201
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Liang F, Wen Y, Dong X, Wang Y, Pan G, Jiang F, Luo H, Jin W, Wang J, Song H. Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29332-29343. [PMID: 33559074 DOI: 10.1007/s11356-020-12038-7] [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: 09/20/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.
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Affiliation(s)
- Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei, 230036, China
| | - Yiyao Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Guangyuan Pan
- Anhui General Station for Agricultural Technology Extension, Hefei, 230001, China
| | - Fangying Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huaying Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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202
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Wang Y, Zhao R, Liu L, Li B, Zhang T. Selective enrichment of comammox from activated sludge using antibiotics. WATER RESEARCH 2021; 197:117087. [PMID: 33819658 DOI: 10.1016/j.watres.2021.117087] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 05/04/2023]
Abstract
While the ubiquitous presence of comammox in engineered systems provides the foundation of developing a novel biological nitrogen removal process, factors contributing to the comammox dynamics in engineered systems have not been well resolved. Here, we investigate the long-term effects of ten different antibiotics on microbial community dynamics in activated sludge and the results show that both types and concentrations of antibiotics affect the taxonomic composition of nitrifiers, including comammox, ammonia-oxidizing bacteria, and canonical nitrite-oxidizing bacteria. Specifically, phylogenetically different comammox Nitrospira were selectively enriched by four types of antibiotics (i.e., ampicillin, kanamycin, lincomycin, and trimethoprim). Comparative genomic analysis of the four newly identified comammox clade A Nitrospira revealed that the comammox enriched by antibiotics shared the conserved key metabolic potentials, such as carbon fixation, complete ammonia oxidation, and utilization of hydrogen as alternative electron donors, among the known comammox organisms. Comammox strains enriched in this study also encoded genes involved in formate and cyanate metabolism that were recently reported in comammox clade A organisms from wastewater treatment systems. Our findings highlight that the comammox in activated sludge ecosystems possess high metabolic versatility than previously recognized and could be selectively enriched by some antibiotics.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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203
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Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX. Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144993. [PMID: 33736320 DOI: 10.1016/j.scitotenv.2021.144993] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.
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Affiliation(s)
- Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chen-Hao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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204
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Wang J, Song J, Yin F, Shen Y, Yang D, Liu W. Insight into how high dissolved oxygen favors the startup of nitritation with aerobic granules. CHEMOSPHERE 2021; 270:128643. [PMID: 33097238 DOI: 10.1016/j.chemosphere.2020.128643] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/03/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
To elucidate how high dissolved oxygen (DO) favors the startup of nitritation with aerobic granular sludge, two granular reactors were operated under low (1-2 mg O2·L-1) and high DO (3-5 mg O2·L-1) conditions with similar effluent ammonium concentrations (>20 mg N·L-1). The results showed that though nitritation with an average nitrite accumulation ratio of above 95% was finally achieved in both reactors, a five-fold start-up time (eleven weeks) was required for the low DO reactor compared to the high DO reactor. Moreover, the nitritation performance was positively correlated with the extent of nitrifiers stratification in granules. The faster startup of nitritation under high DO conditions mainly resulted from the faster formation of well-stratified nitrifiers, with ammonium oxidizing bacteria (AOB) dominating granule surface. High DO operation combined with sufficient ammonium supply ensured the faster growth of AOB, which should provide a competitive advantage to AOB in competing for habitable space (i.e., granule surface). Besides, the lower porosity, larger size, and more active extracellular polymeric substances (particularly proteins) production of granules was observed under the high DO condition. Overall, these findings supported the proposition that the switch from mixed to stratified distribution of nitrifiers in granule was primarily driven by their competition for habitable space rather than by oxygen-limitation.
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Affiliation(s)
- Jianfang Wang
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jiajun Song
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Fangfang Yin
- Suzhou Jing Yan Environmental Protection Technology Co. Ltd, Suzhou, 215009, China
| | - Yaoliang Shen
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, China
| | - Wenru Liu
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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205
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Rose A, Padovan A, Christian K, van de Kamp J, Kaestli M, Tsoukalis S, Bodrossy L, Gibb K. The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry. MICROBIAL ECOLOGY 2021; 81:1029-1041. [PMID: 33170351 PMCID: PMC8062326 DOI: 10.1007/s00248-020-01639-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/04/2020] [Indexed: 05/26/2023]
Abstract
Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.
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Affiliation(s)
- A Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia.
| | - A Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - K Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - J van de Kamp
- CSIRO Oceans and Atmosphere, Hobart, Tasmania, 7004, Australia
| | - M Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - S Tsoukalis
- PowerWater Corporation, Darwin, Northern Territory, 0820, Australia
| | - L Bodrossy
- CSIRO Oceans and Atmosphere, Hobart, Tasmania, 7004, Australia
| | - K Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
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206
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Yin Z, Yang X, Wang X, Wang S. Effects of operating conditions on microbial consortium of the heterotrophic ammonia oxidation process. BIORESOURCE TECHNOLOGY 2021; 328:124823. [PMID: 33592544 DOI: 10.1016/j.biortech.2021.124823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the ammonia removal by the consortium mainly comprising of ammonia-oxidizing bacteria under different initial pH, temperatures and stress of heavy metals. The results showed that the consortium exhibited a strong adaptation for broad pH ranging from 5 to 9. When the temperature dropped to 15℃, its ammonium removal and nitrate accumulation rates decreased by 72.23% and 95.12%, respectively. Meanwhile, the temperature correction coefficients of the ammonium removal and nitrate accumulation rates reached the maximum. In addition, the consortium could survive in the solutions containing 0-1.0 mg·L-1 Cu2+ and 0-5.0 mg·L-1 Fe3+. Moreover, the inhibition of free nitrous acid (FNA) against nitrite oxidation activity was found to be much more significant than that low-temperature treatment. Microbial diversity analysis showed that the bacterial community structure was shift significantly by the temperature drop, especially change the abundance of Nitrosomonas, Paracoccus, Pseudomonas and Nitrospirae.
