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Hu P, Qian Y, Xu Y, Radian A, Yang Y, Gu JD. A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system. WATER RESEARCH X 2024; 24:100237. [PMID: 39155949 PMCID: PMC11327836 DOI: 10.1016/j.wroa.2024.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 08/20/2024]
Abstract
Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.
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Affiliation(s)
- Pengfei Hu
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Youfen Qian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Yanbin Xu
- School of Environmental Sciences and Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Adi Radian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong 510275, People’s Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
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2
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Su X, Huang X, Zhang Y, Yang L, Wen T, Yang X, Zhu G, Zhang J, Tang Y, Li Z, Ding J, Li R, Pan J, Chen X, Huang F, Rillig MC, Zhu YG. Nitrifying niche in estuaries is expanded by the plastisphere. Nat Commun 2024; 15:5866. [PMID: 38997249 PMCID: PMC11245476 DOI: 10.1038/s41467-024-50200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15N- and 13C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.
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Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400715, China
| | - Xinrong Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Yiyue Zhang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Leyang Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Guibing Zhu
- University of the Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Gießen, Germany
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2015, Australia
| | - Zhaolei Li
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400715, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China
| | - Ruilong Li
- School of Marine Science, Guangxi University, Nanning, 530004, China
| | - Junliang Pan
- School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Xinping Chen
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400715, China
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China.
- University of the Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China.
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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3
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Zhao R, Jørgensen SL, Babbin AR. An abundant bacterial phylum with nitrite-oxidizing potential in oligotrophic marine sediments. Commun Biol 2024; 7:449. [PMID: 38605091 PMCID: PMC11009272 DOI: 10.1038/s42003-024-06136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some cores are significantly higher than the theoretical ratio range predicted from physiological traits of AOA and NOB characterized under realistic ocean conditions, indicating that some NOBs are yet to be discovered. Here we report a bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilus) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) additionally appears in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer helps to resolve the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert controls on the nitrite budget.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Steffen L Jørgensen
- Centre for Deep-Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Wang R, Liu J, Zhang Q, Li X, Wang S, Peng Y. Robustness of the anammox process at low temperatures and low dissolved oxygen for low C/N municipal wastewater treatment. WATER RESEARCH 2024; 252:121209. [PMID: 38309058 DOI: 10.1016/j.watres.2024.121209] [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: 09/12/2023] [Revised: 12/25/2023] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Low water temperatures and ammonium concentrations pose challenges for anammox applications in the treatment of low C/N municipal wastewater. In this study, a 10 L-water bath sequencing batch reactor combing biofilm and suspended sludge was designed for low C/N municipal wastewater treatment. The nitrogen removal performance via partial nitrification anammox-(endogenous) denitrification anammox process was investigated with anaerobic-aerobic-anoxic mode at low temperatures and dissolved oxygen (DO). The results showed that with the decrease of temperature from 30 to 15℃, the influent and effluent nitrogen concentrations and nitrogen removal efficiencies were 73.7 ± 6.5 mg/L, 7.8 ± 2.8 mg/L, and 89.4 %, respectively, with aerobic hydraulic retention time of only 6 h and DO concentration of 0.2-0.5 mg/L. Among that, the stable anammox process compensated for the inhibitory effects of the low temperatures on the nitrification and denitrification processes. Notably, from 30 to 15℃, the anammox activity and relative abundance of the dominant Brocadia genus were increased from 39.7 to 45.5 mgN/gVSS/d and 7.3 to 12.0 %, respectively; the single gene expression level of the biofilm increased 9.0 times. The anammox bacteria showed a good adaptation to temperatures reduction. However, nitrogen removal by anammox was not improved by increasing DO (≥ 4 mg/L) at 8-4℃. Overall, the results of this study demonstrate the feasibility of the mainstream anammox process at low temperatures.
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Affiliation(s)
- Rui Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Jinjin Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Xiyao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Shuying Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
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5
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Suarez C, Rosenqvist T, Dimitrova I, Sedlacek CJ, Modin O, Paul CJ, Hermansson M, Persson F. Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor. MICROBIOME 2024; 12:51. [PMID: 38475926 DOI: 10.1186/s40168-024-01762-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms. RESULTS We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers. CONCLUSIONS We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund, Sweden.
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Tage Rosenqvist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Christopher J Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Catherine J Paul
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund, Sweden
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Peoples LM, Seixas MH, Evans KA, Bilbrey EM, Ranieri JR, Tappenbeck TH, Dore JE, Baumann A, Church MJ. Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake. Environ Microbiol 2024; 26:e16616. [PMID: 38517638 DOI: 10.1111/1462-2920.16616] [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: 11/11/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.
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Affiliation(s)
- Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Miranda H Seixas
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Evan M Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - John R Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Tyler H Tappenbeck
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Adam Baumann
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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de Paula RS, E Souza CC, Gonçalves CAX, de Holanda Moura MV, Guañabens ACP, Andrade GR, Nascimento AMA, Cardoso AV, de Paula Reis M, Jorge EC. Diversity and distribution of iron-oxidising bacteria belonging to Gallionellaceae in different sites of a hydroelectric power plant. Braz J Microbiol 2024; 55:639-646. [PMID: 38214875 PMCID: PMC10920547 DOI: 10.1007/s42770-024-01245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Iron (Fe) is the fourth most abundant element on the planet, and iron-oxidising bacteria (FeOB) play an important role in the biogeochemical cycle of this metal in nature. FeOB stands out as Fe oxidisers in microaerophilic environments, and new members of this group have been increasingly discussed in the literature, even though their isolation can still be challenging. Among these bacteria is the Gallionellaceae family, mainly composed of neutrophilic FeOB, highlighting Gallionella ferruginea, and nitrite-oxidiser genera. In the previous metagenomic study of the biofilm and sediments of the cooling system from the Irapé hydroelectric power plant (HPP-Irapé), 5% of the total bacteria sequences were related to Gallionellaceae, being 99% unclassified at genus level. Thus, in the present study, a phylogenetic tree based on this family was constructed, in order to search for shared and unique Gallionellaceae signatures in a deep phylogenetic level affiliation and correlated them with geomorphologic characteristics. The results revealed that Gallionella and Ferrigenium were ubiquitous reflecting their ability to adapt to various locations in the power plant. The cave was considered a hotspot for neutrophilic FeOB since it harboured most of the Gallionellaceae diversity. Microscopic biosignatures were detected only in the CS1 sample, which presented abundance of the stalk-forming Ferriphaselus and of the sheath-forming Crenothrix. Further studies are required to provide more detailed insights on Gallionellaceae distribution and diversity patterns in hydroelectric power plants, particularly its biotechnological potential in this industry.
