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Aguilar-Rangel EJ, Savin-Gámez A, García-Maldonado JQ, Prado B, Vásquez-Murrieta MS, Siebe C, Alcántara-Hernández RJ. Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater. PLoS One 2024; 19:e0299518. [PMID: 38603769 PMCID: PMC11008854 DOI: 10.1371/journal.pone.0299518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 04/13/2024] Open
Abstract
Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.
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Affiliation(s)
- Eduardo J. Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - Alba Savin-Gámez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - José Q. García-Maldonado
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Merida 97310, Yucatán, México
| | - Blanca Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340, Ciudad de México, México
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - Rocío J. Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
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Deng N, Gubry-Rangin C, Song XT, Ju XT, Liu SY, Shen JP, Di HJ, Han LL, Zhang LM. AOB Nitrosospira cluster 3a.2 (D11) dominates N 2O emissions in fertilised agricultural soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120504. [PMID: 38447513 DOI: 10.1016/j.jenvman.2024.120504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.
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Affiliation(s)
- Na Deng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xiao-Tong Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Xiao-Tang Ju
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Ju-Pei Shen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Hong-Jie Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Xiang Y, Zhou T, Deng S, Shao Z, Liu Y, He Q, Chai H. Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process. WATER RESEARCH X 2023; 21:100204. [PMID: 38098882 PMCID: PMC10719579 DOI: 10.1016/j.wroa.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.
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Affiliation(s)
- Yu Xiang
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, China
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Tengzhi Zhou
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Siping Deng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Zhiyu Shao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yiwen Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Qiang He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
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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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5
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Farmer M, Rajasabhai R, Tarpeh W, Tyo K, Wells G. Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes. Front Microbiol 2023; 14:1287491. [PMID: 38033562 PMCID: PMC10687191 DOI: 10.3389/fmicb.2023.1287491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.
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Affiliation(s)
- McKenna Farmer
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Rashmi Rajasabhai
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - William Tarpeh
- Chemical Engineering, Stanford University, Stanford, CA, United States
| | - Keith Tyo
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - George Wells
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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6
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Bhardwaj L, Reddy B, Dubey SK. Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem. ENVIRONMENTAL RESEARCH 2023; 237:117033. [PMID: 37660873 DOI: 10.1016/j.envres.2023.117033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha-1, respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.
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Affiliation(s)
- Laliteshwari Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Bhaskar Reddy
- Virus Research and Diagnostic Laboratory, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh-9, 201310, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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7
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Xue Y, Zheng M, Cheng Z, Li S, Yang S, Liu Y, Qian Y, Huang X. Dynamic Simulation of Nitrifying Microbial Communities for Establishing Acidic Partial Nitritation in Suspended Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17542-17552. [PMID: 37909179 DOI: 10.1021/acs.est.3c01282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Acidic partial nitritation (PN) is a promising technology to achieve low-cost and energy-efficient shortcut nitrogen removal from wastewater. However, a comprehensive understanding of the acidic PN under dynamic changes of pH in a sequencing batch reactor (SBR) is still lacking. In this study, we successfully established acidic PN (NO2- accumulation ratio >80%) under dynamic pH variation from 7.0 to 4.5 in a lab-scale SBR. By accumulating in situ free nitrous acid (FNA) generation based on the dynamic pH change, acidic PN maintained stability even at a low NH4+ concentration of 100 mg N L-1. The microbial community analysis revealed that two ammonium-oxidizing bacteria (AOB) genera, Nitrosospira and Nitrosomonas, successfully coexisted and cooperated during acidic PN. None of the species of nitrite-oxidizing bacteria (NOB) showed adaptation to intermittent inhibition of in situ FNA even under high DO conditions (>4.0 mg O2 L-1). Furthermore, we innovatively incorporated the classic nitrification model with the growth and decay of different nitrifying bacterial species and their inhibition by pH, FNA, and free ammonia (FA) to predict the nitrifying microbial communities shifting for establishing acidic PN. The extended model was calibrated by using short-term batch experiments and was validated by using long-term dynamic data of the nitrifying microbial community during SBR operation. The validated model was further used to identify feasible influent conditions for the SBR PN process, including influent HCO3- concentration, NH4+ concentration and molar ratio (HCO3/NH4+). Outcomes from this study support the optimal design of acidic PN-based short-cut nitrogen removal processes for future application.
