1
|
Wei Y, Chen Y, Xia W, Ye M, Li YY. Dynamic pulse approach to enhancing mainstream Anammox process stability: Integrating sidestream support and tackling nitrite-oxidizing bacteria challenges. BIORESOURCE TECHNOLOGY 2024; 395:130327. [PMID: 38242244 DOI: 10.1016/j.biortech.2024.130327] [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: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Nitrite-oxidizing bacteria (NOB) seriously threaten the partial nitritation and Anammox (PN/A) process, hindering its mainstream application. Herein, a one-stage PN/A reactor was continuously operated for 245 days under nitrogen loading rate lifted from 0.4 g N/L/d to 0.6 g N/L/d and 0.8 g N/L/d with the nitrogen removal efficiency of 71 %, 64 %, and 41 %, respectively. Furthermore, the NOB species over time was identified as Nitrospira_sp._OLB3, exhibiting an increase of the relative abundance from 0.9 % to 4.3 %. The hydroxyapatite (HAP) granules gradually lost their microbiological function of Anammox bacteria then aged, leading to NOB dominance. Therefore, one "pulse therapy" was introduced and combined with "continuous enhancement" of Anammox sludge supported by sidestream to competitively limit the NOB dynamics. The treatment's effect persisted for around two months. The strategy that returning at least 50 % of the impaired HAP granular sludge to the sidestream for recultivation could fulfill the bottlenecks of mainstream PN/A.
Collapse
Affiliation(s)
- Yanxiao Wei
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yujie Chen
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Weizhe Xia
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Min Ye
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| |
Collapse
|
2
|
Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H. Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales. THE ISME JOURNAL 2023; 17:2123-2133. [PMID: 37749300 PMCID: PMC10579370 DOI: 10.1038/s41396-023-01518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.
Collapse
Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Anne Daebeler
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 7, 370 05, Budweis, Czech Republic
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | - Rasmus H Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Vienna, Austria.
| |
Collapse
|
3
|
Zhao J, Guan X, Shi X, Guo W, Luo X. Niche differentiation and influencing factors of nitrite oxidation bacteria Nitrospira in sediments of the Luan River estuary in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:103313-103323. [PMID: 37688699 DOI: 10.1007/s11356-023-29609-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 08/27/2023] [Indexed: 09/11/2023]
Abstract
In the estuarine sediment, the nitrite oxidation process mediated by bacteria significantly influences nitrification. Nitrospira is the most widely distributed nitrite-oxidizing bacteria (NOB) and can adapt to various environments. In this study, the Nitrospira-specific primer nxrB 169F-638R was used to analyze the microbial communities in the sediments of low-, middle-, and high-level zones in the Luan River estuary. The structure of the microbial community and its response to environmental factors were also assessed. The abundance and diversity of Nitrospira were the highest in the low-level zone and lowest in the high-level zone. Lineage II and lineage IV were the dominant Nitrospira at 43.58% and 32.09%, respectively. The distribution pattern of Nitrospira was also affected by complex environmental factors, such as the concentration of NH4+, Fe, and Cu cations. This study provides novel insights into the niche differentiation and adaptation strategies of Nitrospira in an estuarine sediment environment and will help to facilitate single-step nitrification.
Collapse
Affiliation(s)
- Jiawei Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xiaonan Shi
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Wei Guo
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Ximing Luo
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China.
| |
Collapse
|
4
|
Su Z, Liu T, Guo J, Zheng M. Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12557-12570. [PMID: 37589598 PMCID: PMC10470456 DOI: 10.1021/acs.est.3c00636] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing bacteria (NOB). Since NOB were first isolated 130 years ago, the understanding of the phylogenetical and physiological diversities of NOB has been gradually deepened. In recent endeavors of advanced biological nitrogen removal, NOB have been more considered as a troublesome disruptor, and strategies on NOB suppression often fail in practice after long-term operation due to the growth of specific NOB that are able to adapt to even harsh conditions. In line with a review of the history of currently known NOB genera, a phylogenetic tree is constructed to exhibit a wide range of NOB in different phyla. In addition, the growth behavior and metabolic performance of different NOB strains are summarized. These specific features of various NOB (e.g., high oxygen affinity of Nitrospira, tolerance to chemical inhibitors of Nitrobacter and Candidatus Nitrotoga, and preference to high temperature of Nitrolancea) highlight the differentiation of the NOB ecological niche in biological nitrogen processes and potentially support their adaptation to different suppression strategies (e.g., low dissolved oxygen, chemical treatment, and high temperature). This review implicates the acquired physiological characteristics of NOB to their emergence from a genomic and ecological perspective and emphasizes the importance of understanding physiological characterization and genomic information in future wastewater treatment studies.
Collapse
Affiliation(s)
- Zicheng Su
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Tao Liu
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Min Zheng
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| |
Collapse
|
5
|
Daebeler A, Güell‐Bujons Q, Mooshammer M, Zechmeister T, Herbold CW, Richter A, Wagner M, Daims H. Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes. Environ Microbiol 2023; 25:1055-1067. [PMID: 36651641 PMCID: PMC10947350 DOI: 10.1111/1462-2920.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.
Collapse
Affiliation(s)
- Anne Daebeler
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Biology Centre CAS, BudweisInstitute of Soil Biology and BiogeochemistryCzechia
| | - Queralt Güell‐Bujons
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Institut de Ciències del Mar (ICM‐CSIC), Passeig Marítim de la Barceloneta 37‐49BarcelonaCataloniaSpain
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | | | - Craig W. Herbold
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | - Michael Wagner
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Holger Daims
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
| |
Collapse
|
6
|
Wang Y, Zeng X, Ma Q, Zhang Y, Yu W, Zheng Z, Zhang N, Xu L. Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China. Front Microbiol 2023; 14:1095937. [PMID: 36819044 PMCID: PMC9929954 DOI: 10.3389/fmicb.2023.1095937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.
Collapse
Affiliation(s)
- Yanan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xibai Zeng, ✉
| | - Qiang Ma
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wantai Yu
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhong Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyang Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
7
|
Chen H, Liu K, Yang E, Chen J, Gu Y, Wu S, Yang M, Wang H, Wang D, Li H. A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159462. [PMID: 36257429 DOI: 10.1016/j.scitotenv.2022.159462] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.
