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Park Y, Song B, Cha J, An S. Microbiome signature of different stages of hypoxia event in Wonmun Bay. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106673. [PMID: 39216437 DOI: 10.1016/j.marenvres.2024.106673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/24/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
We investigated how microbial communities associated with different hypoxic stages respond to environmental changes across three water depths in Wonmun Bay, South Korea. Analysis of temperature, salinity, dissolved oxygen (DO), and nutrient concentrations revealed prominent seasonal shifts and strong stratification during summer hypoxia. Metabarcoding of prokaryotic 16 S rRNA genes and phototrophic eukaryotic chloroplasts along with quantitative PCR (qPCR) revealed variations in the abundance and composition of these communities. Chloroplast 16 S sequences in May were dominated by land plants (93% of Embryophyta), contrasting with the diverse phytoplankton taxa detected in other months. The water communities in May also had higher total microbial abundance than other months but significantly lower alpha diversity. These results suggest a major influence of freshwater discharge on water communities, pre-conditioning for hypoxia events by promoting organic matter decomposition coupled with DO consumption in bottom water. Subsequently, distinct microbial communities were observed across depths during hypoxia in June and July, while less variability was detected among different depths in September and later months when hypoxia events disappeared. Principal Coordinate analysis (PCoA) demonstrated the distinct patterns of microbial communities in May, June, and July from other months. Both sulfur-oxidizing and sulfate-reducing bacteria (SRB) were prevalent in June while the increase of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was observed in mid and bottom water in July. This data suggests the intricate interaction between sulfur and nitrogen-cycling microbes during the hypoxia events in Wonmun Bay. In conclusion, this study provides valuable insights into the microbial community responses to the varying environmental conditions at different stages of hypoxia events in eutrophic coastal ecosystems.
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Affiliation(s)
- Yunjung Park
- Research Institute for Basic Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Bongkeun Song
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, 23062, United States
| | - Jaeho Cha
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Soonmo An
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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2
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Ji R, Wan J, Liu J, Zheng J, Xiao T, Pan Y, Lin W. Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level. MICROBIOME 2024; 12:158. [PMID: 39182147 PMCID: PMC11344931 DOI: 10.1186/s40168-024-01837-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/14/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques. METHODS Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics. RESULTS We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time. CONCLUSIONS To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.
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Affiliation(s)
- Runjia Ji
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Wan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
| | - Jia Liu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinbo Zheng
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Engineering Laboratory for Deep Resources Equipment and Technology, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Tian Xiao
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Liu S, Hou C, Dong C, Zhao D, Chen Q, Terence Yang JY, Tang K. Integrated multi-omics analyses reveal microbial community resilience to fluctuating low oxygen in the East China sea. ENVIRONMENTAL RESEARCH 2024; 261:119764. [PMID: 39122162 DOI: 10.1016/j.envres.2024.119764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Climate change and eutrophication are accelerating ocean deoxygenation, leading to a global decline in oxygen levels. The East China Sea, frequently experiencing deoxygenation events, harbors diverse microbial communities. However, the response of these communities to the changing deoxygenation dynamics remains poorly understood. Here, we explored the composition and function of microbial communities inhabiting seawaters of the Changjiang Estuary and offshore areas. Our findings suggested that neutral processes significantly influenced the assembly of these communities. The overall bacterial composition demonstrated remarkable high stability across the oxygen gradient. Salinity exhibited a significantly stronger correlation with bacterial community structure than dissolved oxygen. Both metagenomics and metaproteomics revealed that all of the samples exhibited similar functional community structures. Heterotrophic metabolism dominated these sites, as evidenced by a diverse array of transporters and metabolic enzymes for organic matter uptake and utilization, which constituted a significant portion of the expressed proteins. O2 was the primary electron acceptor in bacteria even under hypoxic conditions, evidenced by expression of low- and high-affinity cytochrome oxidases. Proteins associated with anaerobic processes, such as dissimilatory sulfite reductases, were virtually undetectable. Untargeted liquid chromatography with tandem mass spectrometry analysis of seawater samples revealed a diverse range of dissolved organic matter (DOM) components in amino acids, lipids, organic acids, peptides, and carbohydrates, potentially fueling dominant taxa growth. Despite fluctuations in the abundance of specific genera, the remarkable similarity in community structure, function, and DOM suggests that this ecosystem possesses robust adaptive mechanisms that buffer against abrupt changes, even below the well-defined hypoxic threshold in marine ecosystem.
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Affiliation(s)
- Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Congcong Hou
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Duo Zhao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Jin-Yu Terence Yang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China.
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4
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Huang Y, Zhang X, Xin Y, Tian J, Li M. Distinct microbial nitrogen cycling processes in the deepest part of the ocean. mSystems 2024; 9:e0024324. [PMID: 38940525 PMCID: PMC11265455 DOI: 10.1128/msystems.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean. IMPORTANCE The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.
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Affiliation(s)
- Yuhan Huang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Synthetic Biology Research Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xinxu Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Synthetic Biology Research Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yu Xin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, Shandong, China
| | - Jiwei Tian
- MOE Key Laboratory of Physical Oceanography, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Meng Li
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Synthetic Biology Research Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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5
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Lenferink WB, van Alen TA, Jetten MSM, Op den Camp HJM, van Kessel MAHJ, Lücker S. Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria. Antonie Van Leeuwenhoek 2024; 117:104. [PMID: 39043958 PMCID: PMC11266412 DOI: 10.1007/s10482-024-02002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/11/2024] [Indexed: 07/25/2024]
Abstract
Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.
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Affiliation(s)
- Wouter B Lenferink
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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6
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Li J, Xie N, Liu X, Bai M, Hunt DE, Wang G. Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174934. [PMID: 39047843 DOI: 10.1016/j.scitotenv.2024.174934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.
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Affiliation(s)
- Jiaqian Li
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China; Duke University Marine Lab, Beaufort, NC, USA
| | - Ningdong Xie
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Xiuping Liu
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Mohan Bai
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Dana E Hunt
- Duke University Marine Lab, Beaufort, NC, USA.
| | - Guangyi Wang
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China.
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7
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Liu X, Wu M, Guo J. Coupling Nitrate-Dependent Anaerobic Ethane Degradation with Anaerobic Ammonium Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11525-11533. [PMID: 38898713 DOI: 10.1021/acs.est.4c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The microbial oxidation of short-chain gaseous alkanes (SCGAs, consisting of ethane, propane, and butane) serves as an efficient sink to mitigate these gases' emission to the atmosphere, thus reducing their negative impacts on air quality and climate. "Candidatus Alkanivorans nitratireducens" are recently found to mediate nitrate-dependent anaerobic ethane oxidation (n-DAEO). In natural ecosystems, anaerobic ammonium-oxidizing (anammox) bacteria may consume nitrite generated from nitrate reduction by "Ca. A. nitratireducens", thereby alleviating the inhibition caused by nitrite accumulation on the metabolism of "Ca. A. nitratireducens". Here, we demonstrate the coupling of n-DAEO with anammox in a laboratory-scale model system to prevent nitrite accumulation. Our results suggest that a high concentration of ethane (6.9-7.9%) has acute inhibition on anammox activities, thus making the coupling process a significant challenge. By maintaining ethane concentrations within the range of 1.7-5.5%, stable ethane and ammonium oxidation, nitrate reduction, and dinitrogen gas generation without nitrite accumulation were finally achieved. After the accomplished coupling of n-DAEO with anammox, nitrate reduction rates increased by 8.1 times compared to the rate observed with n-DAEO alone. Microbial community profiling via 16S rRNA gene amplicon sequencing showed "Ca. A. nitratireducens" (6.6-12.9%) and anammox bacteria "Candidatus Kuenenia" (3.4-5.6%) were both dominant in the system, indicating they potentially form a syntrophic partnership to jointly contribute to nitrogen removal. Our findings offer insights into the cross-feeding interaction between "Ca. A. nitratireducens" and anammox bacteria in anoxic environments.
