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Cerda Á, Rodríguez C, González M, González H, Serrano J, Leiva E. Feammox bacterial biofilm formation in HFMB. CHEMOSPHERE 2024; 358:142072. [PMID: 38657691 DOI: 10.1016/j.chemosphere.2024.142072] [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: 11/16/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Nitrogen pollution has been increasing with the development of industrialization. Consequently, the excessive deposition of reactive nitrogen in the environment has generated the loss of biodiversity and eutrophication of different ecosystems. In 2005, a Feammox process was discovered that anaerobically metabolizes ammonium. Feammox with the use of hollow fiber membrane bioreactors (HFMB), based on the formation of biofilms of bacterial communities, has emerged as a possible efficient and sustainable method for ammonium removal in environments with high iron concentrations. This work sought to study the possibility of implementing, at laboratory scale, an efficient method by evaluating the use of HFMB. Samples from an internal circulation reactor (IC) incubated in culture media for Feammox bacteria. The cultures were enriched in a batch reactor to evaluate growth conditions. Next, HFMB assembly was performed, and Feammox parameters were monitored. Also, conventional PCR and scanning electron microscopy (SEM) analysis were performed to characterize the bacterial communities associated with biofilm formation. The use of sodium acetate presented the best performance for Feammox activity. The HFMB operation showed an ammonium (NH4+) removal of 50%. SEM analysis of the fibers illustrated the formation of biofilm networks formed by bacteria, which were identified as Albidiferax ferrireducens, Geobacter spp, Ferrovum myxofaciens, Shewanella spp., and Anammox. Functional genes Archaea/Bacteria ammonia monooxygenase, nrxA, hzsB, nirS and nosZ were also identified. The implementation of HFMB Feammox could be used as a sustainable tool for the removal of ammonium from wastewater produced because of anthropogenic activities.
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Affiliation(s)
- Ámbar Cerda
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Carolina Rodríguez
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Macarena González
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Heylin González
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Jennyfer Serrano
- Escuela de Biotecnología, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago 8580745, Chile.
| | - Eduardo Leiva
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile; Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
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Wang Z, Cui T, Wang Q. Optimization of degradation conditions and analysis of degradation mechanism for nitrite by Bacillus aryabhattai 47. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171096. [PMID: 38387569 DOI: 10.1016/j.scitotenv.2024.171096] [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: 12/06/2023] [Revised: 02/17/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Excessive nitrite levels cause significant damage to aquaculture, making it crucial to explore green and reliable nitrite removal technologies. In this study, A Bacillus aryabhattai (designated as the strain 47) isolated from aquaculture wastewater was used as the experimental strain. The nitrite degradation conditions of the strain 47 were optimized, and the optimal conditions are: glucose was 12.74 g/L, fermented special soybean meal was 21.27 g/L, MgCl2 369 mg/L, pH 7.0, incubated at 30 °C with the inoculum size of 2 % and the rotation speed of 170 rpm. Under the optimal conditions, the nitrite concentration of the culture solution was 200 mg/L, and the nitrite removal rate reached 91.4 %. Meanwhile, the mechanism by which Mg2+ enhanced the nitrite degradation ability of the strain 47 was investigated by transcriptomics. An operon structure directed cellular trafficking of Mg2+, and then, the Mg2+-mediated catalytic reaction of multiple enzymes enhanced and improved cellular metabolic processes (e.g. the transport and metabolism of nitrite, central carbohydrate metabolism oxidative phosphorylation). At the same time, with the progress of cell metabolism, cells secreted a series of enzymes related to nitrite transport and metabolism to promote the metabolism of nitrite. And the process of the assimilated nitrate reduction pathway of nitrite degradation in the strain 47 was elaborated at the transcriptome level. This study provided a new insight into nitrite treatment mediated by microbial organisms.
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Affiliation(s)
- Zhenhao Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Qiang Wang
- Guangdong Yuzanchen Biotechnology Co., Ltd, Jiangmen 529100, PR China
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Wu J, Xu W, Xu Y, Su H, Hu X, Cao Y, Zhang J, Wen G. Impact of Organic Carbons Addition on the Enrichment Culture of Nitrifying Biofloc from Aquaculture Water: Process, Efficiency, and Microbial Community. Microorganisms 2024; 12:703. [PMID: 38674647 PMCID: PMC11052406 DOI: 10.3390/microorganisms12040703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L-1 to 2588.0 mg L-1 were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L-1. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L-1 h-1, a net nitrification rate of 2.02 ± 0.20 mg N L-1 h-1, and a specific nitrification rate of 0.72 ± 0.14 mg N g-1 h-1. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture.
