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Antony R, Mongad D, Sanyal A, Dhotre D, Thamban M. Holed up, but thriving: Impact of multitrophic cryoconite communities on glacier elemental cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173187. [PMID: 38750762 DOI: 10.1016/j.scitotenv.2024.173187] [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: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Cryoconite holes (water and sediment-filled depressions), found on glacier surfaces worldwide, serve as reservoirs of microbes, carbon, trace elements, and nutrients, transferring these components downstream via glacier hydrological networks. Through targeted amplicon sequencing of carbon and nitrogen cycling genes, coupled with functional inference-based methods, we explore the functional diversity of these mini-ecosystems within Antarctica and the Himalayas. These regions showcase distinct environmental gradients and experience varying rates of environmental change influenced by global climatic shifts. Analysis revealed a diverse array of photosynthetic microorganisms, including Stramenopiles, Cyanobacteria, Rhizobiales, Burkholderiales, and photosynthetic purple sulfur Proteobacteria. Functional inference highlighted the high potential for carbohydrate, amino acid, and lipid metabolism in the Himalayan region, where organic carbon concentrations surpassed those in Antarctica by up to 2 orders of magnitude. Nitrogen cycling processes, including fixation, nitrification, and denitrification, are evident, with Antarctic cryoconite exhibiting a pronounced capacity for nitrogen fixation, potentially compensating for the limited nitrate concentrations in this region. Processes associated with the respiration of elemental sulfur and inorganic sulfur compounds such as sulfate, sulfite, thiosulfate, and sulfide suggest the presence of a complete sulfur cycle. The Himalayan region exhibits a higher potential for sulfur cycling, likely due to the abundant sulfate ions and sulfur-bearing minerals in this region. The capability for complete iron cycling through iron oxidation and reduction reactions was also predicted. Methanogenic archaea that produce methane during organic matter decomposition and methanotrophic bacteria that utilize methane as carbon and energy sources co-exist in the cryoconite, suggesting that these niches support the complete cycling of methane. Additionally, the presence of various microfauna suggests the existence of a complex food web. Collectively, these results indicate that cryoconite holes are self-sustaining ecosystems that drive elemental cycles on glaciers and potentially control carbon, nitrogen, sulfur, and iron exports downstream.
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Affiliation(s)
- Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India; GFZ German Research Centre for Geosciences, Potsdam, Germany.
| | - Dattatray Mongad
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India
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2
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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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Govednik A, Eler K, Mihelič R, Suhadolc M. Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172054. [PMID: 38569950 DOI: 10.1016/j.scitotenv.2024.172054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.
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Affiliation(s)
- Anton Govednik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Klemen Eler
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Rok Mihelič
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Marjetka Suhadolc
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
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Wang E, Yu B, Zhang J, Gu S, Yang Y, Deng Y, Guo X, Wei B, Bi J, Sun M, Feng H, Song A, Fan F. Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9658-9668. [PMID: 38768036 DOI: 10.1021/acs.est.3c08319] [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: 05/22/2024]
Abstract
Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.
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Affiliation(s)
- Enzhao Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing Yu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiayin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunfeng Yang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ye Deng
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xue Guo
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100864, China
| | - Buqing Wei
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingjing Bi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miaomiao Sun
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huaqi Feng
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Alin Song
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fenliang Fan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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von Kügelgen A, Cassidy CK, van Dorst S, Pagani LL, Batters C, Ford Z, Löwe J, Alva V, Stansfeld PJ, Bharat TAM. Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature 2024; 630:230-236. [PMID: 38811725 PMCID: PMC11153153 DOI: 10.1038/s41586-024-07462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - C Keith Cassidy
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lennart L Pagani
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christopher Batters
- Protein and Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Zephyr Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
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6
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Wang T, Gao M, Shao W, Wang L, Yang C, Wang X, Yao S, Zhang B. Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions. Appl Microbiol Biotechnol 2024; 108:347. [PMID: 38805033 PMCID: PMC11133221 DOI: 10.1007/s00253-024-13184-5] [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: 12/28/2023] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.
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Affiliation(s)
- Tianshu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miao Gao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Shao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunyan Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Shuihong Yao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Tan Q, Wu H, Zheng L, Wang X, Xing Y, Tian Q, Zhang Y. Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum. WATER RESEARCH 2024; 255:121480. [PMID: 38518415 DOI: 10.1016/j.watres.2024.121480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Haoming Wu
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing 100875, PR China.
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Qi Tian
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yaoxin Zhang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
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Zhang A, Zhu M, Zheng Y, Tian Z, Mu G, Zheng M. The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing. BIORESOURCE TECHNOLOGY 2024; 399:130637. [PMID: 38548031 DOI: 10.1016/j.biortech.2024.130637] [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: 01/24/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.
