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Chen X, Gong Y, Li Z, Guo Y, Zhang H, Hu B, Yang W, Cao Y, Mu R. Key function of Kouleothrix in stable formation of filamentous aerobic granular sludge at low superficial gas velocity with polymeric substrates. BIORESOURCE TECHNOLOGY 2024; 397:130466. [PMID: 38373501 DOI: 10.1016/j.biortech.2024.130466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Forming and maintaining stable aerobic granular sludge (AGS) at a low superficial gas velocity (SGV) is challenging, particularly with polymeric substrates. This study cultivated filamentous aerobic granular sludge (FAGS) with filamentous Kouleothrix (Type 1851) at low SGV (0.15 cm/s) utilizing mixed acetate-soluble starch. Within approximately 260 days, notable increases in the relative abundance of Kouleothrix (from 4 % to 10 %) and Ca. Competibacter (from 1 % to 26 %) were observed through 16S rRNA gene analysis. Metagenomic analysis revealed increased expression of functional genes involved in volatile fatty acid (VFA) production (e.g., ackA and pta) and polyhydroxyalkanoate synthesis (e.g., phbB and phbC). Kouleothrix acted as a skeleton for bacterial attachment and was the key fermenting bacteria promoting granulation and maintaining granule stability. This study provides insight into the formation of FAGS with low-energy and non-VFA substrates.
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Affiliation(s)
- Xi Chen
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China.
| | - Yanzhe Gong
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Zhihua Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yingming Guo
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Hongjiang Zhang
- North China Electric Power Research Institute Co., Ltd, Beijing 100045, China
| | - Bin Hu
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Wenhao Yang
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Yinhuan Cao
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Ruihua Mu
- School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an 710048, China
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2
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Pelevina A, Gruzdev E, Berestovskaya Y, Dorofeev A, Nikolaev Y, Kallistova A, Beletsky A, Ravin N, Pimenov N, Mardanov A. New insight into the granule formation in the reactor for enhanced biological phosphorus removal. Front Microbiol 2023; 14:1297694. [PMID: 38163067 PMCID: PMC10755871 DOI: 10.3389/fmicb.2023.1297694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
While granulated activated sludge exhibits high productivity, the processes of granule formation are incompletely studied. The processes of granule formation and succession of communities were investigated in a laboratory sequencing batch reactor (SBR) under conditions for enhanced biological phosphorus removal (EBPR) using microbiological and molecular techniques. Active consumption of acetate, primarily by the phosphate-accumulating organisms (PAO), commenced at day 150 of cultivation. This was indicated by the high ratio of molar P-released/acetate uptake (0.73-0.77 P-mol/C-mol), characteristic of PAO. During this period, two types of granule-like aggregates formed spontaneously out of the activated sludge flocs. The aggregates differed in morphology and microbial taxonomic composition. While both aggregate types contained phosphorus-enriched bacterial cells, PAO prevailed in those of morphotype I, and glycogen-accumulating organisms (GAOs) were predominant in the aggregates of morphotype II. After 250 days, the elimination of the morphotype II aggregates from the reactor was observed. The subsequent selection of the community was associated with the development of the morphotype I aggregates, in which the relative abundance of PAO increased significantly, resulting in higher efficiency of phosphorus removal. Metagenomic analysis revealed a predominance of the organisms closely related to Candidatus Accumulibacter IС and IIС and of Ca. Accumulibacter IIB among the PAO. Based on the content of the genes of the key metabolic pathways, the genomes of potential PAO belonging to the genera Amaricoccus, Azonexus, Thauera, Zoogloea, Pinisolibacter, and Siculibacillus were selected. The patterns of physicochemical processes and the microbiome structure associated with granule formation and succession of the microbial communities were revealed.
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Affiliation(s)
- Anna Pelevina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny Gruzdev
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yulia Berestovskaya
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Dorofeev
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yury Nikolaev
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kallistova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Beletsky
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Ravin
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Pimenov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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3
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Kleikamp HBC, Grouzdev D, Schaasberg P, van Valderen R, van der Zwaan R, Wijgaart RVD, Lin Y, Abbas B, Pronk M, van Loosdrecht MCM, Pabst M. Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome. WATER RESEARCH 2023; 246:120700. [PMID: 37866247 DOI: 10.1016/j.watres.2023.120700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023]
Abstract
The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.