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Affiliation(s)
- Rayan Silva de Paula
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Clara Carvalho E Souza
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Carlos Alberto Xavier Gonçalves
- Coordenação de Biotecnologia, Instituto SENAI de Inovação Em Biossintéticos E Fibras, Centro de Tecnologia da Indústria Química E Têxtil (SENAI CETIQT), Rio de Janeiro, RJ, Brazil
| | - Marcelo Victor de Holanda Moura
- Coordenação de Biotecnologia, Instituto SENAI de Inovação Em Biossintéticos E Fibras, Centro de Tecnologia da Indústria Química E Têxtil (SENAI CETIQT), Rio de Janeiro, RJ, Brazil
| | - Anna Carolina Paganini Guañabens
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Gabriela Rabelo Andrade
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia E Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Antonio Valadão Cardoso
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
- Escola de Design, Universidade Do Estado de Minas Gerais (UEMG), Belo Horizonte, MG, Brazil
| | - Mariana de Paula Reis
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil.
| | - Erika Cristina Jorge
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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8
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Li S, Islam MS, Yang S, Xue Y, Liu Y, Huang X. Potential stimulation of nitrifying bacteria activities and genera by landfill leachate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168620. [PMID: 37977385 DOI: 10.1016/j.scitotenv.2023.168620] [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: 09/07/2023] [Revised: 10/29/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
With the increasing complexity of influent composition in wastewater treatment plants, the potential stimulating effects of refractory organic matter in wastewater on growth characteristics and genera conversion of nitrifying bacteria (ammonium-oxidizing bacteria [AOB] and nitrite-oxidizing bacteria [NOB]) need to be further investigated. In this study, domestic wastewater was co-treated with landfill leachate in the lab-scale reactor, and the competition and co-existence of NOB genera Nitrotoga and Nitrospira were observed. The results demonstrated that the addition of landfill leachate could induce the growth of Nitrotoga, whereas Nitrotoga populations remain less competitive in domestic wastewater operation. In addition, the refractory organic matter in the landfill leachate also would have a potential stimulating effect on the maximum specific growth rate of AOB genus Nitrosomonas (μmax, aob). The μmax, aob of Nitrosomonas in the control group was estimated to be 0.49 d-1 by fitting the ASM model, and the μmax, aob reached 0.66-0.71 d-1 after injection of refractory organic matter in the landfill leachate, while the maximum specific growth rate of NOB (μmax, nob) was always in the range of 1.05-1.13 d-1. These findings have positive significance for the understanding of potential stimulation on nitrification processes and the stable operation of innovative wastewater treatment process.
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Affiliation(s)
- Siqi Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Md Sahidul Islam
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shaolin Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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9
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Yuan S, Zhong Q, Zhang H, Zhu W, Wang W, Zhang S. Deciphering the influencing mechanism of hydraulic retention time on purification performance of a mixotrophic system from the perspective of reaction kinetics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12933-12947. [PMID: 38236564 DOI: 10.1007/s11356-023-31305-x] [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: 07/26/2023] [Accepted: 11/26/2023] [Indexed: 01/19/2024]
Abstract
At present, eutrophication is increasingly serious, so it is necessary to effectively reduce nitrogen and phosphorus in water bodies. In this study, a pyrite/polycaprolactone-based mixotrophic denitrification (PPMD) system using pyrite and polycaprolactone (PCL) as electron donors was developed and compared with pyrite-based autotrophic denitrification (PAD) system and PCL-based heterotrophic denitrification (PHD) system through continuous flow experiment. The removal efficiency of NO3--N (NRE) and PO43--P (PRE) and the contribution proportion of PAD in the PPMD system were significantly increased by prolonging hydraulic retention time (HRT, from 1 to 48 h). When HRT was equal to 24 h, the PPMD system conformed to the zero-order kinetic model, so NRE and PRE were mainly limited by the PAD process. When HRT was equal to 48 h, the PPMD system met the first-order kinetic model with NRE and PRE reaching 98.9 ± 1.1% and 91.8 ± 4.5%, respectively. When HRT = 48 h, the NRE and PRE by PAD system were 82.7 ± 9.1% and 88.5 ± 4.7%, respectively, but the effluent SO42- concentration was as high as 152.1 ± 13.7 mg/L (the influent SO42- concentration was 49.2 ± 3.3 mg/L); the NRE by PHD system was 98.5 ± 1.7%, but the PO43--P could not be removed ideally. The concentrations of NO3--N, total nitrogen, PO43--P, and SO42- in the PPMD system also showed distinct changes along the reactor column. In addition, the microbial diversity analysis showed that prolonging HRT (from 24 to 48 h) increased the abundance of autotrophic denitrifying microorganisms in the PPMD system, ultimately increasing the contribution proportion of PAD.
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Affiliation(s)
- Sicheng Yuan
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Qingbo Zhong
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Hongjun Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Wentao Zhu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Shiyang Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, People's Republic of China.
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10
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Kang W, Xiao Y, Li W, Cheng A, Cheng C, Jia Z, Yu L. Paddy cultivation in degraded karst wetland soil can significantly improve the physiological and ecological functions of carbon-fixing resident microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168187. [PMID: 37972785 DOI: 10.1016/j.scitotenv.2023.168187] [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: 07/04/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
Microorganisms play an important role in carbon fixation in karst wetland soils. However, the carbon fixation capacity of karst wetland soils and active microorganisms involved in the carbon fixation process are poorly understood. In this study, carbon fixation capacity and active microorganisms involved in the fixation of inorganic carbon into organic carbon were studied in native, naturally degraded, and reclaimed karst wetland soils by the combination of stable isotope probing (SIP) and high-throughput sequencing. Under light conditions, the soil carbon fixation capacity ranked: the reclaimed wetland soil (1.58 mg C kg-1 day-1) > native wetland soil (1.43 mg C kg-1 day-1) > degraded wetland soil (0.62 mg C kg-1 day-1). In the dark, the soils ranked: the native wetland soil (0.24 mg C kg-1 day-1) > reclaimed wetland soil (0.18 mg C kg-1 day-1) > degraded wetland soil (0.06 mg C kg-1 day-1). Active microorganisms fixing inorganic carbon in the karst wetland soils were mainly Sulfurovum, Thermovirga, Dethiosulfatibacter, Allochromatium, Methylorubrum, and Bradyrhizobium. Thus, paddy cultivation can restore the carbon fixation capacity of microorganisms in the degraded karst wetland soil. This study provides an experimental basis for improving soil carbon fixation capacity and repairing degraded soil in karst wetlands.
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Affiliation(s)
- Weihua Kang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yutian Xiao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Li
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan 430074, China.
| | - Aoqi Cheng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Congyu Cheng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan 430074, China
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11
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Alfreider A, Harringer M. Vertical Distribution and Seasonal Patterns of Candidatus Nitrotoga in a Sub-Alpine Lake. Microbes Environ 2024; 39:ME23086. [PMID: 38825479 PMCID: PMC11220445 DOI: 10.1264/jsme2.me23086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/01/2024] [Indexed: 06/04/2024] Open
Abstract
The nitrite oxidizing bacterial genus Ca. Nitrotoga was only recently discovered to be widespread in freshwater systems; however, limited information is currently available on the environmental factors and seasonal effects that influence its distribution in lakes. In a one-year study in a dimictic lake, based on monthly sampling along a vertical profile, the droplet digital PCR quantification of Ca. Nitrotoga showed a strong spatio-temporal patchiness. A correlation ana-lysis with environmental parameters revealed that the abundance of Ca. Nitrotoga correlated with dissolved oxygen and ammonium, suggesting that the upper hypolimnion of the lake is the preferred habitat.