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Affiliation(s)
- Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Zhao Cheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Siqi Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shaolin Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yi Qian
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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8
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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9
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [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: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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10
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Newberger DR, Minas IS, Manter DK, Vivanco JM. A Microbiological Approach to Alleviate Soil Replant Syndrome in Peaches. Microorganisms 2023; 11:1448. [PMID: 37374950 DOI: 10.3390/microorganisms11061448] [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: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Replant syndrome (RS) is a global problem characterized by reduced growth, production life, and yields of tree fruit/nut orchards. RS etiology is unclear, but repeated monoculture plantings are thought to develop a pathogenic soil microbiome. This study aimed to evaluate a biological approach that could reduce RS in peach (Prunus persica) orchards by developing a healthy soil bacteriome. Soil disinfection via autoclave followed by cover cropping and cover crop incorporation was found to distinctly alter the peach soil bacteriome but did not affect the RS etiology of RS-susceptible 'Lovell' peach seedlings. In contrast, non-autoclaved soil followed by cover cropping and incorporation altered the soil bacteriome to a lesser degree than autoclaving but induced significant peach growth. Non-autoclaved and autoclaved soil bacteriomes were compared to highlight bacterial taxa promoted by soil disinfection prior to growing peaches. Differential abundance shows a loss of potentially beneficial bacteria due to soil disinfection. The treatment with the highest peach biomass was non-autoclaved soil with a cover crop history of alfalfa, corn, and tomato. Beneficial bacterial species that were cultivated exclusively in the peach rhizosphere of non-autoclaved soils with a cover crop history were Paenibacillus castaneae and Bellilinea caldifistulae. In summary, the non-autoclaved soils show continuous enhancement of beneficial bacteria at each cropping phase, culminating in an enriched rhizosphere which may help alleviate RS in peaches.
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Affiliation(s)
- Derek R Newberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA
| | - Ioannis S Minas
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel K Manter
- Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO 80526, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA
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Zhang Q, Chen M, Leng Y, Wang X, Fu Y, Wang D, Zhao X, Gao W, Li N, Chen X, Fan C, Li Q. Organic substitution stimulates ammonia oxidation-driven N 2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162183. [PMID: 36804975 DOI: 10.1016/j.scitotenv.2023.162183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/01/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.
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Affiliation(s)
- Qi Zhang
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miao Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Youfeng Leng
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; College of Eco-environment Engineering, Guizhou Minzu University, Guiyang 550025, China
| | - Xiaotong Wang
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yajun Fu
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Danfeng Wang
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiongwei Zhao
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenlong Gao
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Ning Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Xin Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Changhua Fan
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China.
| | - Qinfen Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China.
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12
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Nagar S, Bharti M, Negi RK. Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 2023; 107:3273-3289. [PMID: 37052633 DOI: 10.1007/s00253-023-12503-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/18/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023]
Abstract
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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13
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Cleary DFR, Oliveira V, Gomes NCM, Bialecki A, de Voogd NJ. A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges. FEMS Microbiol Ecol 2023; 99:7033423. [PMID: 36758964 PMCID: PMC10022632 DOI: 10.1093/femsec/fiad014] [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: 09/22/2022] [Revised: 01/16/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.
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Affiliation(s)
- D F R Cleary
- Corresponding author. Institute of Environmental Sciences, CML, Leiden University Einsteinweg 2, 2333 CC Leiden, The Netherlands. E-mail:
| | - V Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - N C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - A Bialecki
- Laboratoire de Chimie et de Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France
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14
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Lead or cadmium co-contamination alters benzene and toluene degrading bacterial communities. Biodegradation 2023; 34:357-369. [PMID: 36840890 DOI: 10.1007/s10532-023-10021-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023]
Abstract
Co-contamination of hydrocarbons with heavy metals in soils often complicates and hinders bioremediation. A comprehensive characterization of site-specific degraders at contaminated sites can help determine if in situ bioremediation processes are sufficient. This study aimed to identify differences in benzene and toluene degradation rates and the microbial communities enriched under aerobic conditions when different concentrations of Cd and Pb are introduced. Microcosms were used to study the degradation of 0.23 mM benzene or 0.19 mM toluene under various concentrations of Pb (up to 240 µM) and Cd (up to 440 µM). Soil collected from a stormwater retention basin receiving runoff from a large parking lot was utilized to seed the microcosms. The hydrocarbon degradation time and rates were measured. After further rounds of amendment and degradation of benzene and toluene, 16S rRNA gene amplicon sequencing and quantitative PCR were used to ascertain the microbial communities enriched under the various concentrations of the heavy metals. The initial degradation time for toluene and benzene was 7 to 9 days and 10 to 13 days, respectively. Degradation rates were similar for each hydrocarbon despite the concentration and presence of metal co-contaminant, however, the enriched microbial communities under each condition differed. Microcosms without metal co-contaminant contained a diversity of putative benzene and toluene degrading bacteria. Cd strongly reduced the richness of the microbial communities. With higher levels of heavy metals, genera such as Ralstonia, Cupriavidus, Azoarcus, and Rhodococcus became more dominant under various conditions. The study finds that highly efficient benzene- and toluene-degrading consortia can develop under variations of heavy metal co-contamination, but the consortia are dependent on the heavy metal type and concentrations.