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Affiliation(s)
- Anqi Zhang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Mingyang Zhu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yize Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Zhichao Tian
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Guangli Mu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Maosheng Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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Cai S, Lao Q, Chen C, Zhu Q, Chen F. The impact of algal blooms on promoting in-situ N 2O emissions: A case in Zhanjiang bay, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120935. [PMID: 38648725 DOI: 10.1016/j.jenvman.2024.120935] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Under the influence of many factors, such as climate change, anthropogenic eutrophication, and the development of aquaculture, the area and frequency of algal blooms have showed an increasing trend worldwide, which has become a challenging issue at present. However, the coupled relationship between nitrous oxide (N2O) and algal blooms and the underlying mechanisms remain unclear. To address this issue, 15N isotope cultures and quantitative polymerase chain reaction (qPCR) experiments were conducted in Zhanjiang Bay during algal and non-algal bloom periods. The results showed that denitrification and nitrification-denitrification were the two processes responsible for the in-situ production of N2O during algal and non-algal bloom periods. Stable isotope rate cultivation experiments indicated that denitrification and nitrification-denitrification were promoted in the water during the algal bloom period. The in-situ production of N2O during the algal bloom period was three-fold that during the non-algal bloom period. This may be because fresh particulate organic matter (POM) from the organisms responsible for the algal bloom provides the necessary anaerobic and hypoxic environment for denitrification and nitrification-denitrification in the degradation environment. Additionally, a positive linear correlation between N2O concentrations and ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (nirK and nirS) also supported the significant denitrification and nitrification-denitrification occurring in the water during the algal bloom period. However, the algal bloom changed the main process for the in-situ production of N2O, wherein it shifted from denitrification during the non-algal bloom period to nitrification-denitrification during the algal bloom period. The results of our study will improve our understanding of the processes responsible for the in-situ production of N2O during the algal bloom period, and can help formulate effective policies to mitigate N2O emissions in the bay.
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Affiliation(s)
- Shangjun Cai
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qibin Lao
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chunqing Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qingmei Zhu
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Fajin Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China.
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10
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Tian S, Xia Y, Yu Z, Zhou H, Wu S, Zhang N, Yue X, Deng Y, Xia Y. Improvement and the relationship between chemical properties and microbial communities in secondary salinization of soils induced by rotating vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171019. [PMID: 38382605 DOI: 10.1016/j.scitotenv.2024.171019] [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: 10/11/2023] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.
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Affiliation(s)
- Shihan Tian
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Xia
- College of Tropical Crops, Yunnan Agricultural University, Pu'er 665099, China
| | - Zhong Yu
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Huazhi Biotechnology Co. Ltd, Changsha 410000, China
| | - Hongyin Zhou
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Sirui Wu
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Naiming Zhang
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Xianrong Yue
- Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Yishu Deng
- Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Yunsheng Xia
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China.
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11
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Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Nat Commun 2024; 15:3219. [PMID: 38622143 PMCID: PMC11018855 DOI: 10.1038/s41467-024-47324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Eve Tudor-Matthew
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Luis Jimenez
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Han-Chung Lee
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Erwin Tanuwidjaya
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hanna A Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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12
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Han P, Tang X, Koch H, Dong X, Hou L, Wang D, Zhao Q, Li Z, Liu M, Lücker S, Shi G. Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica. Nat Commun 2024; 15:3143. [PMID: 38609359 PMCID: PMC11014942 DOI: 10.1038/s41467-024-47392-4] [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: 11/26/2023] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3-) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3- via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.
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Affiliation(s)
- Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
- Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Hanna Koch
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-3430, Tulln, Austria
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
- Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Danhe Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Qian Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Zhe Li
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
- Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Guitao Shi
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
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13
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Chen T, Yang X, Zuo Z, Xu H, Yang X, Zheng X, He S, Wu X, Lin X, Li Y, Zhang Z. Shallow wet irrigation reduces nitrogen leaching loss rate in paddy fields by microbial regulation and lowers rate of downward migration of leaching water: a 15N-tracer study. FRONTIERS IN PLANT SCIENCE 2024; 15:1340336. [PMID: 38590742 PMCID: PMC10999577 DOI: 10.3389/fpls.2024.1340336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
China consumes 35% of the world's fertilizer every year; however, most of the nitrogen fertilizers, which are essential for rice cultivation, are not used effectively. In this study, factors affecting the nitrogen leaching loss rate were studied in typical soil and rice varieties in South China. The effects of various irrigation measures on rice growth and nitrogen leaching loss were investigated by conducting experiments with eight groups. These groups included traditional irrigation (TI) and shallow wet irrigation (SWI). The TI is a common irrigation method for farmers in South China, maintaining a water layer of 5-8 cm depth. For SWI, after establishing a shallow water layer usually maintaining at 1-2 cm, paddy is irrigated when the field water level falls to a certain depth, then this process is then repeat as necessary. The nitrogen distribution characteristics were determined using 15N isotope tracing. In addition, the effects of nitrification, denitrification, and microbial composition on soil nitrogen transformation at different depths were studied by microbial functional gene quantification and high-throughput sequencing. The results revealed that in the SWI groups, the total nitrogen leaching loss rate reduced by 0.3-0.8% and the nitrogen use efficiency (NUE) increased by 2.18-4.43% compared with those in the TI groups. After the 15N-labeled nitrogen fertilizer was applied, the main pathways of nitrogen were found to be related to plant absorption and nitrogen residues. Furthermore, paddy soil ammonia-oxidizing archaea were more effective than ammonia-oxidizing bacteria for soil ammonia oxidation by SWI groups. The SWI measures increased the relative abundance of Firmicutes in paddy soil, enhancing the ability of rice to fix nitrogen to produce ammonium nitrogen, thus reducing the dependence of rice on chemical fertilizers. Moreover, SWI enhanced the relative abundance of nirS and nosZ genes within surface soil bacteria, thereby promoting denitrification in the surface soil of paddy fields. SWI also promoted ammonia oxidation and denitrification by increasing the abundance and activity of Proteobacteria, Nitrospirae, and Bacteroidetes. Collectively, SWI effectively reduced the nitrogen leaching loss rate and increase NUE.