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Affiliation(s)
- Zhikai Yin
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xiaolong Yang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xingyu Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China.
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207
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Chen X, Wang K, Li X, Qiao Y, Dong K, Yang L. Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144884. [PMID: 33636785 DOI: 10.1016/j.scitotenv.2020.144884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
To explore the effects of Microcystis blooms on nitrogen (N) cycling in the water column, the community structures of the Microcystis-attached and free-living bacteria in Lake Taihu were assessed and a mesocosm experiment was further conducted on the shore of Lake Taihu. The bacterial communities of Microcystis-attached and free-living bacteria were dominated by heterotrophic bacteria, such as Pseudomonas and Massilia, while the relative abundances of the genera related to traditional autotrophic nitrification were surprisingly low. However, the dramatic increase in nitrate (NO3-) levels at the daytime suggested that in the mesocosms nitrification did occur, during which the heterotrophic nitrifiers played a predominant role as revealed by the acetylene inhibition experiment. The ammonium (NH4+) concentrations were always maintained at a low level, indicating that most of the substrates for daytime nitrification originated from organic N. The total N being removed during the experiment was much less than the sum of daily NO3- reduction, while the decrease in NO3- concentration was much higher than the increase in NH4+ concentration during the night, indicating that assimilation was the main explanation for nocturnal NO3- reduction. Thus, the cycling of organic N (remineralization) - heterotrophic nitrification - NO3- assimilation (reduction) promoted by Microcystis blooms aggravates the diurnal variation of NO3- in the water column.
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Affiliation(s)
- Xiaofeng Chen
- School of Environmental Science and Engineering, Yangzhou University, West Huayang Road 196, Yangzhou 225127, People's Republic of China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Road 163, Nanjing 210146, People's Republic of China.
| | - Kun Wang
- School of Environmental Science and Engineering, Yangzhou University, West Huayang Road 196, Yangzhou 225127, People's Republic of China
| | - Xing Li
- School of Environmental Science and Engineering, Yangzhou University, West Huayang Road 196, Yangzhou 225127, People's Republic of China
| | - Yuqi Qiao
- School of Environmental Science and Engineering, Yangzhou University, West Huayang Road 196, Yangzhou 225127, People's Republic of China
| | - Kunming Dong
- School of Environmental Science and Engineering, Yangzhou University, West Huayang Road 196, Yangzhou 225127, People's Republic of China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Road 163, Nanjing 210146, People's Republic of China
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208
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Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones. THE ISME JOURNAL 2021; 15:1317-1329. [PMID: 33408366 PMCID: PMC8114937 DOI: 10.1038/s41396-020-00852-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 01/29/2023]
Abstract
Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.
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209
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Xing Y, Harper WF. The effects of engineered nanoparticles on nitrification during biological wastewater treatment. Biotechnol Bioeng 2021; 118:2401-2410. [PMID: 33682924 DOI: 10.1002/bit.27746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 10/08/2020] [Accepted: 03/04/2021] [Indexed: 11/12/2022]
Abstract
Technological advancements in the past few decades have made it possible to manufacture nanomaterials at a large scale, and engineered nanoparticles (ENPs) are increasingly found in consumer products, such as cosmetics, sports products, and LED displays. A large amount of these ENPs end up in wastewater and potentially impact the performance of wastewater treatment plants (WWTPs). One important function of the WWTP is nitrification, which is carried out by the actions of two groups of bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Since most ENPs are found to have or are designed to have antimicrobial activities, it is a legitimate concern that ENPs entering WWTPs may have negative impacts on nitrification. In this paper, the effects of ENPs on nitrification are discussed, focusing mainly on autotrophic nitrification by AOBs and NOBs. This review also covers ENP effects on anaerobic ammonium oxidation (anammox). Generally, nitrifiers in pure and mixed cultures can be inhibited by a variety of ENPs, but stress response mechanisms may attenuate toxicity. Long-term studies demonstrated that a wide range of NPs could cause severe deterioration of AOBs and/or NOBs when the influent concentration exceeded an inhibition threshold. Proposed mechanisms include the generation of reactive oxygen species, dissolved metals, physical disruption of cell membranes, bacterial engulfment, and intracellular accumulation of ENPs. Future research needs are also discussed.
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Affiliation(s)
- Yun Xing
- Department of Systems Engineering and Management, Air Force Institute of Technology, Environmental Engineering and Science Program, Wright-Patterson AFB, Ohio, USA
| | - Willie F Harper
- Department of Systems Engineering and Management, Air Force Institute of Technology, Environmental Engineering and Science Program, Wright-Patterson AFB, Ohio, USA
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210
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Stefan L, Hartmann M, Engbersen N, Six J, Schöb C. Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition. Front Microbiol 2021; 12:660749. [PMID: 33936016 PMCID: PMC8081861 DOI: 10.3389/fmicb.2021.660749] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Intensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant-microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and activity, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (three times larger) or soil moisture (three times larger). Furthermore, these processes were context-dependent: in Spain, where resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes and emphasizing the context-dependence of crop-microbe relationships.
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Affiliation(s)
- Laura Stefan
- Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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211
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Wang Q, Han Y, Lan S, Hu C. Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession. Front Microbiol 2021; 12:633428. [PMID: 33815315 PMCID: PMC8009985 DOI: 10.3389/fmicb.2021.633428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO3–. pH and SO42– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.