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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Ribeiro B, Padua A, Oliveira BFRD, Puccinelli G, da Costa Fernandes F, Laport MS, Klautau M. Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges. MICROBIAL ECOLOGY 2023; 85:737-746. [PMID: 35234997 DOI: 10.1007/s00248-022-01980-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.
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Affiliation(s)
- Bárbara Ribeiro
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | - André Padua
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
- Departamento de Biologia Animal, Instituto de Ciências Biológicas E da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, 23897000, Brazil
| | - Bruno Francesco Rodrigues de Oliveira
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, 24210130, Brazil
| | - Gabriela Puccinelli
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | | | - Marinella Silva Laport
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | - Michelle Klautau
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil.
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Liang D, Bowatte S. Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone. Front Microbiol 2022; 13:1036897. [PMID: 36523826 PMCID: PMC9744808 DOI: 10.3389/fmicb.2022.1036897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Ammonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question. METHODS Metabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil. RESULTS AND DISCUSSION We found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed. CONCLUSION These results suggest seed vectored AOB may play a critical role in N cycle.
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Affiliation(s)
- Danni Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Saman Bowatte
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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18
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Xu Y, Wang N, Peng L, Li S, Liang C, Song K, Song S, Zhou Y. Free Nitrous Acid Inhibits Atenolol Removal during the Sidestream Partial Nitritation Process through Regulating Microbial-Induced Metabolic Types. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11614-11624. [PMID: 35900075 DOI: 10.1021/acs.est.1c08845] [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] [Indexed: 06/15/2023]
Abstract
Limited studies have attempted to evaluate pharmaceutical removal during the sidestream partial nitritation (PN) process. In this work, atenolol biodegradation by PN cultures was investigated by maintaining ammonium and pH at different levels. For the first time, free nitrous acid (FNA), other than ammonium, pH, and free ammonia, was demonstrated to inhibit atenolol removal, with biodegradation efficiencies of ∼98, ∼67, and ∼28% within 6 days at average FNA levels of 0, 0.03, and 0.19 mg-N L-1, respectively. Ammonia-oxidizing bacteria (AOB)-induced metabolism was predominant despite varying FNA concentrations. In the absence of ammonium/FNA, atenolol was mostly biodegraded via AOB-induced metabolism (65%) and heterotroph-induced metabolism (33%). AOB-induced metabolism was largely inhibited (down to 29%) at 0.03 mg-N L-1 FNA, while ∼27 and ∼11% were degraded via heterotroph-induced metabolism and AOB-induced cometabolism, respectively. Higher FNA (0.19 mg-N L-1) substantially reduced atenolol biodegradation via heterotroph-induced metabolism (4%), AOB-induced metabolism (16%), and AOB-induced cometabolism (8%). Newly identified products and pathways were related to metabolic types and FNA levels: (i) deamination and decarbonylation (AOB-induced cometabolism, 0.03 mg-N L-1 FNA); (ii) deamination from atenolol acid (heterotrophic biodegradation); and (iii) nitro-substitution (reaction with nitrite). This suggests limiting FNA to realize simultaneous nitrogen and pharmaceutical removal during the sidestream process.
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Affiliation(s)
- Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Ning Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Shengjun Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Chuanzhou Liang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Yan Zhou
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
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Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method. mSphere 2022; 7:e0032422. [PMID: 35938727 PMCID: PMC9429940 DOI: 10.1128/msphere.00324-22] [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] [Indexed: 01/04/2023] Open
Abstract
Until recently, the de facto method for short-read-based amplicon reconstruction was a sequence similarity threshold approach (operational taxonomic units [OTUs]). This has changed with the amplicon sequence variant (ASV) method where distributions are fitted to abundance profiles of individual genes using a noise-error model. While OTU-based approaches are still useful for 16S rRNA/18S rRNA genes, where thresholds of 97% to 99% are used, their use for functional genes is still debatable as there is no consensus on clustering thresholds. Here, we compare OTU- and ASV-based reconstruction approaches and taxonomy assignment methods, the naive Bayesian classifier (NBC) and Bayesian lowest common ancestor (BLCA) algorithm, using a functional gene data set from the microbial nitrogen-cycling community in the Brouage mudflat (France). A range of OTU similarity thresholds and ASVs were used to compare amoA (ammonia-oxidizing archaea [AOA] and ammonia-oxidizing bacteria [AOB]), nxrB, nirS, nirK, and nrfA communities between differing sedimentary structures. Significant effects of the sedimentary structure on weighted UniFrac (WUniFrac) distances were observed for AOA amoA when using ASVs, an OTU at a threshold of 97% sequence identity (OTU-97%), and OTU-85%; AOB amoA when using OTU-85%; and nirS when using ASV, OTU-90%, and OTU-85%. For AOB amoA, significant effects of the sedimentary structures on UniFrac distances were observed when using OTU-97% but not ASVs, and the inverse was found for nrfA. Interestingly, conclusions drawn for nirK and nxrB were consistent between amplicon reconstruction methods. We also show that when the sequences in the reference database are related to the environment in question, the BLCA algorithm leads to more phylogenetically relevant classifications. However, when the reference database contains sequences more dissimilar to the ones retrieved, the NBC obtains more information. IMPORTANCE Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets. In this paper, we argue that the recently developed ASV approach offers a better opportunity to achieve such standardization than OTUs for functional genes. We also propose a comprehensive framework for quality filtering of the sequencing reads based on protein sequence verification.