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Affiliation(s)
- Tianyi Chen
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xiaoming Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Zheng Zuo
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Huijuan Xu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xiangjian Zheng
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Shuran He
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Xin Wu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xueming Lin
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Zhen Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
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14
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Ghimire-Kafle S, Weaver ME, Kimbrel MP, Bollmann A. Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments. Appl Environ Microbiol 2024; 90:e0169823. [PMID: 38349190 PMCID: PMC10952389 DOI: 10.1128/aem.01698-23] [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: 10/06/2023] [Accepted: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.
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Affiliation(s)
| | - Matt E. Weaver
- Department of Microbiology, Miami University, Oxford, Ohio, USA
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15
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Stein LY. Agritech to Tame the Nitrogen Cycle. Cold Spring Harb Perspect Biol 2024; 16:a041668. [PMID: 37788889 PMCID: PMC10910340 DOI: 10.1101/cshperspect.a041668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While the Haber-Bosch process for N-fixation has enabled a steady food supply for half of humanity, substantial use of synthetic fertilizers has caused a radical unevenness in the global N-cycle. The resulting increases in nitrate production and greenhouse gas (GHG) emissions have contributed to eutrophication of both ground and surface waters, the growth of oxygen minimum zones in coastal regions, ozone depletion, and rising global temperatures. As stated by the Food and Agriculture Organization of the United Nations, agriculture releases ∼9.3 Gt CO2 equivalents per year, of which methane (CH4) and nitrous oxide (N2O) account for 5.3 Gt CO2 equivalents. N-pollution and slowing the runaway N-cycle requires a combined effort to replace chemical fertilizers with biological alternatives, which after a 10-yr span of usage could eliminate a minimum of 30% of ag-related GHG emissions (∼1.59 Gt), protect waterways from nitrate pollution, and protect soils from further deterioration. Agritech solutions include bringing biological fertilizers and biological nitrification inhibitors to the marketplace to reduce the microbial conversion of fertilizer nitrogen into GHGs and other toxic intermediates. Worldwide adoption of these plant-derived molecules will substantially elevate nitrogen use efficiency by crops while blocking the dominant source of N2O to the atmosphere and simultaneously protecting the biological CH4 sink. Additional agritech solutions to curtail N-pollution, soil erosion, and deterioration of freshwater supplies include soil-free aquaponics systems that utilize improved microbial inocula to enhance nitrogen use efficiency without GHG production. With adequate and timely investment and scale-up, microbe-based agritech solutions emphasizing N-cycling processes can dramatically reduce GHG emissions on short time lines.
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Affiliation(s)
- Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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16
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Jiang C, Wu J, Ye J, Hong Y. High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay. MARINE POLLUTION BULLETIN 2024; 200:116046. [PMID: 38246016 DOI: 10.1016/j.marpolbul.2024.116046] [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: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.
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Affiliation(s)
- Cuihong Jiang
- 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
| | - 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.
| | - 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
| | - 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.
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17
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Sun D, Rozmoš M, Kotianová M, Hršelová H, Jansa J. Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils. Heliyon 2024; 10:e26485. [PMID: 38444950 PMCID: PMC10912043 DOI: 10.1016/j.heliyon.2024.e26485] [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: 09/12/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.