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Affiliation(s)
- Qiong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingchun Han
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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212
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Bayer B, Saito MA, McIlvin MR, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. THE ISME JOURNAL 2021; 15:1025-1039. [PMID: 33230266 PMCID: PMC8115632 DOI: 10.1038/s41396-020-00828-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
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Affiliation(s)
- Barbara Bayer
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | - Mak A. Saito
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Matthew R. McIlvin
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands
| | - Dawn M. Moran
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | | | - Alyson E. Santoro
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
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213
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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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214
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Qin S, Zhang X, He S, Huang J. Improvement of nitrogen removal with iron scraps in floating treatment wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17878-17890. [PMID: 33398766 DOI: 10.1007/s11356-020-12177-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Floating treatment wetland (FTW) in restoration of low C/N ratio wastewater was deemed to a frequently used method. However, the nitrate removal performance in floating beds was limited due to insufficient organic carbon sources. Iron scraps as a potential electron donor was beneficial to the NO3--N reduction. To research the removal performance and mechanism of denitrification in FTW with iron scraps, FTW with Iris pseudacorus was built, and iron scraps were added as an electron donor to improve nitrogen removal efficiency. The batch experimental results demonstrated that the proper mass ratio of iron scraps to NO3--N was 500:1. With iron scraps, the NO3--N removal efficiency of FTW and control system increased significantly to 98.04% and 44.42% respectively in 2 weeks, while there was no obvious influence on the removal of NH4+-N. After adding iron scraps, the proportion of bacteria in the systems related to iron cycle and the relative abundance of nitrifying and denitrifying bacteria have increased obviously. By calculating the nitrogen balance, nitrogen reduction via plant uptake accounted for 8.79%, and the microbial denitrification was the main nitrogen removal pathway in FTW.
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Affiliation(s)
- Si Qin
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Xiaoyi Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China.
- Shanghai Engineering Research Center of Landscape Water Environment, Shanghai, 200031, People's Republic of China.
| | - Jungchen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
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215
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Li J, Hua ZS, Liu T, Wang C, Li J, Bai G, Lücker S, Jetten MSM, Zheng M, Guo J. Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor. ISME COMMUNICATIONS 2021; 1:7. [PMID: 37938245 PMCID: PMC9723585 DOI: 10.1038/s43705-021-00005-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.
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Affiliation(s)
- Jiyun Li
- School of Environment, Tsinghua University, Beijing, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Tao Liu
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing, China.
| | - Jie Li
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Ge Bai
- School of Environment, Tsinghua University, Beijing, China
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Min Zheng
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| | - Jianhua Guo
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
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216
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Liu L, Sun F, Zhao H, Mi H, He S, Chen Y, Liu Y, Lan H, Zhang M, Wang Z. Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143383. [PMID: 33189382 DOI: 10.1016/j.scitotenv.2020.143383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
Due to the geographical circumstances, the Yangtze River Estuary (YRE) and the adjacent East China Sea are extensively influenced by both anthropogenic activities and environmental factors. To reveal the responses of microbes in surface sediment to environmental factors and their contributions to the biogeochemical cycle in this area, surface sediment and overlying water samples were collected at 21 stations from the estuary to the coastal region. Water and sediment parameters were determined, and 16S rRNA genes of microbes in sediment samples were sequenced using high throughput sequencing technology. The results indicated that ocean currents, sediment density (SD), nutrients, sulfate (SO42-), and salinity were the key factors shaping the microbial communities. Coastal microbes were affected mainly by SD, whereas anthropogenic discharge might have been responsible for a decrease in indigenous microbial diversity in the ocean. Due to the anthropogenic discharge, the most representative bacteria in the nearshore were aerobic and chemoheterotrophic bacteria, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and polyphosphate accumulating organisms. In the offshore, anaerobic bacteria, thermophilic bacteria, halophilic bacteria, sulfate-reducing bacteria, and sulfide oxidizing bacteria were the dominant bacteria, and these were characterized by strong solidarity and cooperative properties within the malnourished environment. In summary, these results provide a new perspective for revealing the biogeochemical significance of the bacterial lineages in the YRE, as well as constructive guidance for the management of the marginal sea ecosystems in distinct regions.
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Affiliation(s)
- Lili Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Feifei Sun
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hanbin Zhao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Haosheng Mi
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siqi He
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Chen
- School of Environment Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hailian Lan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Zhiping Wang
- School of Environment Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
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217
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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218
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Zhang M, Huang JC, Sun S, Rehman MMU, He S, Zhou W. Nitrogen removal through collaborative microbial pathways in tidal flow constructed wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143594. [PMID: 33246723 DOI: 10.1016/j.scitotenv.2020.143594] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
Constructed wetlands are efficient in removing nitrogen from water; however, little is known about nitrogen-cycling pathways for nitrogen loss from tidal flow constructed wetlands. This study conducted molecular and stable isotopic analyses to investigate potential dissimilatory nitrate reduction to ammonium (DNRA), denitrification, nitrification, anaerobic ammonium oxidation (anammox), and their contributions to nitrogen removal by two tidal wetland mesocosms, PA (planted with Phragmites australis) and NP (unplanted), designated to treat Yangtze River Estuary water. Our results show the mesocosms removed ~22.6% of TN from nitrate-dominated river water (1.19 mg·L-1), with better performance obtained in PA than that in NP, which was consistent with the molecular and stable isotopic data. The potential activities of DNRA, anammox, denitrification and nitrification varied between 0.6 and 1.6, 4.6-37.3, 36.4-305.7, and 463.7-945.9 nmol N2 g-1 dry soil d-1, respectively, with higher values obtained in PA than NP. Nitrification accounted for 94.3-99.4% of NH4+ oxidation, with the rest through anammox. Denitrification contributed to 77.9-90.3% of NOx- reduction, compared to 9.2-21.6% and 0.5-1.5% via anammox and DNRA, respectively; 78.4-90.9% of N2 was produced through denitrification, with the rest via anammox. Pearson correlation analyses suggest NH4+ was the major factor regulating nitrification, while NO3- played an important role in the competition between denitrification and DNRA, and NO2- was a key restrictive factor for anammox. Overall, this study reveals the importance of nitrification, denitrification, anammox and DNRA in nitrogen removal, providing new insight into the nitrogen-cycling mechanisms in natural/artificial tidal wetlands.