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Affiliation(s)
- Hugo B C Kleikamp
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - Pim Schaasberg
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ramon van Valderen
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ramon van der Zwaan
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Roel van de Wijgaart
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | | | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
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4
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Tomás-Martínez S, Zwolsman EJ, Merlier F, Pabst M, Lin Y, van Loosdrecht MCM, Weissbrodt DG. Turnover of the extracellular polymeric matrix of granules performing biological phosphate removal. Appl Microbiol Biotechnol 2023; 107:1997-2009. [PMID: 36759376 PMCID: PMC10006046 DOI: 10.1007/s00253-023-12421-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Polyphosphate accumulating organisms (PAOs) are responsible for enhanced biological phosphate removal (EBPR) from wastewater, where they grow embedded in a matrix of extracellular polymeric substances (EPS). EPSs comprise a mixture of biopolymers like polysaccharides or (glyco)proteins. Despite previous studies, little is known about the dynamics of EPS in mixed cultures, and their production by PAOs and potential consumption by flanking microbes. EPSs are biodegradable and have been suggested to be a substrate for other organisms in the community. Studying EPS turnover can help elucidate their biosynthesis and biodegradation cycles. We analyzed the turnover of proteins and polysaccharides in the EPS of an enrichment culture of PAOs relative to the turnover of internal proteins. An anaerobic-aerobic sequencing batch reactor (SBR) simulating EBPR conditions was operated to enrich for PAOs. After achieving a stable culture, carbon source was switched to uniformly 13C-labeled acetate. Samples were collected at the end of each aerobic phase. EPSs were extracted by alkaline treatment. 13C enrichment in proteins and sugars (after hydrolysis of polysaccharides) in the extracted EPS were measured by mass spectrometry. The average turnover rate of sugars and proteins (0.167 and 0.192 d-1 respectively) was higher than the expected value based on the solid removal rate (0.132 d-1), and no significant difference was observed between intracellular and extracellular proteins. This indicates that EPS from the PAO enriched community is not selectively degraded by flanking populations under stable EBPR process conditions. Instead, we observed general decay of biomass, which corresponds to a value of 0.048 d-1. KEY POINTS: • Proteins showed a higher turnover rate than carbohydrates. • Turnover of EPS was similar to the turnover of intracellular proteins. • EPS is not preferentially consumed by flanking populations.
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Affiliation(s)
- Sergio Tomás-Martínez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands.
| | - Erwin J Zwolsman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, 60319, 60203, Compiègne Cedex, CS, France
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9,2629, HZ, Delft, The Netherlands
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5
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Tomás-Martínez S, Chen LM, Pabst M, Weissbrodt DG, van Loosdrecht MCM, Lin Y. Enrichment and application of extracellular nonulosonic acids containing polymers of Accumulibacter. Appl Microbiol Biotechnol 2023; 107:931-941. [PMID: 36484828 DOI: 10.1007/s00253-022-12326-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Pseudaminic and legionaminic acids are a subgroup of nonulosonic acids (NulOs) unique to bacterial species. There is a lack of advances in the study of these NulOs due to their complex synthesis and production. Recently, it was seen that "Candidatus Accumulibacter" can produce Pse or Leg analogues as part of its extracellular polymeric substances (EPS). In order to employ a "Ca. Accumulibacter" enrichment as production platform for bacterial sialic acids, it is necessary to determine which fractions of the EPS of "Ca. Accumulibacter" contain NulOs and how to enrich and/or isolate them. We extracted the EPS from granules enriched with "Ca. Accumulibcater" and used size-exclusion chromatography (SEC) to separate them into different molecular weight (MW) fractions. This separation resulted in two high molecular weight (> 5500 kDa) fractions dominated by polysaccharides, with a NulO content up to 4 times higher than the extracted EPS. This suggests that NulOs in "Ca. Accumulibacter" are likely located in high molecular weight polysaccharides. Additionally, it was seen that the extracted EPS and the NulO-rich fractions can bind and neutralize histones. This opens the possibility of EPS and NulO-rich fractions as potential source for sepsis treatment drugs. KEY POINTS: • NulOs in "Ca. Accumulibacter" are likely located in high MW polysaccharides • SEC allows to obtain high MW polysaccharide-rich fractions enriched with NulOs • EPS and the NulOs-rich fractions are a potential source for sepsis treatment drugs.
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Affiliation(s)
- Sergio Tomás-Martínez
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Le Min Chen
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
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6
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Diaz R, Mackey B, Chadalavada S, Kainthola J, Heck P, Goel R. Enhanced Bio-P removal: Past, present, and future - A comprehensive review. CHEMOSPHERE 2022; 309:136518. [PMID: 36191763 DOI: 10.1016/j.chemosphere.2022.136518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Excess amounts of phosphorus (P) and nitrogen (N) from anthropogenic activities such as population growth, municipal and industrial wastewater discharges, agriculture fertilization and storm water runoffs, have affected surface water chemistry, resulting in episodes of eutrophication. Enhanced biological phosphorus removal (EBPR) based treatment processes are an economical and environmentally friendly solution to address the present environmental impacts caused by excess P present in municipal discharges. EBPR practices have been researched and operated for more than five decades worldwide, with promising results in decreasing orthophosphate to acceptable levels. The advent of molecular tools targeting bacterial genomic deoxyribonucleic acid (DNA) has also helped us reveal the identity of potential polyphosphate-accumulating organisms (PAO) and denitrifying PAO (DPAO) responsible for the success of EBPR. Integration of process engineering and environmental microbiology has provided much-needed confidence to the wastewater community for the successful implementation of EBPR practices around the globe. Despite these successes, the process of EBPR continues to evolve in terms of its microbiology and application in light of other biological processes such as anaerobic ammonia oxidation and on-site carbon capture. This review provides an overview of the history of EBPR, discusses different operational parameters critical for the successful operation of EBPR systems, reviews current knowledge of EBPR microbiology, the influence of PAO/DPAO on the disintegration of microbial communities, stoichiometry, EBPR clades, current practices, and upcoming potential innovations.
