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1.
Appl Microbiol Biotechnol ; 108(1): 334, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38739161

ABSTRACT

Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.


Subject(s)
Bacteria , Bioreactors , Microbiota , Sewage , Sewage/microbiology , Bacteria/classification , Bacteria/metabolism , Bacteria/genetics , Bacteria/isolation & purification , Bioreactors/microbiology , Aerobiosis , Sweden , Glycogen/metabolism , Ammonia/metabolism , Nitrites/metabolism , Nitrates/metabolism , Phosphates/metabolism , Water Purification/methods
2.
Microbiome ; 12(1): 51, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38475926

ABSTRACT

BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms. RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers. CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.


Subject(s)
Ammonia , Anaerobic Ammonia Oxidation , Phylogeny , Sewage/microbiology , Bacteria , Bioreactors/microbiology , Nitrogen , Biofilms , Oxidation-Reduction
3.
Biofilm ; 6: 100161, 2023 Dec 15.
Article in English | MEDLINE | ID: mdl-37859795

ABSTRACT

In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.

4.
Sci Total Environ ; 902: 166483, 2023 Dec 01.
Article in English | MEDLINE | ID: mdl-37611717

ABSTRACT

Primary filtration is a compact pre-treatment process for municipal wastewater, which can lead to high removal of total suspended solids (TSS) if polymer is added prior to filtration. Extensive carbon removal with rotating belt filter (RBF) can be combined with filter primary sludge fermentation at ambient temperature, in order to produce volatile fatty acids (VFAs) as carbon source for biological nutrient removal (BNR). This process was implemented at large pilot-scale and operated for more than a year. The results showed that the RBF efficiently removed particles >10 µm, and that the TSS removal had a strong linear correlation to the influent TSS concentration. Fermentation of the sludge at ambient temperature and five days retention time and addition of the fermentate to the wastewater could nearly double the VFA concentration in the wastewater by adding 31 ± 9 mg VFA-COD/L. Meanwhile, an increase of 2 mg/L of ammonium nitrogen, and 0.7 mg /L of phosphate phosphorus would be added to the wastewater with the fermentate. Adding the fermented sludge to the wastewater stream and removing the particles with RBF makes it possible to utilize nearly all the produced VFAs for BNR, and the feasibility of this configuration was shown at pilot-scale. According to simulations of subsequent BNR, the pre-treatment would lead to lower effluent total nitrogen concentrations. Alternatively, the required BNR volume could be reduced by 11-18 %. The estimated total biogas production was similar for pre-treatment with primary settler and RBF with fermentation. RBF without fermentation gave the most favourable energy balance, but did not reach the same low effluent value for total nitrogen as RBF with fermentation.


Subject(s)
Sewage , Wastewater , Fermentation , Bioreactors , Fatty Acids, Volatile , Nutrients , Phosphorus , Nitrogen/analysis , Carbon , Waste Disposal, Fluid/methods
5.
Biofilm ; 6: 100145, 2023 Dec 15.
Article in English | MEDLINE | ID: mdl-37575957

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.

6.
Water Environ Res ; 95(8): e10914, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37494966

ABSTRACT

This study demonstrates a comparison of energy usage, land footprint, and volumetric requirements of municipal wastewater treatment with aerobic granular sludge (AGS) and conventional activated sludge (CAS) at a full-scale wastewater treatment plant characterized by large fluctuations in nutrient loadings and temperature. The concentration of organic matter in the influent to the AGS was increased by means of hydrolysis and bypassing the pre-settler. Both treatment lines produced effluent concentrations below 5 mg BOD7 L-1 , 10 mg TN L-1 , and 1 mg TP L-1 , by enhanced biological nitrogen- and phosphorus removal. In this case study, the averages of volumetric energy usage over 1 year were 0.22 ± 0.08 and 0.26 ± 0.07 kWh m-3 for the AGS and CAS, respectively. A larger difference was observed for the energy usage per reduced population equivalents (P.E.), which was on average 0.19 ± 0.08 kWh P.E.-1 for the AGS and 0.30 ± 0.08 kWh P.E.-1 for the CAS. However, both processes had the potential for decreased energy usage. Over 1 year, both processes showed similar fluctuations in energy usage, related to variations in loading, temperature, and DO. The AGS had a lower specific area, 0.3 m2  m-3 d-1 , compared to 0.6 m2  m-3 d-1 of the CAS, and also a lower specific volume, 1.3 m3  m-3 d-1 compared to 2.0 m3  m-3 d-1 . This study confirms that AGS at full-scale can be compact and still have comparable energy usage as CAS. PRACTITIONER POINTS: Full-scale case study comparison of aerobic granular sludge (AGS) and conventional activated sludge (CAS), operated in parallel. AGS had 50 % lower footprint compared to CAS. Energy usage was lower in the AGS, but both processes had potential to improve the energy usage efficiency. Both processes showed low average effluent concentrations.