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Affiliation(s)
- Manping Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jung-Chen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Shanshan Sun
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Muhammad Muneeb Ur Rehman
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Weili Zhou
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
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219
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He X, Yin H, Fang C, Xiong J, Han L, Yang Z, Huang G. Metagenomic and q-PCR analysis reveals the effect of powder bamboo biochar on nitrous oxide and ammonia emissions during aerobic composting. BIORESOURCE TECHNOLOGY 2021; 323:124567. [PMID: 33401162 DOI: 10.1016/j.biortech.2020.124567] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
To investigate the emission mechanism of ammonia (NH3) and nitrous oxide (N2O) during aerobic composting and the influence of powder bamboo biochar (PBB) on this process, this paper conducted a systematic study on the nitrogen-transforming functional microbial community, including functional genes, microbial structure and metabolism pathways. PBB reduced N2O and NH3 emissions by 1.25%-8.72% and 10.4%-11.8%, respectively. The quantitative PCR results indicated that the reduced N2O emission by PBB were mainly related to denitrifying genes (nirS, nirK, nosZ, and narG). The metagenome results demonstrated that Nitrosococcus was the main genus that could oxidize ammonia to nitrite decreased by PBB. The PBB significantly affected the nitrogen metabolism pathway, reduced the activity of glutamate dehydrogenase to inhibit the formation of NH4+ to reduce NH3 emission. The higher N2O emission in the control group was also related to the higher relative contents of hydroxylamine reductase and nitrite reductase.
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Affiliation(s)
- Xueqin He
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Hongjie Yin
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Chen Fang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Jinpeng Xiong
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Lujia Han
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Zengling Yang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Guangqun Huang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China.
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220
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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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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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222
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Su Q, Schittich AR, Jensen MM, Ng H, Smets BF. Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2173-2188. [PMID: 33543927 DOI: 10.1021/acs.est.0c06466] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH2OH), nitrite (NO2-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH4+) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (rbio, μmol/g VSS/d) to NH4+ removal (rNH4+, mol/g VSS/d) rate ratios (rbio/rNH4+) is observed for individual OMPs across different systems with similar rNH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.
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Affiliation(s)
- Qingxian Su
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Anna-Ricarda Schittich
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Howyong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Centre for Water Research, Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576 Singapore, Singapore
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
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223
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Soler-Jofra A, Pérez J, van Loosdrecht MCM. Hydroxylamine and the nitrogen cycle: A review. WATER RESEARCH 2021; 190:116723. [PMID: 33352529 DOI: 10.1016/j.watres.2020.116723] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/21/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Aerobic ammonium oxidizing bacteria were first isolated more than 100 years ago and hydroxylamine is known to be an intermediate. The enzymatic steps involving hydroxylamine conversion to nitrite are still under discussion. For a long time it was assumed that hydroxylamine was directly converted to nitrite by a hydroxylamine oxidoreductase. Recent enzymatic evidences suggest that the actual product of hydroxylamine conversion is NO and a third, yet unknown, enzyme further converts NO to nitrite. More recently, ammonium oxidizing archaea and complete ammonium oxidizing bacteria were isolated and identified. Still the central nitrogen metabolism of these microorganisms presents to researchers the same puzzle: how hydroxylamine is transformed to nitrite. Nitrogen losses in the form of NO and N2O have been identified in all three types of aerobic ammonium oxidizing microorganisms and hydroxylamine is known to play a significant role in the formation. Yet, the pathways and the factors promoting the greenhouse gas emissions are to be fully characterized. Hydroxylamine also plays a yet poorly understood role on anaerobic ammonium oxidizing bacteria and is known to inhibit nitrite oxidizing bacteria. In this review, the role of this elusive intermediate in the metabolism of different key players of the nitrogen cycle is discussed, as well as the putative importance of hydroxylamine as a key nitrogen metabolite for microbial interactions within microbial communities and engineered systems. Overall, for the first time putting together the acquired knowledge about hydroxylamine and the nitrogen cycle over the years in a review, setting potential hypothesis and highlighting possible next steps for research.
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Affiliation(s)
- Aina Soler-Jofra
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Julio Pérez
- Department of Chemical, Biological and Environmental Engineering, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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224
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Han P, Wu D, Sun D, Zhao M, Wang M, Wen T, Zhang J, Hou L, Liu M, Klümper U, Zheng Y, Dong HP, Liang X, Yin G. N 2O and NO y production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers. WATER RESEARCH 2021; 190:116728. [PMID: 33326897 DOI: 10.1016/j.watres.2020.116728] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) and NOy (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO2)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N2O and NOy emissions. Yet, little is known about HONO and NO2 production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N2O and NOy production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NOy production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N2O based on results from NH2OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH2OH) and NO transformation enzymatic activities may lead to a buildup of NH2OH/NO which can abiotically react to N2O ; iv) collectively confirm restrained N2O and NOy emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.
