1
|
Hu L, Wang Z, Wang Z, Wang L, Fang J, Liu R. Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench. Curr Microbiol 2024; 81:282. [PMID: 39060557 DOI: 10.1007/s00284-024-03810-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.
Collapse
Affiliation(s)
- Lin Hu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Zhixuan Wang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Zixuan Wang
- Tidal Flat Research Center of Jiangsu Province, Nanjing, Jiangsu, China
| | - Li Wang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, USA
| | - Rulong Liu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China.
| |
Collapse
|
2
|
Liu H, Jing H, Wang F. Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Front Microbiol 2023; 14:1268790. [PMID: 37840747 PMCID: PMC10568479 DOI: 10.3389/fmicb.2023.1268790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.
Collapse
Affiliation(s)
- Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
3
|
Effects of aquatic nitrogen pollution on particle-attached ammonia-oxidizing bacteria in urban freshwater mesocosms. World J Microbiol Biotechnol 2022; 38:64. [DOI: 10.1007/s11274-022-03251-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
|
4
|
Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
Collapse
Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| |
Collapse
|
5
|
Interaction between Microbes, Minerals, and Fluids in Deep-Sea Hydrothermal Systems. MINERALS 2021. [DOI: 10.3390/min11121324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by converting inorganic carbon into organic biomass. Due to the rich variety of chemical sources and steep physico-chemical gradients, a large array of microorganisms thrive in these extreme environments, which includes but are not restricted to chemolithoautotrophs, heterotrophs, and mixotrophs. Past research has revealed the underlying relationship of these microbial communities with the subsurface geology and hydrothermal geochemistry. Endolithic microbial communities at the ocean floor catalyze a number of redox reactions through various metabolic activities. Hydrothermal chimneys harbor Fe-reducers, sulfur-reducers, sulfide and H2-oxidizers, methanogens, and heterotrophs that continuously interact with the basaltic, carbonate, or ultramafic basement rocks for energy-yielding reactions. Here, we briefly review the global deep-sea hydrothermal systems, microbial diversity, and microbe–mineral interactions therein to obtain in-depth knowledge of the biogeochemistry in such a unique and geologically critical subseafloor environment.
Collapse
|
6
|
Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
Collapse
Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| |
Collapse
|
7
|
Wen T, Yang L, Dang C, Yang M, Miki T, Bai H, Nagasaka T. Effect of modified basic oxygen furnace slag on the controlled release of nitrate nitrogen and the functional microbial community in soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 261:110191. [PMID: 32001433 DOI: 10.1016/j.jenvman.2020.110191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 01/05/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The specific surface area and active adsorption sites of basic oxygen furnace (BOF) slag increase after BOF modification. The addition of modified BOF slag to the soil may enable the control of nitrate nitrogen (NO3-N) leaching and also affect the functional microflora in the soil. In this study, soil column leaching experiments were conducted to explore the effects of adding modified slag to the soil on the controlled release of NO3-N and the main functional microbial communities involved in nitrification and denitrification processes. The experimental design included seven column groups: a soil control group (CT); soil groups with 2.5%, 5%, and 10% raw slag (S1, S2, S3); and soil groups with 2.5%, 5%, and 10% modified slag (MS1, MS2, MS3) that were subjected to three cycles of leaching, each of which were comprised of five leaching treatments. After the three cycles of leaching, significantly less NO3-N had leached from the modified slag group compared to the CT and the raw slag groups (P < 0.05). Although both slag treatments increased soil pH and decreased the oxidation reduction potential of the soil leaching solution, the addition of modified slag had less effect on soil pH than the addition of raw slag. During column leaching, the group with modified slag had a higher gene abundance of functional microflora compared with the group with raw slag. Similarly, the modified slag group had a higher diversity and richness of denitrifying bacteria, ammonia-oxidizing archaea, and ammonia-oxidizing bacteria than the raw slag group. In conclusion, the addition of modified slag to soil effectively decreased the NO3-N leaching and had relatively little effect on the functional microbial community in the soil.
Collapse
Affiliation(s)
- Tingting Wen
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, 100083, PR China
| | - Liyun Yang
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, 100083, PR China.