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Affiliation(s)
- Xiawei Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
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8
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Sun Y, Du P, Li H, Zhou K, Shou L, Chen J, Meng Li. Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column. ENVIRONMENTAL RESEARCH 2024; 252:119011. [PMID: 38670213 DOI: 10.1016/j.envres.2024.119011] [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: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO43-, and distance offshore (p < 0.05). Water depth, NH4+, and PO43- were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3- (or NO2-) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.
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Affiliation(s)
- Yihua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Konglin Zhou
- Institute of Oceanography, Minjiang University, No. 200 xiyuangong Road, 350108 Fuzhou, Fujian, PR China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Synthetic Biology Research Center, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China.
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9
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Yang Q, Ling J, Zhang Y, Zhou W, Wei Z, Li J, Zhang Y, Dong J, Qian P. Microbial nitrogen removal in reef-building corals: A light-sensitive process. CHEMOSPHERE 2024; 359:142394. [PMID: 38777199 DOI: 10.1016/j.chemosphere.2024.142394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Scleractinian corals are the main framework-building groups in tropical coral reefs. In the coral holobiont, nitrogen-cycling mediated by microbes is fundamental for sustaining the coral reef ecosystems. However, little direct evidence characterizing the activities of microbial nitrogen removal via complete denitrification and anaerobic ammonium oxidation (anammox) in stony corals has been presented. In this study, multiple incubation experiments using 15N-tracer were conducted to identify and characterize N2 production by denitrification and anammox in the stony coral Pocillopora damicornis. The rates of denitrification and anammox were recorded up to 0.765 ± 0.162 and 0.078 ± 0.009 nmol N2 cm-2 h-1 respectively. Denitrification contributed the majority (∼90%) of N2 production by microbial nitrogen removal in stony corals. The microbial nitrogen removal activities showed diel rhythms, which might correspond to photosynthetic oxygen production. The N2 production rates of anammox and denitrification increased with incubation time. To the authors' knowledge, this study is the first to confirm and characterize the activities of complete denitrification and anammox in stony corals via stable isotope techniques. This study extends the understanding on nitrogen-cycling in coral reefs and how it participates in corals' resilience to environmental stressors.
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Affiliation(s)
- Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhangliang Wei
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Ocean School, Yantai University, Yantai, China.
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Tropical Marine Biological Research Station in Hainan, CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China; Shantou Marine Plants Experiment Station, Chinese Academy of Sciences, Shantou, China.
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
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10
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Intrator N, Jayakumar A, Ward BB. Aquatic nitrous oxide reductase gene ( nosZ) phylogeny and environmental distribution. Front Microbiol 2024; 15:1407573. [PMID: 38835481 PMCID: PMC11148229 DOI: 10.3389/fmicb.2024.1407573] [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: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.
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Affiliation(s)
- Naomi Intrator
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
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11
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Ray M, Manu S, Rastogi G, Umapathy G. Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution. J Mol Evol 2024; 92:121-137. [PMID: 38489069 DOI: 10.1007/s00239-024-10159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.
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Affiliation(s)
- Manisha Ray
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.
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12
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Sarkar J, Mondal M, Bhattacharya S, Dutta S, Chatterjee S, Mondal N, N S, Peketi A, Mazumdar A, Ghosh W. Extremely oligotrophic and complex-carbon-degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments. Arch Microbiol 2024; 206:179. [PMID: 38498215 DOI: 10.1007/s00203-024-03875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2 limitation, obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a ~ 3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates' genomes and the habitat's metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains' survival in the critically carbon-depleted layers below the explored sediment depths (core-bottom organic carbon: 0.5-1.0% w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously reported sources such as Nitrosopumilus species.
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Affiliation(s)
- Jagannath Sarkar
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
| | - Mahamadul Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sabyasachi Bhattacharya
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Subhajit Dutta
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Nibendu Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- International Institute of Innovation and Technology, Kolkata, West Bengal, India
| | - Saran N
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Aditya Peketi
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Aninda Mazumdar
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Wriddhiman Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
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13
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Wang C, He T, Zhang M, Zheng C, Yang L, Yang L. Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123480. [PMID: 38325507 DOI: 10.1016/j.envpol.2024.123480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.
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Affiliation(s)
- Cerong Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Tengxia He
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Manman Zhang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Chunxia Zheng
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Li Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Lu Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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14
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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15
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Cuecas A, Barrau MJ, Gonzalez JM. Microbial divergence and evolution. The case of anammox bacteria. Front Microbiol 2024; 15:1355780. [PMID: 38419632 PMCID: PMC10900513 DOI: 10.3389/fmicb.2024.1355780] [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: 12/14/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Species differentiation and the appearance of novel diversity on Earth is a major issue to understand the past and future of microbial evolution. Herein, we propose the analysis of a singular evolutive example, the case of microorganisms carrying out the process of anammox (anaerobic ammonium oxidation). Anammox represents a singular physiology active on Earth from ancient times and, at present, this group is still represented by a relatively limited number of species carrying out a specific metabolism within the Phylum Planctomycetota. The key enzyme on the anammox pathway is hydrazine dehydrogenase (HDH) which has been used as a model in this study. HDH and rRNA (16S subunit) phylogenies are in agreement suggesting a monophyletic origin. The diversity of this singular phylogenetic group is represented by a few enriched bacterial consortia awaiting to be cultured as monospecific taxa. The apparent evolution of the HDH genes in these anammox bacteria is highly related to the diversification of the anammox clades and their genomes as pointed by phylogenomics, their GC content and codon usage profile. This study represents a clear case where bacterial evolution presents a paralleled genome, gene and species diversification through time from a common ancestor; a scenario that most times is masked by a web-like phylogeny and the huge complexity within the prokaryotes. Besides, this contribution suggests that microbial evolution of the anammox bacteria has followed an ordered, vertical diversification through Earth history and will present a potentially similar speciation fate in the future.
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Affiliation(s)
| | | | - Juan M. Gonzalez
- Institute of Natural Resources and Agrobiology, Spanish National Council for Research, IRNAS-CSIC, Sevilla, Spain
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16
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Oshiki M, Morimoto E, Kobayashi K, Satoh H, Okabe S. Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture. ISME COMMUNICATIONS 2024; 4:ycad007. [PMID: 38304081 PMCID: PMC10833080 DOI: 10.1093/ismeco/ycad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 02/03/2024]
Abstract
Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Emi Morimoto
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Kanae Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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17
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Wan XS, Sheng HX, Liu L, Shen H, Tang W, Zou W, Xu MN, Zheng Z, Tan E, Chen M, Zhang Y, Ward BB, Kao SJ. Particle-associated denitrification is the primary source of N 2O in oxic coastal waters. Nat Commun 2023; 14:8280. [PMID: 38092778 PMCID: PMC10719265 DOI: 10.1038/s41467-023-43997-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.
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Affiliation(s)
- Xianhui S Wan
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
| | - Hua-Xia Sheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Li Liu
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Hui Shen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Weiyi Tang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Wenbin Zou
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Min N Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Zhenzhen Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Mingming Chen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Yao Zhang
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Shuh-Ji Kao
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China.
