| 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. |
- Liebana, Raquel, 1986, et al.
(författare)
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Combined Deterministic and Stochastic Processes Control Microbial Succession in Replicate Granular Biofilm Reactors
- 2019
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Ingår i: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:9, s. 4912-4921
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Tidskriftsartikel (refereegranskat)abstract
- Granular sludge is an efficient and compact biofilm process for wastewater treatment. However, the ecological factors involved in microbial community assembly during the granular biofilm formation are poorly understood, and little is known about the reproducibility of the process. Here, three replicate bioreactors were used to investigate microbial succession during the formation of granular biofilms. We identified three successional phases. During the initial phase, the successional turnover was high and alpha-diversity decreased as a result of the selection of taxa adapted to grow on acetate and form aggregates. Despite these dynamic changes, the microbial communities in the replicate reactors were similar. The second successional phase occurred when the settling time was rapidly decreased to selectively retain granules in the reactors. The influence of stochasticity on succession increased and new niches were created as granules emerged, resulting in temporarily increased alpha-diversity. The third successional phase occurred when the settling time was kept stable and granules dominated the biomass. Turnover was low, and selection resulted in the same abundant taxa in the reactors, but drift, which mostly affected low-abundant community members, caused the community in one reactor to diverge from the other two. Even so, performance was stable and similar between reactors.
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| 3. |
- Liebana, Raquel, 1986, et al.
(författare)
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Integration of aerobic granular sludge and membrane bioreactor for wastewater treatment
- 2018
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Ingår i: Critical Reviews in Biotechnology. - : Informa UK Limited. - 0738-8551 .- 1549-7801. ; 38:6, s. 801-816
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Forskningsöversikt (refereegranskat)abstract
- Environmental deterioration together with the need for water reuse and the increasingly restrictive legislation of water quality standards have led to a demand for compact, efficient and less energy consuming technologies for wastewater treatment. Aerobic granular sludge and membrane bioreactors (MBRs) are two technologies with several advantages, such as small footprint, high-microbial density and activity, ability to operate at high organic- and nitrogen-loading rates, and tolerance to toxicity. However, they also have some disadvantages. The aerobic granular sludge process generally requires post-treatment in order to fulfill effluent standards and MBRs suffer from fouling of the membranes. Integrating the two technologies could be a way of combining the advantages and addressing the main problems associated with both processes. The use of membranes to separate the aerobic granules from the treated water would ensure high-quality effluents suitable for reuse. Moreover, the use of granular sludge in MBRs has been shown to reduce fouling. Several recent studies have shown that the aerobic granular membrane bioreactor (AGMBR) is a promising hybrid process with many attractive features. However, major challenges that have to be addressed include how to achieve granulation and maintain granular stability during continuous operation of reactors. This paper aims to review the current state of research on AGMBR technology while drawing attention to relevant findings and highlight current limitations.
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| 4. |
- Liebana, Raquel, 1986
(författare)
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Microbial Community Assembly during Aerobic Granulation
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Environmental deterioration together with the increasingly restrictive legislation of water quality standards have led to a demand for compact, efficient and less energy consuming technologies for wastewater treatment. Aerobic granular membrane bioreactors (AGMBRs) combine the advantages of aerobic granular sludge and membrane filtration. Although recent studies have shown that AGMBRs are promising, research is needed to develop these systems. One important aspect is the development and stability of aerobic granules in the reactor. The objective of this thesis is to unravel the ecological mechanisms behind the granulation process and the resulting granular structure. The impact of the washout dynamics applied in sequencing batch reactors (SBRs) on the bacterial community, the microbial spatial organization in granules and the reproducibility of the granulation process were analyzed. High throughput sequencing was used to analyze the microbial community structure and dynamics during granulation. Fluorescence in-situ hybridization (FISH) analysis was performed to study the microbial spatial distribution. Results showed that the bacterial community composition of granules and the biomass in the effluent from three parallel SBRs subjected to high washout conditions and different organic loading was very similar but not identical. Retention ratios predicted the spatial location of the taxa in the granules. Bacteria having lower relative abundance in the effluent were located in the granular interior whereas bacteria growing on the granular surface were more susceptible to erosion. Using FISH analyses of intact granules, ammonia oxidising bacteria (AOB) were found in the inner locations of the granules indicating that both oxygen and ammonia were transported across/into the granule allowing aerobic metabolism also in the interior. Interestingly, the predatory bacteria Bdellovibrio sp. was found inside the granules and seemed to be preferentially attacking AOB. Moreover, the reproducibility analysis of three replicate SBRs showed some statistical differences in the reactor performance and in the microbial community diversity and structure. Both deterministic and stochastic processes seemed to be involved in the microbial community assemblage during granulation. Biodiversity decreased due to habitat specialization and competitive exclusion during the acclimatization of the sludge to the reactor conditions. When the washout dynamics were stronger the community assemblage was niche-oriented and once the selection pressures decreased, stochastic processes became more evident, especially for intermediate and rare species. Acinetobacter sp., Comamonadaceae and Rhodocyclaceae families together with the polymer producers Thauera sp., Flavobacterium sp. and the family Xanthomonadaceae seemed to have important roles during the first stages of granulation.