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Affiliation(s)
- Albin Alfreider
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Manuel Harringer
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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12
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Kop LFM, Koch H, Jetten MSM, Daims H, Lücker S. Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses. ISME COMMUNICATIONS 2024; 4:ycad017. [PMID: 38317822 PMCID: PMC10839748 DOI: 10.1093/ismeco/ycad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.
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Affiliation(s)
- Linnea F M Kop
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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13
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Wang K, Li J, Gu X, Wang H, Li X, Peng Y, Wang Y. How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21503-21526. [PMID: 38096379 DOI: 10.1021/acs.est.3c05600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.
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Affiliation(s)
- Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xin Gu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, P. R. China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
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14
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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15
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Liu Q, Chen Y, Xu XW. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Front Microbiol 2023; 14:1273211. [PMID: 38156017 PMCID: PMC10753782 DOI: 10.3389/fmicb.2023.1273211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.
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Affiliation(s)
- Qian Liu
- Donghai Laboratory, Zhoushan, Zhejiang, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuhao Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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16
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Gajbhiye S, Gonzales ED, Toso DB, Kirk NA, Hickey WJ. Identification of NpdA as the protein forming the surface layer in Paracidovorax citrulli and evidence of its occurrence as a surface layer protein in diverse genera of the Betaproteobacteria and Gammaproteobacteria. Access Microbiol 2023; 5:000685.v3. [PMID: 38188235 PMCID: PMC10765051 DOI: 10.1099/acmi.0.000685.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 01/09/2024] Open
Abstract
The phytopathogen Paracidovorax citrulli possesses an ortholog of a newly identified surface layer protein (SLP) termed NpdA but has not been reported to produce a surface layer (S-layer). This study had two objectives. First, to determine if P. citrulli formed an NpdA-based S-layer and, if so, assess the effects of S-layer formation on virulence, production of nanostructures termed nanopods, and other phenotypes. Second, to establish the distribution of npdA orthologs throughout the Pseudomonadota and examine selected candidate cultures for physical evidence of S-layer formation. Formation of an NpdA-based S-layer by P. citrulli AAC00-1 was confirmed by gene deletion mutagenesis (ΔnpdA), proteomics, and cryo-electron microscopy. There were no significant differences between the wild-type and mutant in virulence assays with detached watermelon fruit. Nanopods contiguous with S-layers of multiple biofilm cells were visualized by transmission electron microscopy. Orthologs of npdA were identified in 62 Betaproteobacteria species and 49 Gammaproteobacteria species. In phylogenetic analyses, NpdA orthologs largely segregated into distinct groups. Cryo-electron microscopy imaging revealed an NpdA-like S-layer in all but one of the 16 additional cultures examined. We conclude that NpdA represents a new family of SLP, forming an S-layer in P. citrulli and other Pseudomonadota. While the S-layer did not contribute to virulence in watermelon fruit, a potential role of the P. citrulli S-layer in another dimension of pathogenesis cannot be ruled out. Lastly, formation of cell-bridging nanopods in biofilms is a new property of S-layers; it remains to be determined if nanopods can mediate intercellular movement of materials.
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Affiliation(s)
- Shabda Gajbhiye
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Erin D Gonzales
- Department of Soil Science, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel B Toso
- Department of Soil Science, University of Wisconsin, Madison, Wisconsin, USA
- Present address: California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - Natalie A Kirk
- Department of Soil Science, University of Wisconsin, Madison, Wisconsin, USA
- Present address: Department of Art and Art History, University of Utah, Salt Lake City, Utah, USA
| | - William J Hickey
- Department of Soil Science, University of Wisconsin, Madison, Wisconsin, USA
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17
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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.
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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
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18
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Zheng M, Li H, Duan H, Liu T, Wang Z, Zhao J, Hu Z, Watts S, Meng J, Liu P, Rattier M, Larsen E, Guo J, Dwyer J, Akker BVD, Lloyd J, Hu S, Yuan Z. One-year stable pilot-scale operation demonstrates high flexibility of mainstream anammox application. WATER RESEARCH X 2023; 19:100166. [PMID: 36685722 PMCID: PMC9845764 DOI: 10.1016/j.wroa.2023.100166] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 05/05/2023]
Abstract
Mainstream nitrogen removal via anammox is widely recognized as a promising wastewater treatment process. However, its application is challenging at large scale due to unstable suppression of nitrite-oxidizing bacteria (NOB). In this study, a pilot-scale mainstream anammox process was implemented in an Integrated Fixed-film Activated Sludge (IFAS) configuration. Stable operation with robust NOB suppression was maintained for over one year. This was achieved through integration of three key control strategies: i) low dissolved oxygen (DO = 0.4 ± 0.2 mg O2/L), ii) regular free nitrous acid (FNA)-based sludge treatment, and iii) residual ammonium concentration control (NH4 + with a setpoint of ∼8 mg N/L). Activity tests and FISH demonstrated that NOB barely survived in sludge flocs and were inhibited in biofilms. Despite receiving organic-deficient wastewater from a pilot-scale High-Rate Activated Sludge (HRAS) system as the feed, the system maintained a stable effluent total nitrogen concentration mostly below 10 mg N/L, which was attributed to the successful retention of anammox bacteria. This study successfully demonstrated large-scale long-term mainstream anammox application and generated new practical knowledge for NOB control and anammox retention.
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Affiliation(s)
- Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Corresponding authors.
| | - Huijuan Li
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Urban Utilities, Brisbane, QLD, 4000, Australia
| | - Haoran Duan
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zhiyao Wang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jing Zhao
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zhetai Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shane Watts
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jia Meng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peng Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Maxime Rattier
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Eloise Larsen
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jason Dwyer
- Urban Utilities, Brisbane, QLD, 4000, Australia
| | - Ben Van Den Akker
- South Australian Water Corporation, 250 Victoria Square, Adelaide SA 5000, Australia
| | - James Lloyd
- Melbourne Water, 990 La Trobe St, Docklands, VIC, 3000, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Corresponding authors.
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Corresponding authors.