Collapse
Affiliation(s)
- Hong Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China; Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Ke Liu
- China Machinery International Engineering Design & Research Institute Co., Ltd, Changsha 410007, China
| | - Enzhe Yang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Jing Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Yanling Gu
- School of Materials Science and Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Sha Wu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China.
| | - Min Yang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Hong Wang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Hailong Li
- School of Energy Science and Engineering, Central South University, Changsha 410083, China.
| |
Collapse
|
8
|
Sun W, Jiao L, Wu J, Ye J, Wei M, Hong Y. Existence and distribution of novel phylotypes of Nitrospira in water columnsof the South China Sea. iScience 2022; 25:104895. [PMID: 36039301 PMCID: PMC9418846 DOI: 10.1016/j.isci.2022.104895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/15/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
In the biological nitrogen cycle, nitrite oxidation is performed by nitrite oxidation bacteria, of which Nitrospira is widespread and diverse. Communities of Nitrospira were collected at 25-1500 m depths in the South China Sea. Phylogenetic diversity, community composition, and environmental factors were investigated using high-throughput sequencing targeting the nxrB gene and statistical analyses. The community composition of Nitrospira varied spatially and by depth. Among the 24 OTUs with relatively high abundance, 70% were unclassified and not affiliated with the known Nitrospira genus, suggesting a previously unrecognized high diversity of marine Nitrospira. Five known Nitrospira genera were detected, of which the common marine Nitrospira marina was not the dominant species, whereas Candidatus Nitrospira lenta and Candidatus Nitrospira defluvii dominated in shallow habitats. Comammox Candidatus Nitrospira nitrosa was discovered in the marine ecosystem. The niche differentiation of versatile Nitrospira species was mainly shaped by nitrate, temperature, and DO.
Collapse
Affiliation(s)
- Wei Sun
- Guangdong University of Petrochemical Technology, Maoming 525000, P.R.China.,Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China.,Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| | - Lijing Jiao
- Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China.,Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China.,Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China.,Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| | - Mingken Wei
- Guangdong University of Petrochemical Technology, Maoming 525000, P.R.China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China.,Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| |
Collapse
|
9
|
Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B, He Z. Niche differentiation among comammox ( Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 2022; 13:956860. [PMID: 36187961 PMCID: PMC9515657 DOI: 10.3389/fmicb.2022.956860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.
Collapse
Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United States
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| |
Collapse
|
10
|
Wang C, Lin Q, Yao Y, Xu R, Wu X, Meng F. Achieving simultaneous nitrification, denitrification, and phosphorus removal in pilot-scale flow-through biofilm reactor with low dissolved oxygen concentrations: Performance and mechanisms. BIORESOURCE TECHNOLOGY 2022; 358:127373. [PMID: 35623607 DOI: 10.1016/j.biortech.2022.127373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
In this pilot-scale study, a flow-through biofilm reactor (FTBR) was investigated for municipal wastewater treatment. The removal efficiencies for ammonium, total nitrogen, total phosphorus, and chemical oxygen demand were 87.2 ± 17.9%, 61.1 ± 13.9%, 83.5 ± 11.9%, and 92.6 ± 1.7%, respectively, at low dissolved oxygen concentrations (averaged at 0.59 mg/L), indicating the feasibility and robustness of the FTBR for a simultaneous nitrification, denitrification, and phosphorous removal (SNDPR) process. The co-occurrence network of bacteria in the dynamic biofilm was complex, with equivalent bacterial cooperation and competition. Nevertheless, the bacterial interactions in the suspended sludge were mainly cooperative. The presence of dynamic biofilms increased bacterial diversity by creating niche differentiation, which enriched keystone species closely related to nutrient removal. Overall, this study provides a novel FTBR-based SNDPR process and reveals the ecological mechanisms responsible for nutrient removal.
Collapse
Affiliation(s)
- Chao Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China
| | - Qining Lin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China
| | - Yuanyuan Yao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China
| | - Xueshen Wu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, PR China.
| |
Collapse
|
11
|
Oshiki M, Netsu H, Kuroda K, Narihiro T, Fujii N, Kindaichi T, Suzuki Y, Watari T, Hatamoto M, Yamaguchi T, Araki N, Okabe S. Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors. Environ Microbiol 2022; 24:3735-3750. [PMID: 35672869 DOI: 10.1111/1462-2920.16085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022]
Abstract
Aerobic ammonia and nitrite oxidation reactions are fundamental biogeochemical reactions contributing to the global nitrogen cycle. Although aerobic nitrite oxidation yields 4.8-folds less Gibbs free energy (∆Gr ) than aerobic ammonia oxidation in the NH4 + -feeding marine recirculating trickling biofilter reactors operated in the present study, nitrite-oxidizing and not ammonia-oxidizing Nitrospira (sublineage IV) outnumbered ammonia-oxidizing Nitrosomonas (relative abundance; 53.8% and 7.59% respectively). CO2 assimilation efficiencies during ammonia or nitrite oxidation were 0.077 μmol-14 CO2 /μmol-NH3 and 0.053-0.054 μmol-14 CO2 /μmol-NO2 - respectively, and the difference between ammonia and nitrite oxidation was much smaller than the difference of ∆Gr . Free-energy efficiency of nitrite oxidation was higher than ammonia oxidation (31%-32% and 13% respectively), and high CO2 assimilation and free-energy efficiencies were a determinant for the dominance of Nitrospira over Nitrosomonas. Washout of Nitrospira and Nitrosomonas from the trickling biofilter reactors was also examined by quantitative PCR assay. Normalized copy numbers of Nitrosomonas amoA were 1.5- to 1.7-folds greater than Nitrospira nxrB and 16S rRNA gene in the reactor effluents. Nitrosomonas was more susceptible for washout than Nitrospira in the trickling biofilter reactors, which was another determinant for the dominance of Nitrospira in the trickling biofilter reactors.