Subject(s)
Sewage , Wastewater , Waste Disposal, Fluid , Bioreactors , Nitrogen , Aerobiosis
7.
Water Res ; 242: 120181, 2023 Aug 15.
Article in English | MEDLINE | ID: mdl-37343334

ABSTRACT

Primary treatment of municipal wastewater by rotating belt filtration followed by hydrolysis and acidogenic fermentation of the filter primary sludge (FPS) at ambient temperature was studied at pilot-scale during one year. The seasonal variations of volatile fatty acids (VFAs), nutrient release and soluble COD production as well as microbial community assembly were assessed, leading to novel findings for fermentation at ambient temperature. The reproducibility of VFA production performance was first established by operating the two fermentation reactors under the same conditions, showing similar results regarding VFA production and microbial community structure. One year of operation at 5 d retention time (RT) and 16-29 °C resulted in an average VFA yield of 180±35 mg COD/g VSin and soluble COD yield of 242±40 mg COD/g VSin. The VFA formation was temperature-dependent, with Ï´=1.033±0.005 ( [Formula: see text] . The seasonal variations of the acetic and propionic acid productions were pronounced, whereas the productions of VFAs with longer chains were more stable regardless of temperature. The community structure of the reactor microbiomes was also clearly affected by season and temperature and linked with the production spectrum of VFAs. The ammonium and phosphate releases were stable during the year, leading to a decrease in ratios of soluble COD to NH4+-N and PO43--P during winter. The soluble COD yield was 11% and 27% higher at 5 d RT compared to 3 and 2 d RT respectively, but the corresponding volumetric productivities were lower. The dissimilarities between microbiomes in influent FPS and fermenters were significant even at a short RT of 2 d, and increased with longer RT of 3 and 5 d, primarily caused by selection of bacteria within Bacteroidota in the fermentation reactors.


Subject(s)
Sewage , Wastewater , Fermentation , Sewage/chemistry , Seasons , Reproducibility of Results , Bioreactors , Fatty Acids, Volatile , Acids , Hydrogen-Ion Concentration
8.
FEMS Microbiol Lett ; 3702023 01 17.
Article in English | MEDLINE | ID: mdl-37291701

ABSTRACT

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.


Subject(s)
Metagenome , Planctomycetes , Nitrogen , RNA, Ribosomal, 16S/genetics , Manganese , Iron , Oxidation-Reduction
9.
Environ Sci Technol ; 57(19): 7431-7441, 2023 05 16.
Article in English | MEDLINE | ID: mdl-37130040

ABSTRACT

The occurrence of pharmaceuticals in the aquatic environment is a global water quality challenge for several reasons, such as deleterious effects on ecological and human health, antibiotic resistance development, and endocrine-disrupting effects on aquatic organisms. To optimize their removal from the water cycle, understanding the processes during biological wastewater treatment is crucial. Time-of-flight secondary ion mass spectrometry imaging was successfully applied to investigate and analyze the distribution of pharmaceuticals as well as endogenous molecules in the complex biological matrix of biofilms for wastewater treatment. Several compounds and their localization were identified in the biofilm section, including citalopram, ketoconazole, ketoconazole transformation products, and sertraline. The images revealed the pharmaceuticals gathered in distinct sites of the biofilm matrix. While citalopram penetrated the biofilm deeply, sertraline remained confined in its outer layer. Both pharmaceuticals seemed to mainly colocalize with phosphocholine lipids. Ketoconazole concentrated in small areas with high signal intensity. The approach outlined here presents a powerful strategy for visualizing the chemical composition of biofilms for wastewater treatment and demonstrates its promising utility for elucidating the mechanisms behind pharmaceutical and antimicrobial removal in biological wastewater treatment.


Subject(s)
Waste Disposal, Fluid , Water Pollutants, Chemical , Humans , Waste Disposal, Fluid/methods , Citalopram/analysis , Citalopram/pharmacology , Ketoconazole/analysis , Ketoconazole/pharmacology , Sertraline/analysis , Sertraline/pharmacology , Spectrometry, Mass, Secondary Ion , Water Pollutants, Chemical/analysis , Wastewater , Biofilms , Pharmaceutical Preparations
10.
J Hazard Mater ; 438: 129528, 2022 09 15.
Article in English | MEDLINE | ID: mdl-35999740