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20
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Mehrani MJ, Kowal P, Sobotka D, Godzieba M, Ciesielski S, Guo J, Makinia J. The coexistence and competition of canonical and comammox nitrite oxidizing bacteria in a nitrifying activated sludge system - Experimental observations and simulation studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161084. [PMID: 36565884 DOI: 10.1016/j.scitotenv.2022.161084] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
The second step of nitrification can be mediated by nitrite oxidizing bacteria (NOB), i.e. Nitrospira and Nitrobacter, with different characteristics in terms of the r/K theory. In this study, an activated sludge model was developed to account for competition between two groups of canonical NOB and comammox bacteria. Heterotrophic denitrification on soluble microbial products was also incorporated into the model. Four 5-week washout trials were carried out at dissolved oxygen-limited conditions for different temperatures (12 °C vs. 20 °C) and main substrates (NH4+-N vs. NO2--N). Due to the aggressive reduction of solids retention time (from 4 to 1 d), the biomass concentrations were continuously decreased and stabilized after two weeks at a level below 400 mg/L. The collected experimental data (N species, biomass concentrations, and microbiological analyses) were used for model calibration and validation. In addition to the standard predictions (N species and biomass), the newly developed model also accurately predicted two microbiological indicators, including the relative abundance of comammox bacteria as well as nitrifiers to heterotrophs ratio. Sankey diagrams revealed that the relative contributions of specific microbial groups to N conversion pathways were significantly shifted during the trial. The contribution of comammox did not exceed 5 % in the experiments with both NH4+-N and NO2--N substrates. This study contributes to a better understanding of the novel autotrophic N removal processes (e.g. deammonification) with nitrite as a central intermediate product.
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Affiliation(s)
- Mohamad-Javad Mehrani
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Przemyslaw Kowal
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Dominika Sobotka
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Martyna Godzieba
- Department of Environmental Biotechnology, Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-719 Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-719 Olsztyn, Poland
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jacek Makinia
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland.
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21
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525709. [PMID: 36747706 PMCID: PMC9900912 DOI: 10.1101/2023.01.26.525709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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22
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Gomez-Alvarez V, Siponen S, Kauppinen A, Hokajärvi AM, Tiwari A, Sarekoski A, Miettinen IT, Torvinen E, Pitkänen T. A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland. WATER RESEARCH 2023; 229:119495. [PMID: 37155494 PMCID: PMC10125003 DOI: 10.1016/j.watres.2022.119495] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.
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Affiliation(s)
- Vicente Gomez-Alvarez
- Office of Research and Development, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
- Corresponding author. (V. Gomez-Alvarez)
| | - Sallamaari Siponen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Department of Environmental and Biological Sciences, Kuopio 70211, Finland
| | - Ari Kauppinen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
| | - Anniina Sarekoski
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
| | - Ilkka T. Miettinen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, Kuopio 70211, Finland
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
- Corresponding author at: Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland. (T. Pitkänen)
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23
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Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water. Microorganisms 2023; 11:microorganisms11020287. [PMID: 36838251 PMCID: PMC9960253 DOI: 10.3390/microorganisms11020287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.
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24
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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.
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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.
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25
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Barnum TP, Coates JD. Chlorine redox chemistry is widespread in microbiology. THE ISME JOURNAL 2023; 17:70-83. [PMID: 36202926 PMCID: PMC9751292 DOI: 10.1038/s41396-022-01317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.
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Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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26
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Ide H, Ishii K, Takahashi Y, Fujitani H, Tsuneda S. Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga. Microbes Environ 2023; 38:ME23076. [PMID: 38072409 PMCID: PMC10728634 DOI: 10.1264/jsme2.me23076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.
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Affiliation(s)
- Hiroto Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Yu Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
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27
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Villeneuve K, Violette M, Lazar CS. From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors. Genes (Basel) 2022; 14:1. [PMID: 36672742 PMCID: PMC9858702 DOI: 10.3390/genes14010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.
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Affiliation(s)
| | | | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal, UQAM, C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
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28
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Zhang Q, Zhang J, Zhao L, Liu W, Chen L, Cai T, Ji XM. Microbial dynamics reveal the adaptation strategies of ecological niche in distinct anammox consortia under mainstream conditions. ENVIRONMENTAL RESEARCH 2022; 215:114318. [PMID: 36116498 DOI: 10.1016/j.envres.2022.114318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
The feasibility of anammox-based processes for nitrogen-contained wastewater treatment has been verified with different anammox bacteria, however, the ecological niche of anammox bacteria under mainstream conditions is still elusive. In this study, six sludge samples collected from different habitats were utilized to culture anammox bacteria under mainstream conditions, and two distinct anammox genera (Ca. Kuenenia and Ca. Brocadia) with a relative abundance of 6.31% (C1) and 3.09% (C3), respectively, were identified. Notably, the microbial dynamics revealed that anammox bacteria (AMX), ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), Chloroflexi bacteria (CFX), and heterotrophic denitrification bacteria (HDB) were the core members in anammox consortia. However, Ca. Kuenenia and Ca. Brocadia occupied different ecological niches in anammox consortia. The dissolved oxygen and microbial structures of the anammox-continuous stirred tank reactor systems were the main factors to affect their niche differentiation. Meanwhile, comammox might exist in the systems and occupy the ecological niche of AOB in nitrogen cycling. The network analysis suggested that Ignavibacterium could be the associated bacteria in Ca. Kuenenia-dominated consortia, while Ca. Nitrotoga was that in the Ca. Brocadia-dominated consortia. Our findings reveal a valuable reference for the observation of distinct anammox genera under mainstream conditions, which provides theoretical guidance for the engineering application of mainstream anammox-based processes.
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Affiliation(s)
- Qi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Leizhen Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenru Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Liwei Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianming Cai
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xiao-Ming Ji
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Kowal P, Mehrani MJ, Sobotka D, Ciesielski S, Mąkinia J. Rearrangements of the nitrifiers population in an activated sludge system under decreasing solids retention times. ENVIRONMENTAL RESEARCH 2022; 214:113753. [PMID: 35772505 DOI: 10.1016/j.envres.2022.113753] [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: 01/21/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Due to the key role of nitrite in novel nitrogen removal systems, nitrite oxidizing bacteria (NOB) have been receiving increasing attention. In this study, the coexistence and interactions of nitrifying bacteria were explored at decreasing solids retention times (SRTs). Four 5-week washout experiments were carried out in laboratory-scale (V = 10 L) sequencing batch reactors (SBRs) with mixed liquor from two full-scale activated sludge systems (continuous flow vs SBR). During the experiments, the SRT was gradually reduced from the initial value of 4.0 d to approximately 1.0 d. The reactors were operated under limited dissolved oxygen conditions (set point of 0.6 mg O2/L) and two process temperatures: 12 °C (winter) and 20 °C (summer). At both temperatures, the progressive SRT reduction was inefficient for the out-selection of both canonical NOB and comammox Nitrospira. However, the dominant NOB switched from Nitrospira to Ca. Nitrotoga, whereas the dominant AOB was always Nitrosomonas. The results of this study are important for optimizing NOB suppression strategies in the novel N removal processes, which are based on nitrite accumulation.