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Affiliation(s)
- Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Dianming Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Mengdi Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Lijun Hou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, 01062, Germany
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
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225
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Gonzalez-Silva BM, Jonassen KR, Bakke I, Østgaard K, Vadstein O. Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater. Sci Rep 2021; 11:2979. [PMID: 33536458 PMCID: PMC7859187 DOI: 10.1038/s41598-021-82272-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 12/17/2020] [Indexed: 12/05/2022] Open
Abstract
In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.
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Affiliation(s)
- Blanca M Gonzalez-Silva
- Department of Biotechnology and Food Science, Faculty of Natural Sciences and Technology, NTNU-Norwegian University of Science and Technology, Sem Saelands v. 6/8, N-7491, Trondheim, Norway. .,Department of Civil and Environmental Engineering, NTNU-Norwegian University of Science and Technology, S. P. Andersens veg 5, N-7031, Trondheim, Norway.
| | - Kjell Rune Jonassen
- Department of Biotechnology and Food Science, Faculty of Natural Sciences and Technology, NTNU-Norwegian University of Science and Technology, Sem Saelands v. 6/8, N-7491, Trondheim, Norway.,VEAS, Bjerkåsholmen 125, 3470, Slemmestad, Oslo, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Faculty of Natural Sciences and Technology, NTNU-Norwegian University of Science and Technology, Sem Saelands v. 6/8, N-7491, Trondheim, Norway
| | - Kjetill Østgaard
- Department of Biotechnology and Food Science, Faculty of Natural Sciences and Technology, NTNU-Norwegian University of Science and Technology, Sem Saelands v. 6/8, N-7491, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Faculty of Natural Sciences and Technology, NTNU-Norwegian University of Science and Technology, Sem Saelands v. 6/8, N-7491, Trondheim, Norway
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226
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Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes. Sci Rep 2021; 11:2982. [PMID: 33536606 PMCID: PMC7858572 DOI: 10.1038/s41598-021-82613-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml-1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.
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227
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Zhang L, Cui B, Yuan B, Zhang A, Feng J, Zhang J, Han X, Pan L, Li L. Denitrification mechanism and artificial neural networks modeling for low-pollution water purification using a denitrification biological filter process. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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228
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Netherway T, Bengtsson J, Krab EJ, Bahram M. Biotic interactions with mycorrhizal systems as extended nutrient acquisition strategies shaping forest soil communities and functions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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229
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Newsome L, Bacon CGD, Song H, Luo Y, Sherman DM, Lloyd JR. Natural attenuation of lead by microbial manganese oxides in a karst aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142312. [PMID: 33254903 DOI: 10.1016/j.scitotenv.2020.142312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 05/27/2023]
Abstract
Lead is a toxic environmental contaminant associated with current and historic mine sites. Here we studied the natural attenuation of Pb in a limestone cave system that receives drainage from the ancient Priddy Mineries, UK. Extensive deposits of manganese oxides were observed to be forming on the cave walls and as coatings in the stream beds. Analysis of these deposits identified them as birnessite (δ-MnO2), with some extremely high concentrations of sorbed Pb (up to 56 wt%) also present. We hypothesised that these cave crusts were actively being formed by microbial Mn(II)-oxidation, and to investigate this the microbial communities were characterised by DNA sequencing, enrichment and isolation experiments. The birnessite deposits contained abundant and diverse prokaryotes and fungi, with ~5% of prokaryotes and ~ 10% of fungi closely related to known heterotrophic Mn(II)-oxidisers. A substantial proportion (up to 17%) of prokaryote sequences were assigned to groups known as autotrophic ammonia and nitrite oxidisers, suggesting that nitrogen cycling may play an important role in contributing energy and carbon to the cave crust microbial communities and consequently the formation of Mn(IV) oxides and Pb attenuation. Enrichment and isolation experiments showed that the birnessite deposits contained Mn(II)-oxidising microorganisms, and two isolates (Streptomyces sp. and Phyllobacterium sp.) could oxidise Mn(II) in the presence of 0.1 mM Pb. Supplying the enrichment cultures with acetate as a source of energy and carbon stimulated Mn(II)-oxidation, but excess organics in the form of glucose generated aqueous Mn(II), likely via microbial Mn(IV)-reduction. In this karst cave, microbial Mn(II)-oxidation contributes to the active sequestration and natural attenuation of Pb from contaminated waters, and therefore may be considered a natural analogue for the design of wastewater remediation systems and for understanding the geochemical controls on karst groundwater quality, a resource relied upon by billions of people across the globe.
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Affiliation(s)
- Laura Newsome
- Williamson Research Centre, Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, United Kingdom.
| | - Charles G D Bacon
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, United Kingdom
| | - Hokyung Song
- Williamson Research Centre, Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Yunyao Luo
- Williamson Research Centre, Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - David M Sherman
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, United Kingdom
| | - Jonathan R Lloyd
- Williamson Research Centre, Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
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230
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González-Cabaleiro R, Martinez-Rabert E, Argiz L, van Kessel MA, Smith CJ. A framework based on fundamental biochemical principles to engineer microbial community dynamics. Curr Opin Biotechnol 2021; 67:111-118. [PMID: 33540361 DOI: 10.1016/j.copbio.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
Microbial communities are complex but there are basic principles we can apply to constrain the assumed stochasticity of their activity. By understanding the trade-offs behind the kinetic parameters that define microbial growth, we can explain how local interspecies dependencies arise and shape the emerging properties of a community. If we integrate these theoretical descriptions with experimental 'omics' data and bioenergetics analysis of specific environmental conditions, predictions on activity, assembly and spatial structure can be obtained reducing the a priori unpredictable complexity of microbial communities. This information can be used to define the appropriate selective pressures to engineer bioprocesses and propose new hypotheses which can drive experimental research to accelerate innovation in biotechnology.
