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 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 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.

Methanogenesis in sediments from deep lakes at different temperatures (2–70°C)

1997 ◽  
Vol 36 (6-7) ◽  
pp. 57-64 ◽  
Author(s):  
Alla N. Nozhevnikova ◽  
C. Holliger ◽  
A. Ammann ◽  
A. J. B. Zehnder
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Methane Production ◽  
Low Temperatures ◽  
Main Question ◽  
Deep Lakes ◽  
Temperature Range ◽  
Wide Range ◽  
Thermophilic Conditions ◽  
Different Temperatures

Methanogenic degradation of organic matter occurs in a wide temperature range from psychrophilic to extreme thermophilic conditions. Mesophilic and thermophilic methanogenesis is relatively well investigated, but little is known about low temperature methanogenesis and psychrophilic methanogenic communities. The aim of the present work was to study methanogenesis in a wide range of temperatures with samples from sediments of deep lakes. These sediments may be considered deposits of different types of microorganisms, which are constantly exposed to low temperatures. The main question was how psychrophilic methanogenic microbial communities compare to mesophilic and thermophilic ones. Methanogenesis in a temperature range of 2–70°C was investigated using sediment samples from Baldegger lake (65 m) and Soppen lake (25 m), Switzerland. Methane production from organic matter of sediments occurred at all temperatures tested. An exponential dependence of methane production rate was found between 2 and 30°C. Methanogenesis occurred even at 70°C. At the same time stable methane production from organic matter of sediments was observed at temperatures below 10°C. Methanogenic microbial communities were enriched at different temperatures. The communities enriched at 4–8°C had the highest activity at low temperatures indicating that a specific psychrophilic community exists. Addition of substrates such as cellulose, volatile fatty acids (butyrate, propionate, acetate), methanol and H2/CO2 stimulated methane production at all temperatures. H2/CO2 as well as methanol were directly converted to methane under thermophilic conditions. At low temperatures these substrates were converted to methane by a two-step process. First acetate was formed, followed by methane production from acetate. When acetate concentrations were high, acetoclastic methanogenesis was inhibited at low temperatures. This reaction appears to be one of the “bottle neck” in psychrophilic methanogenesis.

Coagulation/flocculation/ultrafiltration for natural organic matter removal in drinking water production

2004 ◽  
Vol 4 (5-6) ◽  
pp. 215-222 ◽  
Author(s):  
A.R. Costa ◽  
M.N. de Pinho
Keyword(s):  
Drinking Water ◽  
Organic Matter ◽  
Natural Organic Matter ◽  
Membrane Fouling ◽  
Membrane Filtration ◽  
Membrane Surface ◽  
Water Production ◽  
Cellulose Acetate Membranes ◽  
Wide Range ◽  
Drinking Water Production

Membrane fouling by natural organic matter (NOM), namely by humic substances (HS), is a major problem in water treatment for drinking water production using membrane processes. Membrane fouling is dependent on membrane morphology like pore size and on water characteristics namely NOM nature. This work addresses the evaluation of the efficiency of ultrafiltration (UF) and Coagulation/Flocculation/UF performance in terms of permeation fluxes and HS removal, of the water from Tagus River (Valada). The operation of coagulation with chitosan was evaluated as a pretreatment for minimization of membrane fouling. UF experiments were carried out in flat cells of 13.2×10−4 m2 of membrane surface area and at transmembrane pressures from 1 to 4 bar. Five cellulose acetate membranes were laboratory made to cover a wide range of molecular weight cut-off (MWCO): 2,300, 11,000, 28,000, 60,000 and 75,000 Da. Severe fouling is observed for the membranes with the highest cut-off. In the permeation experiments of raw water, coagulation prior to membrane filtration led to a significant improvement of the permeation performance of the membranes with the highest MWCO due to the particles and colloidal matter removal.

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.

A generally applicable pedotransfer function that estimates field capacity and permanent wilting point from soil texture and bulk density

2008 ◽  
Vol 88 (5) ◽  
pp. 761-774 ◽  
Author(s):  
J. A. P. Pollacco
Keyword(s):  
Organic Matter ◽  
Soil Moisture ◽  
Bulk Density ◽  
Soil Texture ◽  
The United States ◽  
Pedotransfer Functions ◽  
Pedotransfer Function ◽  
Data Set ◽  
Wide Range ◽  
Fitting Parameters

Hydrological models require the determination of fitting parameters that are tedious and time consuming to acquire. A rapid alternative method of estimating the fitting parameters is to use pedotransfer functions. This paper proposes a reliable method to estimate soil moisture at -33 and -1500 kPa from soil texture and bulk density. This method reduces the saturated moisture content by multiplying it with two non-linear functions depending on sand and clay contents. The novel pedotransfer function has no restrictions on the range of the texture predictors and gives reasonable predictions for soils with bulk density that varies from 0.25 to 2.16 g cm-3. These pedotransfer functions require only five parameters for each pressure head. It is generally accepted that the introduction of organic matter as a predictor improves the outcomes; however it was found by using a porosity based pedotransfer model, using organic matter as a predictor only modestly improves the accuracy. The model was developed employing 18 559 samples from the IGBP-DIS soil data set for pedotransfer function development (Data and Information System of the International Geosphere Biosphere Programme) database that embodies all major soils across the United States of America. The function is reliable and performs well for a wide range of soils occurring in very dry to very wet climates. Climatical grouping of the IGBP-DIS soils was proposed (aquic, tropical, cryic, aridic), but the results show that only tropical soils require specific grouping. Among many other different non-climatical soil groups tested, only humic and vitric soils were found to require specific grouping. The reliability of the pedotransfer function was further demonstrated with an independent database from Northern Italy having heterogeneous soils, and was found to be comparable or better than the accuracy of other pedotransfer functions found in the literature. Key words: Pedotransfer functions, soil moisture, soil texture, bulk density, organic matter, grouping

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.

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