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Nordio R, Belachqer-El Attar S, Clagnan E, Sánchez-Zurano A, Pichel N, Viviano E, Adani F, Guzmán JL, Acién G. Exploring microbial growth dynamics in a pilot-scale microalgae raceway fed with urban wastewater: Insights into the effect of operational variables. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 369:122385. [PMID: 39243421 DOI: 10.1016/j.jenvman.2024.122385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/12/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Microalgae-based wastewater treatment is a promising technology efficient for nutrient recycling and biomass production. Studies continuously optimize processes to reduce costs and increase productivity. However, changes in the operational conditions affect not only biomass productivity but the dynamics of the overall microbial community. This study characterizes a microalgae culture from an 80 m2 pilot-scale raceway reactor fed with untreated urban wastewater. Operational conditions such as pH, dissolved oxygen control strategies (On-off, PI, Event-based, no control), and culture height were varied to assess microbial population changes. Results demonstrate that increased culture height significantly promotes higher microalgal and bacterial diversity. pH, dissolved oxygen and culture height highly affects nitrifying bacteria activity and nitrogen accumulation. Furthermore, the system exhibited high disinfection capability with average Logarithmic Reduction Values (LRV) of 3.36 for E. coli and 2.57 for Clostridium perfringens. Finally, the fungi species detected included Chytridiomycota and Ascomycota, while purple photosynthetic bacteria were also found in significant abundance within the medium.
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Affiliation(s)
- Rebecca Nordio
- Department of Chemical Engineering, University of Almeria, 04120, Almería, Spain; CIESOL Solar Energy Research Centre, Joint Centre University of Almería-CIEMAT, 04120, Almería, Spain.
| | - Solaima Belachqer-El Attar
- Department of Chemical Engineering, University of Almeria, 04120, Almería, Spain; CIESOL Solar Energy Research Centre, Joint Centre University of Almería-CIEMAT, 04120, Almería, Spain
| | - Elisa Clagnan
- Gruppo Ricicla Labs, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | | | - Natalia Pichel
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos, Madrid, Spain
| | - Emanuele Viviano
- Department of Chemical Engineering, University of Almeria, 04120, Almería, Spain
| | - Fabrizio Adani
- Gruppo Ricicla Labs, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - José Luis Guzmán
- Department of Informatics, University of Almeria, 04120, Almería, Spain
| | - Gabriel Acién
- Department of Chemical Engineering, University of Almeria, 04120, Almería, Spain; CIESOL Solar Energy Research Centre, Joint Centre University of Almería-CIEMAT, 04120, Almería, Spain
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2
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Chavez-Ortiz P, Larsen J, Olmedo-Alvarez G, García-Oliva F. Control of inorganic and organic phosphorus molecules on microbial activity, and the stoichiometry of nutrient cycling in soils in an arid, agricultural ecosystem. PeerJ 2024; 12:e18140. [PMID: 39329143 PMCID: PMC11426319 DOI: 10.7717/peerj.18140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 08/30/2024] [Indexed: 09/28/2024] Open
Abstract
Background The dynamics of carbon (C), nitrogen (N), and phosphorus (P) in soils determine their fertility and crop growth in agroecosystems. These dynamics depend on microbial metabolism, which in turn depends on nutrient availability. Farmers typically apply either mineral or organic fertilizers to increase the availability of nutrients in soils. Phosphorus, which usually limits plant growth, is one of the most applied nutrients. Our knowledge is limited regarding how different forms of P impact the ability of microbes in soils to produce the enzymes required to release nutrients, such as C, N and P from different substrates. Methods In this study, we used the arable layer of a calcareous soil obtained from an alfalfa cropland in Cuatro Cienegas, México, to perform an incubation experiment, where five different phosphate molecules were added as treatments substrates: three organic molecules (RNA, adenine monophosphate (AMP) and phytate) and two inorganic molecules (calcium phosphate and ammonium phosphate). Controls did not receive added phosphorus. We measured nutrient dynamics and soil microbial activity after 19 days of incubation. Results Different P molecules affected potential microbial C mineralization (CO2-C) and enzyme activities, specifically in the organic treatments. P remained immobilized in the microbial biomass (Pmic) regardless of the source of P, suggesting that soil microorganisms were limited by phosphorus. Higher mineralization rates in soil amended with organic P compounds depleted dissolved organic carbon and increased nitrification. The C:N:P stoichiometry of the microbial biomass implied a change in the microbial community which affected the carbon use efficiency (CUE), threshold elemental ratio (TER), and homeostasis. Conclusion Different organic and inorganic sources of P affect soil microbial community structure and metabolism. This modifies the dynamics of soil C, N and P. These results highlight the importance of considering the composition of organic matter and phosphate compounds used in agriculture since their impact on the microbial activity of the soil can also affect plant productivity.