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Affiliation(s)
- Przemyslaw Kowal
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland.
| | - Mohamad-Javad Mehrani
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
| | - Dominika Sobotka
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Ul. Sloneczna 45G, 10-709, Olsztyn, Poland
| | - Jacek Mąkinia
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
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30
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Yang X, Tang Z, Xiao L, Zhang S, Jin J, Zhang S. Effect of electric current intensity on performance of polycaprolactone/FeS 2-based mixotrophic biofilm-electrode reactor. BIORESOURCE TECHNOLOGY 2022; 361:127757. [PMID: 35952860 DOI: 10.1016/j.biortech.2022.127757] [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: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
In this study, a bioelectrochemical system consisting of pyrite-based autotrophic denitrification (PAD) and heterotrophic denitrification (HD) was established to polish nitrate wastewater. The loading of electric current (EC) could stimulate the dissolution of pyrite. Appropriate EC (I ≤ 30 mA) was conducive to nitrate removal, too high EC (I = 40 mA) would inhibit nitrate removal and lead to an obvious accumulation of NO2--N and NH4+-N. Microbial analysis revealed that the increase of EC could inhibit the diversity of heterotrophic microbes, but appropriate EC (I = 10 mA) could increase the diversity of autotrophic microbes. The EC loading was conducive to the enrichment of iron autotrophic denitrifiers (Ferritrophicum), pyrite-oxidizing bacteria (Thiobacillus, Sulfurimonas), and sulfur autotrophic denitrifiers (Dechloromonas, Thiobacillus, and Arenimonas). The EC loading enlarged the contribution of PAD, making PAD a dominant pathway in denitrification.
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Affiliation(s)
- Xin Yang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, China
| | - Zhiwei Tang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, China
| | - Longqu Xiao
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, China
| | - Shaohui Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, China
| | - Jing Jin
- Yunnan Ningmao Environmental Technology Co., Ltd., Kunming 650000, China
| | - Shiyang Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, China.
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31
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Meng J, Hu Z, Wang Z, Hu S, Liu Y, Guo H, Li J, Yuan Z, Zheng M. Determining Factors for Nitrite Accumulation in an Acidic Nitrifying System: Influent Ammonium Concentration, Operational pH, and Ammonia-Oxidizing Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11578-11588. [PMID: 35877959 DOI: 10.1021/acs.est.1c07522] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Acidic nitrification is attracting wide attention because it can enable robust suppression of nitrite-oxidizing bacteria (NOB) in wastewater treatment. This study reports a comprehensive assessment of the novel acidic nitrification process to identify the key factors that govern stable nitrite accumulation. A laboratory-scale moving-bed biofilm reactor receiving low-alkalinity wastewater was continuously operated under acidic conditions (pH < 6) for around two years, including nine stages varying influent and operational conditions. The results revealed that nitrite accumulation was related to three factors, i.e., influent ammonium concentration, operating pH, and ammonia-oxidizing microbial community. These three factors impact nitrite accumulation by altering the in situ concentration of free nitrous acid (FNA), which is a potent inhibitor of NOB. The critical FNA concentration is approximately one part per million (ppm, ∼1 mg HNO2-N/L), above which nitrite accumulation is stably maintained in an acidic nitrifying system. The findings of this study suggest that stable nitrite accumulation via acidic ammonia oxidation can be maintained under a range of influent and operational conditions, as long as a ppm-level of FNA is established. Taking low-strength mainstream wastewater (40-50 mg NH4+-N/L) with limited alkalinity as an example, stable nitrite accumulation was experimentally demonstrated at a pH of 4.35, under which an in situ FNA of 2.3 ± 0.6 mg HNO2-N/L was attained. Under these conditions, Candidatus Nitrosoglobus became the only ammonia oxidizer detectable by 16S rRNA gene sequencing. The results of this study deepen our understanding of acidic nitrifying systems, informing further development of novel wastewater treatment technologies.
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Affiliation(s)
- Jia Meng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Zhetai Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Zhiyao Wang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongguang Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Zhiguo Yuan
- 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
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32
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Korth B, Pous N, Hönig R, Haus P, Corrêa FB, Nunes da Rocha U, Puig S, Harnisch F. Electrochemical and Microbial Dissection of Electrified Biotrickling Filters. Front Microbiol 2022; 13:869474. [PMID: 35711746 PMCID: PMC9197458 DOI: 10.3389/fmicb.2022.869474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Electrified biotrickling filters represent sustainable microbial electrochemical technology for treating organic carbon-deficient ammonium-contaminated waters. However, information on the microbiome of the conductive granule bed cathode remains inexistent. For uncovering this black box and for identifying key process parameters, minimally invasive sampling units were introduced, allowing for the extraction of granules from different reactor layers during reactor operation. Sampled granules were analyzed using cyclic voltammetry and molecular biological tools. Two main redox sites [-288 ± 18 mV and -206 ± 21 mV vs. standard hydrogen electrode (SHE)] related to bioelectrochemical denitrification were identified, exhibiting high activity in a broad pH range (pH 6-10). A genome-centric analysis revealed a complex nitrogen food web and the presence of typical denitrifiers like Pseudomonas nitroreducens and Paracoccus versutus with none of these species being identified as electroactive microorganism so far. These are the first results to provide insights into microbial structure-function relationships within electrified biotrickling filters and underline the robustness and application potential of bioelectrochemical denitrification for environmental remediation.
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Affiliation(s)
- Benjamin Korth
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Narcís Pous
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Girona, Spain
| | - Richard Hönig
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Philip Haus
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Felipe Borim Corrêa
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sebastià Puig
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Girona, Spain
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Elling FJ, Evans TW, Nathan V, Hemingway JD, Kharbush JJ, Bayer B, Spieck E, Husain F, Summons RE, Pearson A. Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols. GEOBIOLOGY 2022; 20:399-420. [PMID: 35060273 DOI: 10.1111/gbi.12484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia- and nitrite-oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia-oxidizing (AOB), nitrite-oxidizing (NOB), and complete ammonia-oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen-containing bacteriohopanepolyols were tentatively identified, of which the so called BHP-743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin-Benson-Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids.
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Affiliation(s)
- Felix J Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Vinitra Nathan
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jordon D Hemingway
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jenan J Kharbush
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, Michigan, USA
| | - Barbara Bayer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Fatima Husain
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roger E Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. mBio 2022; 13:e0237921. [PMID: 35435701 PMCID: PMC9239080 DOI: 10.1128/mbio.02379-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.