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Affiliation(s)
- Rebeca González-Cabaleiro
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK.
| | - Eloi Martinez-Rabert
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
| | - Lucia Argiz
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Maartje Ahj van Kessel
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cindy J Smith
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
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231
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Minimization of N2O Emission through Intermittent Aeration in a Sequencing Batch Reactor (SBR): Main Behavior and Mechanism. WATER 2021. [DOI: 10.3390/w13020210] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To explore the main behavior and mechanism of minimizing nitrous oxide (N2O) emission through intermittent aeration during wastewater treatment, two lab-scale sequencing batch reactors operated at intermittently aerated mode (SBR1), and continuously aerated mode (SBR2) were established. Compared with SBR2, the intermittently aerated SBR1 reached not only a higher total nitrogen removal efficiency (averaged 93.5%) but also a lower N2O-emission factor (0.01–0.53% of influent ammonia), in which short-cut nitrification and denitrification were promoted. Moreover, less accumulation and consumption of polyhydroxyalkanoates, a potential endogenous carbon source promoting N2O emission, were observed in SBR1. Batch experiments revealed that nitrifier denitrification was the major pathway generating N2O while heterotrophic denitrification played as a sink of N2O, and SBR1 embraced a larger N2O-mitigating capability. Finally, quantitative polymerase chain reaction results suggested that the abundant complete ammonia oxidizer (comammox) elevated in the intermittently aerated environment played a potential role in avoiding N2O generation during wastewater treatment. This work provides an in-depth insight into the utilization of proper management of intermittent aeration to control N2O emission from wastewater treatment plants.
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232
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Fujitani H, Nomachi M, Takahashi Y, Hasebe Y, Eguchi M, Tsuneda S. Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions. FEMS Microbiol Lett 2021; 367:5731803. [PMID: 32037440 DOI: 10.1093/femsle/fnaa025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/08/2020] [Indexed: 12/25/2022] Open
Abstract
In artificial engineered systems, nitrification is a key reaction that accounts for the removal of biological nitrogen. Recently, a single microbe capable of oxidizing ammonia to nitrate, known as a complete ammonia oxidizer (comammox), has been discovered. Although the abundance and diversity of comammox Nitrospira in engineered systems have been identified through molecular-based approaches, the enrichment and isolation of comammox Nitrospira remains a challenge. Therefore, the aim of this study was to enrich comammox Nitrospira from nitrifying granules, which were used to increase the efficiency of biological nitrogen removal in wastewater treatment plants. We sought to accomplish this through the use of a fixed-bed continuous feeding bioreactor. Fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing and qPCR of functional genes were utilized to monitor the growth of nitrifiers including comammox Nitrospira. Cloning of comammox amoA genes identified amoA phylogeny of enriched comammox Nitrospira. This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, 305-8566, Japan.,Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yu Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoshiaki Hasebe
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Masahiro Eguchi
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
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233
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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234
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Yu X, Yan M, Cui Y, Liu Z, Liu H, Zhou J, Liu J, Zeng L, Chen Q, Gu Y, Zou L, Zhao K, Xiang Q, Ma M, Li S. Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field. Front Microbiol 2021. [PMID: 35601203 DOI: 10.3389/fmicb.2021.687888/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.
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Affiliation(s)
- Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yongliang Cui
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Zhongyi Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Han Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jie Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jiahao Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lan Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Shuangcheng Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
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235
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Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol 2021; 6:1129-1139. [PMID: 34267357 PMCID: PMC8387239 DOI: 10.1038/s41564-021-00934-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023]
Abstract
Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein's electron transport chain, and elucidate the electron transfer pathways within the complex.
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236
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Lin J, Chen N, Yuan X, Tian Q, Hu A, Zheng Y. Impacts of human disturbance on the biogeochemical nitrogen cycle in a subtropical river system revealed by nitrifier and denitrifier genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141139. [PMID: 32745858 DOI: 10.1016/j.scitotenv.2020.141139] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Human activities have largely modified nitrogen (N) sources supply, cycling and export from land to ocean. Nitrification and denitrification are vital processes alleviating N pollution in aquatic ecosystems but the diverse responses and niche of microbial N retention to human disturbance are still understudied. Here we investigated the changes in N species and functional genes in the urban, agriculture and reservoir river sections of the Jiulong River (southeast China). Our results show that ammonia-oxidizing bacteria (AOB) (Nitrosomonas) were dominant in the urban river section receiving ammonium-rich sewage that enhanced nitrification and subsequent denitrification, while ammonia-oxidizing archaea (AOA) was more abundant than AOB in the river section flowing through areas of pomelo (Citrus maxima) agriculture with low pH, low ammonium and very high nitrate input. Warm temperatures and large total suspended matter (TSM) in the wet season promoted growth of nitrifiers and denitrifiers, which were mostly particle-attached. The potential river N retention through gaseous N removal (PRN2O and PRN2) in the agriculture section with huge N loading was among the lowest. Strong nitrification and denitrification were suspected to occur in the agricultural acid soil system rather than in the river network. In addition, the decreased TSM and N concentration promoted free-living microbes in the reservoir. The highest PRN2 and N2 production observed in the reservoir in the dry season implied that denitrification and anammox occurring in sediments was likely to increase N retention. This study suggests the diverse factors involved in processing of N pollution among diverse landscapes.