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Affiliation(s)
- Daquan Sun
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Martin Rozmoš
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Michala Kotianová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Hana Hršelová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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18
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Beneduce L, Piergiacomo F, Limoni PP, Zuffianò LE, Polemio M. Microbial, chemical, and isotopic monitoring integrated approach to assess potential leachate contamination of groundwater in a karstic aquifer (Apulia, Italy). ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:312. [PMID: 38413499 PMCID: PMC10899417 DOI: 10.1007/s10661-024-12477-6] [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: 09/28/2023] [Accepted: 02/17/2024] [Indexed: 02/29/2024]
Abstract
Landfill sites are subjected to long-term risks of accidental spill of leachate through the soil and consequential contamination of the groundwater. Wide areas surrounding the landfill can seriously be threatened with possible consequences to human health and the environment. Given the potential impact of different coexisting anthropic pollution sources (i.e., agriculture and cattle farming) on the same site, the perturbation of the groundwater quality may be due to multiple factors. Therefore, it is a challenging issue to correctly establish the pollution source of an aquifer where the landfill is not isolated from other anthropic land uses, especially in the case of a karstic coastal aquifer. The present study is aimed at setting in place an integrated environmental monitoring system that included microbiological, chemical, and isotope methods to evaluate potential groundwater pollution in a landfill district in the south of Italy located in Murgia karstic aquifer. Conventional (microbial plate count and physical-chemical analyses) and advanced methods (PCR-ARISA, isotope analysis of δ18O, δ2H, 3H, δ 13C, δ 15N-NO3-, and δ 18O-NO3-) were included in the study. Through data integration, it was possible to reconstruct a scenario in which agriculture and other human activities along with seawater intrusion in the karst aquifer were the main drivers of groundwater pollution at the monitored site. The microbiological, chemical, and isotope results confirmed the absence of leachate effects on groundwater quality, showing the decisive role of fertilizers as potential nitrate sources. The next goal will be to extend long-term integrated monitoring to other landfill districts, with different geological and hydrogeological characteristics and including different sources of pollution, to support the ecological restoration of landfills.
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Affiliation(s)
- L Beneduce
- Department of the Science of Agriculture, Food, Natural Resources and Engineering (DAFNE), University of Foggia, Via Napoli, 25 -71122, Foggia, Italy
| | - F Piergiacomo
- Present address: Faculty of Science and Technology, Free University of Bolzano-Bozen, Piazza Università 1, 39100, Bolzano-Bozen, Italy
| | - P P Limoni
- CNR-IRPI, National Research Council, Research Institute for Hydrogeological Protection, Via Amendola 122/I, 70126, Bari, Italy
| | - L E Zuffianò
- CNR-IRPI, National Research Council, Research Institute for Hydrogeological Protection, Via Amendola 122/I, 70126, Bari, Italy.
| | - M Polemio
- CNR-IRPI, National Research Council, Research Institute for Hydrogeological Protection, Via Amendola 122/I, 70126, Bari, Italy
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19
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Qin W, Wei SP, Zheng Y, Choi E, Li X, Johnston J, Wan X, Abrahamson B, Flinkstrom Z, Wang B, Li H, Hou L, Tao Q, Chlouber WW, Sun X, Wells M, Ngo L, Hunt KA, Urakawa H, Tao X, Wang D, Yan X, Wang D, Pan C, Weber PK, Jiang J, Zhou J, Zhang Y, Stahl DA, Ward BB, Mayali X, Martens-Habbena W, Winkler MKH. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat Microbiol 2024; 9:524-536. [PMID: 38297167 DOI: 10.1038/s41564-023-01593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.
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Affiliation(s)
- Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Stephany P Wei
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Eunkyung Choi
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - Xiangpeng Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | | | - Xianhui Wan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Baozhan Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hanyan Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Lei Hou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wyatt W Chlouber
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xin Sun
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Michael Wells
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Long Ngo
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Xuanyu Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Dongyu Wang
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Chongle Pan
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
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20
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Beeckman F, Drozdzecki A, De Knijf A, Audenaert D, Beeckman T, Motte H. High-throughput assays to identify archaea-targeting nitrification inhibitors. FRONTIERS IN PLANT SCIENCE 2024; 14:1283047. [PMID: 38259951 PMCID: PMC10800436 DOI: 10.3389/fpls.2023.1283047] [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: 08/25/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 -) and then to nitrate (NO3 -). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 - leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Andrzej Drozdzecki
- Screening Core, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Dominique Audenaert
- Screening Core, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
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21
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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [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: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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22
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Johnson J, Jain KR, Patel A, Parmar N, Joshi C, Madamwar D. Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal. World J Microbiol Biotechnol 2023; 40:52. [PMID: 38146029 DOI: 10.1007/s11274-023-03848-1] [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: 03/04/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023]
Abstract
Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.
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Affiliation(s)
- Jenny Johnson
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Kunal R Jain
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Anand Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Nidhi Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, 6th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa (Anand), Gujarat, 388 421, India.
