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Solár J, Pitoňáková T, Pogányová A. Changes in physicochemical parameters of the alpine/mountain stream influenced by summer flash flood in Tatra Mountains (Western Carpathians). ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:655. [PMID: 38913150 PMCID: PMC11196348 DOI: 10.1007/s10661-024-12835-4] [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: 03/06/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
Changes to the physicochemical parameters of water in alpine/mountain streams can provide evidence of ongoing natural and anthropogenic processes in their catchment. In this study, we analysed a mountain stream (Javorinka) on the north-eastern side of the Tatra Mountains (Western Carpathians), which is minimally influenced by human activity. The stream was monitored weekly for 5 years (2017-2021) and evaluated for its seasonal variations in physicochemical parameters. These seasonal variations were influenced by the large summer flash flood in July 2018. We hypothesise that floods are essential for the oligotrophic profile of alpine/mountain streams. To support this idea, our main objective was to compare the seasonal trends of the main physicochemical parameters in the stream before and after floods or periods of high flow. We found evidence to support our hypothesis. For example, there was a significant decrease in the chemical consumption of oxygen and ammonia, and, conversely, an increase in the ratio of saturated oxygen and nitrate concentrations. Stream bed erosion also resulted in increased phosphates (over the next 2 years) and high enrichment of the water by dissolved solids in the spring. Interestingly outside of the main objectives, we observed a significant decrease in sulphates, especially in the summer and autumn of 2020 and 2021, which may be related to suppressed emissions due to the restriction of the COVID-19 lockdown. The observed trends and their changes therefore support the idea that alpine/mountain streams are excellent indicators of ongoing environmental processes, and that occasional summer flash floods support the oligotrophic profile of the stream system.
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Affiliation(s)
- Jaroslav Solár
- Institute of High Mountain Biology, University of Zilina, Tatranská Javorina 7, 059 56, Tatranska Javorina, Slovak Republic.
| | - Tatiana Pitoňáková
- Institute of High Mountain Biology, University of Zilina, Tatranská Javorina 7, 059 56, Tatranska Javorina, Slovak Republic
| | - Andrea Pogányová
- Institute of High Mountain Biology, University of Zilina, Tatranská Javorina 7, 059 56, Tatranska Javorina, Slovak Republic
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2
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Bowen JL, Spivak AC, Bernhard AE, Fulweiler RW, Giblin AE. Salt marsh nitrogen cycling: where land meets sea. Trends Microbiol 2024; 32:565-576. [PMID: 37827901 DOI: 10.1016/j.tim.2023.09.010] [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: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.
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Affiliation(s)
- Jennifer L Bowen
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Rd, Nahant, MA, USA.
| | - Amanda C Spivak
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Anne E Bernhard
- Biology Department, Connecticut College, New London, CT 06320, USA
| | - Robinson W Fulweiler
- Department of Earth and Environment, Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, MA 02543, USA
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3
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Zheng R, Feng Y, Kong L, Wu X, Zhou J, Zhang L, Liu S. Blue-light irradiation induced partial nitrification. WATER RESEARCH 2024; 254:121381. [PMID: 38442606 DOI: 10.1016/j.watres.2024.121381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/08/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.
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Affiliation(s)
- Ru Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Lingrui Kong
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Liguo Zhang
- School of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China.
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Li H, Song X, Wu D, Wei D, Ju X. Digestate induces significantly higher N 2O emission compared to urea under different soil properties and moisture. ENVIRONMENTAL RESEARCH 2024; 241:117617. [PMID: 37967706 DOI: 10.1016/j.envres.2023.117617] [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: 07/12/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
Digestate is considered as an option for recycling resources and a part of the substitution for chemical fertilizers to reduce environmental impacts. However, its application may lead to significant nitrous oxide (N2O) emissions because of its high concentration of ammonium and degradable carbon. The research objectives are to evaluate how N2O emissions respond to digestate as compared to urea application and whether this depends on soil properties and moisture. Either digestate or urea (100 mg N kg-1) was applied with and without a nitrification inhibitor of 3,4-dimethylpyrazole phosphate (DMPP) to three soil types (fluvo-aquic soil, black soil, and latosol) under three different soil moisture conditions (45, 65, and 85% water-filled pore space (WFPS)) through microcosm incubations. Results showed that digestate- and urea-induced N2O emissions increased exponentially with soil moisture in the three studied soils, and the magnitude of the increase was much greater in the alkaline fluvo-aquic soil, coinciding with high net nitrification rate and transient nitrite accumulation. Compared with urea-amended soils, digestate led to significantly higher peaks in N2O and carbon dioxide (CO2) emissions, which might be due to stimulated rapid oxygen consumption and mineralized N supply. Digestate-induced N2O emissions were all more than one time higher than those induced by urea at the three moisture levels in the three studied soils, except at 85% WFPS in the fluvo-aquic soil. DMPP was more effective at mitigating N2O emissions (inhibitory efficacy: 73%-99%) in wetter digestate-fertilized soils. Overall, our study shows the contrasting effect of digestate to urea on N2O emissions under different soil properties and moisture levels. This is of particular value for determining the optimum of applying digestate under varying soil moisture conditions to minimize stimulated N2O emissions in specific soil properties.
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Affiliation(s)
- Haoruo Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaotong Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Di Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Dan Wei
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Xiaotang Ju
- College of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
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5
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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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Solár J, Tomaškovič J. Physicochemical properties of mountain streams in the High and Western Tatras. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1543. [PMID: 38012457 PMCID: PMC10682066 DOI: 10.1007/s10661-023-12158-w] [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: 05/23/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
The aim of this study was to measure the physicochemical properties of 28 mountain streams in Tatra National Park, Slovakia. Sampling sites (119) were selected based on a previous study conducted in 2010. Physical properties (e.g., temperature, conductivity, total dissolved solids, pH, and dissolved oxygen) and chemical components (e.g., nitrogen oxides, ammonia oxides, chloride compounds, and chemical oxygen demand) of the water were determined. Environmental parameters of streams (elevation, slope, aspect, width, depth, flow accumulation, watershed size, bedrock, and presence of mountain lakes) at sampling sites were examined. While comparing results from both periods (2010 and 2017), we found a correlation in data trends, concluding that elevation plays a significant role in almost all investigated parameters. Downstream, streams were more saturated by dissolved solids, CaCO3, and nitrates, increasing the pH level. Despite this well-known trend, we observed significant higher levels of ammonias and chlorides in the alpine zone, especially at sites where higher water temperature and lower values of dissolved oxygen were observed. This occurred in the Eastern Tatras, below mountain lakes, and where watersheds had granite origins. There are indications that denitrification processes were significantly stronger in 2017, but, on the other hand, increased chlorides resulted in stronger inhibition of nitrification processes in alpine zones at sites below mountain lakes.