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Jiang C, Wang X, Wang H, Xu S, Zhang W, Meng Q, Zhuang X. Achieving Partial Nitritation by Treating Sludge With Free Nitrous Acid: The Potential Role of Quorum Sensing. Front Microbiol 2022; 13:897566. [PMID: 35572707 PMCID: PMC9095614 DOI: 10.3389/fmicb.2022.897566] [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: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Partial nitritation is increasingly regarded as a promising biological nitrogen removal process owing to lower energy consumption and better nitrogen removal performance compared to the traditional nitrification process, especially for the treatment of low carbon wastewater. Regulating microbial community structure and function in sewage treatment systems, which are mainly determined by quorum sensing (QS), by free nitrous acid (FNA) to establish a partial nitritation process is an efficient and stable method. Plenty of research papers reported that QS systems ubiquitously existed in ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), and various novel nitrogen removal processes based on partial nitritation were successfully established using FNA. Although the probability that partial nitritation process might be achieved by the regulation of FNA on microbial community structure and function through the QS system was widely recognized and discussed, the potential role of QS in partial nitritation achievement by FNA and the regulation mechanism of FNA on QS system have not been reviewed. This article systematically reviewed the potential role of QS in the establishment of partial nitritation using FNA to regulate activated sludge flora based on the summary and analysis of the published literature for the first time, and future research directions were also proposed.
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Affiliation(s)
- Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xu Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Huacai Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Shengjun Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Qingjie Meng
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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21
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Taylor AE, Mellbye BL. Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature. Front Microbiol 2022; 13:817986. [PMID: 35620102 PMCID: PMC9127996 DOI: 10.3389/fmicb.2022.817986] [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: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.
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Affiliation(s)
- Anne E. Taylor
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Brett L. Mellbye
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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22
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Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. mBio 2022; 13:e0237921. [PMID: 35435701 PMCID: PMC9239080 DOI: 10.1128/mbio.02379-21] [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] [Indexed: 11/27/2022] Open
Abstract
Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.
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23
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Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. THE ISME JOURNAL 2022; 16:958-971. [PMID: 34743174 PMCID: PMC8941013 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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24
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Duhan N, Norton JM, Kaundal R. deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning. Brief Bioinform 2022; 23:6553605. [PMID: 35325031 DOI: 10.1093/bib/bbac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 11/12/2022] Open
Abstract
Nitrogen is essential for life and its transformations are an important part of the global biogeochemical cycle. Being an essential nutrient, nitrogen exists in a range of oxidation states from +5 (nitrate) to -3 (ammonium and amino-nitrogen), and its oxidation and reduction reactions catalyzed by microbial enzymes determine its environmental fate. The functional annotation of the genes encoding the core nitrogen network enzymes has a broad range of applications in metagenomics, agriculture, wastewater treatment and industrial biotechnology. This study developed an alignment-free computational approach to determine the predicted nitrogen biochemical network-related enzymes from the sequence itself. We propose deepNEC, a novel end-to-end feature selection and classification model training approach for nitrogen biochemical network-related enzyme prediction. The algorithm was developed using Deep Learning, a class of machine learning algorithms that uses multiple layers to extract higher-level features from the raw input data. The derived protein sequence is used as an input, extracting sequential and convolutional features from raw encoded protein sequences based on classification rather than traditional alignment-based methods for enzyme prediction. Two large datasets of protein sequences, enzymes and non-enzymes were used to train the models with protein sequence features like amino acid composition, dipeptide composition (DPC), conformation transition and distribution, normalized Moreau-Broto (NMBroto), conjoint and quasi order, etc. The k-fold cross-validation and independent testing were performed to validate our model training. deepNEC uses a four-tier approach for prediction; in the first phase, it will predict a query sequence as enzyme or non-enzyme; in the second phase, it will further predict and classify enzymes into nitrogen biochemical network-related enzymes or non-nitrogen metabolism enzymes; in the third phase, it classifies predicted enzymes into nine nitrogen metabolism classes; and in the fourth phase, it predicts the enzyme commission number out of 20 classes for nitrogen metabolism. Among all, the DPC + NMBroto hybrid feature gave the best prediction performance (accuracy of 96.15% in k-fold training and 93.43% in independent testing) with an Matthews correlation coefficient (0.92 training and 0.87 independent testing) in phase I; phase II (accuracy of 99.71% in k-fold training and 98.30% in independent testing); phase III (overall accuracy of 99.03% in k-fold training and 98.98% in independent testing); phase IV (overall accuracy of 99.05% in k-fold training and 98.18% in independent testing), the DPC feature gave the best prediction performance. We have also implemented a homology-based method to remove false negatives. All the models have been implemented on a web server (prediction tool), which is freely available at http://bioinfo.usu.edu/deepNEC/.