ABSTRACT

Removal performances of organic micropollutants by conventional activated sludge (CAS) and aerobic granular sludge (AGS) were investigated at a full-scale wastewater treatment plant. Lab-scale kinetic experiments were performed to assess the micropollutant transformation rates under oxic and anoxic conditions. Transformation rates were used to model the micropollutant removal in the full-scale processes. Metagenomic sequencing was used to compare the microbial communities and antimicrobial resistance genes of the CAS and AGS systems. Higher transformation ability was observed for CAS compared to AGS for most compounds, both at the full-scale plant and in the complementary batch experiments. Oxic conditions supported the transformation of several micropollutants with faster and/or comparable rates compared to anoxic conditions. The estimated transformation rates from batch experiments adequately predicted the removal for most micropollutants in the full-scale processes. While the compositions in microbial communities differed between AGS and CAS, the full-scale biological reactors shared similar resistome profiles. Even though granular biomass showed lower potential for micropollutant transformation, AGS systems had somewhat higher gene cluster diversity compared to CAS, which could be related to a higher functional diversity. Micropollutant exposure to biomass or mass transfer limitations, therefore played more important roles in the observed differences in OMP removal.


Subject(s)
Sewage , Water Purification , Bioreactors , Waste Disposal, Fluid , Wastewater
11.
NPJ Biofilms Microbiomes ; 8(1): 47, 2022 06 08.
Article in English | MEDLINE | ID: mdl-35676296

ABSTRACT

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.


Subject(s)
Microbiota , Nitrites , Anaerobic Ammonia Oxidation , Bacteria/genetics , Biofilms , Bioreactors/microbiology
12.
Water Res X ; 16: 100146, 2022 Aug 01.
Article in English | MEDLINE | ID: mdl-35761925

ABSTRACT

With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.

13.
Environ Microbiol ; 24(5): 2348-2360, 2022 05.
Article in English | MEDLINE | ID: mdl-35415863

ABSTRACT

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.


Subject(s)
Ammonium Compounds , Metagenome , Ammonium Compounds/metabolism , Anaerobic Ammonia Oxidation , Anaerobiosis , Bacteria , Bacteria, Anaerobic/metabolism , Ecosystem , Oxidation-Reduction
14.
Front Microbiol ; 13: 959211, 2022.
Article in English | MEDLINE | ID: mdl-36590422

ABSTRACT

In single-chamber microbial electrolysis cells (MECs), organic compounds are oxidized at the anode, liberating electrons that are used for hydrogen evolution at the cathode. Microbial communities on the anode and cathode surfaces and in the bulk liquid determine the function of the MEC. The communities are complex, and their assembly processes are poorly understood. We investigated MEC performance and community composition in nine MECs with a carbon cloth anode and a cathode of carbon nanoparticles, titanium, or stainless steel. Differences in lag time during the startup of replicate MECs suggested that the initial colonization by electrogenic bacteria was stochastic. A network analysis revealed negative correlations between different putatively electrogenic Deltaproteobacteria on the anode. Proximity to the conductive anode surface is important for electrogens, so the competition for space could explain the observed negative correlations. The cathode communities were dominated by hydrogen-utilizing taxa such as Methanobacterium and had a much lower proportion of negative correlations than the anodes. This could be explained by the diffusion of hydrogen throughout the cathode biofilms, reducing the need to compete for space.

15.
Microbiome ; 8(1): 148, 2020 Oct 28.
Article in English | MEDLINE | ID: mdl-33115538

ABSTRACT

An amendment to this paper has been published and can be accessed via the original article.

16.
Water Res ; 186: 116348, 2020 Nov 01.
Article in English | MEDLINE | ID: mdl-32911269

ABSTRACT

A model-based study was developed to analyse the behaviour of Moving Bed Biofilm Reactor (MBBR) and Integrated Fixed-Film Activated Sludge (IFAS) reactor configurations for the removal of nitrogen in the main water line of municipal wastewater treatment plants via partial nitritation/anammox (PN/AMX). The basic principles and underlying mechanisms linking operating conditions to process performance were investigated, with particular focus on nitrite oxidizing bacteria (NOB) repression and resulting volumetric conversion rates. The external mass transfer resistance is a major factor differentiating granular sludge PN/AMX processes from MBBR or IFAS systems. The external mass transfer resistance was found to promote the metabolic coupling between anammox (AMX) and ammonia oxidizing bacteria (AOB), crucial for NOB repression in the biofilm. Operation at low bulk DO prevents NOB proliferation in the flocs of IFAS systems as AMX activity limits nitrite availability (the so-called AMX nitrite sink). Importantly, the effectiveness of the AMX nitrite sink strongly depends on the AMX sensitivity to oxygen. Also, over a broad range of operational conditions, the seeding of AOB from the biofilm played a crucial role in maintaining their activity in the flocs. From a practical perspective, while low DO promotes NOB repression, lower nitrogen loads have to be applied to maintain the same effluent quality. Thus, a trade-off between NOB repression and volumetric conversion capacity needs to be defined. To this end, IFAS allow for higher volumetric rates, but the window of operating conditions with effective NOB repression is smaller than that for MBBR. Ultimately, this study identified the principles controlling NOB in MBBR and IFAS systems and the key differences with granular reactors, allowing for the interpretation of (seemingly contradictory) published experimental results.