Collapse
Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.,Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Hirotoshi Netsu
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Naoki Fujii
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Yoshiyuki Suzuki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| |
Collapse
|
12
|
Park S, Cho K, Lee T, Lee E, Bae H. Improved insights into the adaptation and selection of Nitrosomonas spp. for partial nitritation under saline conditions based on specific oxygen uptake rates and next generation sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153644. [PMID: 35122854 DOI: 10.1016/j.scitotenv.2022.153644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Partial nitritation (PN) is a bioprocess that is essential for developing cost-effective biological nitrogen removal processes. Understanding the abundant bacterial communities responsible for nitrification under salt stress conditions is important to achieve a stable PN system for treating saline wastewater. Therefore, in this study, we identified the core nitrifying communities and investigated their correlations with the process parameters in a nitrifying bioreactor that was used for treating saline high-strength ammonia wastewater. A PN system worked efficiently under saline conditions with varying operational factors, such as temperature, dissolved oxygen (DO), and alkalinity. Interestingly, the specific oxygen uptake rate (SOUR) became similar under salt-free and saline media after the salt adaption. Next generation sequencing results suggested that the inactivation of Nitrobacter winogradskyi was a key factor for the PN reaction under salt stress conditions. We also found that Nitrosomonas europaea, a freshwater type ammonia-oxidizing bacteria (AOB), was predominantly found under both salt-free and saline conditions, whereas other halotolerant or halophilic AOB species, including Nitrosomonas nitrosa and Nitrosomonas mobilis, became selectively abundant under saline conditions. This implies that adaptation (training of N. europaea) and selection (presence of N. nitrosa and N. mobilis) were simultaneously attributed to selective ammonia conversion for the PN reaction. The redundancy analysis showed that the salinity and ammonia loading rates were statistically significant process parameters that determined the nitrifying bacterial community, suggesting that these parameters drive the adaptation and selection of the core AOB species during the PN reaction. Furthermore, the correlation analysis revealed that the abundance of N. nitrosa and N. mobilis was critically correlated with the specific oxygen uptake rates in saline media containing ammonia.
Collapse
Affiliation(s)
- Suin Park
- Department of Civil and Environmental Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
| | - Kyungjin Cho
- Center for Water Cycle Research, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Taeho Lee
- Department of Civil and Environmental Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
| | - Eunsu Lee
- R&D Center, POSCO E&C, 241, Incheon tower-daero, Yeonsu-gu, Incheon 22009, Republic of Korea.
| | - Hyokwan Bae
- Department of Civil and Environmental Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea; Institute for Environment and Energy, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
| |
Collapse
|
13
|
Taylor AE, Mellbye BL. Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature. Front Microbiol 2022; 13:817986. [PMID: 35620102 PMCID: PMC9127996 DOI: 10.3389/fmicb.2022.817986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.
Collapse
Affiliation(s)
- Anne E. Taylor
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Brett L. Mellbye
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
14
|
Murakami C, Machida K, Nakao Y, Kindaichi T, Ohashi A, Aoi Y. Mutualistic relationship between Nitrospira and concomitant heterotrophs. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:130-137. [PMID: 34862743 PMCID: PMC9300095 DOI: 10.1111/1758-2229.13030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Nitrifying chemoautotrophs support the growth of diverse concomitant heterotrophs in natural or engineered environments by supplying organic compounds. In this study, we aimed to investigate this microbial association, especially (i) to distinguish whether the relationship between nitrifying chemoautotrophs and heterotrophs is commensal or mutualistic, and (ii) to clarify how heterotrophs promote the growth of autotrophic nitrite-oxidizing bacteria (Nitrospira). Pure cultured Nitrospira (Nitrospira sp. ND1) was employed in this study. Heterotrophs growing with metabolic by-products of Nitrospira as a sole carbon source were isolated from several environmental samples and used to test the growth-promoting activity of Nitrospira. Furthermore, liquid chromatography-mass spectrometry analysis was conducted to evaluate how heterotrophs consumed chemical compounds produced by Nitrospira and newly produced during co-cultivation. Notably, Nitrospira growth was stimulated by co-cultivation with some heterotrophs and the addition of spent media of some strains, suggesting that not only heterotrophs but also Nitrospira received benefits from their mutual co-existence. Furthermore, the data suggested that some of the growth-promoting heterotrophs provided as-yet-unidentified growth-promoting factors to Nitrospira. Overall, Nitrospira and heterotrophs thus appear to exhibit a mutualistic relationship. Such mutualistic relationships between autotrophs and heterotrophs would contribute to the stability and diversity of microbial ecosystems.
Collapse
Affiliation(s)
- Chiho Murakami
- Department of Civil and Environmental EngineeringGraduate School of Engineering Hiroshima UniversityHiroshimaJapan
- Unit of Biotechnology, Graduate School of Integrated Sciences for LifeHiroshima UniversityHiroshimaJapan
- Institute for Sustainable Science and DevelopmentHiroshima UniversityHiroshimaJapan
| | - Koshi Machida
- Waseda Research Institute for Science and EngineeringWaseda UniversityTokyoJapan
| | - Yoichi Nakao
- Waseda Research Institute for Science and EngineeringWaseda UniversityTokyoJapan
| | - Tomonori Kindaichi
- Department of Civil and Environmental EngineeringGraduate School of Engineering Hiroshima UniversityHiroshimaJapan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental EngineeringGraduate School of Engineering Hiroshima UniversityHiroshimaJapan
| | - Yoshiteru Aoi
- Unit of Biotechnology, Graduate School of Integrated Sciences for LifeHiroshima UniversityHiroshimaJapan
- Institute for Sustainable Science and DevelopmentHiroshima UniversityHiroshimaJapan
| |
Collapse
|
15
|
Jia B, Chang X, Fu Y, Heng W, Ye Z, Liu P, Liu L, Al Shoffe Y, Watkins CB, Zhu L. Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears. BMC Microbiol 2022; 22:18. [PMID: 34996363 PMCID: PMC8742312 DOI: 10.1186/s12866-021-02432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/28/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. RESULTS The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. CONCLUSIONS It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.
Collapse
Affiliation(s)
- Bing Jia
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Xiao Chang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Yuanyuan Fu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Wei Heng
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Zhenfeng Ye
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Pu Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Li Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Yosef Al Shoffe
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Liwu Zhu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China.
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
16
|
Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
Collapse
Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| |
Collapse
|
17
|
Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/aem.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
Collapse
|
18
|
Bayer B, Saito MA, McIlvin MR, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. THE ISME JOURNAL 2021; 15:1025-1039. [PMID: 33230266 PMCID: PMC8115632 DOI: 10.1038/s41396-020-00828-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
Collapse
Affiliation(s)
- Barbara Bayer
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | - Mak A. Saito
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Matthew R. McIlvin
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands
| | - Dawn M. Moran
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | | | - Alyson E. Santoro
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| |
Collapse
|
19
|
Akinwole P, Kaplan L, Findlay R. Elucidating stream bacteria utilizing terrestrial dissolved organic matter. World J Microbiol Biotechnol 2021; 37:32. [DOI: 10.1007/s11274-021-02997-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
|
20
|
Wang X, Lu L, Zhou X, Tang X, Kuang L, Chen J, Shan J, Lu H, Qin H, Adams J, Wang B. Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary. Front Microbiol 2021; 11:618287. [PMID: 33584582 PMCID: PMC7873905 DOI: 10.3389/fmicb.2020.618287] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 01/13/2023] Open
Abstract
The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.
