scholarly journals New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

2020 ◽  
Author(s):  
Stefano Campanaro ◽  
Laura Treu ◽  
Luis M Rodriguez-Rojas ◽  
Adam Kovalovszki ◽  
Ryan M Ziels ◽  
...  
Keyword(s):  
Methane Production ◽  
Growth Dynamics ◽  
Metabolic Reconstruction ◽  
Waste Biomass ◽  
Anaerobic Digesters ◽  
Extensive Evaluation ◽  
Archaeal Species ◽  
Wide Range ◽  
Biogas Reactors ◽  
High Flexibility

Abstract BackgroundMicroorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.ResultsHere, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. ConclusionsThe outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

scholarly journals New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

2019 ◽  
Author(s):  
Stefano Campanaro ◽  
Laura Treu ◽  
Luis M Rodriguez-Rojas ◽  
Adam Kovalovszki ◽  
Ryan M Ziels ◽  
...  
Keyword(s):  
Organic Matter ◽  
Methane Production ◽  
Metabolic Reconstruction ◽  
Waste Biomass ◽  
Anaerobic Digesters ◽  
Extensive Evaluation ◽  
Archaeal Species ◽  
Wide Range ◽  
Biogas Reactors ◽  
High Flexibility

Abstract Background Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. Results Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter. Conclusions The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem. Keywords Anaerobic digestion, Metagenome-Assembled Genomes, Biogas, Microbial community structure, Functional reconstruction

scholarly journals The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

2019 ◽  
Author(s):  
Stefano Campanaro ◽  
Laura Treu ◽  
Luis M Rodriguez-R ◽  
Adam Kovalovszki ◽  
Ryan M Ziels ◽  
...  
Keyword(s):  
Organic Matter ◽  
Anaerobic Digestion ◽  
Methane Production ◽  
Metabolic Reconstruction ◽  
Waste Biomass ◽  
Dynamic Composition ◽  
Extensive Evaluation ◽  
Wide Range ◽  
Biogas Reactors ◽  
High Flexibility

AbstractBackgroundMicroorganisms in biogas reactors are essential for degradation of organic matter and methane production through anaerobic digestion process. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.ResultsHere, 134 publicly available datasets derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half were ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter.ConclusionsThe outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic composition and adaptability to the environmental conditions, including temperatures and a wide range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of anaerobic digestion microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

scholarly journals A modular microfluidic system based on a multilayered configuration to generate large-scale perfusable microvascular networks

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Tao Yue ◽  
Da Zhao ◽  
Duc T. T. Phan ◽  
Xiaolin Wang ◽  
Joshua Jonghyun Park ◽  
...  
Keyword(s):  
Large Scale ◽  
Circulatory System ◽  
Vertical Direction ◽  
Microfluidic System ◽  
Vital Role ◽  
Microvascular Networks ◽  
Biological Studies ◽  
Wide Range ◽  
High Flexibility

AbstractThe vascular network of the circulatory system plays a vital role in maintaining homeostasis in the human body. In this paper, a novel modular microfluidic system with a vertical two-layered configuration is developed to generate large-scale perfused microvascular networks in vitro. The two-layer polydimethylsiloxane (PDMS) configuration allows the tissue chambers and medium channels not only to be designed and fabricated independently but also to be aligned and bonded accordingly. This method can produce a modular microfluidic system that has high flexibility and scalability to design an integrated platform with multiple perfused vascularized tissues with high densities. The medium channel was designed with a rhombic shape and fabricated to be semiclosed to form a capillary burst valve in the vertical direction, serving as the interface between the medium channels and tissue chambers. Angiogenesis and anastomosis at the vertical interface were successfully achieved by using different combinations of tissue chambers and medium channels. Various large-scale microvascular networks were generated and quantified in terms of vessel length and density. Minimal leakage of the perfused 70-kDa FITC-dextran confirmed the lumenization of the microvascular networks and the formation of tight vertical interconnections between the microvascular networks and medium channels in different structural layers. This platform enables the culturing of interconnected, large-scale perfused vascularized tissue networks with high density and scalability for a wide range of multiorgan-on-a-chip applications, including basic biological studies and drug screening.

Efficient Directed Densest Subgraph Discovery

2021 ◽  
Vol 50 (1) ◽  
pp. 33-40
Author(s):  
Chenhao Ma ◽  
Yixiang Fang ◽  
Reynold Cheng ◽  
Laks V.S. Lakshmanan ◽  
Wenjie Zhang ◽  
...  
Keyword(s):  
Approximation Algorithms ◽  
State Of The Art ◽  
Exact Algorithms ◽  
Large Datasets ◽  
Dense Subgraph ◽  
Extensive Evaluation ◽  
Wide Range ◽  
Edge Graph ◽  
Community Mining ◽  
Densest Subgraph

Given a directed graph G, the directed densest subgraph (DDS) problem refers to the finding of a subgraph from G, whose density is the highest among all the subgraphs of G. The DDS problem is fundamental to a wide range of applications, such as fraud detection, community mining, and graph compression. However, existing DDS solutions suffer from efficiency and scalability problems: on a threethousand- edge graph, it takes three days for one of the best exact algorithms to complete. In this paper, we develop an efficient and scalable DDS solution. We introduce the notion of [x, y]-core, which is a dense subgraph for G, and show that the densest subgraph can be accurately located through the [x, y]-core with theoretical guarantees. Based on the [x, y]-core, we develop both exact and approximation algorithms. We have performed an extensive evaluation of our approaches on eight real large datasets. The results show that our proposed solutions are up to six orders of magnitude faster than the state-of-the-art.