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Affiliation(s)
- Ruby Diaz
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Brendan Mackey
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Sreeni Chadalavada
- School of Engineering, University of Southern Queensland Springfield, Queensland, 4350, Australia.
| | - Jyoti Kainthola
- Department of Civil Engineering, École Centrale School of Engineering, Mahindra University, Hyderabad, India, 500043
| | - Phil Heck
- Central Valley Water Reclamation Facility, Salt Lake City, UT, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
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7
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Tomás-Martínez S, Chen LM, Neu TR, Weissbrodt DG, van Loosdrecht MCM, Lin Y. Catabolism of sialic acids in an environmental microbial community. FEMS Microbiol Ecol 2022; 98:6571932. [PMID: 35446356 DOI: 10.1093/femsec/fiac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/14/2022] Open
Abstract
Sialic acids are a family of nine-carbon negatively charged carbohydrates. In animals, they are abundant on mucosa surfaces as terminal carbohydrates of mucin glycoproteins. Some commensal and pathogenic bacteria are able to release, take up, and catabolize sialic acids. Recently, sialic acids have been discovered to be widespread among most microorganisms. Although the catabolism of sialic acids has been intensively investigated in the field of host-microbe interactions, very limited information is available on microbial degradation of sialic acids produced by environmental microorganisms. In this study, the catabolic pathways of sialic acids within an microbial community dominated by 'Candidatus Accumulibacter' was evaluated. Protein alignment tools were used to detect the presence of the different proteins involved in the utilization of sialic acids in the flanking populations detected by 16S rRNA gene amplicon sequencing. The results showed the ability of Clostridium to release sialic acids from the glycan chains by the action of a sialidase. Clostridium and Chryseobacterium can take up free sialic acids and utilize them as nutrient. Interestingly, these results display similarities with the catabolism of sialic acids by the gut microbiota. This study points at the importance of sialic acids in environmental communities in the absence of eukaryotic hosts.
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Affiliation(s)
- Sergio Tomás-Martínez
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Le Min Chen
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre of Environmental Research - UFZ, Brueckstrasse 3A, 39114, Magdeburg, Germany
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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8
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OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
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9
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Chen G, Bai R, Zhang Y, Zhao B, Xiao Y. Application of metagenomics to biological wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150737. [PMID: 34606860 DOI: 10.1016/j.scitotenv.2021.150737] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Biological wastewater treatment is a process in which the microbial metabolism of complex communities transforms pollutants into low- or non-toxic products. Due to the absence of an in-depth understanding of the diversity and complexity of microbial communities, it is very likely to ignore the potential mechanisms of microbial community in wastewater treatment. Metagenomics is a technology based on molecular biology, in which massive gene sequences are obtained from environmental samples and analyzed by bioinformatics to determine the composition and function of a microbial community. Metagenomics can identify the state of microbes in their native environments more effectively than traditional molecular methods. This review summarizes the application of metagenomics to assess microbial communities in biological wastewater treatment, such as the biological removal of phosphorus and nitrogen by bacteria, the study of antibiotic resistance genes (ARGs), and the reduction of heavy metals by microbial communities, with an emphasis on the contribution of microbial diversity and metabolic diversity. Technical bottlenecks in the application of metagenomics to biological wastewater treatment are elucidated, and future research directions for metagenomics are proposed, among which the application of multi-omics will be an important research method for future biological wastewater treatment.
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Affiliation(s)
- Geng Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rui Bai
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yiqing Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Biyi Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yong Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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10
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Srinivasan VN, Li G, Wang D, Tooker NB, Dai Z, Onnis-Hayden A, Bott C, Dombrowski P, Schauer P, Pinto A, Gu AZ. Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems. WATER RESEARCH 2021; 206:117725. [PMID: 34653799 DOI: 10.1016/j.watres.2021.117725] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Candidatus Accumulibacter phosphatis (CAP) and its clade-level micro-diversity has been associated with and implicated in functional differences in phosphorus removal performance in enhanced biological phosphorus removal (EBPR) systems. Side-stream EBPR (S2EBPR) is an emerging process that has been shown to present a suite of advantages over the conventional EBPR design, however, large knowledge gaps remain in terms of its underlying ecological mechanisms. Here, we compared and revealed the higher-resolution differences in microbial ecology of CAP between a full-scale side-stream EBPR configuration and a conventional A2O EBPR process that were operated in parallel and with the same influent feed. Even though the relative abundance of CAP, revealed by 16S rRNA gene amplicon sequencing, was similar in both treatment trains, a clade-level analysis, using combined 16S rRNA-gene based amplicon sequencing and oligotyping analysis and metagenomics analysis, revealed the distinct CAP microdiversity between the S2EBPR and A2O configurations that likely attributed to the improved performance in S2EBPR in comparison to conventional EBPR. Furthermore, genome-resolved metagenomics enabled extraction of three metagenome-assembled genomes (MAGs) belonging to CAP clades IIB (RCAB4-2), IIC (RC14) and II (RC18), from full-scale EBPR sludge for the first time, including a distinct Ca. Accumulibacter clade that is dominant and associated only with the S2EBPR configuration. The results also revealed the temporally increasing predominance of RC14, which belonged to Clade IIC, during the implementation of the S2EBPR configuration. Finally, we also show the existence of previously uncharacterized diversity of clades of CAP, namely the clades IIB and as yet unidentified clade of type II, in full-scale EBPR communities, highlighting the unknown diversity of CAP communities in full-scale EBPR systems.