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Affiliation(s)
- Jaroslav Solár
- Institute of High Mountain Biology, University of Zilina, Tatranská Javorina, 7, SK-059 56, Tatranská Javorina, Zilina, Slovakia.
| | - Jakub Tomaškovič
- Institute of High Mountain Biology, University of Zilina, Tatranská Javorina, 7, SK-059 56, Tatranská Javorina, Zilina, Slovakia
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7
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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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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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9
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Lagos S, Tsetsekos G, Mastrogianopoulos S, Tyligada M, Diamanti L, Vasileiadis S, Sotiraki S, Karpouzas DG. Interactions of anthelmintic veterinary drugs with the soil microbiota: Toxicity or enhanced biodegradation? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122135. [PMID: 37406753 DOI: 10.1016/j.envpol.2023.122135] [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: 04/15/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Anthelmintic (AH) compounds are used to control gastrointestinal nematodes (GINs) in livestock production. They are only partially metabolized in animals ending in animal excreta whose use as manures leads to AH dispersal in agricultural soils. Once in soil, AHs interact with soil microorganisms, with the outcome being either detrimental, or beneficial. We aimed to disentangle the mechanisms of these complex interactions. Two soils previously identified as « fast » or « slow», regarding the degradation of albendazole (ABZ), ivermectin (IVM), and eprinomectin (EPM), were subjected to repeated applications at two dose rates (1, 2 mg kg-1and 10, 20 mg kg-1). We hypothesized that this application scheme will lead to enhanced biodegradation in «fast » soils and accumulation and toxicity in «slow » soils. Repeated application of ABZ resulted in different transformation pathways in the two soils and a clear acceleration of its degradation in the «fast » soil only. In contrast residues of IVM and EPM accumulated in both soils. ABZ was the sole AH that induced a consistent reduction in the abundance of total fungi and crenarchaea. In addition, inhibition of nitrification and reduction in the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) by all AHs was observed, while commamox bacteria were less responsive. Amplicon sequencing analysis showed dose-depended shifts in the diversity of bacteria, fungi, and protists in response to AHs application. ABZ presented the most consistent effect on the abundance and diversity of most microbial groups. Our findings provide first evidence for the unexpected toxicity of AHs on key soil microbial groups that might have to be considered in a regulatory context.
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Affiliation(s)
- Stathis Lagos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Georgios Tsetsekos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Spyridon Mastrogianopoulos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Maria Tyligada
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Lamprini Diamanti
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Smaragda Sotiraki
- Laboratory of Parasitology, Hellenic Agricultural Organization-Demeter, Veterinary Research Institute, 57001, Thermi, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece.
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10
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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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11
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Afzal MR, Naz M, Ashraf W, Du D. The Legacy of Plant Invasion: Impacts on Soil Nitrification and Management Implications. PLANTS (BASEL, SWITZERLAND) 2023; 12:2980. [PMID: 37631191 PMCID: PMC10458916 DOI: 10.3390/plants12162980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Plant invasions can have long-lasting impacts on soil nitrification, which plays a critical role in nutrient cycling and plant growth. This review examines the legacy effects of plant invasion on soil nitrification, focusing on the underlying mechanisms, context dependence, and implications for management. We synthesize literature on the positive, negative and neutral legacy effects of plant invasion on soil nitrification, highlighting the complexity of these effects and the need for further research to fully understand them. Positive legacy effects include increased soil microbial biomass or activity, potentially enhancing nutrient availability for plants. However, negative legacy effects, like reduced nitrifier abundance, can result in decreased soil nitrification rates and nutrient availability. In some cases, changes to nitrification during active invasion appear transitory after the removal of invasive plants, indicating neutral short-term legacies. We discuss the context dependence of legacy effects considering factors, including location, specific invasive plant species, and other environmental conditions. Furthermore, we discuss the implications of these legacy effects for management and restoration strategies, such as the removal or control of invasive plants, and potential approaches for restoring ecosystems with legacy effects on soil nitrification. Finally, we highlight future research directions, including further investigation into the mechanisms and context dependence of legacy effects, and the role of plant-microbe interactions. Overall, this review provides insights into the legacy effects of plant invasion on soil nitrification and their implications for ecosystems.
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Affiliation(s)
- Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China;
| | - Misbah Naz
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China;
| | - Waqas Ashraf
- Soil and Water Testing Laboratory for Research, Ayub Agricultural Research Institute Faisalabad, Punjab 38850, Pakistan;
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China;
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Kurtz BE, Landmeyer JE, Culter JK. Precipitation, submarine groundwater discharge of nitrogen, and red tides along the southwest Florida Gulf coast. Heliyon 2023; 9:e16046. [PMID: 37215903 PMCID: PMC10196494 DOI: 10.1016/j.heliyon.2023.e16046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/05/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Blooms of the dinoflagellate Karenia brevis occur almost every year along the southwest Florida Gulf coast. Long-duration blooms with especially high concentrations of K. brevis, known as red tides, destroy marine life through production of neurotoxins. Current hypotheses are that red tides originate in oligotrophic waters far offshore using nitrogen (N) from upwelling bottom water or, alternatively, from blooms of Trichodesmium, followed by advection to nearshore waters. But the amount of N available from terrestrial sources does not appear to be adequate to maintain a nearshore red tide. To explain this discrepancy, we hypothesize that contemporary red tides are associated with release of N from offshore submarine groundwater discharge (SGD) that has accumulated in benthic sediment biomass by dissimilatory nitrate reduction to ammonium (DNRA). The release occurs when sediment labile organic carbon (LOC), used as the electron donor in DNRA, is exhausted. Detritus from the resulting destruction of marine life restores the sediment LOC to continue the cycle of red tides. The severity of individual red tides increases with increased bloom-year precipitation in the geographic region where the SGD originates, while the severity of ordinary blooms is relatively unaffected.