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18
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Govindankutty Menon A, Davis CV, Nürnberg D, Nomaki H, Salonen I, Schmiedl G, Glock N. A deep-learning automated image recognition method for measuring pore patterns in closely related bolivinids and calibration for quantitative nitrate paleo-reconstructions. Sci Rep 2023; 13:19628. [PMID: 37949926 PMCID: PMC10638366 DOI: 10.1038/s41598-023-46605-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Eutrophication is accelerating the recent expansion of oxygen-depleted coastal marine environments. Several bolivinid foraminifera are abundant in these oxygen-depleted settings, and take up nitrate through the pores in their shells for denitrification. This makes their pore density a possible nitrate proxy. This study documents three aspects related to the porosity of bolivinids. 1. A new automated image analysis technique to determine the number of pores in bolivinids is tested. 2. The pore patterns of Bolivina spissa from five different ocean settings are analysed. The relationship between porosity, pore density and mean pore size significantly differs between the studied locations. Their porosity is mainly controlled by the size of the pores at the Gulf of Guayaquil (Peru), but by the number of pores at other studied locations. This might be related to the presence of a different cryptic Bolivina species in the Gulf of Guayaquil. 3. The pore densities of closely related bolivinids in core-top samples are calibrated as a bottom-water nitrate proxy. Bolivina spissa and Bolivina subadvena showed the same correlation between pore density and bottom-water nitrate concentrations, while the pore density of Bolivina argentea and Bolivina subadvena accumeata is much higher.
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Affiliation(s)
- Anjaly Govindankutty Menon
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany.
| | - Catherine V Davis
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, 2800 Faucette Dr, Raleigh, NC, 27695, USA
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, Geb. 8c, Raum 106, 24148, Kiel, Germany
| | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Iines Salonen
- SUGAR, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
| | - Gerhard Schmiedl
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
- Center for Earth System Research and Sustainability, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
| | - Nicolaas Glock
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
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19
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Ye W, Ma X, Liu C, Ye R, Priyadarshani WNC, Jayathilake R, Weerakoon A, Wimalasiri U, Dissanayake PAKN, Pathirana G, Iroshanie RGA, Zhu Y, Li Z, Wang B, Shou L, Ran L, Zhou F, Chen J, Du P. Vertical variation of bacterial production and potential role in oxygen loss in the southern Bay of Bengal. Front Microbiol 2023; 14:1250575. [PMID: 38029132 PMCID: PMC10663246 DOI: 10.3389/fmicb.2023.1250575] [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: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Marine environments wherein long-term microbial oxygen consumption exceeds oxygen replenishment can be associated with oxygen minimum zones (OMZ). The Bay of Bengal OMZ (BOB-OMZ) is one of the most intense OMZs globally. To assess the contribution of bacterial oxygen consumption to oxygen loss in BOB-OMZ, we measured bacterial production (BP), temperature, salinity, and dissolved oxygen (DO) in the whole water column. We then compared the estimated bacterial oxygen demand (BOD) with diapycnal oxygen supply (DOS) at depths of 50-200 m in the southern BOB in January 2020. The average BP was 3.53 ± 3.15 μmol C m-3 h-1 in the upper 200 m of four stations, which was lower than those reported in other tropical waters. The vertical distribution of BP differed between the open ocean and nearshore areas. In the open ocean, temperature and DO were the most important predictors for BP in the whole water column. In the nearshore areas, when DO increased sharply from the suboxic state, extremely high BP occurred at 200 m. The average estimated BOD/DOS could reach up to 153% at depths of 50-200 m, indicating advection and anticyclonic eddies probably are important DO replenishment pathways in the BOB.
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Affiliation(s)
- Wenqi Ye
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Xiao Ma
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - Chenggang Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Ruijie Ye
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - W. N. C. Priyadarshani
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Ruchi Jayathilake
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Ashoka Weerakoon
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Udeshika Wimalasiri
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - P. A. K. N. Dissanayake
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - Gayan Pathirana
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - R. G. A. Iroshanie
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - Yuanli Zhu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Zhongqiao Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Bin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Lihua Ran
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Feng Zhou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564641. [PMID: 37961710 PMCID: PMC10634959 DOI: 10.1101/2023.10.30.564641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Wilbert
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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21
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Jiang Z, Qian L, Cui M, Jiang Y, Shi L, Dong Y, Li J, Wang Y. Bacterial Sulfate Reduction Facilitates Iodine Mobilization in the Deep Confined Aquifer of the North China Plain. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15277-15287. [PMID: 37751521 DOI: 10.1021/acs.est.3c05513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Bacterial sulfate reduction plays a crucial role in the mobilization of toxic substances in aquifers. However, the role of bacterial sulfate reduction on iodine mobilization in geogenic high-iodine groundwater systems has been unexplored. In this study, the enrichment of groundwater δ34SSO4 (15.56 to 69.31‰) and its significantly positive correlation with iodide and total iodine concentrations in deep groundwater samples of the North China Plain suggested that bacterial sulfate reduction participates in the mobilization of groundwater iodine. Similar significantly positive correlations were further observed between the concentrations of iodide and total iodine and the relative abundance of the dsrB gene by qPCR, as well as the composition and abundance of sulfate-reducing bacteria (SRB) predicted from 16S rRNA gene high-throughput sequencing data. Subsequent batch culture experiments by the SRB Desulfovibrio sp. B304 demonstrated that SRB could facilitate iodine mobilization through the enzyme-driven biotic and sulfide-driven abiotic reduction of iodate to iodide. In addition, the dehalogenation of organoiodine compounds by SRB and the reductive dissolution of iodine-bearing iron minerals by biogenic sulfide could liberate bound or adsorbed iodine into groundwater. The role of bacterial sulfate reduction in iodine mobilization revealed in this study provides new insights into our understanding of iodide enrichment in iodine-rich aquifers worldwide.
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Affiliation(s)
- Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Li Qian
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Mengjie Cui
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan ,Hubei 430074, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, Hubei 430074, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Junxia Li
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, Hubei 430074, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan ,Hubei 430074, China
| | - Yanxin Wang
- School of Environmental Studies, China University of Geosciences, Wuhan ,Hubei 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan ,Hubei 430074, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, Hubei 430074, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan ,Hubei 430074, China
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Zhao R, Le Moine Bauer S, Babbin AR. " Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces. Appl Environ Microbiol 2023; 89:e0080023. [PMID: 37470485 PMCID: PMC10467342 DOI: 10.1128/aem.00800-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sven Le Moine Bauer
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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23
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He P, Wang H, Shi J, Xin M, Wang W, Xie L, Wei Q, Huang M, Shi X, Fan Y, Chen H. Prokaryote Distribution Patterns along a Dissolved Oxygen Gradient Section in the Tropical Pacific Ocean. Microorganisms 2023; 11:2172. [PMID: 37764016 PMCID: PMC10534896 DOI: 10.3390/microorganisms11092172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
Oceanic oxygen levels are decreasing significantly in response to global climate change; however, the microbial diversity and ecological functional responses to dissolved oxygen (DO) in the open ocean are largely unknown. Here, we present prokaryotic distribution coupled with physical and biogeochemical variables and DO gradients from the surface to near the bottom of a water column along an approximately 12,000-km transect from 13° N to 18° S in the Tropical Pacific Ocean. Nitrate (11.42%), temperature (10.90%), pH (10.91%), silicate (9.34%), phosphate (4.25%), chlorophyll a (3.66%), DO (3.50%), and salinity (3.48%) significantly explained the microbial community variations in the studied area. A distinct microbial community composition broadly corresponding to the water masses formed vertically. Additionally, distinct ecotypes of Thaumarchaeota and Nitrospinae belonging to diverse phylogenetic clades that coincided with specific vertical niches were observed. Moreover, the correlation analysis revealed large-scale natural feedback in which chlorophyll a (organic matter) promoted Thaumarchaeotal biomass at depths that subsequently coupled with Nitrospina, produced and replenished nitrate for phytoplankton productivity at the surface. Low DO also favored Thaumarchaeota growth and fueled nitrate production.