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Affiliation(s)
- Varun N Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Brown and Caldwell, One Tech Drive, Andover, MA 01810, United States
| | - Guangyu Li
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Nicholas B Tooker
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Department of Civil and Environmental Engineering, University of Massachusetts-Amherst, Amherst, MA 01002, United States
| | - Zihan Dai
- Infrastructure and Environment Division, University of Glasgow, Glasgow G12 8LT, United Kingdom
| | - Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Charles Bott
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23454, United States
| | - Paul Dombrowski
- Woodard & Curran, Inc., 1699 King Street, Enfield, CT 06082, United States
| | - Peter Schauer
- Clean Water Services, 16060 SW 85th Avenue, Tigard, OR 97224, United States
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Cornell University, Ithaca NY 14853, United States.
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11
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Park C, Takeuchi N. Unmasking photogranulation in decreasing glacial albedo and net autotrophic wastewater treatment. Environ Microbiol 2021; 23:6391-6404. [PMID: 34545673 PMCID: PMC9292683 DOI: 10.1111/1462-2920.15780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
In both natural and built environments, microbes on occasions manifest in spherical aggregates instead of substratum‐affixed biofilms. These microbial aggregates are conventionally referred to as granules. Cryoconites are mineral rich granules that appear on glacier surfaces and are linked with expanding surface darkening, thus decreasing albedo, and enhanced melt. The oxygenic photogranules (OPGs) are organic rich granules that grow in wastewater, which enables wastewater treatment with photosynthetically produced oxygen and which presents potential for net autotrophic wastewater treatment in a compact system. Despite obvious differences inherent in the two, cryoconite and OPG pose striking resemblance. In both, the order Oscillatoriales in Cyanobacteria envelope inner materials and develop dense spheroidal aggregates. We explore the mechanism of photogranulation on account of high similarity between cryoconites and OPGs. We contend that there is no universal external cause for photogranulation. However, cryoconites and OPGs, as well as their intravariations, which are all under different stress fields, are the outcome of universal physiological processes of the Oscillatoriales interfacing with goldilocks interactions of stresses. Finding the rules of photogranulation may enhance engineering of glacier and wastewater systems to manipulate their ecosystem impacts.
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Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
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12
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Wang Y, Gao H, F Wells G. Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms. Environ Microbiol 2021; 23:3274-3293. [PMID: 33769674 DOI: 10.1111/1462-2920.15486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023]
Abstract
Unusually high accumulation of the potent greenhouse gas nitrous oxide (N2 O) has previously been documented in denitrifying biological phosphorus (P) removal bioprocesses, but the roles of differential denitrification gene expression patterns and ecological interactions between key functional groups in driving these emissions are not well understood. To address these knowledge gaps, we applied genome-resolved metagenomics and metatranscriptomics to a denitrifying bioprocess enriched in as-yet-uncultivated denitrifying polyphosphate accumulating organisms (PAOs) affiliated with Candidatus Accumulibacter. The six transcriptionally most active populations in the community included three co-occurring Accumulibacter strains affiliated with clades IF (a novel clade identified in this study), IA and IC, a competing glycogen accumulating organism (GAO) affiliated with Competibacteraceae (GAO1), a Gammaproteobacteria PR6 and an Anaerolineae CH7. Strongly elevated expression of nitrite reductase genes compared to nitrous oxide reductase genes was observed in the overall community and in Accumulibacter populations, suggesting a strong role for differential gene expression in driving N2 O accumulation. Surprisingly, while ~90% of the nirS gene transcripts were expressed by the three co-occurring PAO populations, ~93% of the norB gene transcripts were expressed by GAO1 and ~75% of the norZ gene transcripts were mapped to PR6 and several other non-PAO flanking populations. This suggests the potential for cooperation between flanking populations and PAOs in reducing denitrification intermediates. Such cooperation may benefit the community by reducing the accumulation of toxic nitric oxide.
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Affiliation(s)
- Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
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13
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Tomás-Martínez S, Kleikamp HBC, Neu TR, Pabst M, Weissbrodt DG, van Loosdrecht MCM, Lin Y. Production of nonulosonic acids in the extracellular polymeric substances of "Candidatus Accumulibacter phosphatis". Appl Microbiol Biotechnol 2021; 105:3327-3338. [PMID: 33791836 PMCID: PMC8053191 DOI: 10.1007/s00253-021-11249-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/02/2021] [Accepted: 03/17/2021] [Indexed: 11/30/2022]
Abstract
Nonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as an important compound in the extracellular matrix of virtually all microbial life and in "Candidatus Accumulibacter phosphatis", a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of "Ca. Accumulibacter" to produce different types of NulOs. Proteomic analysis showed the ability of "Ca. Accumulibacter" to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of "Ca. Accumulibacter" in particular, and biofilms in general. KEY POINTS: •"Ca. Accumulibacter" has the potential to produce a range of nonulosonic acids. •Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids. •The role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.
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Affiliation(s)
- Sergio Tomás-Martínez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Hugo B C Kleikamp
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre of Environmental Research - UFZ, Brueckstrasse 3A, 39114, Magdeburg, Germany
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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14
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Pelevina AV, Berestovskaya YY, Grachev VA, Dorofeeva IK, Sorokin VV, Dorofeev AG, Kallistova AY, Nikolaev YA, Kotlyarov RY, Beletskii AV, Ravin NV, Pimenov NV, Mardanov AV. A Microbial Consortium Removing Phosphates under Conditions of Cyclic Aerobic-Anaerobic Cultivation. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721010082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Roy S, Guanglei Q, Zuniga-Montanez R, Williams RB, Wuertz S. Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal. Curr Opin Biotechnol 2021; 67:166-174. [PMID: 33582603 DOI: 10.1016/j.copbio.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/02/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is an efficient, cost-effective, and sustainable method for removing excess phosphorus from wastewater. Polyphosphate accumulating organisms (PAOs) exhibit a unique physiology alternating between anaerobic conditions for uptake of carbon substrates and aerobic or anoxic conditions for phosphorus uptake. The implementation of high-throughput sequencing technologies and advanced molecular tools along with biochemical characterization has provided many new perspectives on the EBPR process. These approaches have helped identify a wide range of carbon substrates and electron acceptors utilized by PAOs that in turn influence interactions with microbial community members and determine overall phosphorus removal efficiency. In this review, we systematically discuss the microbial diversity and metabolic response to a range of environmental conditions and process control strategies in EBPR.