Design, implementation, and evaluation of an XG-PON module for the ns-3 network simulator

SIMULATION ◽  
2017 ◽  
Vol 93 (5) ◽  
pp. 409-426 ◽  
Author(s):  
Jerome A Arokkiam ◽  
Pedro Alvarez ◽  
Xiuchao Wu ◽  
Kenneth N Brown ◽  
Cormac J Sreenan ◽  
...  
Keyword(s):  
Optical Network ◽  
Future Internet ◽  
Access Networks ◽  
Passive Optical Network ◽  
Network Simulator ◽  
Optical Access Networks ◽  
Research Topics ◽  
Extensive Evaluation ◽  
Wide Range ◽  
And Performance

10-gigabit-capable Passive Optical Network (XG-PON), one of the latest standards of optical access networks, is regarded as one of the key technologies for future Internet access networks. This paper presents the design and evaluation of our XG-PON module for the ns-3 network simulator. This module is designed and implemented with the aim to provide a standards-compliant, configurable, and extensible module that can simulate XG-PON with reasonable speed and support a wide range of research topics. These include analyzing and improving the performance of XG-PON, studying the interactions between XG-PON and the upper-layer protocols, and investigating its integration with various wireless networks. In this paper, we discuss its design principles, describe the implementation details, and present an extensive evaluation on both functionality and performance.

scholarly journals Microbiota of anaerobic digesters in a full-scale wastewater treatment plant

2017 ◽  
Vol 43 (3) ◽  
pp. 53-60 ◽  
Author(s):  
Piotr Świątczak ◽  
Agnieszka Cydzik-Kwiatkowska ◽  
Paulina Rusanowska
Keyword(s):  
Microbial Community ◽  
Sewage Sludge ◽  
Methane Production ◽  
Treatment Plant ◽  
Full Scale ◽  
Successful Implementation ◽  
Anaerobic Digesters ◽  
Syntrophic Bacteria ◽  
The Stability ◽  
Microbial Groups

AbstractAnaerobic digestion is an important technology for the bio-based economy. The stability of the process is crucial for its successful implementation and depends on the structure and functional stability of the microbial community. In this study, the total microbial community was analyzed during mesophilic fermentation of sewage sludge in full-scale digesters.The digesters operated at 34–35°C, and a mixture of primary and excess sludge at a ratio of 2:1 was added to the digesters at 550 m3/d, for a sludge load of 0.054 m3/(m3·d). The amount and composition of biogas were determined. The microbial structure of the biomass from the digesters was investigated with use of next-generation sequencing.The percentage of methanogens in the biomass reached 21%, resulting in high quality biogas (over 61% methane content). The abundance of syntrophic bacteria was 4.47%, and stable methane production occurred at a Methanomicrobia to Synergistia ratio of 4.6:1.0. The two most numerous genera of methanogens (about 11% total) wereMethanosaetaandMethanolinea, indicating that, at the low substrate loading in the digester, the acetoclastic and hydrogenotrophic paths of methane production were equally important. The high abundance of the orderBacteroidetes, including the classCytophagia(11.6% of all sequences), indicated the high potential of the biomass for efficient degradation of lignocellulitic substances, and for degradation of protein and amino acids to acetate and ammonia.This study sheds light on the ecology of microbial groups that are involved in mesophilic fermentation in mature, stably-performing microbiota in full-scale reactors fed with sewage sludge under low substrate loading.

scholarly journals The aerosol-climate model ECHAM5-HAM

2005 ◽  
Vol 5 (4) ◽  
pp. 1125-1156 ◽  
Author(s):  
P. Stier ◽  
J. Feichter ◽  
S. Kinne ◽  
S. Kloster ◽  
E. Vignati ◽  
...  
Keyword(s):  
Size Distribution ◽  
Climate Model ◽  
Normal Modes ◽  
Anthropogenic Activity ◽  
Climate Modelling ◽  
Extensive Evaluation ◽  
Wide Range ◽  
Log Normal ◽  
Year 2000