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Affiliation(s)
- Jingjie Lin
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, China.
| | - Xin Yuan
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qing Tian
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yi Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
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237
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Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, Zechmeister T, Karst SM, Albertsen M, Nielsen PH, Wagner M, Daims H. Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira. THE ISME JOURNAL 2020; 14:2967-2979. [PMID: 32709974 PMCID: PMC7784846 DOI: 10.1038/s41396-020-0724-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.
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Affiliation(s)
- Anne Daebeler
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Max Planck Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Hanna Koch
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela Steinfeder
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jasmin Schwarz
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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238
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Santos JP, Sousa AGG, Ribeiro H, Magalhães C. The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes. Front Microbiol 2020; 11:574815. [PMID: 33324363 PMCID: PMC7727400 DOI: 10.3389/fmicb.2020.574815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.
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Affiliation(s)
- João Pereira Santos
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department F.A. Forel for Environmental and Aquatic Sciences, Section of Earth and Environmental Sciences, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - António G G Sousa
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Hugo Ribeiro
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Abel Salazar Institute of Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Catarina Magalhães
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,School of Science & Engineering, University of Waikato, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Halitax, NS, Canada
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239
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Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. MICROBIOME 2020; 8:163. [PMID: 33213521 PMCID: PMC7678222 DOI: 10.1186/s40168-020-00936-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. RESULTS Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. CONCLUSIONS These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance. Video Abstract.
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Affiliation(s)
- F H Coutinho
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain.
| | - P J Cabello-Yeves
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Gonzalez-Serrano
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - M López-Pérez
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - T I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - F Rodriguez-Valera
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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240
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Liu Z, Zhang C, Wei Q, Zhang S, Quan Z, Li M. Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140456. [PMID: 32629251 DOI: 10.1016/j.scitotenv.2020.140456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/21/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.
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Affiliation(s)
- Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Cuijing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Qiaoyan Wei
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, PR China
| | - Siyu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China.
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241
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Zakem EJ, Polz MF, Follows MJ. Redox-informed models of global biogeochemical cycles. Nat Commun 2020; 11:5680. [PMID: 33173062 PMCID: PMC7656242 DOI: 10.1038/s41467-020-19454-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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242
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Song L, Pan Z, Dai Y, Chen L, Zhang L, Liao Q, Yu X, Guo H, Zhou G. Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields. PeerJ 2020; 8:e10302. [PMID: 33194446 PMCID: PMC7648459 DOI: 10.7717/peerj.10302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.
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Affiliation(s)
- Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenzhi Pan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Dai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Lin Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing Univerity, Nanjing, Jiangsu, China
| | - Qilin Liao
- Geological Survey of Jiangsu Province, Nanjing, Jiangsu, China
| | - Xiezhi Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing Univerity, Nanjing, Jiangsu, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing Univerity, Nanjing, Jiangsu, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
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Papadopoulou ES, Bachtsevani E, Lampronikou E, Adamou E, Katsaouni A, Vasileiadis S, Thion C, Menkissoglu-Spiroudi U, Nicol GW, Karpouzas DG. Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates. Front Microbiol 2020; 11:581283. [PMID: 33250872 PMCID: PMC7672009 DOI: 10.3389/fmicb.2020.581283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Adamou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Katsaouni
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Cécile Thion
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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244
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Liu X, Zhu H. Treatment of Low C/N Ratio Wastewater by a Carbon Cloth Bipolar Plate Multicompartment Electroenhanced Bioreactor (CBM-EEB). ACS OMEGA 2020; 5:27823-27832. [PMID: 33163765 PMCID: PMC7643109 DOI: 10.1021/acsomega.0c02828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/25/2020] [Indexed: 05/04/2023]
Abstract
The traditional biological denitrification process has the problems of low removal rates and lack of a carbon source when treating wastewater with high ammonia nitrogen concentration and a low carbon-nitrogen ratio. Based on a bio-electrochemical system (BES), a novel carbon cloth bipolar plate multicompartment electroenhanced bioreactor (CBM-EEB) system was constructed. In this study, nitrogen removal efficiency and enrichment of functional bacteria using CBM-EEB under different voltage conditions were investigated. The results from next-generation sequencing indicated that the CBM-EEB included heterotrophic nitrification and aerobic denitrification (HNAD) and was dominated by heterotrophic nitrification aerobic denitrifying bacteria (HNADB). The applied voltage was confirmed as having the ability to regulate the microbial community structure and abundance of functional genes, thereby further enhancing the nitrogen removal efficiency of the system. The total nitrogen removal efficiency was 77.70 ± 1.14, 87.10 ± 0.56, 86.40 ± 0.59, and 89.30 ± 0.53% under applied voltages of 0.4, 0.7, 1.0, and 1.3 V, respectively. All values were significantly higher than the control group (62.86 ± 2.06%). HNADB had the highest abundance among the 17 detected genera related to nitrogen metabolism. Facultative denitrifying bacteria, Pseudoxanthomonas, along with key bacteria of HNADB, such as Flavobacterium, constructed a shortcut simultaneous nitrification-denitrification (SND) process. Poisson analysis and redundancy analysis (RDA) showed that the applied voltage improved the denitrification efficiency by changing the microbial community structure, reducing the abundance of heterotrophic bacteria, and increasing the unit abundance of key functional genes so that less organics were required for the denitrification process. The increased nitrogen removal efficiency in the experimental group was mainly related to simultaneous nitrification-denitrification process and cooperation of microbial communities in the anode and the cathode. This study highlighted the feasibility of CBM-EEB to enhance the HNAD reaction and the response of wastewater with a low C/N ratio to enhance the abundance of microbial bacteria and their functional gene abundance.