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Affiliation(s)
- Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA
| | - Jeanette M Norton
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA.,Bioinformatics Facility, Center for Integrated BioSystems, UT 84322 USA.,Department of Computer Science, College of Science; Utah State University, Logan, UT 84322 USA
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25
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Wang Y, Shi X, Huang X, Huang C, Wang H, Yin H, Shao Y, Li P. Linking microbial community composition to farming pattern in selenium-enriched region: Potential role of microorganisms on Se geochemistry. J Environ Sci (China) 2022; 112:269-279. [PMID: 34955211 DOI: 10.1016/j.jes.2021.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 06/14/2023]
Abstract
Selenium (Se) is an essential micronutrient for lives. Indigenous microbial communities play an important role on Se geochemistry in soils. In this study, the microbial community composition and functions of 53 soil samples were investigated using high-throughput sequencing. Samples were divided into 3 groups with different farming types based on the measured geochemical parameters and microbial functional structures. Results indicated that putative Se related bacteria Bacillus, Dyella, Paenibacillus, Burkholderia and Brevibacillus were dominant in dryland plantation soils which were characterized with higher available Se and low contents of H2O, total organic carbon (TOC), NH4+ and NO2-. In contrast, the putative denitrifier Pseudomonas dominated in flooded paddy soils with higher TOC, NO3- and organic Se, whereas genera Rhizobium, Nitrosospira, and Geobacter preferred woodland soils with higher oxidation-reduction potential (ORP), pH, NH4+ and Fe. Farming patterns resulted in distinct geochemical parameters including moisture, pH, ORP, TOC, and contents of soluble Fe, NO2- and NH4+, shaping the microbial communities, which in turn affected Se forms in soils. This study provides a valuable insight into understanding of Se biogeochemistry in soils and prospective strategy for Se-rich agriculture production.
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Affiliation(s)
- Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xinyan Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xianxin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Chunlei Huang
- Zhejiang Institute of Geological Survey, Hangzhou 311203, China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hanqin Yin
- Zhejiang Institute of Geological Survey, Hangzhou 311203, China
| | - Yixian Shao
- Zhejiang Institute of Geological Survey, Hangzhou 311203, China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.
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26
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Li H, Wang N, Ding J, Liu Y, Ding X, Wei Y, Li J, Ding GC. Spatial Distribution of the Pepper Blight ( Phytophthora capsici) Suppressive Microbiome in the Rhizosphere. FRONTIERS IN PLANT SCIENCE 2022; 12:748542. [PMID: 35126404 PMCID: PMC8813743 DOI: 10.3389/fpls.2021.748542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.
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Affiliation(s)
- Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Tangshan Normal University, Tangshan, China
| | - Ning Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Jia Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Yingjie Liu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Yuquan Wei
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Guo-chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
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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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Bae WB, Park Y, Chandran K, Shin J, Kang SB, Wang J, Kim YM. Temporal triggers of N 2O emissions during cyclical and seasonal variations of a full-scale sequencing batch reactor treating municipal wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149093. [PMID: 34303238 DOI: 10.1016/j.scitotenv.2021.149093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
To investigate the major triggers of nitrous oxide (N2O) production in a full-scale wastewater treatment plant, N2O emissions and wastewater characteristics (ammonia, nitrite, nitrate, total nitrogen, dissolved inorganic carbon, dissolved organic carbon, pH, temperature, dissolved oxygen and specific oxygen uptake rate), the results of variations in the cycling of a sequential batch reactor (SBR, where only full nitrification was performed), were monitored seasonally for 16 months. Major triggers of N2O production were investigated based on a seasonal measured database using a random forest (RF) model and sensitivity analysis, which was applied to identify important input variables. As the result of seasonal monitoring in the full-scale SBR, the N2O emission factor relative to daily total nitrogen removal ranged from 0.05 to 2.68%, corresponding to a range of N2O production rate from 0.02 to 0.70 kg-N/day. Results from the RF model and sensitivity analysis revealed that emissions during nitrification were directly or indirectly related to nitrite accumulation, temperature, ammonia loading rate and the specific oxygen uptake rate ratio between ammonia oxidizing bacteria and nitrite oxidizing bacteria (sOUR-ratio). However, changes in the microbial community did not significantly impact N2O emissions. Based on these results, the sOUR-ratio could represent the major trigger for N2O emission in a full-scale BNR system: a higher sOUR-ratio value with an average of 3.13 ± 0.23 was linked to a higher N2O production rate with an average value of 1.27 ± 0.12 kg-N/day (corresponding to 3.96 ± 1.20% of N2O emission factor relative to daily TN removal), while a lower sOUR-ratio with an average value of 2.39 ± 0.27 was correlated with a lower N2O production average rate of 0.17 ± 0.11 kg-N/day (corresponding to 0.74 ± 0.69% of N2O emission factor) (p-value = 0.00001, Mann-Whitney test).