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Affiliation(s)
- Jiaqi Wu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (J.W.); (J.Z.)
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
| | - Wujie Xu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (J.W.); (J.Z.)
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Yu Xu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
| | - Haochang Su
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Xiaojuan Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Yucheng Cao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Jianshe Zhang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (J.W.); (J.Z.)
| | - Guoliang Wen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (J.W.); (J.Z.)
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.X.); (H.S.); (X.H.); (Y.C.)
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
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Sun C, Zhang S, Yang J, Zhou H, Cheng H, Chen Z, Yu L, Wang Y, Chen X. Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench. ENVIRONMENTAL RESEARCH 2024; 241:117602. [PMID: 37951379 DOI: 10.1016/j.envres.2023.117602] [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: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.
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Affiliation(s)
- Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Libo Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China.
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Liu L, Chen M, Wan XS, Du C, Liu Z, Hu Z, Jiang ZP, Zhou K, Lin H, Shen H, Zhao D, Yuan L, Hou L, Yang JYT, Li X, Kao SJ, Zakem EJ, Qin W, Dai M, Zhang Y. Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre. SCIENCE ADVANCES 2023; 9:eade2078. [PMID: 37585519 PMCID: PMC10431711 DOI: 10.1126/sciadv.ade2078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Nitrite, an intermediate product of the oxidation of ammonia to nitrate (nitrification), accumulates in upper oceans, forming the primary nitrite maximum (PNM). Nitrite concentrations in the PNM are relatively low in the western North Pacific subtropical gyre (wNPSG), where eddies are frequent and intense. To explain these low nitrite concentrations, we investigated nitrification in cyclonic eddies in the wNPSG. We detected relatively low half-saturation constants (i.e., high substrate affinities) for ammonia and nitrite oxidation at 150 to 200 meter water depth. Eddy-induced displacement of high-affinity nitrifiers and increased substrate supply enhanced ammonia and nitrite oxidation, depleting ambient substrate concentrations in the euphotic zone. Nitrite oxidation is more strongly enhanced by the cyclonic eddies than ammonia oxidation, reducing concentrations and accelerating the turnover of nitrite in the PNM. These findings demonstrate a spatial decoupling of the two steps of nitrification in response to mesoscale processes and provide insights into physical-ecological controls on the PNM.
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Affiliation(s)
- Li Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xianhui S. Wan
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Chuanjun Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhiyu Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhendong Hu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | | | - Kuanbo Zhou
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongyang Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hui Shen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Duo Zhao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanying Yuan
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lei Hou
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jin-Yu T. Yang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaolin Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Emily J. Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Wei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
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Zhao Y, Li W, Chen L, Zhou Y. Characterization of heterotrophic nitrification by a thermotolerant Brevibacillus Agri N2 isolated from sewage sludge composting. ENVIRONMENTAL RESEARCH 2022; 214:113903. [PMID: 35863446 DOI: 10.1016/j.envres.2022.113903] [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: 03/25/2022] [Revised: 06/25/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
A thermotolerant strain isolated from sewage sludge (SS) composting was identified as Brevibacillus Agri N2, which showed the efficient capability for heterotrophic nitrification under high-temperature conditions. Incubation at 60 °C, strain N2 could utilize 45.47% of ammonium nitrogen (99.64 mg/L), 68.89% of hydroxylamine nitrogen (51.14 mg/L) and 76.77% of nitrite nitrogen (55.20 mg/L), with a minor part of nitrogen loss for 1.64%, 2.82% and 5.01%, respectively. The successful detection of ammonia monooxygenase, hydroxylamine oxidase, and nitrate oxidoreductase and PCR amplification of amoA, hao and nxrA genes provided evidence of nitrification ability by strain N2. Furthermore, single-factor experiments indicated that the optimal conditions for efficient nitrification performance by strain N2 were succinate as carbon source, 50 °C, C/N 12, pH 8 and 200 r/min. Strain N2 could perform the complete nitrification process, with minimal nitrogen loss at high temperature conditions, which indicated it had the potential for practical application for reducing nitrogen loss of SS composting.
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Affiliation(s)
- Yi Zhao
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Weiguang Li
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Li Chen
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yujie Zhou
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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Kalinowska A, Pierpaoli M, Jankowska K, Fudala-Ksiazek S, Remiszewska-Skwarek A, Łuczkiewicz A. Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154630. [PMID: 35307432 DOI: 10.1016/j.scitotenv.2022.154630] [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: 12/17/2021] [Revised: 02/21/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.