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23
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Akutsu Y, Fujiwara T, Suzuki R, Nishigaya Y, Yamazaki T. Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c554. Appl Environ Microbiol 2023; 89:e0129123. [PMID: 38009977 PMCID: PMC10734522 DOI: 10.1128/aem.01291-23] [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: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea. Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c554, a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.
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Affiliation(s)
- Yukie Akutsu
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takaaki Fujiwara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Rintaro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | | | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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24
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Dong J, Yang B, Wang H, Cao X, He F, Wang L. Reveal molecular mechanism on the effects of silver nanoparticles on nitrogen transformation and related functional microorganisms in an agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166765. [PMID: 37660816 DOI: 10.1016/j.scitotenv.2023.166765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Silver nanoparticles (AgNPs) are widely present in aquatic and soil environment, raising significant concerns about their impacts on creatures in ecosystem. While the toxicity of AgNPs on microorganisms has been reported, their effects on biogeochemical processes and specific functional microorganisms remain relatively unexplored. In this study, a 28-day microcosmic experiment was conducted to investigate the dose-dependent effects of AgNPs (10 mg and 100 mg Ag kg-1 soil) on nitrogen transformation and functional microorganisms in agricultural soils. The molecular mechanisms were uncovered by examining change in functional microorganisms and metabolic pathways. To enable comparison, the toxicity of positive control with an equivalent Ag+ dose from CH3COOAg was also included. The results indicated that both AgNPs and CH3COOAg enhanced nitrogen fixation and nitrification, corresponding to increased relative abundances of associated functional genes. However, they inhibited denitrification via downregulating nirS, nirK, and nosZ genes as well as reducing nitrate and nitrite reductase activities. In contrast to high dose of AgNPs, low levels increased bacterial diversity. AgNPs and CH3COOAg altered the activities of associated metabolic pathways, resulting in the enrichment of specific taxa that demonstrated tolerance to Ag. At genus level, AgNPs increased the relative abundances of nitrogen-fixing Microvirga and Bacillus by 0.02 %-629.39 % and 14.44 %-30.10 %, respectively, compared with control group (CK). The abundances of denitrifying bacteria, such as Rhodoplanes, Pseudomonas, and Micromonospora, decreased by 19.03 % to 32.55 %, 24.73 % to 50.05 %, and 15.66 % to 76.06 %, respectively, compared to CK. CH3COOAg reduced bacterial network complexity, diminished the symbiosis mode compared to AgNPs. The prediction of genes involved in metabolic pathways related to membrane transporter and cell motility showed sensitive to AgNPs exposure in the soil. Further studies involving metabolomics are necessary to reveal the essential effects of AgNPs and CH3COOAg on biogeochemical cycle of elements in agricultural soil.
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Affiliation(s)
- Jinhao Dong
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Baoshan Yang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China.
| | - Hui Wang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China.
| | - Xinlei Cao
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Fei He
- Jinan Environmental Research Academy, Jinan 250098, China
| | - Lijiao Wang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
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25
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Uhlen M, Quake SR. Sequential sequencing by synthesis and the next-generation sequencing revolution. Trends Biotechnol 2023; 41:1565-1572. [PMID: 37482467 DOI: 10.1016/j.tibtech.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023]
Abstract
The impact of next-generation sequencing (NGS) cannot be overestimated. The technology has transformed the field of life science, contributing to a dramatic expansion in our understanding of human health and disease and our understanding of biology and ecology. The vast majority of the major NGS systems today are based on the concept of 'sequencing by synthesis' (SBS) with sequential detection of nucleotide incorporation using an engineered DNA polymerase. Based on this strategy, various alternative platforms have been developed, including the use of either native nucleotides or reversible terminators and different strategies for the attachment of DNA to a solid support. In this review, some of the key concepts leading to this remarkable development are discussed.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA; Chan Zuckerberg Initiative, Redwood City, California, USA, Stanford, CA, USA
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26
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Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
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Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
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Couso LL, Soler-Bistué A, Aptekmann AA, Sánchez IE. Ecology theory disentangles microbial dichotomies. Environ Microbiol 2023; 25:3052-3063. [PMID: 37658654 DOI: 10.1111/1462-2920.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.
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Affiliation(s)
- Luciana L Couso
- Facultad de Agronomía. Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas "Rodolfo A. Ugalde", IIB-IIBIO, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
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28
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [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: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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29
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Wu X, Zhang W, Liu G, Chen T, Li Z. Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China. Microorganisms 2023; 11:2871. [PMID: 38138015 PMCID: PMC10745509 DOI: 10.3390/microorganisms11122871] [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: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.
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Affiliation(s)
- Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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30
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Yang Y, Liu H, Zhang Y, Fang X, Zhong X, Lv J. Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments. Sci Rep 2023; 13:20722. [PMID: 38007550 PMCID: PMC10676402 DOI: 10.1038/s41598-023-44147-x] [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: 02/21/2023] [Accepted: 10/04/2023] [Indexed: 11/27/2023] Open
Abstract
The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Yang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianhui Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianbao Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China.