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Affiliation(s)
- Xueyu Liu
- Biomass Energy Research Center, Tongji University, Shanghai 201804, P. R. China
| | - Hongguang Zhu
- Biomass Energy Research Center, Tongji University, Shanghai 201804, P. R. China
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245
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Wu G, Zhang T, Gu M, Chen Z, Yin Q. Review of characteristics of anammox bacteria and strategies for anammox start-up for sustainable wastewater resource management. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:1742-1757. [PMID: 33201840 DOI: 10.2166/wst.2020.443] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wastewater management has experienced different stages, including pollutant removal, resource recovery, and water nexus. Within these stages, anaerobic ammonia oxidation-based biotechnology can be incorporated for nitrogen removal, which can help achieve sustainable wastewater management, such as reclamation and ecologization of wastewater. Here, the physiology, metabolism, reaction kinetics and microbial interactions of anammox bacteria are discussed, and strategies to start-up the anammox system are presented. Anammox bacteria are slow growers with a high doubling time and a low reaction rate. Although most anammox bacteria grow autotrophically, some types can grow mixotrophically. The reaction stoichiometric coefficients can be affected by loading rates and other biological reactions. Microbial interactions also contribute to enhanced biological nitrogen removal and promote activities of anammox bacteria. The start-up of the anammox process is the key aspect for its practical application, which can be realized through seed selection, system stimulation, and biomass concentration enhancement.
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Affiliation(s)
- Guangxue Wu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China E-mail:
| | - Tianqi Zhang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China E-mail:
| | - Mengqi Gu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China E-mail:
| | - Zhuo Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Qidong Yin
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China E-mail:
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246
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Cui Y, Gao J, Zhang D, Zhao Y, Wang Y. Rapid start-up of partial nitrification process using benzethonium chloride-a novel nitrite oxidation inhibitor. BIORESOURCE TECHNOLOGY 2020; 315:123860. [PMID: 32707510 DOI: 10.1016/j.biortech.2020.123860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Benzethonium chloride (BZC) is an antibacterial compound with extensive applications in various anti-infective products. However, the feasibility of attaining partial nitrification of municipal wastewater using BZC has not been reported. In this work, BZC was used for the first time to attain partial nitrification. Batch experiments indicated nitrite oxidizing bacteria (NOB) was more vulnerable to BZC than ammonia oxidizing bacteria (AOB). When activated sludge was treated only once with 0.023 g BZC·(g MLSS)-1 for 18 h, partial nitrification was attained at the 29th cycle with NAR of 97.46% and sustained 91 cycles in stability tests. Complimentary DNA sequencing analysis revealed the suppression of Nitrospira was the reason for partial nitrification. Oligotyping analysis indicated AOB could likely resist to BZC by both the species shifts and development of tolerance, while most NOB species could not adapt to BZC. This study revealed the feasibility of BZC as a novel NOB inhibitor.
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Affiliation(s)
- Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Da Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yuwei Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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247
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Liu W, Song J, Wang J, Wu P, Shen Y, Yang D. Comparing nitrite-limited and ammonium-limited anammox processes treating low-strength wastewater: Functional and population heterogeneity. CHEMOSPHERE 2020; 258:127290. [PMID: 32535448 DOI: 10.1016/j.chemosphere.2020.127290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/12/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Biomass segregation between granules/biofilm and flocs is widespread in anammox-based processes. The segregation of biomass allows for easy control of processes stability. The goal of this study is to understand the biomass segregation in two anoxic anammox reactors respectively operated in nitrite-limited (RNO2) and ammonium-limited (RNH4) modes treating low-strength wastewater at 20 °C. Results showed that size-based biomass segregation was developed in both reactors. But the functional and population heterogeneity was more significant in the ammonium-limited anammox reactor. The activity and abundance of anammox bacteria in large granules were significantly higher than that in flocs under the ammonium-limited conditions. The large granules played a major role in nitrogen removal in RNH4. By contrast, both large granules and small flocs contributed significantly to the nitrogen loss in the nitrite-limited anammox reactor, since a large number of anammox bacteria existed in both granules and flocs. Besides, a number of Nitrospira-like NOB were also detected in both anoxic anammox reactors, which primarily inhabited in flocs seemingly droved by the availability of oxygen. But the abundance of Nitrospira in RNH4 was much higher than that in RNO2. All these results suggested that selective flocs removal would be necessary for RNH4 to improve its anammox performance but non-essential for RNO2. The two anammox reactors shared the predominant anammox species with the closest relative to Ca. Brocadia sp. 40 (98%). Unexpectedly, the anammox species grew faster in RNH4. But the microbial diversity and evenness was much greater in RNO2, suggesting its higher functional stability.
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Affiliation(s)
- Wenru Liu
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Jiajun Song
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jianfang Wang
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Peng Wu
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Yaoliang Shen
- National & Local Joint Engineering Laboratory for Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, China
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248
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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249
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Lukumbuzya M, Kristensen JM, Kitzinger K, Pommerening-Röser A, Nielsen PH, Wagner M, Daims H, Pjevac P. A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria. WATER RESEARCH 2020; 186:116372. [PMID: 32916620 DOI: 10.1016/j.watres.2020.116372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.
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Affiliation(s)
- Michael Lukumbuzya
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jannie Munk Kristensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Pommerening-Röser
- University of Hamburg, Institute of Plant Science and Microbiology, Microbiology and Biotechnology, Hamburg, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria.
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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250
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Park SJ, Andrei AŞ, Bulzu PA, Kavagutti VS, Ghai R, Mosier AC. Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches. Appl Environ Microbiol 2020; 86:e01667-20. [PMID: 32917751 PMCID: PMC7642081 DOI: 10.1128/aem.01667-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/03/2020] [Indexed: 12/30/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.
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Affiliation(s)
- Soo-Je Park
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA
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