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Affiliation(s)
- Bruce E. Kurtz
- New College of Florida, 5800 Bay Shore Rd., Sarasota, FL 34243, USA
| | | | - James K. Culter
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL 34236, USA
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Bhatta R, Rahman H. Effect of an anti-methanogenic supplement on enteric methane emission, fermentation, and whole rumen metagenome in sheep. Front Microbiol 2022; 13:1048288. [PMID: 36478863 PMCID: PMC9719938 DOI: 10.3389/fmicb.2022.1048288] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
A study was conducted to investigate the impact of an anti-methanogenic product supplementation on enteric methane emissions, whole rumen metagenome and ruminal fermentation in sheep. Twelve adult male sheep were randomly divided into two groups of six animals each. Animals were fed ad libitum on a total mixed ration either without (CON) or with an anti-methanogenic supplement (Harit Dhara-HD). The anti-methanogenic supplement contained 22.1% tannic acid in a 3: 1 ratio of condensed and hydrolysable tannins. The supplementation of product revealed a significant reduction in daily enteric methane emission (21.9 vs. 17.2 g/d) and methane yield (23.2 vs. 18.2) without affecting the nutrient intake and digestibility. However, the propionate concentration in the HD treatment group was significantly higher than in the CON group. On the contrary, the ammonia nitrogen concentration was lower. The anti-methanogenic supplement significantly decreased the ruminal protozoa in the HD treatment group. Whole rumen metagenome analysis revealed that the core bacterial (Bacteroidetes and Firmicutes) and archaeal communities (Methanobrevibacter and Methanosarcina) were comparable between the CON and HD treatment groups. However, the supplementation of anti-methanogenic product led to a considerable reduction in the abundance of Proteobacteria, whereas the abundance of Lentisphaerae was greater. The supplementation significantly decreased the abundance of Methanocaldococcus, Methanococcoides, Methanocella, and Methanoregula methanogens. A total of 36 KO related to methanogenesis were identified in this study. The activities of formate dehydrogenase (EC 1.8.98.6) and tetrahydromethanopterin S-methyltransferase (EC 2.1.1.86) were significantly lowered by the anti-methanogenic product supplementation in sheep. In conclusion, the anti-methanogenic supplement has the potential to decrease enteric methane emission (~22%) at the recommended level (5% of DM) of supplementation. The contribution of minor methanogens vulnerable to supplementation to rumen methanogenesis is not known; hence, the culturing of these archaea should be taken on priority for determining the impact on overall rumen methanogenesis.
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Affiliation(s)
- Pradeep Kumar Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | | | - Atul Purushottam Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India,*Correspondence: Atul Purushottam Kolte,
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Habibar Rahman
- International Livestock Research Institute, New Delhi, India
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Microbiota Modulation in Blueberry Rhizosphere by Biocontrol Bacteria. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbial interactions in agricultural soils can play important roles in the control of soil-borne phytopathogenic diseases. Yields from blueberry plantations from southern Spain have been impacted by the pathogenic fungus, Macrophomina phaseolina. The use of chemical fungicides has been the common method for preventing fungal infections, but due to their high environmental impact, legislation is increasingly restricting its use. Biocontrol alternatives based on the use of microorganisms is becoming increasingly important. Using the metabarcoding technique, fungi and bacteria were characterized (via 16S and ITS regions, respectively) from rhizosphere soils of healthy and dead blueberry plants infected by M. phaseolina, and which had undergone three different treatments: two biocontrol strategies—one of them a mix of Pseudomonas aeruginosa and Bacillus velezensis and the other one with Bacillus amyloliquefaciens—and a third treatment consisting of the application of a nutrient solution. The treatments produced changes in the bacterial microbiota and, to a lesser extent, in the fungi. The abundance of Fusarium was correlated with dead plants, likely favoring the infection by M. phaseolina. The presence of other microorganisms in the soil, such as the fungi Archaeorhizomyces or the bacteria Actinospica, were correlated with healthy plants and could promote their survival. The different genera detected between dead and healthy plants opens the possibility of studying new targets that can act against infection and identify potential microorganisms that can be used in biocontrol strategies.
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Arbuscular Mycorrhiza and Nitrification: Disentangling Processes and Players by Using Synthetic Nitrification Inhibitors. Appl Environ Microbiol 2022; 88:e0136922. [PMID: 36190238 PMCID: PMC9599619 DOI: 10.1128/aem.01369-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both plants and their associated arbuscular mycorrhizal (AM) fungi require nitrogen (N) for their metabolism and growth. This can result in both positive and negative effects of AM symbiosis on plant N nutrition. Either way, the demand for and efficiency of uptake of mineral N from the soil by mycorrhizal plants are often higher than those of nonmycorrhizal plants. In consequence, the symbiosis of plants with AM fungi exerts important feedbacks on soil processes in general and N cycling in particular. Here, we investigated the role of the AM symbiosis in N uptake by Andropogon gerardii from an organic source (15N-labeled plant litter) that was provided beyond the direct reach of roots. In addition, we tested if pathways of 15N uptake from litter by mycorrhizal hyphae were affected by amendment with different synthetic nitrification inhibitors (dicyandiamide [DCD], nitrapyrin, or 3,4-dimethylpyrazole phosphate [DMPP]). We observed efficient acquisition of 15N by mycorrhizal plants through the mycorrhizal pathway, independent of nitrification inhibitors. These results were in stark contrast to 15N uptake by nonmycorrhizal plants, which generally took up much less 15N, and the uptake was further suppressed by nitrapyrin or DMPP amendments. Quantitative real-time PCR analyses showed that bacteria involved in the rate-limiting step of nitrification, ammonia oxidation, were suppressed similarly by the presence of AM fungi and by nitrapyrin or DMPP (but not DCD) amendments. On the other hand, abundances of ammonia-oxidizing archaea were not strongly affected by either the AM fungi or the nitrification inhibitors. IMPORTANCE Nitrogen is one of the most important elements for all life on Earth. In soil, N is present in various chemical forms and is fiercely competed for by various microorganisms as well as plants. Here, we address competition for reduced N (ammonia) between ammonia-oxidizing prokaryotes and arbuscular mycorrhizal fungi. These two functionally important groups of soil microorganisms, participating in nitrification and plant mineral nutrient acquisition, respectively, have often been studied in separation in the past. Here, we showed, using various biochemical and molecular approaches, that the fungi systematically suppress ammonia-oxidizing bacteria to an extent similar to that of some widely used synthetic nitrification inhibitors, whereas they have only a limited impact on abundance of ammonia-oxidizing archaea. Competition for free ammonium is a plausible explanation here, but it is also possible that the fungi produce some compounds acting as so-called biological nitrification inhibitors.