Collapse
Affiliation(s)
- Xinxin Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China.,Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Xue Zhou
- College of Agricultural Engineering, Hohai University, Nanjing, China
| | - Xiufeng Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Junhui Chen
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hua Qin
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jonathan Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
21
|
Fujitani H, Nomachi M, Takahashi Y, Hasebe Y, Eguchi M, Tsuneda S. Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions. FEMS Microbiol Lett 2021; 367:5731803. [PMID: 32037440 DOI: 10.1093/femsle/fnaa025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/08/2020] [Indexed: 12/25/2022] Open
Abstract
In artificial engineered systems, nitrification is a key reaction that accounts for the removal of biological nitrogen. Recently, a single microbe capable of oxidizing ammonia to nitrate, known as a complete ammonia oxidizer (comammox), has been discovered. Although the abundance and diversity of comammox Nitrospira in engineered systems have been identified through molecular-based approaches, the enrichment and isolation of comammox Nitrospira remains a challenge. Therefore, the aim of this study was to enrich comammox Nitrospira from nitrifying granules, which were used to increase the efficiency of biological nitrogen removal in wastewater treatment plants. We sought to accomplish this through the use of a fixed-bed continuous feeding bioreactor. Fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing and qPCR of functional genes were utilized to monitor the growth of nitrifiers including comammox Nitrospira. Cloning of comammox amoA genes identified amoA phylogeny of enriched comammox Nitrospira. This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.
Collapse
Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, 305-8566, Japan.,Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yu Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoshiaki Hasebe
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Masahiro Eguchi
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| |
Collapse
|
22
|
Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
Collapse
Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| |
Collapse
|
23
|
Choi D, Lee C, Jung J. Innovative start-up strategies for single-stage deammonification with conventional activated sludge: Results of a pilot-scale demonstration. BIORESOURCE TECHNOLOGY 2020; 309:123423. [PMID: 32361617 DOI: 10.1016/j.biortech.2020.123423] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
This study investigated innovative start-up strategies of a pilot-scale sequencing batch reactor (SBR) for single-stage deammonification using activated sludge as the sole inoculum source. In 24 m3 aerobic oxidizing bacteria cultivation plant, nitrogen loss efficiency was suggested to be an indicator for determining duration of cultivation. In 12 m3 ANAMMOX (ANaerobic AMMonium OXidation) cultivation plant, combined strategy (sequential fed-batch and continuous modes) was adopted to promote ANAMMOX activity from activated sludge. Both the cultivated sludge were inoculated in 24 m3 pilot-plant for single-stage SBR with deammonification. The feed distribution strategy was used to cultivate ANAMMOX bacteria selectively resulting in nitrogen removal rate of 0.73 kg/m3/d and nitrogen removal efficiency of 86.5 ± 1.9% within 254 days. Candidatus Brocadia sp. 40 was enriched from undetectable to 22.7% relative abundance. These findings indicated that fast start-up of the deammonification process was possible without ANAMMOX seed sludge in pilot-scale reactor with various variables.
Collapse
Affiliation(s)
- Daehee Choi
- Department of Environmental Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan-Si, Gyeongbuk 38541, South Korea
| | - Chulwoo Lee
- Doosan Heavy Industries and Construction, South Korea
| | - Jinyoung Jung
- Department of Environmental Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan-Si, Gyeongbuk 38541, South Korea.
| |
Collapse
|
24
|
Takahashi Y, Fujitani H, Hirono Y, Tago K, Wang Y, Hayatsu M, Tsuneda S. Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils. Front Microbiol 2020; 11:1737. [PMID: 32849373 PMCID: PMC7396549 DOI: 10.3389/fmicb.2020.01737] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/02/2020] [Indexed: 12/02/2022] Open
Abstract
In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.
Collapse
Affiliation(s)
- Yu Takahashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| |
Collapse
|
25
|
Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
Collapse
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
| |
Collapse
|
26
|
Ishii K, Fujitani H, Sekiguchi Y, Tsuneda S. Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate. Environ Microbiol 2020; 22:2365-2382. [PMID: 32285573 DOI: 10.1111/1462-2920.15015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022]
Abstract
Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.
Collapse
Affiliation(s)
- Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hirotsugu Fujitani
- Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| |
Collapse
|
27
|
Yang Y, Daims H, Liu Y, Herbold CW, Pjevac P, Lin JG, Li M, Gu JD. Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems. mBio 2020; 11:e03175-19. [PMID: 32184251 PMCID: PMC7078480 DOI: 10.1128/mbio.03175-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/06/2020] [Indexed: 11/20/2022] Open
Abstract
The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.
Collapse
Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, Hsinchu City, Taiwan
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
| |
Collapse
|
28
|
Sanders T, Fiencke C, Hüpeden J, Pfeiffer EM, Spieck E. Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia. Microorganisms 2019; 7:E699. [PMID: 31847402 PMCID: PMC6955795 DOI: 10.3390/microorganisms7120699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/01/2023] Open
Abstract
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.
Collapse
Affiliation(s)
- Tina Sanders
- Helmholtz Zentrum Geesthacht, Institut für Küstenforschung, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Claudia Fiencke
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Jennifer Hüpeden
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
| | - Eva Maria Pfeiffer
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Eva Spieck
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
| |
Collapse
|
29
|
Barbarroja P, Zornoza A, Aguado D, Borrás L, Alonso JL. A multivariate approach of changes in filamentous, nitrifying and protist communities and nitrogen removal efficiencies during ozone dosage in a full-scale wastewater treatment plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1500-1508. [PMID: 31272009 DOI: 10.1016/j.envpol.2019.06.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/27/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
The application of low ozone dosage to minimize the problems caused by filamentous foaming was evaluated in two bioreactors of an urban wastewater treatment plant. Filamentous and nitrifying bacteria, as well as protist and metazoa, were monitored throughout a one-year period by FISH and conventional microscopy to examine the effects of ozone application on these specific groups of microorganisms. Multivariate data analysis was used to determine if the ozone dosage was a key factor determining the low carbon and nitrogen removal efficiencies observed throughout the study period, as well as to evaluate its impact on the biological communities monitored. The results of this study suggested that ozonation did not significantly affect the COD removal efficiency, although it had a moderate effect on ammonia removal efficiency. Filamentous bacteria were the community most influenced by ozone (24.9% of the variance explained by ozone loading rate), whilst protist and metazoa were less affected (11.9% of the variance explained). Conversely, ozone loading rate was not a factor in determining the nitrifying bacterial community abundance and composition, although this environmental variable was correlated with ammonia removal efficiency. The results of this study suggest that different filamentous morphotypes were selectively affected by ozone.