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35
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Begmatov S, Dorofeev AG, Kadnikov VV, Beletsky AV, Pimenov NV, Ravin NV, Mardanov AV. The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow. Sci Rep 2022; 12:3458. [PMID: 35236881 PMCID: PMC8891259 DOI: 10.1038/s41598-022-07132-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022] Open
Abstract
Microbial communities in wastewater treatment plants (WWTPs) play a key role in water purification. Microbial communities of activated sludge (AS) vary extensively based on plant operating technology, influent characteristics and WWTP capacity. In this study we performed 16S rRNA gene profiling of AS at nine large-scale WWTPs responsible for the treatment of municipal sewage from the city of Moscow, Russia. Two plants employed conventional aerobic process, one plant-nitrification/denitrification technology, and six plants were operated with the University of Cape Town (UCT) anaerobic/anoxic/oxic process. Microbial communities were impacted by the technology and dominated by the Proteobacteria, Bacteroidota and Actinobacteriota. WWTPs employing the UCT process enabled efficient removal of not only organic matter, but also nitrogen and phosphorus, consistently with the high content of ammonia-oxidizing Nitrosomonas sp. and phosphate-accumulating bacteria. The latter group was represented by Candidatus Accumulibacter, Tetrasphaera sp. and denitrifiers. Co-occurrence network analysis provided information on key hub microorganisms in AS, which may be targeted for manipulating the AS stability and performance. Comparison of AS communities from WWTPs in Moscow and worldwide revealed that Moscow samples clustered together indicating that influent characteristics, related to social, cultural and environmental factors, could be more important than a plant operating technology.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexander G Dorofeev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
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36
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Keuter S, Koch H, Sass K, Wegen S, Lee N, Lücker S, Spieck E. Some like it cold: The cellular organization and physiological limits of cold-tolerant nitrite-oxidizing Nitrotoga. Environ Microbiol 2022; 24:2059-2077. [PMID: 35229435 DOI: 10.1111/1462-2920.15958] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
Chemolithoautotrophic production of nitrate is accomplished by the polyphyletic functional group of nitrite-oxidizing bacteria (NOB). A widely distributed and important NOB clade in nitrogen removal processes at low temperatures is Nitrotoga, which however remains understudied due to the scarcity of cultivated representatives. Here, we present physiological, ultrastructural and genomic features of Nitrotoga strains from various habitats, including the first marine species enriched from an aquaculture system. Immunocytochemical analyses localized the nitrite-oxidizing enzyme machinery in the wide irregularly shaped periplasm, apparently without contact to the cytoplasmic membrane, confirming previous genomic data suggesting a soluble nature. Interestingly, in two strains we also observed multicellular complexes with a shared periplasmic space, which seem to form through incomplete cell division and might enhance fitness or survival. Physiological tests revealed differing tolerance limits towards dissolved inorganic nitrogen concentrations and confirmed the generally psychrotolerant nature of the genus was. Moreover, comparative analysis of 15 Nitrotoga genomes showed, e.g., a unique gene repertoire of the marine strain that could be advantageous in its natural habitat and confirmed the lack of genes for assimilatory nitrite reduction in a strain found to require ammonium for growth. Overall, these novel insights largely broaden our knowledge of Nitrotoga and elucidate the metabolic variability, physiological limits and thus potential ecological roles of this group of nitrite oxidizers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sabine Keuter
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Hanna Koch
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Katharina Sass
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Simone Wegen
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Natuschka Lee
- Department of Ecology and Environmental Science and Research Infrastructure Fluorescence in situ Hybridization (FISH), Chemical Biological Centre, Umeå University, Umeå, Sweden.,Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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37
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The Variation in Groundwater Microbial Communities in an Unconfined Aquifer Contaminated by Multiple Nitrogen Contamination Sources. WATER 2022. [DOI: 10.3390/w14040613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Aquifers provide integral freshwater resources and host ecosystems of largely uncharacterized, truncated endemic microorganisms. In recent history, many aquifers have become increasingly contaminated from various anthropogenic sources. To better understand the impacts of nitrogen contamination on native groundwater ecosystems, 16S rRNA sequencing of the groundwater microbial communities was carried out. Samples were taken from an aquifer known to be contaminated with nitrogen from multiple sources, including fertilizers and wastewater treatment plant effluents. In total, two primary contaminants were identified: NH4+ (<0.1–3.7–26 mg L−1 NH4+ min-median-max), and NO3− (<0.01–18–150 mg L−1 NO3− min-median-max). These contaminants were found to be associated with a decrease/increase in microbial species richness within affected groundwater for NH4+/NO3−, respectively. Important phyla were identified, including Proteobacteria, which had the highest abundance within samples unaffected by NH4+ (36–81% NH4+ unaffected, 4–33% NH4+ affected), and Planctomycetes (0.05–10% NH4+ unaffected, 43–72% NH4+ affected), which had the highest abundance within the NH4+ affected samples, likely due to its ability to perform anaerobic ammonia oxidation (ANAMMOX). Planctomycetes were identified as a potential indicator for the presence of NH4+ contamination. The analysis and characterization of sequencing data alongside physicochemical data showed potential to increase the depth of our understanding of contaminant behavior and fate within a contaminated aquifer using this type of data and analysis.
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38
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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39
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Martinez‐Rabert E, Smith CJ, Sloan WT, González‐Cabaleiro R. Biochemistry shapes growth kinetics of nitrifiers and defines their activity under specific environmental conditions. Biotechnol Bioeng 2022; 119:1290-1300. [PMID: 35092010 PMCID: PMC9303882 DOI: 10.1002/bit.28045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022]
Abstract
Is it possible to find trends between the parameters that define microbial growth to help us explain the vast microbial diversity? Through an extensive database of kinetic parameters of nitrifiers, we analyzed if the dominance of specific populations of nitrifiers could be predicted and explained. We concluded that, in general, higher growth yield (YXS) and ammonia affinity (a0NH3) and lower growth rate (µmax) are observed for ammonia‐oxidizing archaea (AOA) than bacteria (AOB), which would explain their considered dominance in oligotrophic environments. However, comammox (CMX), with the maximum energy harvest per mole of ammonia, and some AOB, have higher a0NH3 and lower µmax than some AOA. Although we were able to correlate the presence of specific terminal oxidases with observed oxygen affinities (a0O2) for nitrite‐oxidizing bacteria (NOB), that correlation was not observed for AOB. Moreover, the presumed dominance of AOB over NOB in O2‐limiting environments is discussed. Additionally, lower statistical variance of a0O2 values than for ammonia and nitrite affinities was observed, suggesting nitrogen limitation as a stronger selective pressure. Overall, specific growth strategies within nitrifying groups were not identified through the reported kinetic parameters, which might suggest that mostly, fundamental differences in biochemistry are responsible for underlying kinetic parameters.
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Affiliation(s)
- Eloi Martinez‐Rabert
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - Cindy J. Smith
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - William T. Sloan
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - Rebeca González‐Cabaleiro
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft The Netherlands
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40
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Xi H, Zhou X, Arslan M, Luo Z, Wei J, Wu Z, Gamal El-Din M. Heterotrophic nitrification and aerobic denitrification process: Promising but a long way to go in the wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150212. [PMID: 34536867 DOI: 10.1016/j.scitotenv.2021.150212] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 05/27/2023]
Abstract
The traditional biological nitrogen removal (BNR) follows the conventional scheme of sequential nitrification and denitrification. In recent years, novel processes such as anaerobic ammonia oxidation (anammox), complete oxidation of ammonia to nitrate in one organism (comammox), heterotrophic nitrification and aerobic denitrification (HN-AD), and dissimilatory nitrate reduction to ammonium (DNRA) are gaining tremendous attention after the discovery of metabolically versatile bacteria. Among them, HN-AD offers several advantages because individual bacteria could achieve one-stage nitrogen removal under aerobic conditions in the presence of organic carbon. In this review, besides classical BNR processes, we summarized the existing literature on HN-AD bacteria which have been isolated from diverse habitats. A particular focus was given on the diversity and physiology of HN-AD bacteria, influences of physiological and biochemical factors on their growth, nitrogen removal performances, as well as limitations and strategies in unraveling HN-AD metabolic pathways. We also presented case studies of HN-AD application in wastewater treatment facilities, pointed out forthcoming challenges of HN-AD in these systems, and presented modulation strategies for HN-AD application in engineering. This review may help improve the existing design of wastewater treatment plants by harnessing HN-AD bacteria for effective nitrogen removal.
