMWW) in a packed bed biofilm reactor (PBBR) and the identification of different microorganisms involved in the digestion process is an attractive field for research. RESULTS: A PBBR treating OMWW under different organic loading rates (OLRs) (0.94-9.36 gCOD/(L d)), showed high stability during an extensive time (723 days) without any sign of acidification. High volumetric biogas and methane (CH 4 ) productions, 4.1 and 2.4 L N /(L reactor d), respectively were registered at the highest OLR. Meanwhile, high chemical oxygen demand (COD) removal (62.5-79.7%) was obtained throughout the experiment. Phenolic compounds removal was much higher during the first steps of the experiment (75.9-84.2%), and decreased as the OLR increased to about 38%. High homogeneity of biofilm thickness and Bacteria and extracellular polymeric substance distribution were demonstrated by confocal laser scanning microscopy. Results of real-time quantitative polymerase chain reaction (PCR) and 16S rRNA amplicon analyses showed that Bacteria, mainly consisting of Firmicutes, Proteobacteria, Bacteroidetes andChloroflexi phylum, was about eight times more abundant than Archaea in the reactor liquid phase, while Bacteria to Archaea ratio was almost one in the biofilm. This points to a major degradation of organic substances in the liquid, while methanogenesis occurred mainly within the biofilm. In the liquid, acetoclastic methanogens were more abundant than hydrogenotrophic ones, while both groups showed likely very similar contributions in the biofilm.CONCLUSION: Promising results have been presented throughout this work providing information about the long-term operation of PBBR-granular activated carbon treating OMWW and analyzing, in an efficient manner, the structure and the composition of the microbial community involved in OMWW digestion.

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Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis

Cited by 28 publications

References 44 publications

Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

Binning enables efficient host genome reconstruction in cnidarian holobionts

Performance and microbial analysis during long‐term anaerobic digestion of olive mill wastewater in a packed‐bed biofilm reactor

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