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Papadopoulou ES, Bachtsevani E, Papazlatani CV, Rousidou C, Brouziotis A, Lampronikou E, Tsiknia M, Vasileiadis S, Ipsilantis I, Menkissoglu-Spiroudi U, Ehaliotis C, Philippot L, Nicol GW, Karpouzas DG. The Effects of Quinone Imine, a New Potent Nitrification Inhibitor, Dicyandiamide, and Nitrapyrin on Target and Off-Target Soil Microbiota. Microbiol Spectr 2022; 10:e0240321. [PMID: 35856708 PMCID: PMC9431271 DOI: 10.1128/spectrum.02403-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Dicyandiamide (DCD) and nitrapyrin (NP) are nitrification inhibitors (NIs) used in agriculture for over 40 years. Recently, ethoxyquin (EQ) was proposed as a novel potential NI, acting through its derivative quinone imine (QI). Still, the specific activity of these NIs on the different groups of ammonia-oxidizing microorganisms (AOM), and mostly their effects on other soil microbiota remain unknown. We determined the impact of QI, and comparatively of DCD and NP, applied at two doses (regular versus high), on the function, diversity, and dynamics of target (AOM), functionally associated (nitrite-oxidizing bacteria-NOB), and off-target prokaryotic and fungal communities in two soils mainly differing in pH (5.4 versus 7.9). QI was equally effective to DCD but more effective than NP in inhibiting nitrification in the acidic soil, while in the alkaline soil QI was less efficient than DCD and NP. This was attributed to the higher activity of QI toward AOA prevailing in the acidic soil. All NIs induced significant effects on the composition of the AOB community in both soils, unlike AOA, which were less responsive. Beyond on-target effects, we noted an inhibitory effect of all NIs on the abundance of NOB in the alkaline soil, with Nitrobacter being more sensitive than Nitrospira. QI, unlike the other NIs, induced significant changes in the composition of the bacterial and fungal communities in both soils. Our findings have serious implications for the efficiency and future use of NIs on agriculture and provide unprecedented evidence for the potential off-target effects of NIs on soil microbiota. IMPORTANCE NIs could improve N use efficiency and decelerate N cycling. Still, we know little about their activity on the distinct AOM groups and about their effects on off-target soil microorganisms. Here, we studied the behavior of a new potent NI, QI, compared to established NIs. We show that (i) the variable efficacy of NIs across soils with different pH reflects differences in the inherent specific activity of the NIs to AOA and AOB; (ii) beyond AOM, NIs exhibit negative effects on other nitrifiers, like NOB; (iii) QI was the sole NI that significantly affected prokaryotic and fungal diversity. Our findings (i) highlight the need for novel NI strategies that consider the variable sensitivity of AOM groups to the different NIs (ii) identify QI as a potent AOA inhibitor, and (iii) stress the need for monitoring NIs' impact on off-target soil microorganisms to ensure sustainable N fertilizers use and soil ecosystem functioning.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
- Laboratory of Environmental Microbiology, Department of Environmental Sciences, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Christina V. Papazlatani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Constantina Rousidou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonios Brouziotis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Myrto Tsiknia
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Ioannis Ipsilantis
- Laboratory of Soil Sciences, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Constantinos Ehaliotis
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Graeme W. Nicol
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, CNRS UMR 5005, Université de Lyon, Lyon, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Lei J, Fan Q, Yu J, Ma Y, Yin J, Liu R. A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria. Front Microbiol 2022; 13:962146. [PMID: 35928162 PMCID: PMC9343776 DOI: 10.3389/fmicb.2022.962146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N2O) and perform the first step of nitrification, but their contribution to N2O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N2O emissions and increased 71.4% of soil NH4+ concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N2O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N2O emissions with NI addition was significantly correlated with AOB changes (R2 = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in NH4+ concentration and AOB amoA gene abundance after NI application (R2 = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.
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Xing G, Lu J, Xuan L, Chen J, Xiong J. Sediment prokaryotic assembly, methane cycling, and ammonia oxidation potentials in response to increasing antibiotic pollution at shrimp aquafarm. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128885. [PMID: 35421673 DOI: 10.1016/j.jhazmat.2022.128885] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 05/28/2023]
Abstract
Antibiotic pollution poses serious threats to public health and ecological processes. However, systematic research regarding the interactive effects of increasing nutrient and antibiotic pollutions on the prokaryotic community, particularly taxa that contribute to greenhouse gas emissions, is lacking. By exploring the complex interactions that occur between interkingdom bacteria and archaea, biotic and abiotic factors, the responses of sediment prokaryotic assembly were determined along a significant antibiotic pollution gradient. Bacterial and archaeal communities were primarily governed by sediment antibiotic pollution, ammonia, phosphate, and redox potential, which further affected enzyme activities. The two communities nonlinearly responded to increasing antibiotic pollution, with significant tipping points of 3.906 and 0.979 mg/kg antibiotics, respectively. The combined antibiotic concentration-discriminatory taxa of bacteria and archaea accurately (98.0% accuracy) diagnosed in situ antibiotic concentrations. Co-abundance analysis revealed that the methanogens, methanotrophs, sulfate-reducing bacteria, and novel players synergistically contributed to methane cycling. Antibiotic pollution caused the dominant role of ammonia-oxidizing archaea in ammonia oxidation at these alkaline sediments. Collectively, the significant tipping points and bio-indicators afford indexes for regime shift and quantitative diagnosis of antibiotic pollution, respectively. Antibiotic pollution could expedite methane cycling and mitigate nitrous oxide yield, which are previously unrecognized ecological effects. These findings provide new insights into the interactive biological and ecological consequences of increasing nutrient and antibiotic pollutions.