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Affiliation(s)
- Haipeng Xi
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Xiangtong Zhou
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China.
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Zhijun Luo
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Jing Wei
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Zhiren Wu
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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41
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Thieringer PH, Honeyman AS, Spear JR. Spatial and Temporal Constraints on the Composition of Microbial Communities in Subsurface Boreholes of the Edgar Experimental Mine. Microbiol Spectr 2021; 9:e0063121. [PMID: 34756066 PMCID: PMC8579930 DOI: 10.1128/spectrum.00631-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. Attention is required to understand the near subsurface and its continuity with surface systems, where numerous novel microbial members with unique physiological modifications remain to be identified. This surface-subsurface relationship raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (∼150 m below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric groundwater feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined that unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Desulfosporosinus, Candidatus Nitrotoga, and Chelatococcus associated with endemic subsurface communities. Two other boreholes presented sequences related to nonsubsurface-originating microbiota. High concentration of sulfate along with detected sulfur reducing and oxidizing microorganisms suggests that sulfur related metabolic strategies are prominent within these near-subsurface boreholes. Overall, results indicate that microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20 cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments. IMPORTANCE The Edgar Experimental Mine, Idaho Springs, CO, provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near subsurface are connected to surface hydrological influences is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves, and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relate to both fluid-rock equilibration, and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.
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Affiliation(s)
- Patrick H. Thieringer
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Alexander S. Honeyman
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
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Hu Z, Duan H, Wang Z, Zhao J, Ye L, Yuan Z, Zheng M, Hu S. Centralized iron-dosing into returned sludge brings multifaceted benefits to wastewater management. WATER RESEARCH 2021; 203:117536. [PMID: 34403845 DOI: 10.1016/j.watres.2021.117536] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 05/06/2023]
Abstract
Iron salts (i.e. FeCl3) are the most used chemicals in the urban wastewater system. Iron is commonly dosed into sewage or the mainstream system, which provides multiple benefits such as enhanced phosphorus removal and improved sludge settleability/dewaterability. This study reported and demonstrated a new approach that dosed FeCl3 into returned sludge in order to bring two more benefits to wastewater management: short-cut nitrogen removal via the nitrite pathway and less biomass production. This approach is achieved based on our findings that with similar amount of FeCl3, centralized iron dosing into a sidestream sludge unit generated iron concentration two orders of magnitude higher than the common mainstream dosing (e.g. 10-40 mg Fe/L-wastewater), leading to sludge acidification (pH = 2.1) with Fe (III) hydrolysis. Together with accumulated nitrite in the supernatant of the sludge, ppm-level of free nitrous acid was generated and thus enabled sludge disintegration, cell lysis, and selective elimination of nitrite-oxidizing bacteria (NOB). Long-term effects on nitrifying bacteria and overall reactor performance were evaluated using two laboratory reactor experiments for over one year. The experimental reactor showed stable nitrite accumulation with an average NO2-/(NO2- + NO3-) ratio above 80% and ∼30% observed biomass yield reduction compared to those in control reactors. In addition, the centralized sludge dosing strategy still provided benefits such as improved settleability and dewaterability of sludge and enhanced phosphorus removal.
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Affiliation(s)
- Zhetai Hu
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia
| | - Haoran Duan
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia; School of Chemical Engineering, The University of Queensland, St Lucia QLD 4072, Australia
| | - Zhiyao Wang
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia
| | - Jing Zhao
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia
| | - Liu Ye
- School of Chemical Engineering, The University of Queensland, St Lucia QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia
| | - Min Zheng
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia.
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St Lucia QLD 4072, Australia
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43
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Wei SP, Stensel HD, Ziels RM, Herrera S, Lee PH, Winkler MKH. Partitioning of nutrient removal contribution between granules and flocs in a hybrid granular activated sludge system. WATER RESEARCH 2021; 203:117514. [PMID: 34407486 DOI: 10.1016/j.watres.2021.117514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Sludge granulation in continuous-flow systems is an emerging technology to intensify existing activated sludge infrastructure for nutrient removal. In these systems, the nutrient removal contributions and partitioning of microbial functions between granules and flocs can offer insights into process implementations. To this end, a reactor system that simulates the continuous-flow environment using an equal amount of initial granule and floc biomass was investigated. The two operational strategies for maintaining granule growth in the continuous-flow system were (a) the higher solids retention time (SRT) for the granules versus flocs, as well as (b) selective feeding of carbon to the granules. The SRT of the large granule fractions (>425 µm, LG) and floc/small granule fractions (<425 µm, FSG) were controlled at 20 and 2.7-6.0 days, respectively. Long term operation of the hybrid granule/floc system achieved high PO43- and NH4+ removal efficiencies. Higher polyphosphate-accumulating organisms (PAO) activity was observed in the FSG than LG, while ammonia-oxidizing bacteria (AOB) activities were similar in the two biomass fractions. Nitrite shunt was observed in the FSG, possibly due to out-competition by the high NOB activity in LG. More importantly, washing out the FSG caused a reduction in LG's AOB and PAO activity, indicating a possible dependency of LG on FSG for maintaining its nutrient removal capacity. Our findings highlighted the partitioning and potential competition/cooperation of key microbial functional groups between LG and FSG, facilitating nutrient removal in a hybrid granular activated sludge system, as well as implications for practical application of the treatment platform.
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Affiliation(s)
- Stephany P Wei
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - H David Stensel
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA.
| | - Ryan M Ziels
- University of British Columbia, Department of Civil Engineering, Vancouver BC V6T 1Z4, Canada.
| | - Stephanie Herrera
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - Po-Heng Lee
- Imperial College London, Department of Civil and Environmental Engineering, Skempton Building, South Kensington Campus, London SW7 2AZ, United Kingdom.
| | - Mari-K H Winkler
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA.
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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.