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Beeckman F, Drozdzecki A, De Knijf A, Corrochano-Monsalve M, Bodé S, Blom P, Goeminne G, González-Murua C, Lücker S, Boeckx P, Stevens CV, Audenaert D, Beeckman T, Motte H. Drug discovery-based approach identifies new nitrification inhibitors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118996. [PMID: 37725864 DOI: 10.1016/j.jenvman.2023.118996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Andrzej Drozdzecki
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Samuel Bodé
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Pascal Boeckx
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian V Stevens
- Synthesis, Bioresources and Bioorganic Chemistry Research Group (SynBioC), Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dominique Audenaert
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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32
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Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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33
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Jenull S, Bauer T, Silbermayr K, Dreer M, Stark TD, Ehling-Schulz M. The toxicological spectrum of the Bacillus cereus toxin cereulide points towards niche-specific specialisation. Environ Microbiol 2023; 25:2231-2249. [PMID: 37354053 DOI: 10.1111/1462-2920.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/06/2023] [Indexed: 06/26/2023]
Abstract
Most microbes share their environmental niches with very different forms of life thereby engaging in specialised relationships to enable their persistence. The bacterium Bacillus cereus occurs ubiquitously in the environment with certain strain backgrounds causing foodborne and opportunistic infections in humans. The emetic lineage of B. cereus is capable of producing the toxin cereulide, which evokes emetic illnesses. Although food products favouring the accumulation of cereulide are known, the ecological role of cereulide and the environmental niche of emetic B. cereus remain elusive. To better understand the ecology of cereulide-producing B. cereus, we systematically assayed the toxicological spectrum of cereulide on a variety of organisms belonging to different kingdoms. As cereulide is a potassium ionophore, we further tested the effect of environmental potassium levels on the action of cereulide. We found that adverse effects of cereulide exposure are species-specific, which can be exacerbated with increased environmental potassium. Additionally, we demonstrate that cereulide is produced within an insect cadaver indicating its potential ecological function for a saprophytic lifestyle. Collectively, distinct cereulide susceptibilities of other organisms may reflect its role in enabling competitive niche specialization of emetic B. cereus.
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Affiliation(s)
- Sabrina Jenull
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tobias Bauer
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Katja Silbermayr
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Maximilian Dreer
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Timo D Stark
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
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34
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Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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35
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [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: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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Sieradzki ET, Nuccio EE, Pett-Ridge J, Firestone MK. Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development. mSystems 2023; 8:e0031523. [PMID: 37754554 PMCID: PMC10654102 DOI: 10.1128/msystems.00315-23] [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: 03/30/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.
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Affiliation(s)
- Ella T. Sieradzki
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, UC Merced, Merced, California, USA
- Innovative Genomics Institute, UC Berkeley, Berkeley, California, USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
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37
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Han X, Beck K, Bürgmann H, Frey B, Stierli B, Frossard A. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front Microbiol 2023; 14:1279041. [PMID: 37942081 PMCID: PMC10627841 DOI: 10.3389/fmicb.2023.1279041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.
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Affiliation(s)
- Xingguo Han
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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38
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Singh D, Kaushik R, Chakdar H, Saxena AK. Unveiling novel insights into haloarchaea (Halolamina pelagica CDK2) for alleviation of drought stress in wheat. World J Microbiol Biotechnol 2023; 39:328. [PMID: 37792124 DOI: 10.1007/s11274-023-03781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023]
Abstract
Plant growth promoting microorganisms have various implications for plant growth and drought stress alleviation; however, the roles of archaea have not been explored in detail. Herein, present study was aimed for elucidating potential of haloarchaea (Halolamina pelagica CDK2) on plant growth under drought stress. Results showed that haloarchaea inoculated wheat plants exhibited significant improvement in total chlorophyll (100%) and relative water content (30.66%) compared to the uninoculated water-stressed control (30% FC). The total root length (2.20-fold), projected area (1.60-fold), surface area (1.52-fold), number of root tips (3.03-fold), number of forks (2.76-fold) and number of links (1.45-fold) were significantly higher in the inoculated plants than in the uninoculated water stressed control. Additionally, the haloarchaea inoculation resulted in increased sugar (1.50-fold), protein (2.40-fold) and activity of antioxidant enzymes such as superoxide dismutase (1.93- fold), ascorbate peroxidase (1.58-fold), catalase (2.30-fold), peroxidase (1.77-fold) and glutathione reductase (4.70-fold), while reducing the accumulation of proline (46.45%), glycine betaine (35.36%), lipid peroxidation (50%), peroxide and superoxide radicals in wheat leaves under water stress. Furthermore, the inoculation of haloarchaea significantly enhanced the expression of stress-responsive genes (DHN, DREB, L15, and TaABA-8OH) and wheat vegetative growth under drought stress over the uninoculated water stressed control. These results provide novel insights into the plant-archaea interaction for plant growth and stress tolerance in wheat and pave the way for future research in this area.