Subject(s)
Ammonium Compounds , Nitrites , Bacteria/genetics , Biofilms , Bioreactors , Nitrogen , Oxidation-Reduction , Sewage
17.
Microbiome ; 8(1): 132, 2020 09 11.
Article in English | MEDLINE | ID: mdl-32917275

ABSTRACT

BACKGROUND: High-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. RESULTS: Using 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. CONCLUSIONS: Hill-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. Video Abstract.


Subject(s)
Archaea/isolation & purification , Bacteria/isolation & purification , Computer Simulation , Microbiota , Software
18.
Sci Total Environ ; 714: 136342, 2020 Apr 20.
Article in English | MEDLINE | ID: mdl-31982771

ABSTRACT

Nitrogen removal from the mainstream of municipal wastewater with partial nitritation-anammox (PNA) would be highly beneficial with regard to the uses of energy and organic carbon. However, the challenges of process instability, low nitrogen removal rates (NRR) and unwanted aerobic nitrite oxidation need to be solved to reach large-scale implementation. Here, we have operated pilot-scale moving bed biofilm reactors (MBBRs) for mainstream treatment, together with sidestream treatment of sludge liquor from anaerobic digestors, for over 900 days to investigate process stability, reactor performance and microbial community structure at realistic conditions. The MBBR biofilm contained stable and high relative abundances of anammox bacteria (10-32%) consisting of two major Brocadia sp. populations, and several populations of aerobic ammonia-oxidising bacteria (AOB) within Nitrosomonas sp. (0.2-3.1%), as assessed by 16S rDNA amplicon sequencing. In addition, nitrite-oxidising bacteria (NOB) consisting of Nitrospira sp. (0.4-0.8%) and Nitrotoga sp. (up to 0.4%) were present. Nitrogen was removed at a peak rate of 0.66 g N m-2 d-1 (0.13 kg N m-3 d-1) with a nitrate production over ammonium consumption of 15% by the NOB, at operation with continuous aeration at 15 °C. However, during most periods with continuous aeration, the NRR was lower (≈ 0.45 g N m-2 d-1), with larger relative nitrate production (≈40%), presumably due to problems to maintain stable residual ammonium concentrations during wet-weather mainstream flows. Changing reactor operation to intermittent aeration decreased the NRR but did not help in suppressing the NOB. The study shows that with MBBRs, stable mainstream PNA can be attained at realistic NRR, but with need for post-treatment of nitrate, since effective NOB suppression was hard to achieve.


Subject(s)
Biofilms , Ammonium Compounds , Bioreactors , Nitrites , Nitrogen , Oxidation-Reduction , Wastewater
19.
Microb Biotechnol ; 12(5): 962-975, 2019 09.
Article in English | MEDLINE | ID: mdl-31228355

ABSTRACT

In microbial fuel cells (MFCs), microorganisms generate electrical current by oxidizing organic compounds. MFCs operated with different electron donors harbour different microbial communities, and it is unknown how that affects their response to starvation. We analysed the microbial communities in acetate- and glucose-fed MFCs and compared their responses to 10 days starvation periods. Each starvation period resulted in a 4.2 ± 1.4% reduction in electrical current in the acetate-fed MFCs and a 10.8 ± 3.9% reduction in the glucose-fed MFCs. When feed was resumed, the acetate-fed MFCs recovered immediately, whereas the glucose-fed MFCs required 1 day to recover. The acetate-fed bioanodes were dominated by Desulfuromonas spp. converting acetate into electrical current. The glucose-fed bioanodes were dominated by Trichococcus sp., functioning as a fermenter, and a member of Desulfuromonadales, using the fermentation products to generate electrical current. Suspended biomass and biofilm growing on non-conductive regions within the MFCs had different community composition than the bioanodes. However, null models showed that homogenizing dispersal of microorganisms within the MFCs affected the community composition, and in the glucose-fed MFCs, the Trichococcus sp. was abundant in all locations. The different responses to starvation can be explained by the more complex pathway requiring microbial interactions to convert glucose into electrical current.


Subject(s)
Acetates/metabolism , Bacteria/classification , Bacteria/metabolism , Bioelectric Energy Sources/microbiology , Glucose/metabolism , Microbiota , Bacteria/isolation & purification , Electricity , Energy Metabolism , Microbial Interactions
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