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Affiliation(s)
- Agnieszka Kalinowska
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Katarzyna Jankowska
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Sylwia Fudala-Ksiazek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Anna Remiszewska-Skwarek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Aneta Łuczkiewicz
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Liu H, Zeng W, Zhan M, Li J, Fan Z, Peng Y. Analysis of nitrite oxidation process and nitrification performance by nitrogen and oxygen isotope fractionation effect. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152511. [PMID: 34990690 DOI: 10.1016/j.scitotenv.2021.152511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The N and O isotope fractionation effects in NO2--N oxidation and nitrification performance of an activated sludge system treating municipal wastewater are unknown. The nitrifying sludge was cultured under different temperature (33 ± 1 °C, 25 ± 1 °C,and 18 ± 1 °C) and dissolved oxygen (DO: 0.5-1 mg/L, 3-4 mg/L, and 7-8 mg/L). The inverse kinetic isotope effects of N and O (15εNO2 and 18εNO2) were -0.62‰ to -7.08‰ and -0.87‰ to -1.68‰ in the process of NO2--N oxidation, respectively. 15εNO3 gradually increased with increasing of temperature (15εNO3-33°C (14.49‰) > 15εNO3-25°C (10.43‰) > 15εNO3-18°C (7.3‰)), while the 15εNO3:18εNO3 was maintained at 1.02-5.32. The increase of temperature improved the nitrification activity, which promoted the fractionation effect, but the change of DO did not highlight this difference. The exchange of NO2--N and H2O (XNOB) was 32.5 ± 1.5%, and the kinetic isotope effect of H2O participating in the reaction (18εk, H2O, 2) was 22.57 ± 1.79‰, indicating that H2O was involved in the NO2--N oxidation rather than DO. In summary, the elevated temperature enhanced the fractionation effect of NO2--N oxidation. This study provides a new perspective to reveal the mechanism of NO2--N oxidation, optimize the process of nitrogen removal from wastewater and further control water eutrophication.
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Affiliation(s)
- Hong Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Mengjia Zhan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jianmin Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Zhiwei Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
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10
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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11
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Zhao D, Gao P, Xu L, Qu L, Han Y, Zheng L, Gong X. Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148097. [PMID: 34412405 DOI: 10.1016/j.scitotenv.2021.148097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/19/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O2 saturation), medium oxygen (MO, close to 75% O2 saturation), and low oxygen (LO, close to 50% O2 saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.
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Affiliation(s)
- Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ping Gao
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lingyun Qu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Yajing Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Liwen Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China.
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12
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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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13
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Sun X, Kop LFM, Lau MCY, Frank J, Jayakumar A, Lücker S, Ward BB. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. THE ISME JOURNAL 2019; 13:2391-2402. [PMID: 31118472 PMCID: PMC6776041 DOI: 10.1038/s41396-019-0443-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.
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Affiliation(s)
- Xin Sun
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.
| | - Linnea F M Kop
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Maggie C Y Lau
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-Sea Science and Engineering, Chinese Academic of Sciences, Sanya, Hainan, 572000, China
| | - Jeroen Frank
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Amal Jayakumar
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Bess B Ward
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
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14
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Hur M, Park SJ. Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System. Microorganisms 2019; 7:microorganisms7090357. [PMID: 31527468 PMCID: PMC6780547 DOI: 10.3390/microorganisms7090357] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022] Open
Abstract
Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.
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Affiliation(s)
- Moonsuk Hur
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Incheon 22689, Korea.
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea.
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15
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Kang MS, Hur M, Park SJ. Rhizocompartments and environmental factors affect microbial composition and variation in native plants. J Microbiol 2019; 57:550-561. [DOI: 10.1007/s12275-019-8646-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 11/27/2022]
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16
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Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI. Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. FEMS Microbiol Ecol 2019; 94:4969676. [PMID: 29668882 DOI: 10.1093/femsec/fiy063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/26/2023] Open
Abstract
Hopanoids, including the extended side chain-containing bacteriohopanepolyols, are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle. Here, we use metagenomic data from the Red Sea to investigate the ecology of hopanoid producers in an environmental setting that is biogeochemically distinct from those investigated previously. The distributions of hopanoid production and nitrite oxidation genes in the Red Sea are closely correlated, and the majority of hopanoid producers are taxonomically affiliated with the major marine nitrite oxidizers, Nitrospinae and Nitrospirae. These results suggest that the relationship between hopanoid production and nitrite oxidation is conserved across varying biogeochemical conditions in dark ocean microbial ecosystems.