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Affiliation(s)
- Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Qiu Guanglei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Rohan Bh Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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Adler A, Holliger C. Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back. Front Microbiol 2020; 11:574361. [PMID: 33324361 PMCID: PMC7726351 DOI: 10.3389/fmicb.2020.574361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/12/2020] [Indexed: 01/31/2023] Open
Abstract
Aerobic granular sludge (AGS) is a promising alternative wastewater treatment to the conventional activated sludge system allowing space and energy saving. Basic understanding of AGS has mainly been obtained using simple wastewater containing acetate and propionate as carbon source. Yet, the aspect and performances of AGS grown in such model systems are different from those obtained in reactor treating real wastewater. The impact of fermentable and hydrolyzable compounds on already formed AGS was assessed separately by changing the composition of the influent from simple wastewater containing volatile fatty acids to complex monomeric wastewater containing amino acids and glucose, and then to complex polymeric wastewater containing also starch and peptone. The reversibility of the observed changes was assessed by changing the composition of the wastewater from complex monomeric back to simple. The introduction of fermentable compounds in the influent left the settling properties and nutrient removal performance unchanged, but had a significant impact on the bacterial community. The proportion of Gammaproteobacteria diminished to the benefit of Actinobacteria and the Saccharibateria phylum. On the other hand, the introduction of polymeric compounds altered the settling properties and denitrification efficiency, but induced smaller changes in the bacterial community. The changes induced by the wastewater transition were only partly reversed. Seven distinct stables states of the bacterial community were detected during the 921 days of experiment, four of them observed with the complex monomeric wastewater. The transitions between these states were not only caused by wastewater changes but also by operation failures and other incidences. However, the nutrient removal performance and settling properties of the AGS were globally maintained due to the functional redundancy of its bacterial community.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Environmental Engineering Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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17
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Revealing the Metabolic Flexibility of " Candidatus Accumulibacter phosphatis" through Redox Cofactor Analysis and Metabolic Network Modeling. Appl Environ Microbiol 2020; 86:AEM.00808-20. [PMID: 33008826 DOI: 10.1128/aem.00808-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Environmental fluctuations in the availability of nutrients lead to intricate metabolic strategies. "Candidatus Accumulibacter phosphatis," a polyphosphate-accumulating organism (PAO) responsible for enhanced biological phosphorus removal (EBPR) from wastewater treatment systems, is prevalent in aerobic/anaerobic environments. While the overall metabolic traits of these bacteria are well described, the nonavailability of isolates has led to controversial conclusions on the metabolic pathways used. In this study, we experimentally determined the redox cofactor preferences of different oxidoreductases in the central carbon metabolism of a highly enriched "Ca Accumulibacter phosphatis" culture. Remarkably, we observed that the acetoacetyl coenzyme A reductase engaged in polyhydroxyalkanoate (PHA) synthesis is NADH preferring instead of showing the generally assumed NADPH dependency. This allows rethinking of the ecological role of PHA accumulation as a fermentation product under anaerobic conditions and not just a stress response. Based on previously published metaomics data and the results of enzymatic assays, a reduced central carbon metabolic network was constructed and used for simulating different metabolic operating modes. In particular, scenarios with different acetate-to-glycogen consumption ratios were simulated, which demonstrated optima using different combinations of glycolysis, glyoxylate shunt, or branches of the tricarboxylic acid (TCA) cycle. Thus, optimal metabolic flux strategies will depend on the environment (acetate uptake) and on intracellular storage compound availability (polyphosphate/glycogen). This NADH-related metabolic flexibility is enabled by the NADH-driven PHA synthesis. It allows for maintaining metabolic activity under various environmental substrate conditions, with high carbon conservation and lower energetic costs than for NADPH-dependent PHA synthesis. Such (flexible) metabolic redox coupling can explain the competitiveness of PAOs under oxygen-fluctuating environments.IMPORTANCE Here, we demonstrate how microbial storage metabolism can adjust to a wide range of environmental conditions. Such flexibility generates a selective advantage under fluctuating environmental conditions. It can also explain the different observations reported in PAO literature, including the capacity of "Ca Accumulibacter phosphatis" to act like glycogen-accumulating organisms (GAOs). These observations stem from slightly different experimental conditions, and controversy arises only when one assumes that metabolism can operate only in a single mode. Furthermore, we also show how the study of metabolic strategies is possible when combining omics data with functional cofactor assays and modeling. Genomic information can only provide the potential of a microorganism. The environmental context and other complementary approaches are still needed to study and predict the functional expression of such metabolic potential.