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| 5. |
- Liebana, Raquel, 1986
(författare)
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Microbial Ecology of Granular Sludge
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Granular sludge is an efficient and compact biofilm process for wastewater treatment. Despite the well-established methods for granule cultivation, the ecological processes underpinning the microbial community assembly during granulation are poorly understood. Unveiling fundamental aspects of the microbial ecology of granular sludge will contribute to the improvement of the granulation methods and to the technological upgrade. In this thesis, reviews of the available literature were undertaken to assess critical points of current knowledge about the combination of aerobic granular sludge and membrane filtration, and to gain further knowledge on the ecology of the granular sludge and the granular structure. In parallel, three sequencing batch reactors were employed in different experiments and molecular biology techniques, such as high-throughput DNA sequencing, fluorescence in-situ hybridization and confocal laser scanning microscopy, were used. The reproducibility of the reactors was tested, showing the reactors to be generally reproducible for the abundant community members and for the reactor functions when constant conditions were applied. However, when subjected to periodic disturbances, the replicate reactors did not display a high degree in reproducibility in microbial community. Granulation responded to deterministic factors driven by the reactor conditions. During the start-up of the reactors, microorganisms were washed-out randomly and the granulation started as a response to the shear forces applied in the reactor. Simultaneously, there was a deterministic selection of microorganisms involved in aggregate development and for those that were well adapted to grow at the specific reactor conditions. It was also observed that stochastic processes, i.e. drift, had considerable effect on the less abundant community members. Moreover, stochasticity seemed to be important when the community was subjected to periodical disturbances. Also, bacterial predators appeared as part of the core community and they were found to predate on bacteria that were exerting important reactor functions. Ammonia-oxidizing bacteria were observed in the inner locations of the granules, which did not follow the commonly accepted multilayer model of stratification of different functional groups. The granules were able to withstand high pressures showing a high stability and strength when submitted to different water fluxes. In a separate study, it was shown that the choice of bioinformatics pipelines and dissimilarity indices affects the conclusions drawn from experimental data and the use of Hill-based indices was proposed for robust data analysis.
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| 6. |
- Liebana, Raquel, 1986, et al.
(författare)
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Resistance of aerobic granular sludge microbiomes to periodic loss of biomass
- 2023
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Ingår i: Biofilm. - 2590-2075. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.
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| 7. |
- Liebana, Raquel, 1986, et al.
(författare)
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Stability of nitrifying granules exposed to water flux through a coarse pore mesh.
- 2015
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The study of the strength and stability of aerobic granules is essential for the application of aerobic granular sludge membrane bioreactors (AGMBR). In this study, a coarse pore nylon mesh membrane was used to study the differences in compressibility and breakage of 78 aerobic granules submitted to different water fluxes. Confocal laser scanning microscopy was employed to investigate the distribution of extracellular polymeric substances of cryosectioned granules. The tested granules were able to withstand fluxes much higher than those typically applied in MBRs, with pressures ranging from 0.2 to 4.5 kN m-2 before breakage. Cells, β-polysaccharides and proteins were present in higher abundance in the outer layers, while calcium ions were abundant in the outer- as well as the inner layers of the granule. The results shows that the use of coarse pore meshes operated at very high flux is a feasible technique for biomass separation in AGMBR.
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| 8. |
- Liebana, Raquel, 1986, et al.