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Affiliation(s)
- Guorui Xing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lixia Xuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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Sarkar S, Kamke A, Ward K, Rudick AK, Baer SG, Ran Q, Feehan B, Thapa S, Anderson L, Galliart M, Jumpponen A, Johnson L, Lee STM. Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress. Microbiol Spectr 2022; 10:e0239121. [PMID: 35442065 PMCID: PMC9241903 DOI: 10.1128/spectrum.02391-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species' range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought. IMPORTANCE In this study, we used a 10-year long reciprocal garden system, and reports that different ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii can maintain or recruit distinct bacterial but not fungal rhizobiomes after 10 years in an arid environment. We used both 16S rRNA and ITS2 amplicons to analyze the bacterial and fungal communities in the rhizospheres of the respective ecotypes. We showed that A. gerardii might regulate the bacterial community to adapt to the arid environment, in which some ecotypes were not adapted to. Our study also suggested a possible tradeoff between the generalist and the specialist bacterial communities in specific environments, which could benefit the plant host. Our study will provide insights into the plant host regulation of the rhizosphere bacterial and fungal communities, especially during frequent drought conditions anticipated in the future.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Aoesta K. Rudick
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sara G. Baer
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - QingHong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Brandi Feehan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shiva Thapa
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Lauren Anderson
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Matthew Galliart
- Department of Biological Sciences, Fort Hays State University, Hays, Kansas, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Loretta Johnson
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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Ecological Impacts of Aged Freshwater Biofilms on Estuarine Microbial Communities Elucidated Through Microcosm Experiments: A Microbial Invasion Perspective. Curr Microbiol 2022; 79:210. [PMID: 35666311 DOI: 10.1007/s00284-022-02903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 05/12/2022] [Indexed: 11/03/2022]
Abstract
Inadvertent introductions of alien species via biofilms as a vector released through ballast water are of environmental importance, yet their consequences are not much known. In the present study, biofilm communities developed in an inland freshwater port under in situ and dark conditions were subjected to long-term dark incubations. Subsequently, the impact of these aged biofilms as vectors on estuarine water column communities were evaluated using microcosm experiments in the laboratory. Variations in biofilm and planktonic microbial communities were quantified using quantitative PCR.Upon prolonged dark incubation, a shift in bacterial diversity with an increase in tolerant bacterial communities better adapted to stress was observed. Actinobacteria were the dominant taxa in both aged biofilms upon dark incubations. The laboratory studies indicated that on exposure of these biofilms to estuarine water, resuscitation of Vibrio alginolyticus, V. parahaemolyticus, and V. cholerae from a dormant state existing in these biofilms to culturable form was observed. Moreover, the results revealed that both the biofilm types can pose a threat to the environment, but the degree of risk can be attributed to the imbalance caused by significant changes in the surrounding estuarine microbial communities. Consequently, this may result in either proliferation or decline of some genera with different metabolic potential and resuscitation of pathogenic forms not present earlier, thereby influencing the ecology of the environment. Quantifying these effects in the field using biofilm metagenomes with an emphasis on virulent species and understanding traits that enable them to adapt to changing environments is a way forward.
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Effect of Nitrogen Fertilization on Savvatiano (Vitis vinifera L.) Grape and Wine Composition. BEVERAGES 2022. [DOI: 10.3390/beverages8020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Nitrogen nutrition is one of the most effective cultural practices in vineyards. The vine nitrogen status influences the berries’ quality characteristics and the produced wines. The current study investigated the effect of traditional nitrogen fertilization in the form of ammonium sulfate compared to nitrogen fertilization coupled with the nitrification inhibitor 3,4-Dimethylpyrazole phosphate (DMPP) on the agronomic characteristics of grapes and the produced wines of the white variety Savvatiano from a productive vineyard in the Attiki region. Must and wine quality was evaluated by a chemical analysis and sensorial evaluation by trained panelists. The different forms of nitrogen fertilizers did not significantly affect the aroma and sensory profile in contrast to unfertilized grapevines. In addition, the applied fertilization increased some important aroma compounds in the wine, compared to no fertilization. The significance of this work is to add information about the effect of nitrogen fertilization on the wine volatile composition of the Greek white grapevine Savvatiano.
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22
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Fisk LM, Barton L, Maccarone LD, Jenkins SN, Murphy DV. Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil. Sci Rep 2022; 12:7299. [PMID: 35508560 PMCID: PMC9068766 DOI: 10.1038/s41598-022-10711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
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Affiliation(s)
- L M Fisk
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - L Barton
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - L D Maccarone
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S N Jenkins
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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23
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Shao Q, Sun D, Fang C, Feng Y, Wang C. Biodiversity and Biogeography of Abundant and Rare Microbial Assemblages in the Western Subtropical Pacific Ocean. Front Microbiol 2022; 13:839562. [PMID: 35432250 PMCID: PMC9006148 DOI: 10.3389/fmicb.2022.839562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance-decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Ningbo Institute of Oceanography, Ningbo, China
| | - Dong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chen Fang
- College of Oceanography, Hohai University, Nanjing, China
| | - Yunzhi Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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24
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Hossain S, Chow CWK, Cook D, Sawade E, Hewa GA. Review of Nitrification Monitoring and Control Strategies in Drinking Water System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074003. [PMID: 35409686 PMCID: PMC8997939 DOI: 10.3390/ijerph19074003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Nitrification is a major challenge in chloraminated drinking water systems, resulting in undesirable loss of disinfectant residual. Consequently, heterotrophic bacteria growth is increased, which adversely affects the water quality, causing taste, odour, and health issues. Regular monitoring of various water quality parameters at susceptible areas of the water distribution system (WDS) helps to detect nitrification at an earlier stage and allows sufficient time to take corrective actions to control it. Strategies to monitor nitrification in a WDS require conducting various microbiological tests or assessing surrogate parameters that are affected by microbiological activities. Additionally, microbial decay factor (Fm) is used by water utilities to monitor the status of nitrification. In contrast, approaches to manage nitrification in a WDS include controlling various factors that affect monochloramine decay rate and ammonium substrate availability, and that can inhibit nitrification. However, some of these control strategies may increase the regulated disinfection-by-products level, which may be a potential health concern. In this paper, various strategies to monitor and control nitrification in a WDS are critically examined. The key findings are: (i) the applicability of some methods require further validation using real WDS, as the original studies were conducted on laboratory or pilot systems; (ii) there is no linkage/formula found to relate the surrogate parameters to the concentration of nitrifying bacteria, which possibly improve nitrification monitoring performance; (iii) improved methods/monitoring tools are required to detect nitrification at an earlier stage; (iv) further studies are required to understand the effect of soluble microbial products on the change of surrogate parameters. Based on the current review, we recommend that the successful outcome using many of these methods is often site-specific, hence, water utilities should decide based on their regular experiences when considering economic and sustainability aspects.