Collapse
Affiliation(s)
- Paula Barbarroja
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain.
| | - Andrés Zornoza
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain
| | - Daniel Aguado
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain
| | - Luis Borrás
- Departamento de Ingeniería Química, Universitat de València, Avda de la Universidad s/n, 46100, Burjassot, Valencia, Spain
| | - José Luis Alonso
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain.
| |
Collapse
|
30
|
Han P, Yu Y, Zhou L, Tian Z, Li Z, Hou L, Liu M, Wu Q, Wagner M, Men Y. Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8695-8705. [PMID: 31294971 DOI: 10.1021/acs.est.9b01037] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.
Collapse
Affiliation(s)
- Ping Han
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology , University of Vienna , Althanstrasse 14 , 1090 Vienna , Austria
| | - Yaochun Yu
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Lijun Zhou
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology , University of Vienna , Althanstrasse 14 , 1090 Vienna , Austria
- State Key Laboratory of Lake Science and Environment , Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008 , China
| | - Zhenyu Tian
- Center for Urban Waters , University of Washington Tacoma , Tacoma , Washington 98421 , United States
| | - Zhong Li
- Metabolomics Center , University of Illinois , Urbana , Illinois 61801 , United States
| | | | | | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment , Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008 , China
- Sino-Danish Center for Education and Science , University of Chinese Academy of Science , Beijing 100190 , China
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology , University of Vienna , Althanstrasse 14 , 1090 Vienna , Austria
- The Comammox Research Platform of the University of Vienna , 1090 Vienna , Austria
- Department of Biotechnology, Chemistry and Bioscience , Aalborg University , 9100 Aalborg , Denmark
| | - Yujie Men
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| |
Collapse
|
31
|
Law Y, Matysik A, Chen X, Swa Thi S, Ngoc Nguyen TQ, Qiu G, Natarajan G, Williams RBH, Ni BJ, Seviour TW, Wuertz S. High Dissolved Oxygen Selection against Nitrospira Sublineage I in Full-Scale Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8157-8166. [PMID: 31184114 DOI: 10.1021/acs.est.9b00955] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A single Nitrospira sublineage I OTU was found to perform nitrite oxidation in full-scale domestic wastewater treatment plants (WWTPs) in the tropics. This taxon had an apparent oxygen affinity constant lower than that of the full-scale domestic activated sludge cohabitating ammonium oxidizing bacteria (AOB) (0.09 ± 0.02 g O2 m-3 versus 0.3 ± 0.03 g O2 m-3). Thus, nitrite oxidizing bacteria (NOB) may in fact thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions selected for and high aeration inhibited the NOB in a long-term lab-scale reactor. The relative abundance of Nitrospira sublineage I gradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. The morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their oxygen affinities. NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to the Nitrosomonas-like AOB clusters, which maintained a porous and nonspherical morphology. In conclusion, the effect of oxygen on AOB/NOB population dynamics depends on which OTU predominates given that oxygen affinities are species-specific, and this should be elucidated when devising operating strategies to achieve mainstream partial nitritation.
Collapse
Affiliation(s)
- Yingyu Law
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Artur Matysik
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Xueming Chen
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Gayathri Natarajan
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering , National University of Singapore , Singapore 119077 , Singapore
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering , University of Technology Sydney , Sydney , New South Wales 2007 , Australia
| | - Thomas William Seviour
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798 , Singapore
| |
Collapse
|
32
|
Li J, Zhang L, Peng Y, Yang S, Wang X, Li X, Zhang Q. NOB suppression in partial nitritation-anammox (PNA) process by discharging aged flocs: Performance and microbial community dynamics. CHEMOSPHERE 2019; 227:26-33. [PMID: 30981967 DOI: 10.1016/j.chemosphere.2019.04.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/04/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
The partial nitritation-anammox (PNA) process is the most promising technique to treat municipal sewage; however, nitrite oxidizing bacteria (NOB) are a hindrance to achieve PNA. This study investigated the effects of selectively discharging flocs (<200 μm) to washout NOB in a sequencing batch reactor (SBR) over 200 d. The experiment was divided into three phases with different floc sludge retention times (SRTs; 30, 20 and 30 d). When the SRT of the flocs was reduced from 30 to 20 d to washout NOB, a significant reduction of ammonia oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in the flocs was found. This indicates that a low floc SRT (20 d) leads to the loss of AOB and anammox bacteria in the flocs (<200 μm) and destroys PNA. Activity tests and qPCR analysis revealed the variations of functional bacteria in the granules and flocs, indicating that the enrichment of AOB, NOB, anammox bacteria in the granules is caused by the long-term discharging of flocs. High-throughput sequencing analysis revealed that the microbial shift of Tetrasphaera was significant in the flocs and may be connected to the enrichment of anammox bacteria and the stability of the PNA requires further research. All the obtained NOB sequences were affiliated with the genera Nitrospira and could further influence the PNA system. Overall, this study provides an in-depth understanding of the impact of discharging flocs to washout NOB and promotes the application of combing granules/floc PNA in sewage treatment.
Collapse
Affiliation(s)
- Jialin Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China.
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Shenhua Yang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiaoling Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiyao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| |
Collapse
|
33
|
Low Temperature and Neutral pH Define " Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii. Appl Environ Microbiol 2019; 85:AEM.02569-18. [PMID: 30824434 DOI: 10.1128/aem.02569-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
Collapse
|
34
|
Liu W, Chen W, Yang D, Shen Y. Functional and compositional characteristics of nitrifiers reveal the failure of achieving mainstream nitritation under limited oxygen or ammonia conditions. BIORESOURCE TECHNOLOGY 2019; 275:272-279. [PMID: 30594837 DOI: 10.1016/j.biortech.2018.12.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
For understanding the potential of achieving nitritation under different oxygen and ammonia levels, two activated sludge reactors with high (RH) and low (RL) dissolved oxygen (DO) were parallelly operated. During over two months continuous operation, rare nitrite accumulation was observed in both reactors. K-strategists Nitrosomonas oligotropha and r-strategists Nitrosomonas europaea were enriched in the RH and RL, respectively, yet their response to DO variations was almost identical. Although K-strategists Nitrospira defluvii dominated both reactors, species cultured with low-DO exhibited higher oxygen affinity. Instead of DO, ammonia and nitrite availability should be the key factor for the selective enrichment of these nitrifiers. Taken together, the limiting ammonia for ammonia oxidizing bacteria and the better oxygen-uptake capacity of nitrite oxidizing bacteria wasrespectively responsible for the failure of nitrite accumulation in the RH and RL. This study supported that high DO coupled with excess ammonia would favor the achievement of mainstream nitritation.