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Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Huan Wang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Jie Shi
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Ming Xin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Weimin Wang
- Center for Ocean and Climate Research, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China;
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Qinsheng Wei
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Mu Huang
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Xuefa Shi
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Yaqin Fan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Hao Chen
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
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24
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Vinha B, Rossi S, Gori A, Hanz U, Pennetta A, De Benedetto GE, Mienis F, Huvenne VAI, Hebbeln D, Wienberg C, Titschack J, Freiwald A, Piraino S, Orejas C. Trophic ecology of Angolan cold-water coral reefs (SE Atlantic) based on stable isotope analyses. Sci Rep 2023; 13:9933. [PMID: 37336945 DOI: 10.1038/s41598-023-37035-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/14/2023] [Indexed: 06/21/2023] Open
Abstract
Cold-water coral (CWC) reefs of the Angolan margin (SE Atlantic) are dominated by Desmophyllum pertusum and support a diverse community of associated fauna, despite hypoxic conditions. In this study, we use carbon and nitrogen stable isotope analyses (δ13C and δ15N) to decipher the trophic network of this relatively unknown CWC province. Although fresh phytodetritus is available to the reef, δ15N signatures indicate that CWCs (12.90 ± 1.00 ‰) sit two trophic levels above Suspended Particulate Organic Matter (SPOM) (4.23 ± 1.64 ‰) suggesting that CWCs are highly reliant on an intermediate food source, which may be zooplankton. Echinoderms and the polychaete Eunice norvegica occupy the same trophic guild, with high δ13C signatures (-14.00 ± 1.08 ‰) pointing to a predatory feeding behavior on CWCs and sponges, although detrital feeding on 13C enriched particles might also be important for this group. Sponges presented the highest δ15N values (20.20 ± 1.87 ‰), which could be due to the role of the sponge holobiont and bacterial food in driving intense nitrogen cycling processes in sponges' tissue, helping to cope with the hypoxic conditions of the reef. Our study provides first insights to understand trophic interactions of CWC reefs under low-oxygen conditions.
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Affiliation(s)
- Beatriz Vinha
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (DiSTeBA), Università del Salento, 73100, Lecce, Italy.
- Hanse Wissenschaftskolleg - Institute for Advanced Study, 27753, Delmenhorst, Germany.
| | - Sergio Rossi
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (DiSTeBA), Università del Salento, 73100, Lecce, Italy
- Instituto de Ciências Do Mar, LABOMAR, Universidade Federal do Ceará, Fortaleza, 60165-081, Brazil
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, 00196, Rome, Italy
| | - Andrea Gori
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (DiSTeBA), Università del Salento, 73100, Lecce, Italy
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, 08028, Barcelona, Spain
- Institut de Recerca de La Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Ulrike Hanz
- Department of Ocean Systems, NIOZ Royal Netherlands Institute for Sea Research, Texel, 1790AB, the Netherlands
- Bentho-Pelagic Processes, Alfred Wegener Institute for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Antonio Pennetta
- Laboratorio di Spettrometria di Massa Analitica e Isotopica, Dipartimento di Beni Culturali, Università del Salento, 73100, Lecce, Italy
| | - Giuseppe E De Benedetto
- Laboratorio di Spettrometria di Massa Analitica e Isotopica, Dipartimento di Beni Culturali, Università del Salento, 73100, Lecce, Italy
| | - Furu Mienis
- Department of Ocean Systems, NIOZ Royal Netherlands Institute for Sea Research, Texel, 1790AB, the Netherlands
| | - Veerle A I Huvenne
- Hanse Wissenschaftskolleg - Institute for Advanced Study, 27753, Delmenhorst, Germany
- Ocean BioGeosciences, National Oceanography Centre, Southampton, S014 3ZH, UK
| | - Dierk Hebbeln
- MARUM - Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Claudia Wienberg
- MARUM - Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Jürgen Titschack
- MARUM - Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Senckenberg Am Meer, Marine Research Department, 26382, Wilhelmshaven, Germany
| | - André Freiwald
- Senckenberg Am Meer, Marine Research Department, 26382, Wilhelmshaven, Germany
| | - Stefano Piraino
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (DiSTeBA), Università del Salento, 73100, Lecce, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, 00196, Rome, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Covadonga Orejas
- Hanse Wissenschaftskolleg - Institute for Advanced Study, 27753, Delmenhorst, Germany
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, (IEO-CSIC), 33212, Gijón, Spain
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Liu N, Sun Z, Zhang H, Klausen LH, Moonhee R, Kang S. Emerging high-ammonia‑nitrogen wastewater remediation by biological treatment and photocatalysis techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162603. [PMID: 36871738 DOI: 10.1016/j.scitotenv.2023.162603] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The bacterial and photocatalysis techniques have been widely applied into the remediation of ammonia nitrogen wastewater. Although traditional microbial methods had been verified useful; more efficient, energy-saving and controllable candidate treatment methods are still urgently needed to cover the increasingly diverse ammonia nitrogen pollution cases. The bacterial treatment technique for ammonia nitrogen mainly depends on the ammonia nitrogen oxidation-reduction (e.g. nitrification, denitrification) by nitrifying bacteria and denitrifying bacteria, but these reactions suffer from slow denitrifying kinetic process and uncontrolled disproportionation reaction. In comparison, the photocatalysis technique based on photoelectrons is more efficient and has some advantages, such as low temperature reaction and long life, while the photocatalysis technique can not perform multiple complex biochemical reactions. Despite much scientific knowledge obtained about this issue recently, such research has yet not been widely adopted in the industry because of many concerns about subsequent catalyst stability and economic feasibility. This review summarized and discussed the very recent achievements and key problems on remediation of high-ammonia‑nitrogen wastewater and oxidation driven by bacterial treatment and photocatalysis techniques, as well as the most promising future directions for these two techniques, especially the potential of jointly bacterial-photocatalysis techniques.
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Affiliation(s)
- Nian Liu
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, 200093 Shanghai, PR China; Institute of Photochemistry and Photocatalysts, University of Shanghai for Science and Technology, 200093 Shanghai, PR China
| | - Zhen Sun
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, 200090 Shanghai, PR China
| | - Huan Zhang
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, 200093 Shanghai, PR China; Institute of Photochemistry and Photocatalysts, University of Shanghai for Science and Technology, 200093 Shanghai, PR China
| | | | - Ryu Moonhee
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 570-752, Republic of Korea
| | - Shifei Kang
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, 200093 Shanghai, PR China; Institute of Photochemistry and Photocatalysts, University of Shanghai for Science and Technology, 200093 Shanghai, PR China.
