| 1. |
- Modin, Oskar, 1980, et al.
(författare)
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Hill-based dissimilarity indices and null models for analysis of microbial community assembly
- 2020
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundHigh-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.ResultsUsing amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.ConclusionsHill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.
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| 2. |
- Rahimi, Shadi, 1982, et al.
(författare)
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Co-culturing Bacillus subtilis and wastewater microbial community in a bio-electrochemical system enhances denitrification and butyrate formation
- 2020
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Ingår i: Chemical Engineering Journal. - : Elsevier BV. - 1385-8947. ; 397
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Tidskriftsartikel (refereegranskat)abstract
- Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. subtilis was able to rapidly remove nitrate from wastewater. In these conditions, B. subtilis overexpressed nitrogen assimilatory and respiratory genes including nasD, nasE, narG, narH, and narI, which arguably accounted for the observed boost in denitrification. Next, we attempted to use the ammonium- and nitrate-enriched wastewater samples bio-augmented with B. subtilis in the cathodic compartment of bioelectrochemical systems (BES) operated in anaerobic condition. B. subtilis only had low relative abundance in the microbial community, but bio-augmentation promoted the growth of Clostridium butyricum and C. beijerinckii, which became the dominant species. Both bio-augmentation with B. subtilis and electrical current from the cathode in the BES promoted butyrate production during fermentation of glucose. A concentration of 3.4 g/L butyrate was reached with a combination of cathodic current and bio-augmentation in ammonium-enriched wastewater. With nitrate-enriched wastewater, the BES effectively removed nitrate reaching 3.2 mg/L after 48 h. In addition, 3.9 g/L butyrate was produced. We propose that bio-augmentation of wastewater with B. subtilis in combination with bioelectrochemical processes could both boost denitrification in nitrate-containing wastewater and enable commercial production of butyrate from carbohydrate- containing wastewater, e.g. dairy industry discharges. These results suggest that B. subtilis bio-augmentation in our BES promotes simultaneous wastewater treatment and butyrate production. © 2020 The Authors
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| 3. |
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| 4. |
- Modin, Oskar, 1980, et al.
(författare)
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Sorption and Release of Organics by Primary, Anaerobic, and Aerobic Activated Sludge Mixed with Raw Municipal Wastewater
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 10:3, s. e0119371-
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Tidskriftsartikel (refereegranskat)abstract
- New activated sludge processes that utilize sorption as a major mechanism for organics removal are being developed to maximize energy recovery from wastewater organics, or as enhanced primary treatment technologies. To model and optimize sorption-based activated sludge processes, further knowledge about sorption of organics onto sludge is needed. This study compared primary-, anaerobic-, and aerobic activated sludge as sorbents, determined sorption capacity and kinetics, and investigated some characteristics of the organics being sorbed. Batch sorption assays were carried out without aeration at a mixing velocity of 200 rpm. Only aerobic activated sludge showed net sorption of organics. Sorption of dissolved organics occurred by a near-instantaneous sorption event followed by a slower process that obeyed 1st order kinetics. Sorption of particulates also followed 1st order kinetics but there was no instantaneous sorption event; instead there was a release of particles upon mixing. The 5-min sorption capacity of activated sludge was 6.5±10.8 mg total organic carbon (TOC) per g volatile suspend solids (VSS) for particulate organics and 5.0±4.7 mgTOC/gVSS for dissolved organics. The observed instantaneous sorption appeared to be mainly due to organics larger than 20 kDa in size being sorbed, although molecules with a size of about 200 Da with strong UV absorbance at 215–230 nm were also rapidly removed.
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| 5. |
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| 6. |
- Saheb Alam, Soroush, 1986
(författare)
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A long journey from bioanode to biocathode
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Better utilization of renewable sources of energy and recovery of resources from waste streams are important challenges for researchers. Bioelectrochemical systems (BESs) are new technologies which e.g. could be used to produce green energy from waste sources or store renewable electricity as chemical fuels. They rely on microorganisms which can catalyse oxidation/reduction reactions on anodes/cathodes. BESs have a wide range of potential applications such as sensing, bioremediation, recovery of nutrients and metals, valorisation of wastewater organics, and production of energy carriers and other chemicals. However, further research is needed before these applications can be realized. The goal of this thesis was to understand the effect of three different dynamic conditions and disturbances that bioanodes and biocathodes may encounter namely storage, starvation, and potential change. Storage and starvation are disturbances that can affect biological electrodes in all kinds of systems, and it is important to understand their consequences for performance. Changing electrode potential has been shown as a promising method for start-up of biocathodes from enriched bioanodes, but little is known about the long-term performance and changes in microbial community composition as the biocathode develops. First, the possibility for storage of acetate-oxidizing bioanodes using refrigeration, glycerol freezing, and acetone dehydration was investigated. It was shown that storage of acetate-oxidizing bioanodes was possible. Bioanodes stored using refrigeration were the only electrodes that showed biological activity right after five weeks of storage. Then, starvation of acetate-and glucose-fed bioanodes was investigated. It was shown that the acetate- and glucose-fed bioanodes can survive 10 days starvation. However, the overall performance of the glucose-fed bioanodes deteriorated more after each starvation phase compared to the acetate-fed bioanodes. The conversion of acetate- and glucose-fed bioanodes to biocathodes was also compared. Immediately after the potential change, the glucose-fed bioanodes showed better cathodic activity but over time the performance converged. Then, we compared the conversion of bioanodes to biocathodes with direct start-up of biocathodes from a wastewater inoculum. Bare electrodes started-up faster compared to pre-enriched bioanodes. In the end, both types of enrichment procedures led to very similar biocathode communities, which were completely different from the bioanode communities. Indeed, for the microbial communities, it was a long journey from bioanode to biocathodes. Hydrogen appeared to be an important intermediate in the biocathode biofilms, therefore, start-up of biocathodes with pre-enriched hydrogenotrophic cultures was investigated. Hydrogenotrophic microorganisms could facilitate start-up of the biocathodes. All the microbial electrolysis cells inoculated by the enrichment cultures started to generate noticeable current directly after inoculation. In summary, the bioelectrodes in our experiments were robust and could handle storage and starvation periods although the results depended on the experimental conditions, the feed, and the microbial communities. Conversion of bioanodes into biocathodes was less successful and resulted in a complete transition of the microbial community on the electrode. Start-up of biocathodes with hydrogen-oxidizing enrichment cultures was a more successful strategy.