Collapse
Affiliation(s)
- Wenru Liu
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Wenjing Chen
- School of Environmental Engineering and Science, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Dianhai Yang
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yaoliang Shen
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou 215009, China
| |
Collapse
|
35
|
Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
Collapse
|
36
|
Zhang G, Li B, Liu J, Luan M, Yue L, Jiang XT, Yu K, Guan Y. The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems. MICROBIOME 2018; 6:222. [PMID: 30545419 PMCID: PMC6292113 DOI: 10.1186/s40168-018-0610-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerate or inhibit corrosion. RESULTS The long-term effects of the bacterial community on cast iron corrosion in reclaimed wastewater distribution systems were investigated from both spatial (yellow layer vs. black layer) and temporal (1-year dynamic process) dimensions of the iron coupon-reclaimed wastewater microcosm using high-throughput sequencing and flow cytometry approaches. Cast iron coupons in the NONdisinfection and UVdisinfection reactors suffered more severe corrosion than did those in the NaClOdisinfection reactor. The bacterial community significantly promoted cast iron corrosion, which was quantified for the first time in the practical reclaimed wastewater and found to account for at least 30.5% ± 9.7% of the total weight loss. The partition of yellow and black layers of cast iron corrosion provided more accurate information on morphology and crystal structures for corrosion scales. The black layer was dense, and the particles looked fusiform, while the yellow layer was loose, and the particles were ellipse or spherical. Goethite was the predominant crystalline phase in black layers, while corrosion products mainly existed as an amorphous phase in yellow layers. The bacterial community compositions of black layers were distinctly separated from yellow layers regardless of disinfection methods. The NONdisinfection and UVdisinfection reactors had a more similar microbial composition and variation tendency for the same layer type than did the NaClOdisinfection reactor. Biofilm development can be divided into the initial start-up stage, mid-term development stage, and terminal stable stage. In total, 12 potential functional genera were selected to establish a cycle model for Fe, N, and S metabolism. Desulfovibrio was considered to accelerate the transfer of Fe0 to Fe2+ and speed up weight loss. CONCLUSION The long-term effect of disinfection processes on corrosion behaviors of cast iron in reclaimed wastewater distribution systems and the hidden mechanisms were deciphered for the first time. This study established a cycle model for Fe, N, and S metabolism that involved 12 functional genera and discovered the significant contribution of Desulfovibrio in promoting corrosion.
Collapse
Affiliation(s)
- Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Mingqiang Luan
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Long Yue
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Xiao-Tao Jiang
- Microbiome Research Centre, St George and Sutherland Clinical School, Department of Medicine, University of New South Wales, Sydney, Australia
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Yuntao Guan
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| |
Collapse
|
37
|
Pan H, Liu H, Liu Y, Zhang Q, Luo Y, Liu X, Liu Y, Xu J, Di H, Li Y. Understanding the relationships between grazing intensity and the distribution of nitrifying communities in grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1157-1164. [PMID: 29660872 DOI: 10.1016/j.scitotenv.2018.04.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Nitrifying microbes are of critical importance in regulating efficient nitrogen (N) cycling, which plays a crucial role in plant productivity and maintaining soil sustainability. Long-term different intensities of grazing can strongly influence the microbial communities, while our understanding of the complex nitrifying community in the grazed grassland soil environment is still limited. To investigate whether and how long-term grazing with different intensities influence soil nitrifying communities, high-throughput sequencing and quantitative PCR analyses were performed on soil samples from permanent grassland soils under four grazing intensities: 0 (G0), 1.5 (G1), 6 (G2) and 9 (G3) sheepha-1. Results showed that the G3 treatment significantly reduced the soil nutrient content and increased the soil bulk density, changes that are not sustainable in the long run. The G1 treatment, on the other hand, significantly increased the soil nutrient content and would improve soil fertility. Some functional microbes were specifically enriched after long term grazing, like Nitrospirae (phylum) to Nitrospira (class) in the G2 samples and Chromatiales (order) to Nitrosococcus (genus) in the G3 soils. The numerically dominant Nitrosococcus watsonii lineage of ammonia oxidizing bacteria (AOB) was observed in this grassland soil. The redundancy analysis (RDA) together with the structural equation modeling (SEM) analysis showed that grazing intensity was important in mediating the distribution of soil microorganisms and affected nitrifying communities by impacting soil physicochemical characteristics (e.g., bulk density, NH4+-N). These results showed the shifts of nitrifying communities across different grazing intensities, and could aid in the determination of an optimal grazing intensity for these grazed grassland soils.
Collapse
Affiliation(s)
- Hong Pan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haiyang Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaowei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qichun Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Xingmei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yimeng Liu
- School of Economics and Resource Management, Beijing Normal University, Beijing 100875, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Hongjie Di
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| |
Collapse
|
38
|
Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. ISME JOURNAL 2018. [PMID: 29515170 DOI: 10.1038/s41396-018-0083-3] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss.
Collapse
|
39
|
Cai M, Ng SK, Lim CK, Lu H, Jia Y, Lee PKH. Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification. Front Microbiol 2018. [PMID: 29535685 PMCID: PMC5835065 DOI: 10.3389/fmicb.2018.00280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of Nitrosomonas-like AOB as well as Nitrobacter-like NOB in the cultures, including the first draft genome of Nitrobacter vulgaris. The nitrifiers exhibited different growth rates with different ammonium (NH4+) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO3-) concentration. The half-saturation constant (Ks for NH4+), the maximum growth rate (μmax), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.