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Affiliation(s)
- Sharif Hossain
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Correspondence:
| | - Christopher W. K. Chow
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - David Cook
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Emma Sawade
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Guna A. Hewa
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
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25
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Exploring the Distinct Distribution of Archaeal Communities in Sites Contaminated with Explosives. Biomolecules 2022; 12:biom12040489. [PMID: 35454078 PMCID: PMC9028785 DOI: 10.3390/biom12040489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 01/25/2023] Open
Abstract
Most of the research on bioremediation and estimation of microbial diversity in waste contaminated sites is focused on the domain Bacteria, whereas details on the relevance of Archaea are still lacking. The present study examined the archaeal diversity and predicted metabolic pathways in two discrete sites (SITE1 and SITE2) contaminated with explosives (RDX and HMX) by amplicon-targeted sequencing of 16S rRNA genes. In total, 14 soil samples were processed, and 35,758 OTUs were observed, among which 981 OTUs were classified as Archaea, representing ~2.7% of the total microbial diversity in our samples. The majority of OTUs belonged to phyla Euryarchaeota (~49%), Crenarchaeota (~24%), and Thaumarchaeota (~23%), while the remaining (~4%) OTUs were affiliated to Candidatus Parvarchaeota, Candidatus Aenigmarchaeota, and Candidatus Diapherotrites. The comparative studies between explosives contaminated and agricultural soil samples (with no history of explosives contamination) displayed significant differences between the compositions of the archaeal communities. Further, the metabolic pathways pertaining to xenobiotic degradation were presumably more abundant in the contaminated sites. Our data provide a first comprehensive report of archaeal communities in explosives contaminated sites and their putative degradation role in such ecosystems which have been as yet unexplored.
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26
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Kim J, Heo YM, Yun J, Lee H, Kim JJ, Kang H. Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland. MICROBIAL ECOLOGY 2022; 83:436-446. [PMID: 34003315 DOI: 10.1007/s00248-021-01770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.
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Affiliation(s)
- Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Young Mok Heo
- College of Life Sciences & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hanbyul Lee
- College of Life Sciences & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jae-Jin Kim
- College of Life Sciences & Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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27
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Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
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Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
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28
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Kraft B, Jehmlich N, Larsen M, Bristow LA, Könneke M, Thamdrup B, Canfield DE. Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 2022; 375:97-100. [PMID: 34990242 DOI: 10.1126/science.abe6733] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the world’s oceans and are key players in the nitrogen cycle. Their energy metabolism—the oxidation of ammonia to nitrite—requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. By carrying out incubations for which oxygen concentrations were resolved to the nanomolar range, we show that after oxygen depletion, Nitrosopumilus maritimus produces dinitrogen and oxygen, which is used for ammonia oxidation. The pathway is not completely resolved but likely has nitric oxide and nitrous oxide as key intermediates. N. maritimus joins a handful of organisms known to produce oxygen in the dark. On the basis of this ability, we reevaluate the role of N. maritimus in oxygen-depleted marine environments.
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Affiliation(s)
- Beate Kraft
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research UFZ GmbH, Leipzig, Germany
| | - Morten Larsen
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Martin Könneke
- Marine Archaea Group, Center for Marine Environmental Sciences (MARUM), and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Bo Thamdrup
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Donald E Canfield
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.,Key Laboratory of Petroleum Geochemistry, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, China.,Danish Institute of Advanced Study, University of Southern Denmark, Odense, Denmark
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29
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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30
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Han Y, Zhang M, Chen X, Zhai W, Tan E, Tang K. Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea. ENVIRONMENT INTERNATIONAL 2022; 158:106889. [PMID: 34619534 DOI: 10.1016/j.envint.2021.106889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Eutrophication-induced water deoxygenation occurs continually in coastal oceans, and alters community structure, metabolic processes, and the energy shunt, resulting in a major threat to the ecological environment. Seasonal deoxygenation events have occurred in the Bohai Sea (China), however, how these affect the functional activity of microorganisms remains unclear. Here, through the use of absolute quantification of 16S rRNA genes amplicon sequencing and metatranscriptomics approaches, we investigated the structure of the microbial community and the patterns of transcriptional activity in deoxygenated seawaters. The dominant phyla were Proteobacteria (average value, 1.4 × 106 copies ml-1), Cyanobacteria (3.7 × 105 copies ml-1), Bacteroidetes (2.7 × 105 copies ml-1), and the ammonia-oxidizing archaea Thaumarchaeota (1.9 × 105 copies ml-1). Among the various environmental factors, dissolved oxygen, pH and temperature displayed the most significant correlation with microbial community composition and functional activity. Metatranscriptomic data showed high transcriptional activity of Thaumarchaeota in the deoxygenated waters, with a significant increase in the expression of core genes representing ammonia oxidation, ammonia transport, and carbon fixation (3-hydroxypropionic acid/4-hydroxybutyric acid cycle) pathways. The transcripts of Cyanobacteria involved in photosynthesis and carbon fixation (Calvin-Benson-Bassham cycle) significantly decreased in low oxygen waters. Meanwhile, the transcripts for the ribulose bisphosphate carboxylase-encoding gene shifted from being assigned to photoautotrophic to chemoautotrophic organisms in surface and bottom waters, respectively. Moreover, the transcription profile indicated that heterotrophs play a critical role in transforming low-molecular-weight dissolved organic nitrogen. Elevated abundances of transcripts related to microbial antioxidant activity corresponded to an enhanced aerobic metabolism of Thaumarchaeota in the low oxygen seawater. In general, our transcriptional evidences showed a population increase of Thaumarchaeota, especially the coastal ecotype of ammonia oxidizers, in low oxygen aquatic environments, and indicated an enhanced contribution of chemolithoautotrophic carbon fixation to carbon flow.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Weidong Zhai
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, Shandong, PR China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, Hainan, PR China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China.
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31
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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32
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Destan E, Yuksel B, Tolar BB, Ayan E, Deutsch S, Yoshikuni Y, Wakatsuki S, Francis CA, DeMirci H. Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Sci Rep 2021; 11:22849. [PMID: 34819551 PMCID: PMC8613188 DOI: 10.1038/s41598-021-02180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway.
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Affiliation(s)
- Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Sam Deutsch
- Nutcracker Therapeutics, Inc 5858 Horton Street, Suite 540, Emeryville, CA, 94608, USA
| | - Yasuo Yoshikuni
- The US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, CA, 94305, USA.