Abstract. The aerosol-climate modelling system ECHAM5-HAM is introduced. It is based on a flexible microphysical approach and, as the number of externally imposed parameters is minimised, allows the application in a wide range of climate regimes. ECHAM5-HAM predicts the evolution of an ensemble of microphysically interacting internally- and externally-mixed aerosol populations as well as their size-distribution and composition. The size-distribution is represented by a superposition of log-normal modes. In the current setup, the major global aerosol compounds sulfate (SU), black carbon (BC), particulate organic matter (POM), sea salt (SS), and mineral dust (DU) are included. The simulated global annual mean aerosol burdens (lifetimes) for the year 2000 are for SU: 0.80 Tg(S) (3.9 days), for BC: 0.11 Tg (5.4 days), for POM: 0.99 Tg (5.4 days), for SS: 10.5 Tg (0.8 days), and for DU: 8.28 Tg (4.6 days). An extensive evaluation with in-situ and remote sensing measurements underscores that the model results are generally in good agreement with observations of the global aerosol system. The simulated global annual mean aerosol optical depth (AOD) is with 0.14 in excellent agreement with an estimate derived from AERONET measurements (0.14) and a composite derived from MODIS-MISR satellite retrievals (0.16). Regionally, the deviations are not negligible. However, the main patterns of AOD attributable to anthropogenic activity are reproduced.

scholarly journals Two-Side Laser Processing Method for Producing High Aspect Ratio Microholes

2017 ◽  
Vol 5 (4) ◽  
Author(s):  
Vahid Nasrollahi ◽  
Pavel Penchev ◽  
Stefan Dimov ◽  
Lars Korner ◽  
Richard Leach ◽  
...  
Keyword(s):  
Cross Sections ◽  
Laser Processing ◽  
Industrial Applications ◽  
Laser Drilling ◽  
Special Focus ◽  
Geometrical Accuracy ◽  
Aspect Ratios ◽  
Wide Range ◽  
High Flexibility ◽  
Accuracy And Repeatability

Laser microprocessing is a very attractive option for a growing number of industrial applications due to its intrinsic characteristics, such as high flexibility and process control and also capabilities for noncontact processing of a wide range of materials. However, there are some constrains that limit the applications of this technology, i.e., taper angles on sidewalls, edge quality, geometrical accuracy, and achievable aspect ratios of produced structures. To address these process limitations, a new method for two-side laser processing is proposed in this research. The method is described with a special focus on key enabling technologies for achieving high accuracy and repeatability in two-side laser drilling. The pilot implementation of the proposed processing configuration and technologies is discussed together with an in situ, on-machine inspection procedure to verify the achievable positional and geometrical accuracy. It is demonstrated that alignment accuracy better than 10 μm is achievable using this pilot two-side laser processing platform. In addition, the morphology of holes with circular and square cross sections produced with one-side laser drilling and the proposed method was compared in regard to achievable aspect ratios and holes' dimensional and geometrical accuracy and thus to make conclusions about its capabilities.

Effects of sulfate concentration and sludge retention time on the interaction between methane production and sulfate reduction for butyrate

1994 ◽  
Vol 30 (8) ◽  
pp. 45-54 ◽  
Author(s):  
O. Mizuno ◽  
Y. Y. Li ◽  
T. Noike
Keyword(s):  
Sulfate Reduction ◽  
Retention Time ◽  
Methane Production ◽  
Electron Flow ◽  
Degradation Pathway ◽  
Sulfate Concentration ◽  
High Concentration ◽  
Total Electron ◽  
Sludge Retention Time ◽  
Wide Range

The effects of sulfate concentration and COD/S ratio on the anaerobic degradation of butyrate were investigated by using 2.0 L anaerobic chemostat-type reactor at 35°C. The study was conducted over a wide range of the COD/S ratio (1.5 to 148) by varying COD concentrations (2500–10000 mg/L) and sulfate concentrations (68–1667 mg-S/L) in the substrate. The sludge retention time at each COD/S ratio was changed from 5 to 20 days. The interaction between methane producing bacteria (MPB) and sulfate-reducing bacteria (SRB) was evidently influenced by COD/S ratio in the substrate. When COD/S ratio was 6.0 or more, methane production was the predominate reaction and over 80% of the total electron flow was used by MPB. At the COD/S ratio of 1.5, SRB utilzed over 50% of the total electron flow. A large amount of sulfate reduction resulted in not only the decrease of methane production, but also the rapid increase of the bacterial growth. The degradation pathway of butyrate and the composition of bacterial populations in the reactor were also dominated by COD/S ratio. In sulfate depleted condition, butyrate was degraded to methane via acetate and hydrogen by MPB. On the other hand, butyrate was firstly degraded into sulfide and acetate in sulfate rich conditions by SRB, and the produced acetate was then degraded by acetate consuming MPB and SRB. The methanogenesis from acetate was inhibited by the high concentration of sulfide.

Nanoparticles in Methane Production from Anaerobic Digesters

2020 ◽  
pp. 202-232
Author(s):  
Efraín Reyes Cruz ◽  
Lilia Ernestina Montañez Hernández ◽  
Inty Omar Hernández De Lira ◽  
Nagamani Balagurusamy
Keyword(s):  
Methane Production ◽  
Anaerobic Digesters
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