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Affiliation(s)
- Devendra Singh
- ICAR- Central Arid Zone Research Institute, 342003, Jodhpur, Rajasthan, India
- ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Kushmaur, Mau, Uttar Pradesh, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Kushmaur, Mau, Uttar Pradesh, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Kushmaur, Mau, Uttar Pradesh, India.
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Liu H, Jing H, Wang F. Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Front Microbiol 2023; 14:1268790. [PMID: 37840747 PMCID: PMC10568479 DOI: 10.3389/fmicb.2023.1268790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.
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Affiliation(s)
- Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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40
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Zhang S, Wang F, Wang Y, Chen X, Xu P, Miao H. Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117871. [PMID: 37030237 DOI: 10.1016/j.jenvman.2023.117871] [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: 01/04/2023] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.
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Affiliation(s)
- Shengman Zhang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Yuchun Wang
- China Institute of Water Resources and Hydropower Research, Beijing, 100038, China.
| | - Xueping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Peifan Xu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Haocheng Miao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
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41
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Kan J, Peck EK, Zgleszewski L, Peipoch M, Inamdar S. Mill dams impact microbiome structure and depth distribution in riparian sediments. Front Microbiol 2023; 14:1161043. [PMID: 37455732 PMCID: PMC10339028 DOI: 10.3389/fmicb.2023.1161043] [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: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function. Methods Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States. Results We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification. Discussion Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.
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Affiliation(s)
- Jinjun Kan
- Stroud Water Research Center, Avondale, PA, United States
| | - Erin K Peck
- University of Delaware, Plant and Soil Sciences, Newark, DE, United States
| | | | - Marc Peipoch
- Stroud Water Research Center, Avondale, PA, United States
| | - Shreeram Inamdar
- University of Delaware, Plant and Soil Sciences, Newark, DE, United States
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Ma M, Zhao Y, Jiang X, Guan D, Yuan M, Cao F, Li L, Zhou J, Ding J, Li J. Fertilization altered co-occurrence patterns and microbial assembly process of ammonia-oxidizing microorganisms. Sci Rep 2023; 13:8234. [PMID: 37217543 DOI: 10.1038/s41598-022-26293-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/13/2022] [Indexed: 05/24/2023] Open
Abstract
Ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) are important intermediate links in the nitrogen cycle. Apart from the AOA and AOB communities in soil, we further investigated co-occurrence patterns and microbial assembly processes subjected to inorganic and organic fertilizer treatments for over 35 years. The amoA copy numbers and AOA and AOB communities were found to be similar for the CK and organic fertilizer treatments. Inorganic fertilizers decreased the AOA gene copy numbers by 0.75-0.93-fold and increased the AOB gene copy numbers by 1.89-3.32-fold compared to those of the CK treatment. The inorganic fertilizer increased Nitrososphaera and Nitrosospira. The predominant bacteria in organic fertilizer was Nitrosomonadales. Furthermore, the inorganic fertilizer increased the complexity of the co-occurrence pattern of AOA and decreased the complexity pattern of AOB comparing with organic fertilizer. Different fertilizer had an insignificant effect on the microbial assembly process of AOA. However, great difference exists in the AOB community assembly process: deterministic process dominated in organic fertilizer treatment and stochastic processes dominated in inorganic fertilizer treatment, respectively. Redundancy analysis indicated that the soil pH, NO3-N, and available phosphorus contents were the main factors affecting the changes in the AOA and AOB communities. Overall, this findings expanded our knowledge concerning AOA and AOB, and ammonia-oxidizing microorganisms were more disturbed by inorganic fertilizers than organic fertilizers.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Yubin Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Yuan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, Heilongjiang, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, 273165, China
| | - Jianli Ding
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
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43
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Wang Z, Li Y, Zheng W, Ji Y, Duan M, Ma L. Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China. Sci Rep 2023; 13:8064. [PMID: 37202434 DOI: 10.1038/s41598-023-35134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha-1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha-1 (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha-1 (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.
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Affiliation(s)
- Zhan Wang
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Guyuan Branch, Ningxia Academy of Agricultural and Forestry Sciences, Guyuan, 756000, China
| | - Yinkun Li
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Wengang Zheng
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuru Ji
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Minjie Duan
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Urban Ecosystem Positioning Observation and Research Station, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Li Ma
- Wuzhong National Agricultural Science and Technology Park Management Committee, Wuzhong, 751100, Ningxia, China
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Zheng P, Zhang Q, Zou J, Han Q, Han J, Wang Q, Yao L, Yu G, Liang Y. A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162385. [PMID: 36842598 DOI: 10.1016/j.scitotenv.2023.162385] [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: 12/26/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.