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Affiliation(s)
- Wo Bin Bae
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-Gwagiro, Gwangju 61005, Republic of Korea
| | - Yongeun Park
- School of Civil and Environmental Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University in the City of New York, New York, NY 10027, USA
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Sung Bong Kang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-Gwagiro, Gwangju 61005, Republic of Korea
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
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29
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Chawley P, Rana A, Jagadevan S. Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review. Crit Rev Biotechnol 2021; 42:931-952. [PMID: 34641754 DOI: 10.1080/07388551.2021.1976099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.
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Affiliation(s)
- Parmita Chawley
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Anu Rana
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
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30
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Wang X, Bai J, Xie T, Wang W, Zhang G, Yin S, Wang D. Effects of biological nitrification inhibitors on nitrogen use efficiency and greenhouse gas emissions in agricultural soils: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112338. [PMID: 34015632 DOI: 10.1016/j.ecoenv.2021.112338] [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: 01/29/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
To maintain and increase crop yields, large amounts of nitrogen fertilizers have been applied to farmland. However, the nitrogen use efficiency (NUE) of chemical fertilizer remains very low, which may lead to serious environmental problems, including nitrate pollution, air quality degradation and greenhouse gas (GHG) emissions. Nitrification inhibitors can alleviate nitrogen loss by inhibiting nitrification; thus, biological nitrification inhibition by plants has gradually attracted increasing attention due to its low cost and environmental friendliness. Research progress on BNI is reviewed in this article, including the source, mechanisms, influencing factors and application of BNIs. In addition, the impact of BNI on agriculture and GHG emissions is summarized from the perspective of agricultural production and environmental protection, and the key future research prospects of BNIs are also noted.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Tian Xie
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Shuo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dawei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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31
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Wang N, Gao J, Liu Y, Wang Q, Zhuang X, Zhuang G. Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review. CHEMOSPHERE 2021; 274:129970. [PMID: 33979914 DOI: 10.1016/j.chemosphere.2021.129970] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhao ZC, Xie GJ, Liu BF, Xing DF, Ding J, Han HJ, Ren NQ. A review of quorum sensing improving partial nitritation-anammox process: Functions, mechanisms and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142703. [PMID: 33069466 DOI: 10.1016/j.scitotenv.2020.142703] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Partial nitritation-anammox (PNA) is a promising and energy-efficient process for the sustainable nitrogen removal. However, its wide applications are still limited by the long start-up period and instability of long-term operation. Quorum sensing (QS), as a way of cell-to-cell communication generally regulating various microbial behaviors, has been increasingly investigated in PNA process, because QS may substantially manipulate the metabolism of microorganisms and overcome the limitations of PNA process. This critical review provides a comprehensive analysis of QS in PNA systems, and identifies the challenges and opportunities for the optimization of PNA process based on QS. The analysis is grouped based on the configurations of PNA process, including partial nitritation, anammox and single-stage PNA systems. QS is confirmed to regulate various properties of PNA systems, including microbial activity, microbial growth rate, microbial aggregation, microbial interactions and the robustness under adverse conditions. Major challenges in the mechanisms of QS, such as QS circuits, target genes and the response to environmental inputs, are identified. Potential applications of QS, such as short-term addition of certain acyl-homoserine lactones (AHLs) or substances containing AHLs, transient unfavorable conditions to stimulate the secretion of AHLs, are also proposed. This review focuses on the theoretical and practical cognation for QS in PNA systems, and serves as a stepping stone for further QS-based strategies to enhance nitrogen removal through PNA process.
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Affiliation(s)
- Zhi-Cheng Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hong-Jun Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, 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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Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
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Hu H, Luo F, Liu Y, Zeng X. Function of quorum sensing and cell signaling in wastewater treatment systems. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:515-531. [PMID: 33600358 DOI: 10.2166/wst.2020.601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Quorum sensing (QS) is a communication mode between microorganisms to regulate bacteria ecological relations and physiological behaviors, thus achieve the physiological function that single bacteria cannot complete. This phenomenon plays important roles in the formation of biofilm and granular sludge, and may be related to enhancement of some functional bacteria activity in wastewater treatment systems. There is a need to better understand bacterial QS in engineered reactors, and to assess how designs and operations might improve the removal efficiency. This article reviewed the recent advances of QS in several environmental systems and mainly analyzed the regulation mechanism of QS-based strategies for biofilm, granular sludge, functional bacteria, and biofouling control. The co-existences of multiple signal molecules in wastewater treatment (WWT) processes were also summarized, which provide basis for the future research on the QS mechanism of multiple signal molecules' interaction in WWT. This review would present some prospects and suggestions which are of practical significance for further application.