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Okabe S, Ye S, Lan X, Nukada K, Zhang H, Kobayashi K, Oshiki M. Oxygen tolerance and detoxification mechanisms of highly enriched planktonic anaerobic ammonium-oxidizing (anammox) bacteria. ISME COMMUNICATIONS 2023; 3:45. [PMID: 37137967 PMCID: PMC10156729 DOI: 10.1038/s43705-023-00251-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Oxygen is a key regulatory factor of anaerobic ammonium oxidation (anammox). Although the inhibitory effect of oxygen is evident, a wide range of oxygen sensitivities of anammox bacteria have been reported so far, which makes it difficult to model the marine nitrogen loss and design anammox-based technologies. Here, oxygen tolerance and detoxification mechanisms of four genera of anammox bacteria; one marine species ("Ca. Scalindua sp.") and four freshwater anammox species ("Ca. Brocadia sinica", "Ca. Brocadia sapporoensis", "Ca. Jettenia caeni", and "Ca. Kuenenia stuttgartiensis") were determined and then related to the activities of anti-oxidative enzymes. Highly enriched planktonic anammox cells were exposed to various levels of oxygen, and oxygen inhibition kinetics (50% inhibitory concentration (IC50) and upper O2 limits (DOmax) of anammox activity) were quantitatively determined. A marine anammox species, "Ca. Scalindua sp.", exhibited much higher oxygen tolerance capability (IC50 = 18.0 µM and DOmax = 51.6 µM) than freshwater species (IC50 = 2.7-4.2 µM and DOmax = 10.9-26.6 µM). The upper DO limit of "Ca. Scalindua sp." was much higher than the values reported so far (~20 µM). Furthermore, the oxygen inhibition was reversible even after exposed to ambient air for 12-24 h. The comparative genome analysis confirmed that all anammox species commonly possess the genes considered to function for reduction of O2, superoxide anion (O2•-), and H2O2. However, the superoxide reductase (Sor)-peroxidase dependent detoxification system alone may not be sufficient for cell survival under microaerobic conditions. Despite the fact that anaerobes normally possess no or little superoxide dismutase (Sod) or catalase (Cat), only Scalindua exhibited high Sod activity of 22.6 ± 1.9 U/mg-protein with moderate Cat activity of 1.6 ± 0.7 U/mg-protein, which was consistent with the genome sequence analysis. This Sod-Cat dependent detoxification system could be responsible for the higher O2 tolerance of Scalindua than other freshwater anammox species lacking the Sod activity.
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Affiliation(s)
- Satoshi Okabe
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
| | - Shaoyu Ye
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Xi Lan
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Keishi Nukada
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Haozhe Zhang
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Kanae Kobayashi
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Mamoru Oshiki
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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Dithugoe CD, Bezuidt OKI, Cavan EL, Froneman WP, Thomalla SJ, Makhalanyane TP. Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions. mSphere 2023:e0042022. [PMID: 37093039 DOI: 10.1128/msphere.00420-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.
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Affiliation(s)
- Choaro D Dithugoe
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Oliver K I Bezuidt
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Emma L Cavan
- Imperial College London, Berks, Silwood Park, Berkshire, United Kingdom
| | - William P Froneman
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
| | - Sandy J Thomalla
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
| | - Thulani P Makhalanyane
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
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Yang J, Yu Q, Su W, Wang S, Wang X, Han Q, Qu J, Li H. Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163631. [PMID: 37086993 DOI: 10.1016/j.scitotenv.2023.163631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.
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Affiliation(s)
- Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiapeng Qu
- Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai 810008, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China.
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30
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Cano V, Nolasco MA, Kurt H, Long C, Cano J, Nunes SC, Chandran K. Comparative assessment of energy generation from ammonia oxidation by different functional bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161688. [PMID: 36708822 DOI: 10.1016/j.scitotenv.2023.161688] [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: 09/27/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Bioelectrochemical ammonia oxidation (BEAO) in a microbial fuel cell (MFC) is a recently discovered process that has the potential to reduce energy consumption in wastewater treatment. However, level of energy and limiting factors of this process in different microbial groups are not fully understood. This study comparatively investigated the BEAO in wastewater treatment by MFCs enriched with different functional groups of bacteria (confirmed by 16S rRNA gene sequencing): electroactive bacteria (EAB), ammonia oxidizing bacteria (AOB), and anammox bacteria (AnAOB). Ammonia oxidation rates of 0.066, 0.083 and 0.082 g NH4+-N L-1 d-1 were achieved by biofilms enriched with EAB, AOB, and AnAOB, respectively. With influent 444 ± 65 mg NH4+-N d-1, nitrite accumulation between 84 and 105 mg N d-1 was observed independently of the biofilm type. The AnAOB-enriched biofilm released electrons at higher potential energy levels (anode potential of 0.253 V vs. SHE) but had high internal resistance (Rint) of 299 Ω, which limits its power density (0.2 W m-3). For AnAOB enriched biofilm, accumulation of nitrite was a limiting factor for power output by allowing conventional anammox activity without current generation. AOB enriched biofilm had Rint of 18 ± 1 Ω and yielded power density of up to 1.4 W m-3. The activity of the AOB-enriched biofilm was not dependent on the accumulation of dissolved oxygen and achieved 1.5 fold higher coulombic efficiency when sulfate was not available. The EAB-enriched biofilm adapted to oxidize ammonia without organic carbon, with Rint of 19 ± 1 Ω and achieved the highest power density of 11 W m-3. Based on lab-scale experiments (scaling-up factors not considered) energy savings of up to 7 % (AnAOB), 44 % (AOB) and 475 % (EAB) (positive energy balance), compared to conventional nitrification, are projected from the applications of BEAO in wastewater treatment plants.
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Affiliation(s)
- Vitor Cano
- University of São Paulo, School of Arts, Sciences and Humanities, Av. Arlindo Béttio, 1000, Sao Paulo, SP 03828-000, Brazil; Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States.
| | - Marcelo A Nolasco
- University of São Paulo, School of Arts, Sciences and Humanities, Av. Arlindo Béttio, 1000, Sao Paulo, SP 03828-000, Brazil.
| | - Halil Kurt
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States.
| | - Chenghua Long
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States.
| | - Julio Cano
- University of São Paulo, School of Arts, Sciences and Humanities, Av. Arlindo Béttio, 1000, Sao Paulo, SP 03828-000, Brazil.
| | - Sabrina C Nunes
- University of São Paulo, School of Arts, Sciences and Humanities, Av. Arlindo Béttio, 1000, Sao Paulo, SP 03828-000, Brazil.
| | - Kartik Chandran
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States.
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31
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Nagar S, Bharti M, Negi RK. Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 2023; 107:3273-3289. [PMID: 37052633 DOI: 10.1007/s00253-023-12503-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/18/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023]
Abstract
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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Li X, Liu C, Xie H, Sun Y, Xu S, Liu G. Nitrogen removal of thermal hydrolysis-anaerobic digestion liquid: A review. CHEMOSPHERE 2023; 320:138097. [PMID: 36764619 DOI: 10.1016/j.chemosphere.2023.138097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/07/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Thermal hydrolysis (TH) pretreatment, as an anaerobic digestion (AD) pretreatment, has not only been verified in the laboratory but also frequently employed in actual engineering. However, the properties of anaerobic digestion liquid (ADL), such as high organic matter concentration, high ammonia nitrogen (NH4+-N) concentration, and low carbon-nitrogen ratio (C/N), have posed some difficulties in the follow-up treatment. To address the above issues, the autotrophic nitrogen removal (ANR) process is developed to treat ADL. Due to the NH4+-N, organic materials, toxic and harmful substances in the ADL that might directly impact the activity of functional bacteria, the ADL should be treated before being fed into the ANR process. This paper provided a focused review of the thermal hydrolysis-anaerobic digestion process (TH-ADP) mechanism and the ANR mechanism, summarized the existing difficulties in the treatment of thermal hydrolysis-anaerobic digestion liquid (TH-ADL), assessed the research status thoroughly, and offered the potential solutions to the problems.
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Affiliation(s)
- Xiangkun Li
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Changkuo Liu
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Hongwei Xie
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Yujie Sun
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Shiwei Xu
- Beijing Capital Eco-environment Protection Group Co., Itd, China
| | - Gaige Liu
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China.