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Affiliation(s)
- Jenan J Kharbush
- Department of Earth and Plantary Sciences, Harvard University, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Mohamed Fauzi Haroon
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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17
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Operation mode of a step-feed anoxic/oxic process with distribution of carbon source from anaerobic zone on nutrient removal and microbial properties. Sci Rep 2019; 9:1153. [PMID: 30718641 PMCID: PMC6362077 DOI: 10.1038/s41598-018-37841-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022] Open
Abstract
This study investigated the operation mode of a step-feed anoxic/oxic (A/O) process with distribution of the carbon source from the anaerobic zone in terms of the treatment effects on sewage with low carbon and high nitrogen and phosphorus. After seven phases of operation, an optimal flow distribution ratio of 75%:25% was obtained from the anaerobic zone, and the concentrations of chemical oxygen demand, ammonia nitrogen, total nitrogen, and total phosphorous in the effluent were 20.8, 0.64, 14.2, and 0.89 mg/L, respectively. The presence of an internal reflux system in the deaeration zone improved the treatment. 16S rRNA high-throughput sequencing revealed that the microbial communities in aerobic zone I(O1) of the first-step A/O sludge were different from those in aerobic zone I (O2) of the second-step A/O sludge, whereas microbial communities of the seed sludge were similar to those in O2 of the second-step A/O sludge. The richness and diversity of microbial communities in O1 of the first-step A/O sludge samples were higher than those in O2 of the second-step A/O and seed sludge. At the optimal flow distribution ratio, the microbial abundance and treatment removal efficiency were the highest.
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18
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Boddicker AM, Mosier AC. Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution. THE ISME JOURNAL 2018; 12:2864-2882. [PMID: 30050164 PMCID: PMC6246548 DOI: 10.1038/s41396-018-0240-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.
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Affiliation(s)
- Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA.
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19
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Yu WJ, Lee JW, Nguyen NL, Rhee SK, Park SJ. The characteristics and comparative analysis of methanotrophs reveal genomic insights into Methylomicrobium sp. enriched from marine sediments. Syst Appl Microbiol 2018; 41:415-426. [DOI: 10.1016/j.syapm.2018.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
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20
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Yepsen DV, Levipan HA, Molina V. Nitrospina bacteria in a rocky intertidal habitat (Quintay Bay, central Chile). Microbiologyopen 2018; 8:e00646. [PMID: 29799171 PMCID: PMC6436435 DOI: 10.1002/mbo3.646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/27/2018] [Accepted: 03/30/2018] [Indexed: 11/06/2022] Open
Abstract
Nitrospina bacteria are among the most important nitrite oxidizers in coastal and open-ocean environments, but the relevance of the genus contrasts with the scarceness of information on their ecophysiology and habitat range. Thus far, Nitrospina bacteria have been the only nitrite oxidizers detected at high abundance in Chilean coastal waters. These levels are often higher than at other latitudes. In this study, the abundance of 16S-rRNA gene transcripts of Nitrospina (hereafter just transcripts) was measured by reverse transcription quantitative PCR in a rocky intertidal gradient and compared with the nearshore counterpart off central Chile (~33°S). Rocky pond transcripts were also compared with the taxonomic composition of the macrobiota and bacterioplankton (by 16S-rRNA gene-based T-RFLP) in the intertidal gradient. Transcripts increased from warmer, saltier, and low-nitrite ponds in the upper intertidal zone (19.5 ± 1.6°C, 39.0 ± 1.0 psu, 0.98 ± 0.17 μmol/L) toward cooler, less salty, and high-nitrite ponds (17.8 ± 2.6°C, 37.7 ± 0.82 psu, 1.23 ± 0.21 μmol/L) from middle and low zones. These varied from ~1,000 up to 62,800 transcripts. This increasing trend in the number of transcripts toward the lower zone was positively associated with the Shannon's diversity index for the macrobiota (r = .81, p < .01). Moreover, an important increase in the average number of transcripts was observed in ponds with a greater number of fish in the upper (7,846 transcripts during 2013) and lower zones (62,800 transcripts during 2015). Altogether, intertidal and nearshore transcripts were significantly correlated with nitrite concentrations (r = .804, p ˂ .01); rocky pond transcripts outnumbered nearshore ones by almost two orders of magnitude. In summary, rocky ponds favored both the presence and activity of Nitrospina bacteria that are tolerant to environmental stress. This in turn was positively influenced by the presence of ammonia- or urea-producing macrobiota.
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Affiliation(s)
- Daniela V Yepsen
- Programa de Doctorado en Ciencias con mención en Manejo de Recursos Acuáticos Renovables, Universidad de Concepción, Concepción, Chile
| | - Héctor A Levipan
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Valparaíso, Chile
| | - Verónica Molina
- Programa de Biodiversidad, Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
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