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Affiliation(s)
- Huizhi Hu
- Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China; Hubei Key Laboratory of Regional Development and Environmental Response, Wuhan 430062, China
| | - Feng Luo
- Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China
| | - Yirong Liu
- Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China
| | - Xiangguo Zeng
- Wuhan planning and design co., LTD, Wuhan 430010, China E-mail:
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Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A. Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO 2, but strongly affected by drought. THE ISME JOURNAL 2020; 14:3038-3053. [PMID: 32770119 PMCID: PMC7784676 DOI: 10.1038/s41396-020-00735-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.
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Affiliation(s)
- Joana Séneca
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christos Zioutis
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Eva Simon
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Altirdning 11, 8952, Irdning, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Wolfgang Wanek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
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Papadopoulou ES, Bachtsevani E, Lampronikou E, Adamou E, Katsaouni A, Vasileiadis S, Thion C, Menkissoglu-Spiroudi U, Nicol GW, Karpouzas DG. Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates. Front Microbiol 2020; 11:581283. [PMID: 33250872 PMCID: PMC7672009 DOI: 10.3389/fmicb.2020.581283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Adamou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Katsaouni
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Cécile Thion
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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Performance and Microbial Community of Different Biofilm Membrane Bioreactors Treating Antibiotic-Containing Synthetic Mariculture Wastewater. MEMBRANES 2020; 10:membranes10100282. [PMID: 33066341 PMCID: PMC7602114 DOI: 10.3390/membranes10100282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 11/17/2022]
Abstract
The performance of pollutant removals, tetracycline (TC) and norfloxacin (NOR) removals, membrane fouling mitigation and the microbial community of three Anoxic/Oxic membrane bioreactors (AO-MBRs), including a moving bed biofilm MBR (MBRa), a fixed biofilm MBR (MBRb) and an AO-MBR (MBRc) for control, were compared in treating antibiotic-containing synthetic mariculture wastewater. The results showed that MBRb had the best effect on antibiotic removal and membrane fouling mitigation compared to the other two bioreactors. The maximum removal rate of TC reached 91.65% and the maximum removal rate of NOR reached 45.46% in MBRb. The addition of antibiotics had little effect on the removal of chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N)—both maintained more than 90% removal rate during the entire operation. High-throughput sequencing demonstrated that TC and NOR resulted in a significant decrease in the microbial diversity and the microbial richness MBRs. Flavobacteriia, Firmicutes and Azoarcus, regarded as drug-resistant bacteria, might play a crucial part in the removal of antibiotics. In addition, the dynamics of microbial community had a great change, which included the accumulation of resistant microorganisms and the gradual reduction or disappearance of other microorganisms under antibiotic pressure. The research provides an insight into the antibiotic-containing mariculture wastewater treatment and has certain reference value.
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Duan P, Zhang Q, Xiong Z. Temperature decouples ammonia and nitrite oxidation in greenhouse vegetable soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139391. [PMID: 32446093 DOI: 10.1016/j.scitotenv.2020.139391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
The influence of temperature on soil ammonia (NH3) and nitrite (NO2-) oxidation and related NO2- accumulation in soils remain unclear. The soil potential NH3 oxidation (PAO) and NO2- oxidation (PNO) rates were evaluated over a temperature gradient of 5-45 °C in six greenhouse vegetable soils using inhibitors. The values of temperature sensitivity traits such as temperature minimum (Tmin), temperature optimum (Topt), and maximum absolute temperature sensitivity (Tm_sens) were also fitted to the square root growth (SQRT) and macromolecular rate theory (MMRT) models. The ammonia-oxidizing archaea (AOA) and bacteria (AOB) were determined by quantifying amoA, and nitrite-oxidizing bacteria (NOB) were determined by quantifying the nxrA and nxrB. Both models identified that Topt for PAO (34.0 °C) was significantly greater than that for PNO (26.0 °C). The Tm_sens (23.4 ± 2.1 °C) and Tmin (1.0 ± 2.0 °C) for PAO were higher than those for PNO (16.8 ± 3.2 °C and - 11.7 ± 6.7 °C). PAO was positively correlated with AOB-amoA at 20-30 °C and with AOA-amoA at 30-35 °C, while PNO was positively correlated with nxrB at 5-30 °C. Additionally, NO2- and N2O were positively correlated with the (AOA + AOB amoA) to (nxrA + nxrB) ratio, and the concentration of N2O was positively correlated with NO2- accumulation. These results highlight that elevated temperatures resulted in the uncoupling of NH3 oxidation and NO2- oxidation, leading to NO2- accumulation, which could stimulate N2O emissions.