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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
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45
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Lantz MA, Boddicker AM, Kain MP, Berg OMC, Wham CD, Mosier AC. Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. Front Microbiol 2021; 12:709371. [PMID: 34484146 PMCID: PMC8415719 DOI: 10.3389/fmicb.2021.709371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Nitrogen cycling microbes, including nitrite-oxidizing bacteria (NOB), perform critical ecosystem functions that help mitigate anthropogenic stresses and maintain ecosystem health. Activity of these beneficial nitrogen cycling microbes is dictated in part by the microorganisms’ response to physicochemical conditions, such as temperature, pH, and nutrient availability. NOB from the newly described Candidatus Nitrotoga genus have been detected in a wide range of habitats across the globe, yet only a few organisms within the genus have been physiologically characterized. For freshwater systems where NOB are critical for supporting aquatic life, Ca. Nitrotoga have been previously detected but little is known about the physiological potential of these organisms or their response to changing environmental conditions. Here, we determined functional response to environmental change for a representative freshwater species of Ca. Nitrotoga (Ca. Nitrotoga sp. CP45, enriched from a Colorado river). The physiological findings demonstrated that CP45 maintained nitrite oxidation at pH levels of 5–8, at temperatures from 4 to 28°C, and when incubated in the dark. Light exposure and elevated temperature (30°C) completely halted nitrite oxidation. Ca. Nitrotoga sp. CP45 maintained nitrite oxidation upon exposure to four different antibiotics, and potential rates of nitrite oxidation by river sediment communities were also resilient to antibiotic stress. We explored the Ca. Nitrotoga sp. CP45 genome to make predictions about adaptations to enable survival under specific conditions. Overall, these results contribute to our understanding of the versatility of a representative freshwater Ca. Nitrotoga sp. Identifying the specific environmental conditions that maximize NOB metabolic rates may ultimately direct future management decisions aimed at restoring impacted systems.
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Affiliation(s)
- Munira A Lantz
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Michael P Kain
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Owen M C Berg
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Courtney D Wham
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
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46
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Worsley SF, Macey MC, Prudence SMM, Wilkinson B, Murrell JC, Hutchings MI. Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome. Front Mol Biosci 2021; 8:686110. [PMID: 34222338 PMCID: PMC8241931 DOI: 10.3389/fmolb.2021.686110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/27/2021] [Indexed: 02/01/2023] Open
Abstract
Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonized more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonization by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Michael C Macey
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Samuel M M Prudence
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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47
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Huang L, Zhang G, Bai J, Xia Z, Wang W, Jia J, Wang X, Liu X, Cui B. Desalinization via freshwater restoration highly improved microbial diversity, co-occurrence patterns and functions in coastal wetland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142769. [PMID: 33168246 DOI: 10.1016/j.scitotenv.2020.142769] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Saltwater intrusion has greatly impacted the functions of coastal wetland soils worldwide by increasing the salt stress; desalinization via freshwater restoration has been suggested to recover saline wetland soils and biodiversity, but its effectiveness is debated. To evaluate the desalinization effectiveness, we characterized the microbial communities and activities using high throughput 16S rRNA gene sequencing and 15N isotopic techniques in freshwater restored (≥10 years) and unrestored wetlands, and then compared the data with reported values of original freshwater wetlands in one of the most dynamic coastal areas, Yellow river estuary (YRE). Our data revealed that freshwater input significantly increased the soil organic carbon (SOC; P < 0.05) after 10 years of restoration, yet it was still 10 times lower than the reported values of original freshwater wetlands. In general, microbial community showed higher diversities and more co-occurrence interactions in the restored than unrestored wetlands. The recovered phylogenetic diversity and the relative abundance of Chloroflexi (9.8-16.3%), Actinobacteria (5.5-10%), Latescibacteria (0.5-1.5%), Nitrospirae (0.9-1.4%) were up to the similar levels of original freshwater wetlands in YRE. Specifically, Gemmatimonadetes_denitrifier clones, as the representatives of denitrifiers, were recovered up to 0.3% with 20 times higher concomitant denitrification rate than anammox rate, significantly contributing to the nitrate removal in restored wetlands; however the rate will be reduced by 80% with a short-term saltwater intrusion. Our study highlighted that freshwater input effectively improved the microbial diversity and their functions and provided a good insight into the desalinization effectiveness via freshwater restoration in coastal wetlands worldwide. ORIGINALITY-SIGNIFICANCE STATEMENT: Salinization is globally spreading with approximately one billion hectares area covered with saline and/or sodic soils on the earth, and the negative effects of salinity on soil microbial communities and their activities have been frequently reported in previous studies all around the world; however, it remains largely unknown about whether the microbial communities and their activities can be recovered or not in soil suffered salinization. Desalinization via freshwater restoration is supposed to offer a good solution to soil salinization in coastal area, but the effectiveness is debated. Here, we are presenting the long-term of field study related to the desalinization effects on microbial diversity, co-occurrence and functions, and find desalinization via freshwater restoration can recover most of microbial communities up to the similar levels of that in original freshwater wetlands, and highly improved microbial diversity and their functions, which sheds a positive light on soil desalinization via freshwater restoration at microenvironments.
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Affiliation(s)
- Laibin Huang
- School of Environment, Beijing Normal University, Beijing, China; Department of Land, Air and Water Resources, University of California-Davis, California, USA.
| | - Guangliang Zhang
- School of Environment, Beijing Normal University, Beijing, China
| | - Junhong Bai
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256600, China.
| | - Zhijian Xia
- School of Environment, Beijing Normal University, Beijing, China
| | - Wei Wang
- School of Environment, Beijing Normal University, Beijing, China
| | - Jia Jia
- School of Environment, Beijing Normal University, Beijing, China
| | - Xin Wang
- School of Environment, Beijing Normal University, Beijing, China
| | - Xinhui Liu
- School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- School of Environment, Beijing Normal University, Beijing, China
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48
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Sakoula D, Koch H, Frank J, Jetten MSM, van Kessel MAHJ, Lücker S. Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification. THE ISME JOURNAL 2021; 15:1010-1024. [PMID: 33188298 PMCID: PMC8115096 DOI: 10.1038/s41396-020-00827-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.
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Affiliation(s)
- Dimitra Sakoula
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.10420.370000 0001 2286 1424Present Address: Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Hanna Koch
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Jeroen Frank
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Mike S. M. Jetten
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maartje A. H. J. van Kessel
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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49
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Sheik CS, Badalamenti JP, Telling J, Hsu D, Alexander SC, Bond DR, Gralnick JA, Lollar BS, Toner BM. Novel Microbial Groups Drive Productivity in an Archean Iron Formation. Front Microbiol 2021; 12:627595. [PMID: 33859627 PMCID: PMC8042283 DOI: 10.3389/fmicb.2021.627595] [Citation(s) in RCA: 6] [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: 11/09/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.
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Affiliation(s)
- Cody S. Sheik
- Department of Biology and the Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jon Telling
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Hsu
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Scott C. Alexander
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Daniel R. Bond
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jeffrey A. Gralnick
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | | | - Brandy M. Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
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50
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Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. THE ISME JOURNAL 2021; 15:732-745. [PMID: 33067588 PMCID: PMC8026999 DOI: 10.1038/s41396-020-00809-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Cameron R Strachan
- Department for Farm Animals and Public Health, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Rasmus H Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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