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Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
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Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch. Processes (Basel) 2023. [DOI: 10.3390/pr11010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.
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Lumactud RA, Gorim LY, Thilakarathna MS. Impacts of humic-based products on the microbial community structure and functions toward sustainable agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.977121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Humic-based products (HPs) are carbon-rich organic amendments in the forms of extracted humic substances from manure, compost, and raw and extracted forms of lignites, coals and peats. HPs are widely used in agriculture and have beneficial effects on plants. While the agronomic benefits of HPs have been widely reported, information on their impact on the soil microbial community composition and functions is lacking, despite claims made by companies of humic substances as biostimulants. In this review, we explored published research on microbial responses with HPs application in an agronomic context. Although research data are sparse, current results suggest indirect impacts of HPs on microbial community composition and activities. HPs application changes the physico-chemical properties of the soil and influence root exudation, which in turn impact the microbial structure and function of the soil and rhizosphere. Application of HPs to the soil as biostimulants seemed to favor plant/soil beneficial bacterial community composition. HPs impacts on microbial activities that influence soil biogeochemical functioning remain unclear; existing data are also inconsistent and contradictory. The structural properties of HPs caused inconsistencies in their reported impacts on soil properties and plants. The sources of HPs and forms (whether extracted or raw), soil type, geographic location, crop species, and management strategies, among others, affect microbial communities affecting HPs efficacy as biostimulants. A more holistic approach to research encompassing multiple influential factors and leveraging the next-generation sequencing technology is needed to unravel the impacts of HPs on the soil microbiome. Addressing these knowledge gaps facilitates sustainable and efficient use of HPs as organic agricultural amendments reducing the use of chemical fertilizers.
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36
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Canfield DE, Kraft B. The 'oxygen' in oxygen minimum zones. Environ Microbiol 2022; 24:5332-5344. [PMID: 36054074 PMCID: PMC9828761 DOI: 10.1111/1462-2920.16192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/31/2022] [Indexed: 01/12/2023]
Abstract
Aerobic processes require oxygen, and anaerobic processes are typically hindered by it. In many places in the global ocean, oxygen is completely removed at mid-water depths forming anoxic oxygen minimum zones (A-OMZs). Within the oxygen gradients linking oxygenated waters with A-OMZs, there is a transition from aerobic to anaerobic microbial processes. This transition is not sharp and there is an overlap between processes using oxygen and those using other electron acceptors. This review will focus on the oxygen control of aerobic and anaerobic metabolisms and will explore how this overlap impacts both the carbon and nitrogen cycles in A-OMZ environments. We will discuss new findings on non-phototrophic microbial processes that produce oxygen, and we focus on how oxygen impacts the loss of fixed nitrogen (as N2 ) from A-OMZ waters. There are both physiological and environmental controls on the activities of microbial processes responsible for N2 loss, and the environmental controls are active at extremely low levels of oxygen. Understanding how these controls function will be critical to understanding and predicting how fixed-nitrogen loss in the oceans will respond to future global warming.
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Affiliation(s)
- Don E. Canfield
- Department of Biology and NordceeUniversity of Southern Denmark, Campusvej 55OdenseDenmark,Danish Institute for Advanced Studies (DIAS)Denmark,PetrochinaBeijingChina
| | - Beate Kraft
- Department of Biology and NordceeUniversity of Southern Denmark, Campusvej 55OdenseDenmark
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Nikitczuk MP, Bebout GE, Geiger CA, Ota T, Kunihiro T, Mustard JF, Halldórsson SA, Nakamura E. Nitrogen Incorporation in Potassic and Micro- and Meso-Porous Minerals: Potential Biogeochemical Records and Targets for Mars Sampling. ASTROBIOLOGY 2022; 22:1293-1309. [PMID: 36074082 PMCID: PMC9618379 DOI: 10.1089/ast.2021.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
We measured the N concentrations and isotopic compositions of 44 samples of terrestrial potassic and micro- and meso-porous minerals and a small number of whole-rocks to determine the extent to which N is incorporated and stored during weathering and low-temperature hydrothermal alteration in Mars surface/near-surface environments. The selection of these minerals and other materials was partly guided by the study of altered volcanic glass from Antarctica and Iceland, in which the incorporation of N as NH4+ in phyllosilicates is indicated by correlated concentrations of N and the LILEs (i.e., K, Ba, Rb, Cs), with scatter likely related to the presence of exchanged, occluded/trapped, or encapsulated organic/inorganic N occurring within structural cavities (e.g., in zeolites). The phyllosilicates, zeolites, and sulfates analyzed in this study contain between 0 and 99,120 ppm N and have δ15Nair values of -34‰ to +65‰. Most of these minerals, and the few siliceous hydrothermal deposits that were analyzed, have δ15N consistent with the incorporation of biologically processed N during low-temperature hydrothermal or weathering processes. Secondary ion mass spectrometry on altered hyaloclastites demonstrates the residency of N in smectites and zeolites, and silica. We suggest that geological materials known on Earth to incorporate and store N and known to be abundant at, or near, the surface of Mars should be considered targets for upcoming Mars sample return with the intent to identify any signs of ancient or modern life.
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Affiliation(s)
- Matthew P. Nikitczuk
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Gray E. Bebout
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Charles A. Geiger
- Universität Salzburg, Fachbereich Chemie und Physik der Materialien, Salzburg, Austria
| | - Tsutomu Ota
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Takuya Kunihiro
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - John F. Mustard
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island, USA
| | - Sæmundur A. Halldórsson
- Nordic Volcanological Center, Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland
| | - Eizo Nakamura
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Japan
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Piscoya E, von Dassow P, Aldunate M, Vargas CA. Physical-chemical factors influencing the vertical distribution of phototrophic pico-nanoplankton in the Oxygen Minimum Zone (OMZ) off Northern Chile: The relative influence of low pH/low O 2 conditions. MARINE ENVIRONMENTAL RESEARCH 2022; 180:105710. [PMID: 35932510 DOI: 10.1016/j.marenvres.2022.105710] [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: 01/17/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The vertical distribution of phytoplankton is of fundamental importance in the structure, dynamic, and biogeochemical pathways in marine ecosystems. Nevertheless, what are the main factors determining this distribution remains as an open question. Here, we evaluated the relative influence of environmental factors that might control the coexistence and vertical distribution of pico-nanoplankton associated with the OMZ off northern Chile. Our results showed that in the upper layer Synechococcus-like cells were numerically important at all sampling stations. Pico-nano eukaryotes and phototrophic nanoflagellates (PNF) also showed high abundances in the upper layer decreasing in abundance down to the upper oxycline, while only Prochlorococcus showed high abundances under oxycline and within the oxygen-depleted layer. Statistical analyses evidenced that temperature, oxygen, and carbonate chemistry parameters (pH and dissolved inorganic carbon, DIC) influenced significantly the vertical distribution of phototrophic pico-nanoplankton. Additionally, we experimentally-evaluated the combined effect of low pH/low O2 conditions on a nanophytoplankton species, the haptophyte Imantonia sp. Under control conditions (pH = 8.1; O2 = 287.5 μM, light = 169.6 μEm-2s-1), Imantonia sp. in vivo fluorescence increased over fifty times, inducing supersaturated O2 conditions (900 μM) and an increasing pH (8.5), whereas upon an experimental treatment mimicking OMZ conditions (pH = 7.5; O2 = 55.6 μM; light = 169.6 μEm-2s-1), in vivo fluorescence declined dramatically, suggesting that Imantonia sp. did not survive. Although preliminary, our study provides evidence about the role of low pH/low O2 conditions on the vertical distribution of nanophytoplankton, which deserve future attention through both fieldwork and more extended experimental experiences.