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Affiliation(s)
- Pamela Chavez-Ortiz
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico, Ciudad de México, Mexico
| | - John Larsen
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Gabriela Olmedo-Alvarez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N., Irapuato, Guanajuato, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
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3
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Kuppe CW, Postma JA. Benefits and limits of biological nitrification inhibitors for plant nitrogen uptake and the environment. Sci Rep 2024; 14:15027. [PMID: 38951138 PMCID: PMC11217430 DOI: 10.1038/s41598-024-65247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
Plant growth and high yields are secured by intensive use of nitrogen (N) fertilizer, which, however, pollutes the environment, especially when N is in the form of nitrate. Ammonium is oxidized to nitrate by nitrifiers, but roots can release biological nitrification inhibitors (BNIs). Under what conditions does root-exudation of BNIs facilitate nitrogen N uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant's life cycle. We determined the sensitivity of N uptake and loss to variations in the parameter values, testing a broad range of soil-plant-microbial conditions, including concentrations, diffusion, sorption, nitrification, population growth, and uptake kinetics. An increase in BNI exudation reduces net N loss and, under most conditions, increases plant N uptake. BNIs decrease uptake in the case of (1) low ammonium concentrations, (2) high ammonium adsorption to the soil, (3) rapid nitrate- or slow ammonium uptake by the plant, and (4) a slowly growing or (5) fast-declining nitrifier population. Bactericidal inhibitors facilitate uptake more than bacteriostatic ones. Some nitrification, however, is necessary to maximize uptake by both ammonium and nitrate transporter systems. An increase in BNI exudation should be co-selected with improved ammonium uptake. BNIs can reduce N uptake, which may explain why not all species exude BNIs but have a generally positive effect on the environment by increasing rhizosphere N retention.
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Affiliation(s)
- Christian W Kuppe
- Institute of Bio- and Geosciences-Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Faculty 1, RWTH Aachen University, Aachen, Germany.
| | - Johannes A Postma
- Institute of Bio- and Geosciences-Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
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4
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Nguyen AH, Oh S. Side effects of the addition of an adsorbent for the nitrification performance of a microbiome in the treatment of an antibiotic mixture. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133034. [PMID: 38035522 DOI: 10.1016/j.jhazmat.2023.133034] [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: 09/08/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023]
Abstract
This work determined the effect of biochar (BC) as an adsorbent on the nitrifying microbiome in regulating the removal, transformation, fate, toxicity, and potential environmental consequences of an antibiotic mixture containing oxytetracycline (OTC) and sulfamethoxazole (SMX). Despite the beneficial role of BC as reported in the literature, the present study revealed side effects for the nitrifying microbiome and its functioning arising from the presence of BC. Long-term monitoring revealed severe disruption to nitratation via the inhibition of both nitrite oxidizers (e.g., Nitrospira defluvii) and potential comammox species (e.g., Ca. Nitrospira nitrificans). Byproducts (BPs) more toxic than the parent compounds were found to persist at a high relative abundance, particularly in the presence of BC. Quantitative structure-activity relationship modeling determined that the physicochemical properties of the toxic BPs significantly differed from those of OTC and SMX. The results suggested that the BPs tended to mobilize and accumulate on the surface of the solids in the system (i.e., the BC and biofilm), disrupting the nitrifiers growing at the interface. Collectively, this study provides novel insights, demonstrating that the addition of adsorbents to biological systems may not necessarily be beneficial; rather, they may generate side effects for specific bacteria that have important ecosystem functions.
