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- Modin, Oskar, 1980, et al.
(author)
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Hill-based dissimilarity indices and null models for analysis of microbial community assembly
- 2020
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In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
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Journal article (peer-reviewed)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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| 3. |
- Wilen, Britt-Marie, 1966, et al.
(author)
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The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality
- 2018
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In: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 102:12, s. 5005-5020
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Journal article (peer-reviewed)abstract
- Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.
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| 4. |
- Modin, Oskar, 1980, et al.
(author)
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A novel bioelectrochemical BOD sensor operating with voltage input
- 2012
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In: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 46:18, s. 6113-6120
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Journal article (peer-reviewed)abstract
- Biochemical oxygen demand (BOD) is a measure of biodegradable compounds in water and is, for example, a common parameter to design and assess the performance of wastewater treatment plants. The conventional method to measure BOD is time consuming (5 or 7 days) and requires trained personnel. Bioelectrochemical BOD sensors designed as microbial fuel cells (MFCs), which are systems where bacteria convert organic matter into an electrical current, have emerged as an alternative to the conventional technique. In this study, a new type of bioelectrochemical BOD sensor with features that overcome some of the limitations of current MFC-type designs was developed: (1) An external voltage was applied to overcome internal resistances and allow bacteria to generate current at their full capacity, and (2) the ion exchange membrane was omitted to avoid pH shifts that wouldotherwise limit the applicability of the sensor for wastewaters with low alkalinity. The sensor was calibrated with an aerated nutrient medium containing acetate as the BOD source. Linear correlation (R2 = 0.97) with charge was obtained for BOD concentrations ranging from 32 to 1280 mg/L in a reaction time of 20 h. Lowering the reaction time to 5 h resulted in lowering the measurable BOD concentration range to 320 mg/L (R2 = 0.99). Propionate, glucose, and ethanol could also be analyzed by the sensor that was acclimated to acetate. The study demonstrates a way to design more robust and simple bioelectrochemicalBOD sensors that do not suffer from the usual limitations of MFCs (high internal resistance and pH shifts).
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| 5. |
- Saheb Alam, Soroush, 1986, et al.
(author)
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A variety of hydrogenotrophic enrichment cultures catalyse cathodic reactions
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Journal article (peer-reviewed)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. |
- Saheb Alam, Soroush, 1986, et al.
(author)
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Effects of storage on mixed-culture biological electrodes
- 2015
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Journal article (peer-reviewed)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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| 9. |
- Almstrand, Robert, et al.
(author)
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Three-dimensional stratification of bacterial biofilm populations in a moving bed biofilm reactor for nitritation-anammox.
- 2014
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In: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 15:2, s. 2191-206
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Journal article (peer-reviewed)abstract
- Moving bed biofilm reactors (MBBRs) are increasingly used for nitrogen removal with nitritation-anaerobic ammonium oxidation (anammox) processes in wastewater treatment. Carriers provide protected surfaces where ammonia oxidizing bacteria (AOB) and anammox bacteria form complex biofilms. However, the knowledge about the organization of microbial communities in MBBR biofilms is sparse. We used new cryosectioning and imaging methods for fluorescence in situ hybridization (FISH) to study the structure of biofilms retrieved from carriers in a nitritation-anammox MBBR. The dimensions of the carrier compartments and the biofilm cryosections after FISH showed good correlation, indicating little disturbance of biofilm samples by the treatment. FISH showed that Nitrosomonas europaea/eutropha-related cells dominated the AOB and Candidatus Brocadia fulgida-related cells dominated the anammox guild. New carriers were initially colonized by AOB, followed by anammox bacteria proliferating in the deeper biofilm layers, probably in anaerobic microhabitats created by AOB activity. Mature biofilms showed a pronounced three-dimensional stratification where AOB dominated closer to the biofilm-water interface, whereas anammox were dominant deeper into the carrier space and towards the walls. Our results suggest that current mathematical models may be oversimplifying these three-dimensional systems and unless the multidimensionality of these systems is considered, models may result in suboptimal design of MBBR carriers.
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| 10. |
- Ardiati, Fenny Clara, et al.
(author)
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Evaluation of batch and fed-batch rotating drum biological contactor using immobilized Trametes hirsuta EDN082 for non-sterile real textile wastewater treatment
- 2024
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In: Journal of Environmental Chemical Engineering. - 2213-3437 .- 2213-2929. ; 12:4
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Journal article (peer-reviewed)abstract
- White rot fungi, in both free and immobilized forms, excel in degrading dyes through adsorption and enzyme degradation. However, existing studies often focus on synthetic wastewater within sterile lab conditions. This study extends the application of Trametes hirsuta EDN082 immobilized in light-expanded clay aggregates (myco-LECAs) packed in a rotating drum biological contactor (RDBC) for treating real textile wastewater under non-sterile conditions to simulate industrial treatment scenarios. Experiments included batch and fed-batch RDBC to assess the impact of additional glucose and stepwise dilution on quality indicators like pH, chemical oxygen demand (COD), ammonia nitrogen (NH4+-N), color, and solids. In fed-batch RDBC with 0.5 % additional glucose, myco-LECAs achieved a maximum of 94 % COD removal (day 15), 99 % NH4+-N reduction (day 33), and 39 % decolorization without additional glucose. In comparison, myco-LECAs in batch RDBC highlighted 89 % NH4+-N reduction in 9 days without pH adjustment or additional nutrients. The pH maintained between 6−9, with no toxicity in Artemia salina, and 97−100 % removal of E. coli. Compared to Indonesian textile wastewater discharge limits, the technology achieved effective ammonia removal below 8 mg/L. This suggests that immobilized T. hirsuta EDN082 in LECAs presents a viable, non-sterile treatment for real textile wastewater.
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