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Huo T, Zhao Y, Tang X, Zhao H, Ni S, Gao Q, Liu S. Metabolic acclimation of anammox consortia to decreased temperature. ENVIRONMENT INTERNATIONAL 2020; 143:105915. [PMID: 32652345 DOI: 10.1016/j.envint.2020.105915] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Widespread application of anammox process has been primarily limited to the high sensitivity of anammox consortia to fluctuations of temperature. However, the metabolic acclimation of anammox consortia to decreased temperature remains unclear, which is the core of developing potential strategies for improving their low-temperature resistance. Here, we operated anammox reactors at 25 °C and 35 °C to explore the acclimation mechanism of anammox consortia in terms of metabolic responses and cross-feedings. Accordingly, we found that the adaptation of anammox consortia to ambient temperature (25 °C) was significantly linked to energy conservation strategy, resulting in decreased extracellular polymeric substance secretion, accumulation of ATP and amino acids. The expression patterns of cold shock proteins and core enzymes caused the apparent metabolic advantage of Candidatus Brocadia fulgida for acclimation to ambient temperature compared to other anammox species. Importantly, strengthened cross-feedings of amino acids, nitrite and glycine betaine benefited adaptation of anammox consortia to ambient temperature. Our work not only uncovers the temperature-adaptive mechanisms of anammox consortia, but also emphasizes the important role of metabolic cross-feeding in the temperature adaptation of microbial community.
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Affiliation(s)
- Tangran Huo
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yunpeng Zhao
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xi Tang
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Huazhang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
| | - Sitong Liu
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
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19
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Profiling population-level diversity and dynamics of Accumulibacter via high throughput sequencing of ppk1. Appl Microbiol Biotechnol 2019; 103:9711-9722. [DOI: 10.1007/s00253-019-10183-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/09/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022]
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20
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Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY, Zhang T. Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. MICROBIOME 2019; 7:122. [PMID: 31462278 PMCID: PMC6714388 DOI: 10.1186/s40168-019-0730-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation anammox (PNA) reactors have received considerable attention for their crucial roles in energy-efficient nitrogen removal from wastewater. However, a comprehensive understanding of how abiotic and biotic factors shape bacterial community assembly in PNA reactors is not well reported. RESULTS Here, we used integrated multi-omics (i.e., high-throughput 16S rRNA gene, metagenomic, metatranscriptomic, and metaproteomic sequencing) to reveal how abiotic and biotic factors shape the bacterial community assembly in a lab-scale one-stage PNA reactor treating synthetic wastewater. Analysis results of amplicon sequences (16S rRNA gene) from a time-series revealed distinct relative abundance patterns of the key autotrophic bacteria, i.e., anammox bacteria and ammonia-oxidizing bacteria (AOB), and the associated heterotrophic populations in the seed sludge and the sludge at the new stable state after deterioration. Using shotgun metagenomic sequences of anammox sludge, we recovered 58 metagenome-assembled genomes (MAGs), including 3 MAGs of anammox bacteria and 3 MAGs of AOB. The integrated metagenomic, metatranscriptomic, and metaproteomic data revealed that nitrogen metabolism is the most active process in the studied PNA reactor. The abundant heterotrophs contribute to the reduction of nitrate to nitrite/ammonium for autotrophic bacteria (anammox bacteria and AOB). Genomic and transcriptomic data revealed that the preference for electron donors of the dominant heterotrophs in different bacterial assemblages (seed and new stable state) varied along with the shift in anammox bacteria that have different metabolic features in terms of EPS composition. Notably, the most abundant heterotrophic bacteria in the reactor were more auxotrophic than the less abundant heterotrophs, regarding the syntheses of amino acids and vitamins. In addition, one of the abundant bacteria observed in the bacterial community exhibited highly transcribed secretion systems (type VI). CONCLUSIONS These findings provide the first insight that the bacterial communities in the PNA reactor are defined by not only abiotic factors (operating mode) but also metabolic interactions, such as nitrogen metabolism, exchange of electron donors, and auxotrophies.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Qigui Niu
- School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, 266237 Shandong Province People’s Republic of China
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Mishty Negi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579 Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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21
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Gonzalez-Gil L, Krah D, Ghattas AK, Carballa M, Wick A, Helmholz L, Lema JM, Ternes TA. Biotransformation of organic micropollutants by anaerobic sludge enzymes. WATER RESEARCH 2019; 152:202-214. [PMID: 30669042 DOI: 10.1016/j.watres.2018.12.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/30/2018] [Accepted: 12/27/2018] [Indexed: 05/27/2023]
Abstract
Biotransformation of organic micropollutants (OMPs) in wastewater treatment plants ultimately depends on the enzymatic activities developed in each biological process. However, few research efforts have been made to clarify and identify the role of enzymes on the removal of OMPs, which is an essential knowledge to determine the biotransformation potential of treatment technologies. Therefore, the purpose of the present study was to investigate the enzymatic transformation of 35 OMPs under anaerobic conditions, which have been even less studied than aerobic systems. Initially, 13 OMPs were identified to be significantly biotransformed (>20%) by anaerobic sludge obtained from a full-scale anaerobic digester, predestining them as potential targets of anaerobic enzymes. Native enzymes were extracted from this anaerobic sludge to perform transformation assays with the OMPs. In addition, the effect of detergents to recover membrane enzymes, as well as the effects of cofactors and inhibitors to promote and suppress specific enzymatic activities were evaluated. In total, it was possible to recover enzymatic activities towards 10 out of these 13 target OMPs (acetyl-sulfamethoxazole and its transformation product sulfamethoxazole, acetaminophen, atenolol, clarithromycin, citalopram, climbazole, erythromycin, and terbutryn, venlafaxine) as well as towards 8 non-target OMPs (diclofenac, iopamidol, acyclovir, acesulfame, and 4 different hydroxylated metabolites of carbamazepine). Some enzymatic activities likely involved in the anaerobic biotransformation of these OMPs were identified. Thereby, this study is a starting point to unravel the still enigmatic biotransformation of OMPs in wastewater treatment systems.