- Biosciences Division, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
| | | | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
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Liao X, Chen Y, Ruan H, Malghani S. Incapability of biochar to mitigate biogas slurry induced N 2O emissions: Field investigations after 7 years of biochar application in a poplar plantation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148572. [PMID: 34214806 DOI: 10.1016/j.scitotenv.2021.148572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Nitrous oxide (N2O) is a potent atmospheric greenhouse gas that is largely emitted from soils due to the enhanced use of reactive nitrogen in agriculture and plantations. In this study, we evaluated the N2O mitigation ability of biochar after 7 years of application in a poplar plantation. The field experiment was based on combinations of three biochar (0, 80, and 120 t ha-1) and four biogas slurry (0, 125, 250, and 375 m3 ha-1) rates following a factorial design. N2O flux rates were measured for seven consecutive months using in situ static chambers. Soil physicochemical characteristics, potential nitrification rate (PNR), denitrification (DEA), and N2O reduction were recorded once each in September 2019 and January 2020 via lab incubations. In addition, qPCR assays were used to assess the abundance of key nitrifying and denitrifying functional genes. Biochar application after 7 years had no significant effects on N2O flux rates, PNR, and DEA rates. However, a triggering effect of biogas slurry on soil N2O emission was observed, although there was no correlation between biogas slurry rates and N2O emission rates. Factorial ANOVA showed a significant effect of biogas slurry and its interaction with biochar on the relative abundance of bacterial denitrifying and nitrifying functional genes. Additionally, significant correlations of N2O emission rates with PNR rates and NO3- concentration indicated that nitrification was the dominant pathway of N2O emission. Thus, a single biochar application did not mitigate N2O emission rates induced by biogas slurry on a long-term scale.
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Affiliation(s)
- Xiaolin Liao
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yajuan Chen
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Saadatullah Malghani
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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Kerou M, Ponce-Toledo RI, Zhao R, Abby SS, Hirai M, Nomaki H, Takaki Y, Nunoura T, Jørgensen SL, Schleper C. Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages. THE ISME JOURNAL 2021; 15:2792-2808. [PMID: 33795828 PMCID: PMC8397731 DOI: 10.1038/s41396-021-00962-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/12/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.
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Affiliation(s)
- Melina Kerou
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rafael I. Ponce-Toledo
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rui Zhao
- grid.7914.b0000 0004 1936 7443Department of Earth Science, K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway ,grid.33489.350000 0001 0454 4791Present Address: School of Marine Science and Policy, University of Delaware, Lewes, DE USA
| | - Sophie S. Abby
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria ,grid.463716.10000 0004 4687 1979Present Address: University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Miho Hirai
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hidetaka Nomaki
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- grid.410588.00000 0001 2191 0132Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Steffen L. Jørgensen
- grid.7914.b0000 0004 1936 7443Department of Earth Science, K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Christa Schleper
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
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Liu G, Wu X, Li D, Jiang L, Huang J, Zhuang L. Long-Term Low Dissolved Oxygen Operation Decreases N 2O Emissions in the Activated Sludge Process. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6975-6983. [PMID: 33904707 DOI: 10.1021/acs.est.0c07279] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas and a dominant ozone-depleting substance. Nitrification in the activated sludge process (ASP) is an important N2O emission source. This study demonstrated that a short-term low dissolved oxygen (DO) increased the N2O emissions by six times, while long-term low DO operation decreased the N2O emissions by 54% (P < 0.01). Under long-term low DO, the ammonia oxidizer abundance in the ASP increased significantly, and thus, complete nitrification was recovered and no NH3 or nitrite accumulated. Moreover, long-term low DO decreased the abundance of ammonia-oxidizing bacteria (AOB) by 28%, while increased the abundance of ammonia-oxidizing archaea (AOA) by 507%, mainly due to their higher oxygen affinity. As a result, AOA outnumbered AOB with the AOA/AOB amoA gene ratio increasing to 19.5 under long-term low DO. The efficient nitrification and decreased AOB abundance might not increase N2O production via AOB under long-term low DO conditions. The enriched AOA could decrease the N2O emissions because they were reported to lack canonical nitric oxide (NO) reductase genes that convert NO to N2O. Probably because of AOA enrichment, the positive and significant (P = 0.02) correlation of N2O emission and nitrite concentration became insignificant (P = 0.332) after 80 days of low DO operation. Therefore, ASPs can be operated with low DO and extended sludge age to synchronously reduce N2O production and carbon dioxide emissions owing to lower aeration energy without compromising the nitrification efficiency.
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Affiliation(s)
- Guoqiang Liu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Xianwei Wu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Deyong Li
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Lugao Jiang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Ju Huang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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Liu J, Liu W, Zhang Y, Chen C, Wu W, Zhang TC. Microbial communities in rare earth mining soil after in-situ leaching mining. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142521. [PMID: 33035989 DOI: 10.1016/j.scitotenv.2020.142521] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China.
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, China
| | - Yingbin Zhang
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Tian C Zhang
- Department of Civil & Environmental Engineering, University of Nebraska-Lincoln, Omaha, USA
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38
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Reyes C, Hodgskiss LH, Kerou M, Pribasnig T, Abby SS, Bayer B, Kraemer SM, Schleper C. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. THE ISME JOURNAL 2020; 14:2659-2674. [PMID: 32665710 PMCID: PMC7785015 DOI: 10.1038/s41396-020-0715-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/09/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
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Affiliation(s)
- Carolina Reyes
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Sophie S Abby
- University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Barbara Bayer
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Department of Limnology and Oceanography, Division of Bio-oceanography, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106-9620, USA
| | - Stephan M Kraemer
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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Wang H, Bier R, Zgleszewski L, Peipoch M, Omondi E, Mukherjee A, Chen F, Zhang C, Kan J. Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments. Front Microbiol 2020; 11:576661. [PMID: 33193193 PMCID: PMC7642518 DOI: 10.3389/fmicb.2020.576661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 11/23/2022] Open
Abstract
In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Raven Bier
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | - Laura Zgleszewski
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | - Marc Peipoch
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | | | | | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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40
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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. mBio 2020; 11:mBio.02371-20. [PMID: 33051370 PMCID: PMC7554672 DOI: 10.1128/mbio.02371-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
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Ma M, Wendehenne D, Philippot L, Hänsch R, Flemetakis E, Hu B, Rennenberg H. Physiological significance of pedospheric nitric oxide for root growth, development and organismic interactions. PLANT, CELL & ENVIRONMENT 2020; 43:2336-2354. [PMID: 32681574 DOI: 10.1111/pce.13850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Nitric oxide (NO) is essential for plant growth and development, as well as interactions with abiotic and biotic environments. Its importance for multiple functions in plants means that tight regulation of NO concentrations is required. This is of particular significance in roots, where NO signalling is involved in processes, such as root growth, lateral root formation, nutrient acquisition, heavy metal homeostasis, symbiotic nitrogen fixation and root-mycorrhizal fungi interactions. The NO signal can also be produced in high levels by microbial processes in the rhizosphere, further impacting root processes. To explore these interesting interactions, in the present review, we firstly summarize current knowledge of physiological processes of NO production and consumption in roots and, thereafter, of processes involved in NO homeostasis in root cells with particular emphasis on root growth, development, nutrient acquisition, environmental stresses and organismic interactions.