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Affiliation(s)
- Anh H Nguyen
- Department of Civil Engineering, College of Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, South Korea
| | - Seungdae Oh
- Department of Civil Engineering, College of Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, South Korea.
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5
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Peoples LM, Seixas MH, Evans KA, Bilbrey EM, Ranieri JR, Tappenbeck TH, Dore JE, Baumann A, Church MJ. Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake. Environ Microbiol 2024; 26:e16616. [PMID: 38517638 DOI: 10.1111/1462-2920.16616] [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: 11/11/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.
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Affiliation(s)
- Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Miranda H Seixas
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Evan M Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - John R Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Tyler H Tappenbeck
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Adam Baumann
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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Alfreider A, Harringer M. Vertical Distribution and Seasonal Patterns of Candidatus Nitrotoga in a Sub-Alpine Lake. Microbes Environ 2024; 39:ME23086. [PMID: 38825479 PMCID: PMC11220445 DOI: 10.1264/jsme2.me23086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/01/2024] [Indexed: 06/04/2024] Open
Abstract
The nitrite oxidizing bacterial genus Ca. Nitrotoga was only recently discovered to be widespread in freshwater systems; however, limited information is currently available on the environmental factors and seasonal effects that influence its distribution in lakes. In a one-year study in a dimictic lake, based on monthly sampling along a vertical profile, the droplet digital PCR quantification of Ca. Nitrotoga showed a strong spatio-temporal patchiness. A correlation ana-lysis with environmental parameters revealed that the abundance of Ca. Nitrotoga correlated with dissolved oxygen and ammonium, suggesting that the upper hypolimnion of the lake is the preferred habitat.
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Affiliation(s)
- Albin Alfreider
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Manuel Harringer
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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7
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Macêdo WV, Schmidt JS, Jensen SB, Biller P, Vergeynst L. Is nitrification inhibition the bottleneck of integrating hydrothermal liquefaction in wastewater treatment plants? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119046. [PMID: 37832286 DOI: 10.1016/j.jenvman.2023.119046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Sewage sludge management poses challenges due to its environmental impact, varying composition, and stringent regulatory requirements. In this scenario, hydrothermal liquefaction (HTL) is a promising technology for producing biofuel and extracting phosphorus from sewage sludge. However, the toxic nature of the resulting process water (HTL-PW) raises concerns about integrating HTL into conventional wastewater treatment processes. This study investigated the inhibitory effects of HTL-PW on the activity of the main microbial functions in conventional activated sludge. Upon recirculation of the HTL-PW from the excess sludge into the wastewater treatment plant, the level of COD in the influent is expected to increase by 157 mgO2⋅L-1, resulting in 44% nitrification inhibition (IC50 of 197 mg⋅L-1). However, sorption of inhibitory compounds on particles can reduce nitrification inhibition to 27% (IC50 of 253 mg⋅L-1). HTL-PW is a viable carbon source for denitrification, showing nearly as high denitrification rates as acetate and only 17% inhibition at 157 mgO2⋅L-1 COD. Under aerobic conditions, heterotrophic organic nitrogen and organic matter conversion remains unaffected up to 223 mgO2⋅L-1 COD, with COD removal higher than 94%. This study is the first to explore the full integration of HTL in wastewater treatment plants for biofuel production from the excess activated sludge. Potential nitrification inhibition is concerning, and further long-term studies are needed to fully investigate the impacts.
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Affiliation(s)
- Williane Vieira Macêdo
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark.