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Affiliation(s)
- Lorena Gonzalez-Gil
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, Santiago de Compostela, E-15782, Spain.
| | - Daniel Krah
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, Koblenz, D-56068, Germany
| | - Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, Koblenz, D-56068, Germany
| | - Marta Carballa
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, Santiago de Compostela, E-15782, Spain
| | - Arne Wick
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, Koblenz, D-56068, Germany
| | - Lissa Helmholz
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, Koblenz, D-56068, Germany
| | - Juan M Lema
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, Santiago de Compostela, E-15782, Spain
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, Koblenz, D-56068, Germany
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Integrated Omic Analyses Provide Evidence that a " Candidatus Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions. mSystems 2019; 4:mSystems00193-18. [PMID: 30944872 PMCID: PMC6446978 DOI: 10.1128/msystems.00193-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/13/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of "Candidatus Accumulibacter phosphatis" to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of "Ca. Accumulibacter phosphatis" in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published "Ca. Accumulibacter phosphatis" genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a "Ca. Accumulibacter phosphatis" strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor's performance suggested the ability of the enriched "Ca. Accumulibacter phosphatis" strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads ("Ca. Accumulibacter phosphatis" UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb 3 cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that "Ca. Accumulibacter phosphatis" UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE "Candidatus Accumulibacter phosphatis" is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that "Ca. Accumulibacter phosphatis" is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.
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Ou D, Li W, Li H, Wu X, Li C, Zhuge Y, Liu YD. Enhancement of the removal and settling performance for aerobic granular sludge under hypersaline stress. CHEMOSPHERE 2018; 212:400-407. [PMID: 30149313 DOI: 10.1016/j.chemosphere.2018.08.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/29/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
The aerobic granular sludge (AGS) dominated by halophilic microorganisms, was successfully cultivated in a lab-scale sequencing batch reactor (SBR) under varying salinity levels (from 0% to 6% (w/v)). Removal performance of AGS improved with the increase of salinity and increased up to 42.86 mg g-1 VSS h-1 at 6% salinity. Increased salinity resulted in better settling performance of AGS in terms of the sludge volume index (SVI), which was initially 148.80 mL/g at 0% salinity and gradually decreased to 59.1 mL/g at 6% salinity. The increase of salinity stimulated bacteria to secret excessive extracellular polymeric substances (EPS), with its highest production of 725.5 mg/(g·VSS) at 5% salinity. The total protein (PN) exhibited highly positive correlation with the total EPS (R = 0.951), indicating that selective secretion of some functional PN played a key constituent in resisting the external osmotic pressure and improving sludge performance. Salinicola, accounted for up to 91% relative abundance at 6% salinity, showed the high positive correlation (R = 0.953) with salinity. The enrichment of such halophilic or halotolerant microbial community assured both stable and improved removal performance in the AGS system. The enrichment of salt response pathways and altered metabolic processes for salt-tolerant bacteria indicated that the microbial community formed special metabolic pattern under long-term hypersaline stress to maintain favourable cellular activity and removal performance.
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Affiliation(s)
- Dong Ou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Wei Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Xiao Wu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Cheng Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Yangyang Zhuge
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Yong-di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
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24
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Lin X, Wang Y, Ma X, Yan Y, Wu M, Bond PL, Guo J. Evidence of differential adaptation to decreased temperature by anammox bacteria. Environ Microbiol 2018; 20:3514-3528. [PMID: 30051608 DOI: 10.1111/1462-2920.14306] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 06/05/2018] [Indexed: 11/27/2022]
Abstract
Low temperature is recognized as one of the major barriers for the application of the anaerobic ammonium oxidation (anammox) process to treat mainstream wastewater. Studies are yet to reveal the underlying biological limitations and molecular mechanisms associated with the inhibition of low temperature on the anammox process. In this study, metaproteomics was used to examine proteome modulation patterns of the anammox community occurring at different temperatures. The anammox community remarkably altered their proteomes when the temperature decreased from 35 °C to 20 °C. This was especially for proteins involved in energy conversion, transcription and translation and inorganic ion transport. However, at 15 °C the anammox activities became distinctly inhibited, and there was evidence of energy limitations and severe stress in Candidatus Kuenenia and to a lesser degree in Candidatus Brocadia. Candidatus Jettenia exhibited more changes in its proteome at 15 °C. From the proteomes, at the lower temperatures there was evidence of stress caused by toxic nitrogen compounds or reactive oxygen species in the anammox bacteria. Hydroxylamine oxidoreductase (HAO)-like proteins and an oxidative stress response protein (a catalase) were in high abundance to potentially ameliorate these inhibitory effects. This study offers metaproteomic insight into the anammox community-based physiological response to decreasing temperatures.