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Affiliation(s)
- Pengpeng Duan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Takahashi Y, Fujitani H, Hirono Y, Tago K, Wang Y, Hayatsu M, Tsuneda S. Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils. Front Microbiol 2020; 11:1737. [PMID: 32849373 PMCID: PMC7396549 DOI: 10.3389/fmicb.2020.01737] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/02/2020] [Indexed: 12/02/2022] Open
Abstract
In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.
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Affiliation(s)
- Yu Takahashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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Zhao B, Xie F, Zhang X, Yue X. Enhancing the nitrogen removal from swine wastewater digested liquid in a trickling biofilter with a soil layer. RSC Adv 2020; 10:23782-23791. [PMID: 35517362 PMCID: PMC9054833 DOI: 10.1039/d0ra03333b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
Trickling biofilters (TFs) allow for a simultaneous nitrification and denitrification (SND) process, and offer a favorable solution for the treatment of swine-wastewater digested liquid due to their simple operation and low cost. In this study, a soil trickling biofilter (STF) was developed to enhance nitrogen removal. A gravel trickling filter (GTF) and a woodchip trickling filter (WTF) were also constructed and operated synchronously to demonstrate the advantage of micron-sized media. The results showed that the STF had a higher ammonium nitrogen (NH4 +-N) removal capacity of 21.4%, 24.9%, and 18.3% in comparison to the GTF when the influent NH4 +-N was 192.9 mg L-1, 500.2 mg L-1 and 802.1 mg L-1, respectively. The total nitrogen (TN) removal capacity of the STF was 104.6%, 89.4%, and 37.5% higher than that of the WTF. Thus, the addition of micron-sized soil to TF could increase the systemic nitrogen removal capacity.
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Affiliation(s)
- Bowei Zhao
- College of Environmental Science and Engineering, Taiyuan University of Technology 79 Yingzexi Road Taiyuan 030000 P. R. China +86 0351-3176586
| | - Fei Xie
- College of Environmental Science and Engineering, Taiyuan University of Technology 79 Yingzexi Road Taiyuan 030000 P. R. China +86 0351-3176586
| | - Xiao Zhang
- College of Environmental Science and Engineering, Taiyuan University of Technology 79 Yingzexi Road Taiyuan 030000 P. R. China +86 0351-3176586
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology 79 Yingzexi Road Taiyuan 030000 P. R. China +86 0351-3176586
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43
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Wang L, Lim CK, Klotz MG. High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. Microorganisms 2020; 8:E693. [PMID: 32397339 PMCID: PMC7285500 DOI: 10.3390/microorganisms8050693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world's oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C-107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
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Affiliation(s)
- Lin Wang
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Martin G. Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
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Barnard S, Van Goethem MW, de Scally SZ, Cowan DA, van Rensburg PJ, Claassens S, Makhalanyane TP. Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiol Ecol 2020; 96:5818763. [DOI: 10.1093/femsec/fiaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P < 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P < 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.
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Affiliation(s)
- Sebastian Barnard
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Storme Z de Scally
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Peet Jansen van Rensburg
- Focus Area Human Metabolomics, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Sarina Claassens
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
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45
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Metaproteomic insights into ammonia oxidising bacterial consortium developed for bioaugmenting nitrification in aquaculture systems. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00481-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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46
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Wendeborn S. Chemie, Biologie und Regulierung der Nitrifikation von Ammonium im Boden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201903014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sebastian Wendeborn
- Fachhochschule Nordwestschweiz FHNWHochschule für Life SciencesInstitut für Chemie und Bioanalytik Hofackerstrasse 30 CH-4132 Muttenz Schweiz
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Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. GLOBAL CHANGE BIOLOGY 2020; 26:103-118. [PMID: 31638306 DOI: 10.1111/gcb.14877] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/30/2019] [Indexed: 05/02/2023]
Abstract
Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N2 O emissions.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Lyon, France
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48
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Sedlacek CJ, McGowan B, Suwa Y, Sayavedra-Soto L, Laanbroek HJ, Stein LY, Norton JM, Klotz MG, Bollmann A. A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria. MICROBIAL ECOLOGY 2019; 78:985-994. [PMID: 30976841 DOI: 10.1007/s00248-019-01378-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.
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Affiliation(s)
- Christopher J Sedlacek
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Brian McGowan
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
| | - Yuichi Suwa
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Luis Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Jeanette M Norton
- Department of Plants, Soil and Climate, Utah State University, Logan, UT, 84322-4820, USA
| | - Martin G Klotz
- School of Molecular Biosciences, Washington State University, Richland, WA, 99354, USA
| | - Annette Bollmann
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA.
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Wendeborn S. The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil. Angew Chem Int Ed Engl 2019; 59:2182-2202. [PMID: 31116902 DOI: 10.1002/anie.201903014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/15/2019] [Indexed: 11/11/2022]
Abstract
Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.
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Affiliation(s)
- Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
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50
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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