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| 7. |
- Saheb Alam, Soroush, 1986, et al.
(författare)
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A variety of hydrogenotrophic enrichment cultures catalyse cathodic reactions
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Biocathodes where living microorganisms catalyse reduction of CO2 can potentially be used to produce valuable chemicals. Microorganisms harbouring hydrogenases may play a key role for biocathode performance since H-2 generated on the electrode surface can act as an electron donor for CO2 reduction. In this study, the possibility of catalysing cathodic reactions by hydrogenotrophic methanogens, acetogens, sulfate-reducers, denitrifiers, and acetotrophic methanogens was investigated. The cultures were enriched from an activated sludge inoculum and performed the expected metabolic functions. All enrichments formed distinct microbial communities depending on their electron donor and electron acceptor. When the cultures were added to an electrochemical cell, linear sweep voltammograms showed a shift in current generation close to the hydrogen evolution potential (-1 V versus SHE) with higher cathodic current produced at a more positive potential. All enrichment cultures except the denitrifiers were also used to inoculate biocathodes of microbial electrolysis cells operated with H+ and bicarbonate as electron acceptors and this resulted in current densities between 0.1-1A/m(2). The microbial community composition of biocathodes inoculated with different enrichment cultures were as different from each other as they were different from their suspended culture inoculum. It was noteworthy that Methanobacterium sp. appeared on all the biocathodes suggesting that it is a key microorganism catalysing biocathode reactions.
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| 8. |
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| 9. |
- Saheb Alam, Soroush, 1986, et al.
(författare)
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Effect of start-up strategies and electrode materials on carbon dioxide reduction on biocathodes
- 2018
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Ingår i: Applied and Environmental Microbiology. - 1098-5336 .- 0099-2240. ; 84:4
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Tidskriftsartikel (refereegranskat)abstract
- The enrichment of CO 2 -reducing microbial biocathodes is challenging. Previous research has shown that a promising approach could be to first enrich bioanodes and then lower the potential so the electrodes are converted into biocathodes. However, the effect of such a transition on the microbial community on the electrode has not been studied. The goal of this study was thus to compare the start-up of biocathodes from preenriched anodes with direct start-up from bare electrodes and to investigate changes in microbial community composition. The effect of three electrode materials on the long-term performance of the biocathodes was also investigated. In this study, preenrichment of acetate-oxidizing bioanodes did not facilitate the start-up of biocathodes. It took about 170 days for the preenriched electrodes to generate substantial cathodic current, compared to 83 days for the bare electrodes. Graphite foil and carbon felt cathodes produced higher current at the beginning of the experiment than did graphite rods. However, all electrodes produced similar current densities at the end of the over 1-year-long study (2.5 A/m 2 ). Methane was the only product detected during operation of the biocathodes. Acetate was the only product detected after inhibition of the methanogens. Microbial community analysis showed that Geobacter sp. dominated the bioanodes. On the biocathodes, the Geobacter sp. was succeeded by Methanobacterium spp., which made up more than 80% of the population. After inhibition of the methanogens, Acetobacterium sp. became dominant on the electrodes (40% relative abundance). The results suggested that bioelectrochemically generated H 2 acted as an electron donor for CO 2 reduction.
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| 10. |
- Saheb Alam, Soroush, 1986, et al.
(författare)
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Effects of storage on mixed-culture biological electrodes
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Storage methods are important to preserve the viability and biochemical characteristics of microbial cultures between experiments or during periods when bioreactors are inactive. Most of the research on storage has focused on isolates; however, there is an increasing interest in methods for mixed cultures, which are of relevance in environmental biotechnology. The purpose of this study was to investigate the effect of different storage methods on electrochemically active enrichment cultures. Acetate-oxidizing bioanodes generating a current density of about 5 A m−2 were enriched in a microbial electrolysis cell. The effect of five weeks of storage was evaluated using electrochemical techniques and microbial community analysis. Storage by refrigeration resulted in quicker re-activation than freezing in 10% glycerol, while the bioelectrochemical activity was entirely lost after storage using dehydration. The results showed that the bioelectrochemical activity of bioanodes stored at low temperature could be retained. However, during the re-activation period the bioanodes only recovered 75% of the current density generated before storage and the bacterial communities were different in composition and more diverse after storage than before.
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