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Affiliation(s)
- Edson Piscoya
- Graduate Program in Oceanography, Department of Oceanography, Universidad de Concepción, Casilla 160-C, Concepcion, Chile; Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile
| | - Peter von Dassow
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Department of Ecology, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile; Research Fellow, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Montserrat Aldunate
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile
| | - Cristian A Vargas
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile; Coastal Socio-ecological Millennium Institute (SECOS), P. Universidad Católica de Chile, Chile.
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Chen Z, Dolfing J, Zhuang S, Wu Y. Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:172-180. [PMID: 38075597 PMCID: PMC10702904 DOI: 10.1016/j.eehl.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/13/2022] [Accepted: 09/29/2022] [Indexed: 01/03/2024]
Abstract
Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.
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Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle Upon Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
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Song M, Sun B, Li R, Qian Z, Bai Z, Zhuang X. Successions and interactions of phyllospheric microbiome in response to NH 3 exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155805. [PMID: 35561907 DOI: 10.1016/j.scitotenv.2022.155805] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Phyllosphere and numerous phyllospheric microbiomes present a huge potential for air pollution mitigation. Despite research investigating the microbial compositions in the phyllosphere, the successions and interactions of the phyllospheric microbiome under ammonia gas (NH3) stress remain poorly understood. Herein, we performed 16S rDNA, the internal transcribed spacer (ITS) profiling and a quantitative microbial element cycling (QMEC) method to reveal successions, co-occurrence, and N-cycling functions changes of phyllospheric bacteria and fungi during NH3 exposure. The NH3 input mainly elevated ammonium (NH4+-N) and total nitrogen (TN) levels on the leaf surface. The exposure in the phyllosphere decreased fungal concentration with a homogeneity increase while enhanced bacterial concentration with a noticeable richness drop. Both short-term (2-week) and long-term (6-week) exposure induced significant changes in microbial compositions. Bacterial genera (Nocardioides, Pseudonocardia) and fungal genera (Alternaria, Acremonium) dominated throughout the exposure. Intensive microbial interactions compared to that in the natural phyllosphere were observed via network analysis. Our results showed that N-cycling functional genes were largely stimulated by the exposure and might, in turn contribute to NH3 pollution buffer and alleviation via microbial metabolism. This study extended the knowledge on microbial responses to NH3 exposure in the phyllosphere and enlightened phylloremediation on NH3 through the microbial role.
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Affiliation(s)
- Manjiao Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Sun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Qian
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Xiongan Institute of Innovation, Xiongan New Area, 071000, China.
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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41
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Nonthakaew N, Panbangred W, Songnuan W, Intra B. Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets’ rhizosphere microbiome. Front Microbiol 2022; 13:967415. [PMID: 36090067 PMCID: PMC9453592 DOI: 10.3389/fmicb.2022.967415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.
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Affiliation(s)
- Napawit Nonthakaew
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
| | - Watanalai Panbangred
- Research, Innovation, and Partnerships Office (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
- *Correspondence: Bungonsiri Intra,
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Yang J, Li G, Sheng Y, Zhang F. Response and contribution of bacterial and archaeal communities to eutrophication in urban river sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119397. [PMID: 35513192 DOI: 10.1016/j.envpol.2022.119397] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/21/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Excessive loading of nitrogen (N) and phosphorus (P) that leads to eutrophication mutually interacts with sediment microbial community. To unravel the microbial community structures and interaction networks in the urban river sediments with the disturbance of N and P loadings, we used high-throughput sequencing analysis and ecological co-occurrence network methods to investigate the responses of diversity and community composition of bacteria and archaea and identify the keystone species in river sediments. The alpha-diversity of archaea significantly decreased with the increased total nitrogen (TN), whereas the operational taxonomic unit (OTU) number of bacteria increased with the increase of available phosphorus (AP). The beta-diversity of archaea and bacteria was more sensitive to N content than P content. The relative abundance of predominant bacterial and archaeal taxa varied differently in terms of different N and P contents. Complexity and connectivity of bacteria and archaea interaction networks showed significant variations with eutrophication, and competition between bacteria became more significant with the increase of N content. The sensitive and the highest connective species (keystone species) were identified for different N and P loadings. Total carbon (TC), water content (WC), microbial alpha-diversity and interaction networks played pivotal roles in the N and P transformation in urban river sediments.
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Affiliation(s)
- Juejie Yang
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Fang Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Monteiro GGTN, Barros DJ, Gabriel GVM, Venturini AM, Veloso TGR, Vazquez GH, Oliveira LC, Neu V, Bodelier PLE, Mansano CFM, Tsai SM, Navarrete AA. Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities. Front Microbiol 2022; 13:913453. [PMID: 35979497 PMCID: PMC9376453 DOI: 10.3389/fmicb.2022.913453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 -), which can be further oxidized to nitrate (NO3 -). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 - and NO3 -, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 +) and NO3 --and NO2 --dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.
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Affiliation(s)
| | - Dayane J. Barros
- Graduate Program in Biodiversity and Biotechnology (BIONORTE), Federal University of Tocantins (UFT), Palmas, Brazil
| | - Gabriele V. M. Gabriel
- Graduate Program in Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Andressa M. Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, United States
| | - Tomás G. R. Veloso
- Graduate Program in Agricultural Microbiology, Federal University of Viçosa, Viçosa, Brazil
| | - Gisele H. Vazquez
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
| | - Luciana C. Oliveira
- Department of Physics, Chemistry, and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Vania Neu
- Federal Rural University of Amazonia (UFRA), Belém, Brazil
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | - Acacio A. Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
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Lin G, Lin X. Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment. WATER RESEARCH 2022; 218:118520. [PMID: 35525032 DOI: 10.1016/j.watres.2022.118520] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Coastal wetland reclamation contributed to development of aquaculture industry, and the residual bait accumulation in aquaculture processes could influence biogeochemical elements cycling, which threaten ecological functions and services in aquaculture and adjacent ecosystems. However, systematic studies for changes in sediment microbial community structure and greenhouse gasses (GHGs) production, as well as environmental parameters following bait input at time scale are still rare. A 90-day incubation experiment was conducted using sediment collected from coastal wetland in Qi'ao Island in southern China, followed by the observations of temporal variations of physicochemical properties, sediment microbial community, and GHGs production in response to different amounts of bait input (0, 20, and 40 mg bait g-1 wet sediment). The results showed that dissolved oxygen of overlying water was profoundly decreased owing to bait input, while dissolved organic carbon of overlying water and several sediment properties (e.g., organic matter, sulfide, and ammonium) varied in reverse patterns. Meanwhile, bait input led to significant loss of microbial community richness and diversity, and strongly altered microbial compositions from aerobic, slow-growing, and oligotrophic (Actinobacteriota, Chloroflexi, and Acidobacteriota) to anaerobic, fast-growing, and copiotrophic (Firmicutes and Bacteroidota). Moreover, both GHGs production and global warming potential were significantly enhanced by bait input, implying that aquaculture ecosystem is an important hotspot for global GHGs emission. Overall, bait input triggered quick responses of physicochemical properties, sediment microbial community, and GHGs production, followed by long-term resilience of the ecosystem. This study could provide new insight into temporal interactive effects of bait input on physicochemical properties, microbial community, and GHGs production, which can enhance the understanding of the temporal dynamics and ecological impacts of coastal aquaculture activities and emphasize the necessity of sustainable assessment and management in aquaculture ecosystems.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China.