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Maomao Yang
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, 100083, PR China
| | - Takahiro Miki
- Department of Metallurgy, Graduate School of Engineering, Tohoku University, 02 Aoba-yama, Sendai, 980-8579, Japan
| | - Hao Bai
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, 100083, PR China
| | - Tetsuya Nagasaka
- Department of Metallurgy, Graduate School of Engineering, Tohoku University, 02 Aoba-yama, Sendai, 980-8579, Japan
| |
Collapse
|
8
|
Zhao MM, Chen YP, Xue LG, Fan TT. Three kinds of ammonia oxidizing microorganisms play an important role in ammonia nitrogen self-purification in the Yellow River. CHEMOSPHERE 2020; 243:125405. [PMID: 31995872 DOI: 10.1016/j.chemosphere.2019.125405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
To develop the microbial resources of the Yellow River, seven water samples were collected along the Lanzhou region of the river from upstream to downstream for testing. Analysis of various physico-chemical indexes was conducted, and key parameters influencing the water quality were selected through principal component analysis, after which the decisive factors impacting water quality were determined by correlation and regression analysis. The results indicated that (1) DO, NH3-N, NO2--N, TN, TC, As, Cr6+ and Pb were the main physico-chemical factors influencing water quality in the Lanzhou region, with NH3-N having the greatest effect. (2) Ammonia-oxidizing microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonia-oxidizing bacteria (AMX)] were found to mediate the transformation of NH3-N in the studied section. AOA was the primary microbe community among the two aerobic ammonia-oxidizing microorganisms (AOA and AOB) in the Yellow River. (3) Phylogenetic analysis showed that there were some known groups, and there were still many unknown species in the water of the studied section, especially within the AMX population. (4) Correlation analysis revealed that AOA has strong adaptability to unhealthy environments, and that some environmental factors (higher concentrations of carbon, nitrogen and some heavy metals) could increase the AOA gene abundance. Overall, these results suggested there are rich ammonia-oxidizing microbial resources, especially AOA, in the Lanzhou section of the Yellow River, which have the potential for application in nitrogen sewage treatment.
Collapse
Affiliation(s)
- Meng M Zhao
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Yi-Ping Chen
- SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China.
| | - Lin-Gui Xue
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Tao T Fan
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| |
Collapse
|
9
|
Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems 2020; 5:5/1/e00795-19. [PMID: 31911466 PMCID: PMC6946796 DOI: 10.1128/msystems.00795-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.
Collapse
|
10
|
Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
Collapse
Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
| |
Collapse
|
11
|
Liu Y, Liu J, Yao P, Ge T, Qiao Y, Zhao M, Zhang XH. Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas. Syst Appl Microbiol 2018; 41:658-668. [PMID: 30172418 DOI: 10.1016/j.syapm.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/19/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.
Collapse
Affiliation(s)
- Yuyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiantian Ge
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
12
|
Wang J, Kan J, Zhang X, Xia Z, Zhang X, Qian G, Miao Y, Leng X, Sun J. Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal. Front Microbiol 2017; 8:415. [PMID: 28360898 PMCID: PMC5352681 DOI: 10.3389/fmicb.2017.00415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.
Collapse
Affiliation(s)
- Jing Wang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jinjun Kan
- Stroud Water Research Center Avondale, PA, USA
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Zhiqiang Xia
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xuecheng Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Gang Qian
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Yanyi Miao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xiaoyun Leng
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| |
Collapse
|
13
|
Yu S, Yao P, Liu J, Zhao B, Zhang G, Zhao M, Yu Z, Zhang XH. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas. Front Microbiol 2016; 7:137. [PMID: 26904010 PMCID: PMC4751261 DOI: 10.3389/fmicb.2016.00137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO[Formula: see text]), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ(15)NTN and SiO[Formula: see text], and nitrate and δ(13)C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO[Formula: see text]. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.
Collapse
Affiliation(s)
- Shaolan Yu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Peng Yao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of ChinaQingdao, China; Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of ChinaQingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Jiwen Liu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Bin Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Guiling Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of ChinaQingdao, China; Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of ChinaQingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Zhigang Yu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Xiao-Hua Zhang
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
| |
Collapse
|
14
|
Hu W, He Y, Chen D, Mo C, Guo Y, Ma D. Diversity of ammonia-oxidizing bacteria in relation to soil environment in Ebinur Lake Wetland. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1124738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
15
|
Luo ZH, Xu W, Li M, Gu JD, Zhong TH. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean. Antonie van Leeuwenhoek 2015; 108:329-42. [PMID: 26014493 DOI: 10.1007/s10482-015-0485-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.
Collapse
Affiliation(s)
- Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen, 361005, People's Republic of China,
| | | | | | | | | |
Collapse
|