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Affiliation(s)
- Ximao Lin
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, People's Republic of China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, People's Republic of China
| | - Xiao Ma
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, People's Republic of China
| | - Yuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, People's Republic of China
| | - Min Wu
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, People's Republic of China
| | - Philip L Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, QLD, St. Lucia, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, QLD, St. Lucia, 4072, Australia
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25
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Sun Y, Guan Y, Wang D, Liang K, Wu G. Potential roles of acyl homoserine lactone based quorum sensing in sequencing batch nitrifying biofilm reactors with or without the addition of organic carbon. BIORESOURCE TECHNOLOGY 2018; 259:136-145. [PMID: 29549833 DOI: 10.1016/j.biortech.2018.03.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 05/03/2023]
Abstract
Two lab-scale nitrifying sequencing batch biofilm reactors, with (SBBR_CN) or without the addition of organics (SBBR_N), were operated to investigate potential roles of acyl homoserine lactone (AHL) based quorum sensing. AHLs of N-[(RS)-3-Hydroxybutyryl]-L-homoserine lactone, N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-L-homoserine lactone (C8-HSL) were detected in both reactors. C6-HSL and C8-HSL were also detected in batch experiments, especially with stimulated nitrite oxidizing bacteria activities. Quorum sensing affected biofilm formation mainly through the regulation of extracellular protein production. By the metagenomics analysis, many identified genera and species could participate in quorum sensing, quorum quenching and extracellular polymeric substances (EPS) production. A high quorum quenching activity was obtained in SBBR_CN, whereas a high quorum sensing activity in SBBR_N. Nitrosomonas-like ammonia oxidizing bacteria, Nitrospira-like nitrite oxidizing bacteria and Comammox harbored genes for AHL synthesis and EPS production. Possible relationships among AHLs synthesis, biofilm formation and nitrifiers activity were proposed.
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Affiliation(s)
- Yuepeng Sun
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Yuntao Guan
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Dan Wang
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Kai Liang
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Guangxue Wu
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
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26
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Designer microbiomes for environmental, energy and health biotechnology. Curr Opin Microbiol 2018; 43:117-123. [DOI: 10.1016/j.mib.2017.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/08/2017] [Accepted: 12/20/2017] [Indexed: 01/19/2023]
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27
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Wang Z, Dunne A, van Loosdrecht MCM, Saikaly PE. Effect of Salt on the Metabolism of ' Candidatus Accumulibacter' Clade I and II. Front Microbiol 2018; 9:479. [PMID: 29616002 PMCID: PMC5865004 DOI: 10.3389/fmicb.2018.00479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/28/2018] [Indexed: 11/29/2022] Open
Abstract
Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, ‘Candidatus Accumulibacter phosphatis’ Clade I and II (hereafter referred to as PAOI and PAOII) were highly enriched (∼90% in relative abundance as determined by quantitative FISH) in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P) and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5–6% at 0.256 mol/L NaCl or KCl) while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29–30% at 0.256 mol/L NaCl or KCl). In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K+) and sodium (Na+) ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance.
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Affiliation(s)
- Zhongwei Wang
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aislinn Dunne
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Pascal E Saikaly
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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28
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Mardanov AV, Beletskii AV, Kallistova AY, Kotlyarov RY, Nikolaev YA, Kevbrina MV, Agarev AM, Ravin NV, Pimenov NV. Dynamics of the composition of a microbial consortium during start-up of a single-stage constant flow laboratory nitritation/anammox setup. Microbiology (Reading) 2016. [DOI: 10.1134/s002626171606014x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Metabolic Responses of Bacterial Cells to Immobilization. Molecules 2016; 21:molecules21070958. [PMID: 27455220 PMCID: PMC6273605 DOI: 10.3390/molecules21070958] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 01/15/2023] Open
Abstract
In recent years immobilized cells have commonly been used for various biotechnological applications, e.g., antibiotic production, soil bioremediation, biodegradation and biotransformation of xenobiotics in wastewater treatment plants. Although the literature data on the physiological changes and behaviour of cells in the immobilized state remain fragmentary, it is well documented that in natural settings microorganisms are mainly found in association with surfaces, which results in biofilm formation. Biofilms are characterized by genetic and physiological heterogeneity and the occurrence of altered microenvironments within the matrix. Microbial cells in communities display a variety of metabolic differences as compared to their free-living counterparts. Immobilization of bacteria can occur either as a natural phenomenon or as an artificial process. The majority of changes observed in immobilized cells result from protection provided by the supports. Knowledge about the main physiological responses occurring in immobilized cells may contribute to improving the efficiency of immobilization techniques. This paper reviews the main metabolic changes exhibited by immobilized bacterial cells, including growth rate, biodegradation capabilities, biocatalytic efficiency and plasmid stability.
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30
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Albertsen M, McIlroy SJ, Stokholm-Bjerregaard M, Karst SM, Nielsen PH. "Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. Front Microbiol 2016; 7:1033. [PMID: 27458436 PMCID: PMC4930944 DOI: 10.3389/fmicb.2016.01033] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/20/2016] [Indexed: 01/16/2023] Open
Abstract
Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial “Candidatus Accumulibacter phosphatis” (Accumulibacter) and the model GAO being the gammaproteobacterial “Candidatus Competibacter phosphatis”. Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set.
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Affiliation(s)
- Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Simon J McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Mikkel Stokholm-Bjerregaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark; Krüger A/SAalborg, Denmark
| | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
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31
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Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism. Appl Environ Microbiol 2016; 82:4126-4132. [PMID: 27129963 DOI: 10.1128/aem.00493-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem.
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