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Affiliation(s)
- Ming Ma
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, China
| | - David Wendehenne
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Dijon, France
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Dijon, France
| | - Robert Hänsch
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, China
- Institute for Plant Biology, Technische Universität, Braunschweig, Germany
| | - Emmanouil Flemetakis
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, China
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Bin Hu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, China
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Sedlacek CJ. It Takes a Village: Discovering and Isolating the Nitrifiers. Front Microbiol 2020; 11:1900. [PMID: 32849473 PMCID: PMC7431685 DOI: 10.3389/fmicb.2020.01900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.
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Affiliation(s)
- Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Wu L, Chen X, Wei W, Liu Y, Wang D, Ni BJ. A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9175-9190. [PMID: 32657581 DOI: 10.1021/acs.est.0c03948] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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Wang X, Wang S, Jiang Y, Zhou J, Han C, Zhu G. Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138563. [PMID: 32334221 DOI: 10.1016/j.scitotenv.2020.138563] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 05/27/2023]
Abstract
The newly identified complete ammonia oxidation (comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented our knowledge of nitrification in the global nitrogen (N) cycle. However, understanding the contribution and ecological roles of comammox in complex soil environments is still in its infancy. Here, the community structure and function of comammox and the interactions with other ammonia oxidation processes in rhizosphere and non-rhizosphere soils of four different crop fields (maize, cotton, soybean, and millet) were investigated in summer and winter. The only identified comammox species Candidatus Nitrospira nitrificans was widely distributed in all sampled soils. Comammox bacterial abundance was lower than that of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). The measured comammox potential rate ranged from 0.01 ± 0.002 to 0.40 ± 0.02 mg N kg-1 d-1, contributing <19.2 and 22.1% to ammonia oxidation in summer and winter, the remainder being due to AOA and AOB. The potential rate and community composition of comammox bacteria were significantly different on a temporal scale, while crop species and soil types (rhizosphere and non-rhizosphere) showed no obvious influences. In terms of oxidation rates, AOA (1.2 ± 0.7 mg N kg-1 d-1) dominated the ammonia oxidation in agricultural soils over AOB (0.31 ± 0.1 mg N kg-1 d-1) and comammox (0.2 ± 0.1 mg N kg-1 d-1). Both anammox bacterial abundance and activity were below the detection limits, indicating a negligible contribution of anammox in agricultural rhizosphere soils. The identification of comammox bacterial abundance and activity in situ enriches our knowledge of nitrification in agricultural systems.
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Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yingying Jiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiemin Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chang Han
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhong S, Chen Q, Hu J, Liu S, Qiao S, Ni J, Sun W. Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments. J Appl Microbiol 2020; 129:1657-1673. [PMID: 32533753 DOI: 10.1111/jam.14742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/20/2020] [Accepted: 06/03/2020] [Indexed: 01/30/2023]
Abstract
AIMS This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors. METHODS AND RESULTS We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables. CONCLUSIONS Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum. SIGNIFICANCE AND IMPACT OF THE STUDY Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.
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Affiliation(s)
- S Zhong
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Q Chen
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - J Hu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - S Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - S Qiao
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - J Ni
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - W Sun
- State Key Lab Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People's Republic of China
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Martínez-Espinosa RM. Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments. Int J Mol Sci 2020; 21:ijms21124228. [PMID: 32545812 PMCID: PMC7349289 DOI: 10.3390/ijms21124228] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/12/2020] [Indexed: 12/23/2022] Open
Abstract
Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; ; Tel.: +34-965903400 (ext. 1258)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Potgieter SC, Dai Z, Venter SN, Sigudu M, Pinto AJ. Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs. mSphere 2020; 5:e00274-20. [PMID: 32350093 PMCID: PMC7193043 DOI: 10.1128/msphere.00274-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023] Open
Abstract
Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas) and nitrite-oxidizing bacteria (i.e., Nitrospira) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira-like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas, and Rhizobiales-like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems.IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems.
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Affiliation(s)
- Sarah C Potgieter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Zihan Dai
- Infrastructure and Environment Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Ameet J Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, USA
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Zhang E, Thibaut LM, Terauds A, Raven M, Tanaka MM, van Dorst J, Wong SY, Crane S, Ferrari BC. Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases. MICROBIOME 2020; 8:37. [PMID: 32178729 PMCID: PMC7076931 DOI: 10.1186/s40168-020-00809-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of biodiversity and the niche-neutral processes underlying these communities remain unclear. In this study, we combine multivariate analyses, co-occurrence networks and fitted species abundance distributions on an extensive set of bacterial, micro-eukaryote and archaeal amplicon sequencing data to unravel soil microbiome patterns of nine sites across two east Antarctic regions, the Vestfold Hills and Windmill Islands. To our knowledge, this is the first microbial biodiversity report on the hyperarid Vestfold Hills soil environment. RESULTS Our findings reveal distinct regional differences in phylogenetic composition, abundance and richness amongst microbial taxa. Actinobacteria dominated soils in both regions, yet Bacteroidetes were more abundant in the Vestfold Hills compared to the Windmill Islands, which contained a high abundance of novel phyla. However, intra-region comparisons demonstrate greater homogeneity of soil microbial communities and measured environmental parameters between sites at the Vestfold Hills. Community richness is largely driven by a variable suite of parameters but robust associations between co-existing members highlight potential interactions and sharing of niche space by diverse taxa from all three microbial domains of life examined. Overall, non-neutral processes appear to structure the polar soil microbiomes studied here, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. Eukaryotic and archaeal communities reveal weaker niche-driven signatures accompanied by multimodality, suggesting the emergence of neutrality. CONCLUSION We provide new information on assemblage patterns, environmental drivers and non-random occurrences for Antarctic soil microbiomes, particularly the Vestfold Hills, where basic diversity, ecology and life history strategies of resident microbiota are largely unknown. Greater understanding of these basic ecological concepts is a pivotal step towards effective conservation management.
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Affiliation(s)
- Eden Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Loïc M Thibaut
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Aleks Terauds
- Australian Antarctic Division, Department of Environment, Antarctic Conservation and Management, 203 Channel Highway, Kingston, TAS, 7050, Australia
| | - Mark Raven
- Commonwealth Scientific and Industrial Research Organisation, Mineralogical Services, Urrbrae, SA, 5064, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sin Yin Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sally Crane
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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50
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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