(författare)
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Unravelling the interactions among microbial populations found in activated sludge during biofilm formation
- 2016
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 92:9
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Tidskriftsartikel (refereegranskat)abstract
- Microorganisms colonize surfaces and develop biofilms through interactions that are not yet thoroughly understood, with important implications for water and wastewater systems. This study investigated the interactions between N-acyl homoserine lactone (AHL)-producing bacteria, yeasts and protists, and their contribution to biofilm development. Sixty-one bacterial strains were isolated from activated sludge and screened for AHL production, with Aeromonas sp. found to be the dominant AHL producer. Shewanella xiamenensis, Aeromonas allosaccharophila, Acinetobacter junii and Pseudomonas aeruginosa recorded the highest adherence capabilities, with S. xiamenensis being the most effective in surface colonization. Additionally, highly significant interactions (i.e. synergic or antagonistic) were described for dual and multistrain mixtures of bacterial strains (P. aeruginosa, S. xiamenensis, A. junii and Pseudomonas stutzeri), as well as for strongly adherent bacteria co-cultured with yeasts. In this last case, the adhered biomass in co-cultures was lower than the monospecific biofilms of bacteria and yeast, with biofilm observations by microscopy suggesting that bacteria had an antagonist effect on the whole or part of the yeast population. Finally, protist predation by Euplotes sp. and Paramecium sp. on Aeromonas hydrophila biofilms not only failed to reduce biofilm formation, but also recorded unexpected results leading to the development of aggregates of high density and complexity.Single- and multi-species microbial biofilms developed by different prokaryotic/eukaryotic microorganisms were investigated in order to study the interactions across populations and their contribution to biofilm development.Single- and multi-species microbial biofilms developed by different prokaryotic/eukaryotic microorganisms were investigated in order to study the interactions across populations and their contribution to biofilm development.
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| 9. |
- Szabo, Enikö Barbara, 1985, et al.
(författare)
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Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors
- 2017
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Ingår i: Amb Express. - : Springer Science and Business Media LLC. - 2191-0855. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Granulation of activated sludge is an increasingly important area within the field of wastewater treatment. Granulation is usually achieved by high hydraulic selection pressure, which results in the wash-out of slow settling particles. The effect of the harsh wash-out conditions on the granular sludge ecosystem is not yet fully understood, but different bacterial groups may be affected to varying degrees. In this study, we used high-throughput amplicon sequencing to follow the community composition in granular sludge reactors for 12 weeks, both in the granular phase and the suspended phase (effluent). The microbiome of the washed out biomass was similar but not identical to the microbiome of the granular biomass. Certain taxa (e.g. Flavobacterium spp. and Bdellovibrio spp.) had significantly (p < 0.05) higher relative abundance in the granules compared to the effluent. Fluorescence in situ hybridization images indicated that these taxa were mainly located in the interior of granules and therefore protected from erosion. Other taxa (e.g. Meganema sp. and Zooglea sp.) had significantly lower relative abundance in the granules compared to the effluent, and appeared to be mainly located on the surface of granules and therefore subject to erosion. Despite being washed out, these taxa were among the most abundant members of the granular sludge communities and were likely growing fast in the reactors. The ratio between relative abundance in the granular biomass and in the effluent did not predict temporal variation of the taxa in the reactors, but it did appear to predict the spatial location of the taxa in the granules.
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| 10. |
- Szabo, Enikö Barbara, 1985, et al.
(författare)
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Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The granular sludge process is an effective, low-footprint alternative to conventional activated sludge wastewater treatment. The architecture of the microbial granules allows the co-existence of different functional groups, e.g., nitrifying and denitrifying communities, which permits compact reactor design. However, little is known about the factors influencing community assembly in granular sludge, such as the effects of reactor operation strategies and influent wastewater composition. Here, we analyze the development of the microbiomes in parallel laboratory-scale anoxic/aerobic granular sludge reactors operated at low (0.9 kg m(-3) d(-1)), moderate (1.9 kg m(-3) d(-1)) and high (3.7 kg m(-3) d(-1)) organic loading rates (OLRs) and the same ammonium loading rate (0.2 kg NH4-N m-3 d(-1)) for 84 days. Complete removal of organic carbon and ammonium was achieved in all three reactors after start-up, while the nitrogen removal (denitrification) efficiency increased with the OLR: 0% at low, 38% at moderate, and 66% at high loading rate. The bacterial communities at different loading rates diverged rapidly after start-up and showed less than 50% similarity after 6 days, and below 40% similarity after 84 days. The three reactor microbiomes were dominated by different genera (mainly Meganema, Thauera, Paracoccus, and Zoogloea), but these genera have similar ecosystem functions of EPS production, denitrification and polyhydroxyalkanoate (PHA) storage. Many less abundant but persistent taxa were also detected within these functional groups. The bacterial communities were functionally redundant irrespective of the loading rate applied. At steady-state reactor operation, the identity of the core community members was rather stable, but their relative abundances changed considerably over time. Furthermore, nitrifying bacteria were low in relative abundance and diversity in all reactors, despite their large contribution to nitrogen turnover. The results suggest that the OLR has considerable impact on the composition of the granular sludge communities, but also that the granule communities can be dynamic even at steady-state reactor operation due to high functional redundancy of several key guilds. Knowledge about microbial diversity with specific functional guilds under different operating conditions can be important for engineers to predict the stability of reactor functions during the start-up and continued reactor operation.
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