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Wu J, Hong Y, He X, Liu X, Ye J, Jiao L, Li Y, Wang Y, Ye F, Yang Y, Du J. Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 2022; 25:104333. [PMID: 35602962 PMCID: PMC9118673 DOI: 10.1016/j.isci.2022.104333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022] Open
Abstract
The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiang He
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lijing Jiao
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Juan Du
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf. Appl Environ Microbiol 2022; 88:e0021622. [PMID: 35404072 PMCID: PMC9088280 DOI: 10.1128/aem.00216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.
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Zhang Y, Zhao H, Hu W, Wang Y, Zhang H, Zhou X, Fei J, Luo G. Understanding how reed-biochar application mitigates nitrogen losses in paddy soil: Insight into microbially-driven nitrogen dynamics. CHEMOSPHERE 2022; 295:133904. [PMID: 35157877 DOI: 10.1016/j.chemosphere.2022.133904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/13/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Biochar application to chemical-amended paddy soils has been proposed as a potential strategy to enhance nitrogen (N) retention and nitrogen use efficiency (NUE) by crops. However, optimal concentrations for these enhancements and the potential drivers are not well understood. Herein, a column-based pot experiment was carried out to investigate the impacts of reed-biochar application rate on N losses and dynamics in paddy soils treated by chemical fertilizer, and particularly, to explore the dominant factors of the processes. The addition of 2-4% reed-biochar had the most significant effects on mitigating N loss by leaching. Reed-biochar amendment increased soil total N and mineral N (NH4+-N and NO3--N) content, and denitrifying gene abundance, and the increments of those variables were positively related to the application rate. Soil treated with 1-4% reed-biochar at harvest period showed higher gene abundances of ammonia-oxidizing and dissimilatory nitrate reduction to ammonium (DNRA) and higher activity of β-1,4-N-acetyl-glucosaminidase (NAG) and leucine aminopeptidase compared with the 4-8% application rate. The amoA-AOA gene abundance, NAG activity, and total carbon (C) content were the main predictors of total N and mineral N accumulated leakage. Total C content was the main predictor of soil total N and mineral N content, followed by the pH and NAG activity. These results suggest that adding 2-4% reed-biochar was more beneficial to mitigate N loss and thus enhance soil N storage and availability. This study highlights the importance of understanding how microbial populations mediate N transformation to decipher biochar-driven NUE enhancement in paddy soils.
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Affiliation(s)
- Yuping Zhang
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Hang Zhao
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Wang Hu
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Yizhe Wang
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Hanfeng Zhang
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Xuan Zhou
- Institute of Soil and Fertilizer, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jiangchi Fei
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources and Environment, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
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Effect of Bacillus subtilis Zeolite Used for Sediment Remediation on Sulfide, Phosphate, and Nitrogen Control in a Microcosm. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074163. [PMID: 35409843 PMCID: PMC8998431 DOI: 10.3390/ijerph19074163] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022]
Abstract
Eutrophication is an emerging worldwide issue concerning the excessive accumulation of various pollutants in sediments, owing to the release of industrial or household wastewaters to coastal areas. The coastal sediment of Goseong Bay in the Republic of Korea is organically enriched with pollutants, including heavy metals, sulfide, phosphate, and ammonia. Microbial remediation and capping techniques have been suggested as effective routes for sediment remediation. In this study, Bacillus subtilis zeolite (BZ) was used as a sediment capping material, and effective remediation of coastal sediment was observed in a 40-day laboratory microcosm experiment. A significant decrease in the sediment water content and reduced concentration of acid volatile sulfide were observed in the BZ-capped sediment. In the overlying water and pore water, significant decreases in phosphate and dissolved inorganic nitrogen (DIN; NO2-N + NO3-N and NH4-N) concentrations were observed in the BZ-treated experiment. Based on our findings, we conclude that BZ could be an effective capping material for coastal sediment remediation.
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Stüeken EE, Viehmann S, Hohl SV. Contrasting nutrient availability between marine and brackish waters in the late Mesoproterozoic: Evidence from the Paranoá Group, Brazil. GEOBIOLOGY 2022; 20:159-174. [PMID: 34661335 DOI: 10.1111/gbi.12478] [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: 02/24/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Understanding the delayed rise of eukaryotic life on Earth is one of the most fundamental questions about biological evolution. Numerous studies have presented evidence for oxygen and nutrient limitations in seawater during the Mesoproterozoic era, indicating that open marine settings may not have been able to sustain a eukaryotic biosphere with complex, multicellular organisms. However, many of these data sets represent restricted marine basins, which may bias our view of habitability. Furthermore, it remains untested whether rivers could have supplied significant nutrient fluxes to coastal habitats. To better characterize the sources of the major nutrients nitrogen and phosphorus, we turned to the late Mesoproterozoic Paranoá Group in Brazil (~1.1 Ga), which was deposited on a passive margin of the São Francisco craton. We present carbon, nitrogen and sulphur isotope data from an open shelf setting (Fazenda Funil) and from a brackish-water environment with significant riverine input (São Gabriel). Our results show that waters were well-oxygenated and nitrate was bioavailable in the open ocean setting at Fazenda Funil; the redoxcline appears to have been deeper and further offshore compared to restricted marine basins elsewhere in the Mesoproterozoic. In contrast, the brackish site at São Gabriel received only limited input of marine nitrate and sulphate. Nevertheless, previous reports of acritarchs reveal that this brackish-water setting was habitable to eukaryotic life. Paired with previously published cadmium isotope data, which can be used as a proxy for phosphorus cycling, our results suggest that complex organisms were perhaps not strictly dependent on marine nutrient supplies. Riverine influxes of P and possibly other nutrients likely rendered coastal waters perhaps equally habitable to the Mesoproterozoic open ocean. This conclusion supports the notion that eukaryotic organisms may have thrived in brackish or perhaps even freshwater environments.
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Affiliation(s)
- Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, UK
| | - Sebastian Viehmann
- Department of Geology, University of Vienna, Vienna, Austria
- Department of Lithospheric Research, University of Vienna, Vienna, Austria
| | - Simon V Hohl
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Sun H, Jiang S. A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:221-232. [PMID: 35072673 DOI: 10.1039/d1em00518a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of the denitrification process is catalyzed by two enzymes with different structures and unrelated evolutionary relationships, namely, the Cu-type nitrite reductase encoded by the nirK gene and the cytochrome cd1-type nitrite reductase encoded by the nirS gene. Although some relevant reviews have been published on denitrifiers, most of these reviews do not include statistical analysis, and do not compare the nirS and nirK communities in-depth. However, a systematic study of the nirS-type and nirK-type denitrifying communities and their response to environmental factors in different ecosystems is needed. In this review, a scientometric approach combined with case studies was used to study the nirS-type and nirK-type denitrifiers. The scientometric approach demonstrated that Pseudomonas, Paracoccus, and Thauera are the most frequently mentioned nirS-type denitrifiers, while Pseudomonas and Bradyrhizobium are the top two most frequently mentioned nirK-type denitrifiers. Among various environmental factors, the concentrations of nitrite, nitrate and carbon sources were widely reported factors that can influence the abundance and structure of nirS-type and nirK-type denitrifying communities. Case studies indicated that Bradyrhizobium was the major genus detected by high-throughput sequencing in both nirS and nirK-type denitrifiers in soil systems. nirS-type denitrifiers are more sensitive to the soil type, soil moisture, pH, and rhizosphere effect than nirK. To clarify the relationships between denitrifying communities and environmental factors, the DNA stable isotope probe combined with metagenomic sequencing is needed for new denitrifier detections.
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Affiliation(s)
- Haishu Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing 100048, China.
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