Collapse
Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Yangyang Jia
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| |
Collapse
|
40
|
Lawson CE, Lücker S. Complete ammonia oxidation: an important control on nitrification in engineered ecosystems? Curr Opin Biotechnol 2018; 50:158-165. [PMID: 29414055 DOI: 10.1016/j.copbio.2018.01.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/09/2018] [Accepted: 01/15/2018] [Indexed: 11/17/2022]
Abstract
Nitrification has long been considered to be mediated by two distinct microbial guilds, the ammonia-oxidizing bacteria and archaea, and the nitrite-oxidizing bacteria. The process has been widely applied as an environmental biotechnology for ammonium removal during water and wastewater treatment. Recently, bacteria capable of complete nitrification of ammonia to nitrate (a process termed complete ammonia oxidation, or comammox) have been discovered. These novel nitrifiers have been identified in a range of engineered, natural freshwater and terrestrial ecosystems, challenging previously held knowledge on the key microorganisms and biochemical pathways controlling nitrification. This paper discusses the distribution of comammox bacteria with a focus on engineered ecosystems, as well as emerging insights from recent genomic and experimental studies on their ecophysiology.
Collapse
Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
| |
Collapse
|
41
|
Pfanzagl V, Holcik L, Maresch D, Gorgone G, Michlits H, Furtmüller PG, Hofbauer S. Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments. Arch Biochem Biophys 2018; 640:27-36. [PMID: 29331688 DOI: 10.1016/j.abb.2018.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 01/08/2023]
Abstract
Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity. Based on available biochemical data and phylogenetic analyses a sequence motif (-Y-P-M/F-X-K/R-) is defined for ChdCs. We show for the first time that in diderm bacteria an active coproheme decarboxylase is present and that the archaeal ChdC homolog from Sulfolobus solfataricus is inactive and its physiological role remains elusive. This shows the limitation of phylogenetic prediction of an enzymatic activity, since the identified sequence motif is equally conserved across all previously defined clades.
Collapse
Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Laurenz Holcik
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulia Gorgone
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| |
Collapse
|
42
|
Ushiki N, Fujitani H, Shimada Y, Morohoshi T, Sekiguchi Y, Tsuneda S. Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. Front Microbiol 2018; 8:2637. [PMID: 29375506 PMCID: PMC5767232 DOI: 10.3389/fmicb.2017.02637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023] Open
Abstract
The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.
Collapse
Affiliation(s)
- Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yu Shimada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, Tochigi, Japan
| | - Yuji Sekiguchi
- Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| |
Collapse
|
43
|
Fowler SJ, Palomo A, Dechesne A, Mines PD, Smets BF. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ Microbiol 2018; 20:1002-1015. [PMID: 29314644 DOI: 10.1111/1462-2920.14033] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 11/26/2022]
Abstract
The recent discovery of completely nitrifying Nitrospira demands a re-examination of nitrifying environments to evaluate their contribution to nitrogen cycling. To approach this challenge, tools are needed to detect and quantify comammox Nitrospira. We present primers for the simultaneous quantification and diversity assessement of both comammox Nitrospira clades. The primers cover a wide range of comammox diversity, spanning all available high quality sequences. We applied these primers to 12 groundwater-fed rapid sand filters, and found comammox Nitrospira to be abundant in all filters. Clade B comammox comprise the majority (∼75%) of comammox abundance in all filters. Nitrosomonadaceae were present in all filters, although at low abundance (mean = 1.8%). Ordination suggests that temperature impacts the structure of nitrifying communities, and in particular that increasing temperature favours Nitrospira. The nitrogen content of the filter material, sulfate concentration and surface ammonium loading rates shape the structure of the comammox guild in the filters. This work provides an assay for simultaneous detection and diversity assessment of clades A and B comammox Nitrospira, expands our current knowledge of comammox Nitrospira diversity and demonstrates a key role for comammox Nitrospira in nitrification in groundwater-fed biofilters.
Collapse
Affiliation(s)
- Susan Jane Fowler
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Paul D Mines
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| |
Collapse
|
44
|
Han S, Luo X, Liao H, Nie H, Chen W, Huang Q. Nitrospira are more sensitive than Nitrobacter to land management in acid, fertilized soils of a rapeseed-rice rotation field trial. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:135-144. [PMID: 28475907 DOI: 10.1016/j.scitotenv.2017.04.086] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/04/2017] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
Nitrite oxidation is recognized as an essential process of biogeochemical nitrogen cycling in agricultural ecosystems. How nitrite-oxidizing bacteria (NOB) respond to land managements (the effect from the long-term straw incorporation and environmental variability caused by the shift from the upland stage to the paddy stage) in a rapeseed-rice rotation field remains unclear. We found the nitrite oxidation (NO) in soils increased from the upland stage to the paddy stage. An inhibitory effect of the long-term straw incorporation on NO was detectable in the upland stage. The abundance of Nitrospira was always greater than Nitrobacter, and it was affected by the rice-growing and straw incorporation while Nitrobacter was not. NO correlated positively with the abundance of Nitrospira and with soluble sulfate (SO42-), soil moisture, pH and NH4+. The high-throughput sequencing analysis of the nitrite oxidoreductase nxrA and nxrB genes for Nitrobacter- and Nitrospira-like NOB was performed respectively. The dominating (relative abundance>1%) operational taxonomic units (OTUs) from Nitrobacter were closely related to Nitrobacter hamburgensis, whereas those from Nitrospira were affiliated with or related to lineage II, lineage V and several unknown groups. Heatmap analysis showed that a few dominant Nitrobacter OTUs were affected by the straw treatment or the rice-growing, and half of the dominant Nitrospira ones were explained by at least one of the variables. Multi-response permutation procedure (MRPP) and redundancy analyses showed that the Nitrospira-like NOB community changes were significantly shaped by the land managements and the soil chemical properties, including pH, moisture and NH4+, whereas that of the Nitrobacter-like NOB community was not. These results suggested that Nitrospira are more sensitive than Nitrobacter to land management in acid and fertilized soils of a rapeseed-rice rotation field trial.
Collapse
Affiliation(s)
- Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailing Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
45
|
Hasebe Y, Meguro H, Kanai Y, Eguchi M, Osaka T, Tsuneda S. High-rate nitrification of electronic industry wastewater by using nitrifying granules. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:3171-3180. [PMID: 29210703 DOI: 10.2166/wst.2017.431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nitrifying granules have a high sedimentation property and an ability to maintain a large amount of nitrifying bacteria in a reaction tank. Our group has examined the formation process of nitrifying granules and achieved high-rate nitrification for an inorganic synthetic wastewater using these granules. In this research, a pilot-scale test plant with an 850-liter reaction tank was assembled in a semiconductor manufacturing factory in order to conduct a continuous water conduction test using real electronics industry wastewater. The aim was to observe the formation of nitrifying granules and determine the maximum ammonia removal rate. The average granule diameter formed during the experiment was 780 μm and the maximum ammonia removal rate was observed to be 1.5 kgN·m-3·day-1 at 20 °C, which is 2.5-5 times faster than traditional activated sludge methods. A fluorescence in situ hybridization analysis showed that β-proteobacterial ammonia oxidizing bacteria and the Nitrospira-like nitrite-oxidizing bacteria dominate the bacteria population in the granules, and their strong aggregation capacity might confer some benefits to the formation of these nitrifying granules.