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Affiliation(s)
- Peihan Zheng
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiaxing Zou
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qi Han
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiarong Han
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qixin Wang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Liting Yao
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guangwei Yu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuhai Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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45
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Wang Y, Zeng X, Zhang Y, Zhang N, Xu L, Wu C. Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil. J Environ Sci (China) 2023; 127:15-29. [PMID: 36522049 DOI: 10.1016/j.jes.2022.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/17/2023]
Abstract
Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.
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Affiliation(s)
- Yanan Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Xibai Zeng
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China.
| | - Yang Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Nan Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Liyang Xu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Cuixia Wu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
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46
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Wen L, Yang L, Chen C, Li J, Fu J, Liu G, Kan Q, Ho CT, Huang Q, Lan Y, Cao Y. Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods. Crit Rev Food Sci Nutr 2023:1-17. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.
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Affiliation(s)
- Linfeng Wen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lixin Yang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Cong Chen
- Guangdong Eco-engineering Polytechnic, Guangzhou, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Jiangyan Fu
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Guo Liu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qixin Kan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Yaqi Lan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
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47
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Gineyts R, Niboyet A. Nitrification, denitrification, and related functional genes under elevated CO 2 : A meta-analysis in terrestrial ecosystems. GLOBAL CHANGE BIOLOGY 2023; 29:1839-1853. [PMID: 36537009 DOI: 10.1111/gcb.16568] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 05/28/2023]
Abstract
Global change may have profound effects on soil nitrogen (N) cycling that can induce positive feedback to climate change through increased nitrous oxide (N2 O) emissions mediated by nitrification and denitrification. We conducted a meta-analysis of the effects of elevated CO2 on nitrification and denitrification based on 879 observations from 58 publications and 46 independent elevated CO2 experiments in terrestrial ecosystems. We investigated the effects of elevated CO2 alone or combined with elevated temperature, increased precipitation, drought, and N addition. We assessed the response to elevated CO2 of gross and potential nitrification, potential denitrification, and abundances of related functional genes (archaeal amoA, bacterial amoA, nirK, nirS, and nosZ). Elevated CO2 increased potential nitrification (+28%) and the abundance of bacterial amoA functional gene (+62%) in cropland ecosystems. Elevated CO2 increased potential denitrification when combined with N addition and higher precipitation (+116%). Elevated CO2 also increased the abundance of nirK (+25%) and nirS (+27%) functional genes in terrestrial ecosystems and of nosZ (+32%) functional gene in cropland ecosystems. The increase in the abundance of nosZ under elevated CO2 was larger at elevated temperature and high N (+62%). Four out of 14 two-way interactions tested between elevated CO2 and elevated temperature, elevated CO2 and increased precipitation, and elevated CO2 and N addition were marginally significant and mostly synergistic. The effects of elevated CO2 on potential nitrification and abundances of bacterial amoA and nirS functional genes increased with mean annual temperature and mean annual precipitation. Our meta-analysis thus suggests that warming and increased precipitation in large areas of the world could reinforce positive responses of nitrification and denitrification to elevated CO2 and urges the need for more investigations in the tropical zone and on interactive effects among multiple global change factors, as we may largely underestimate the effects of global change on soil N2 O emissions.
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Affiliation(s)
- Robin Gineyts
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Paris, France
- AgroParisTech, Palaiseau, France
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Paris, France
- AgroParisTech, Palaiseau, France
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48
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Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, Schleper C. Unexpected complexity of the ammonia monooxygenase in archaea. THE ISME JOURNAL 2023; 17:588-599. [PMID: 36721060 PMCID: PMC10030591 DOI: 10.1038/s41396-023-01367-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.
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Affiliation(s)
- Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Weiqiang Chen
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
| | - Rafael I Ponce-Toledo
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Stefanie Wienkoop
- Molecular Systems Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
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D'Alò F, Zucconi L, Onofri S, Canini F, Cannone N, Malfasi F, Morais DK, Starke R. Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36999249 DOI: 10.1111/1758-2229.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, Viterbo, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, Viterbo, Italy
- Institute of Polar Sciences, National Research Council of Italy (CNR-ISP), Messina, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, Viterbo, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, Viterbo, Italy
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Como, CO, Italy
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Como, CO, Italy
| | - Daniel Kumazawa Morais
- Biological Institute of São Paulo - Vila Mariana, São Paulo, Brazil
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Robert Starke
- Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
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50
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Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake. mSystems 2023; 8:e0099222. [PMID: 36927063 PMCID: PMC10134853 DOI: 10.1128/msystems.00992-22] [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: 03/18/2023] Open
Abstract
Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.
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