Collapse
Affiliation(s)
- Yoshiaki Hasebe
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara 252-0332, Japan E-mail:
| | - Hiroaki Meguro
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara 252-0332, Japan E-mail:
| | - Yuuki Kanai
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara 252-0332, Japan E-mail:
| | - Masahiro Eguchi
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara 252-0332, Japan E-mail:
| | - Toshifumi Osaka
- Department of Life Science and Medical Bioscience, Waseda Univ., Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda Univ., Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| |
Collapse
|
46
|
Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H. AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment. Front Microbiol 2017; 8:1508. [PMID: 28824606 PMCID: PMC5543084 DOI: 10.3389/fmicb.2017.01508] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/27/2017] [Indexed: 12/03/2022] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
Collapse
Affiliation(s)
- Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Clemens Schauberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Lianna Poghosyan
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Craig W. Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Michaela Steinberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| |
Collapse
|
47
|
Bao P, Wang S, Ma B, Zhang Q, Peng Y. Achieving partial nitrification by inhibiting the activity of Nitrospira-like bacteria under high-DO conditions in an intermittent aeration reactor. J Environ Sci (China) 2017; 56:71-78. [PMID: 28571872 DOI: 10.1016/j.jes.2016.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 09/17/2016] [Accepted: 09/23/2016] [Indexed: 05/20/2023]
Abstract
It is generally accepted that a low dissolved oxygen (DO) concentration is more beneficial for achieving partial nitrification than high-DO. In this study, partial nitrification was not established under low-DO conditions in an intermittent aeration reactor for treating domestic wastewater. During the operational period of low-DO conditions (DO: 0.3±0.14mg/L), stable complete nitrification was observed. The abundance of Nitrospira-like bacteria, which were the major nitrite-oxidizing bacteria, increased from 1.03×106 to 2.64×106cells/mL. At the end of the low-DO period, the batch tests showed that high-DO concentration (1.5, 2.0mg/L) could inhibit nitrite oxidation, and enhance ammonia oxidation. After switching to the high-DO period (1.8±0.32mg/L), partial nitrification was gradually achieved. Nitrospira decreased from 2.64×106 to 8.85×105cells/mL. It was found that suddenly switching to a high-DO condition could inhibit the activity and abundance of Nitrospira-like bacteria, resulting in partial nitrification.
Collapse
Affiliation(s)
- Peng Bao
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 10024, China.
| | - Shuying Wang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 10024, China.
| | - Bin Ma
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 10024, China
| | - Qiong Zhang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 10024, China
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 10024, China
| |
Collapse
|
48
|
Ushiki N, Jinno M, Fujitani H, Suenaga T, Terada A, Tsuneda S. Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation. J Biosci Bioeng 2017; 123:581-589. [DOI: 10.1016/j.jbiosc.2016.12.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
|
49
|
Winkler MKH, Boets P, Hahne B, Goethals P, Volcke EIP. Effect of the dilution rate on microbial competition: r-strategist can win over k-strategist at low substrate concentration. PLoS One 2017; 12:e0172785. [PMID: 28333960 PMCID: PMC5363889 DOI: 10.1371/journal.pone.0172785] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/09/2017] [Indexed: 11/18/2022] Open
Abstract
The conditions present in both in vitro and in vivo ecosystems determine the microbial population harbouring it. One commonly accepted theory is that a species with a high substrate affinity and low growth rate (k-strategist) will win the competition against a second species with a lower substrate affinity and higher growth rate (r-strategist) if both species are subjected to low substrate concentrations. In this study two nitrite oxidizing bacteria (NOB), Nitrospira defluvii (k-strategist) and Nitrobacter vulgaris (r-strategist), were cultivated in a continuous reactor systems. The minimal hydraulic retention time (HRT) required for maintaining the slower growing Nitrospira was first determined. A reactor containing Nitrobacter was set to the same HRT and Nitrospira was injected to evaluate the effect of the dilution rate on the competition between both species. By following the microbial population dynamics with qPCR analysis, it was shown that not only the substrate affinity drives the competition between k- and r-strategists but also the dilution rate. Experimental data and numerical simulations both revealed that the washout of Nitrobacter was significantly delayed at dilution rates close to the μmax of Nitrospira. The competition could be even reverted towards Nitrobacter (r-strategist) despite of low nitrite concentrations and dilution rates lower than the μmax of Nitrospira.
Collapse
Affiliation(s)
- Mari.-K. H. Winkler
- Department of Biosystems Engineering, Ghent University, Gent, Belgium
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Pieter Boets
- Department of Applied Ecology and Biotechnology, Ghent University, Gent, Belgium
| | - Birk Hahne
- Department of Biosystems Engineering, Ghent University, Gent, Belgium
- Department of Applied Ecology and Biotechnology, Ghent University, Gent, Belgium
| | - Peter Goethals
- Department of Applied Ecology and Biotechnology, Ghent University, Gent, Belgium
| | | |
Collapse
|
50
|
Park MR, Park H, Chandran K. Molecular and Kinetic Characterization of Planktonic Nitrospira spp. Selectively Enriched from Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2720-2728. [PMID: 28124895 DOI: 10.1021/acs.est.6b05184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nitrospira spp. are chemolithoautotrophic nitrite-oxidizing bacteria (NOB), which are ubiquitous in natural and engineered environments. However, there exist few independent biokinetic studies on Nitrospira spp., likely because their isolation and selective enrichment from environmental consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 μm. On the basis of respirometric assays, estimated maximum specific growth rate (μmax), nitrite half saturation coefficient (KS), oxygen half saturation coefficient (KO), and biomass yield coefficient (Y) of the enriched cultures were 0.69 ± 0.10 d-1, 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O2/L, and 0.14 ± 0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and thermodynamic parameters can help toward the development and application of energy-efficient biological nutrient removal processes through effective Nitrospira out-selection.
Collapse
Affiliation(s)
- Mee-Rye Park
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
| | - Hongkeun Park
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
| |
Collapse
|