| | - Jennie Spicker Schmidt
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Sara Brorson Jensen
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Patrick Biller
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Leendert Vergeynst
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
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8
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Li G, Wei M, Wei G, Chen Z, Shao Z. Efficient heterotrophic nitrification by a novel bacterium Sneathiella aquimaris 216LB-ZA1-12 T isolated from aquaculture seawater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115588. [PMID: 37839193 DOI: 10.1016/j.ecoenv.2023.115588] [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: 05/13/2023] [Revised: 09/10/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
High concentration of ammonia poses a common threat to the healthy breeding of marine aquaculture organisms. Since aquaculture water is rich in organic matter, heterotrophic nitrifying bacteria might play a crucial role in ammonia removal. However, their roles in ammonia oxidation remain unknown. Here, we report a novel strain isolated from shrimp aquaculture seawater, identified as Sneathiella aquimaris 216LB-ZA1-12T, capable of heterotrophic nitrification. It is the first characterized heterotrophic nitrifier of the order Sneathiellales in the class Alphaproteobacteria. It exhibits high activity in heterotrophic nitrification, removing nearly 94% of ammonium-N under carbon-constrained conditions in 8 days with no observed nitrite accumulation. The heterotrophic nitrification pathway, inferred based on detection and genomic data was as follows: NH4+→NH2OH→NO→NO2-→NO3-. While this pathway aligns with the classical nitrification pathway, while the significant difference lies in the absence of classical HAO and HOX encoding genes in the genome, which is common in heterotrophic nitrifying bacteria. In summary, this bacterium is not only valuable for studying the nitrifying mechanism, but also holds potential for practical applications in ammonia removal in marine aquaculture systems and saline wastewater.
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Affiliation(s)
- Guizhen Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Mengjiao Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; College of Oceans and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Zhen Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
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9
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Pérez-Alfaro JE, Villaseca A, Gaytán R, Martínez-Jardines MA, Buitrón G, Texier AC, Cuervo-López FM. Nitrification activity in the presence of 2-chlorophenol using whole nitrifying cells and cell-free extracts: batch and SBR assays. 3 Biotech 2023; 13:364. [PMID: 37840880 PMCID: PMC10575828 DOI: 10.1007/s13205-023-03764-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/29/2023] [Indexed: 10/17/2023] Open
Abstract
Kinetic assays with a nitrifying consortium with whole nitrifying cells amended with 5 mg 2-CP-C/L and 100, 200, 300, or 500 mg NH4+-N/L were carried out in batch and nitrifying sequencing batch reactor (SBR) cultures. No nitrification activity was observed in batch assays with 100 mg NH4+-N/L and 5 mg 2-CP-C/L. Nevertheless, increasing the ammonium concentration from 200 to 500 mg NH4+-N/L allowed simultaneous ammonium and nitrite oxidation even in the presence of 5 mg 2-CP-C/L plus the halogenated compound consumption. Under these conditions, the ammonium monooxygenase enzyme participated in 2-CP consumption. Complete nitrification and simultaneous elimination of 5 mg 2-CP-C/L were achieved in the SBR amended with 200-500 mg NH4+-N/L. The inhibitory effect of 2-CP on the nitrite oxidation process completely disappeared under these conditions. Assays with nitrifying cell-free extracts, ammonium (100 mg NH4+-N/L), and 2-CP (5 mg 2-CP-C/L) were also conducted. In the absence of 2-CP, the nitrifying cell-free extracts maintained up to 60% of the nitrifying activity compared to whole-cells. Contrary to whole-cell assays, cell-free extracts were capable of simultaneously oxidizing ammonium and consuming 2-CP. However, the inhibitory effect of 2-CP on nitrification was still present as lower specific rates of ammonium consumption and nitrate production were obtained. Thus, these assays indicate that the presence of 2-CP affects both, the ammonium transport mechanism and the activity of nitrifying enzymes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03764-z.
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Affiliation(s)
- J. E. Pérez-Alfaro
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
| | - A. Villaseca
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
| | - Raúl Gaytán
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
| | - M. A. Martínez-Jardines
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
| | - G. Buitrón
- Unidad Académica del Instituto de Ingeniería, Universidad Nacional Autónoma de México, 76230 Querétaro, Querétaro México
| | - A.-C. Texier
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
| | - F. M. Cuervo-López
- Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, CP 09310 Mexico City, México
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10
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Woo AYM, Aguilar Ramos MA, Narayan R, Richards-Corke KC, Wang ML, Sandoval-Espinola WJ, Balskus EP. Targeting the human gut microbiome with small-molecule inhibitors. NATURE REVIEWS. CHEMISTRY 2023; 7:319-339. [PMID: 37117817 DOI: 10.1038/s41570-023-00471-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.
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Affiliation(s)
- Amelia Y M Woo
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Rohan Narayan
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Michelle L Wang
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | - Walter J Sandoval-Espinola
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
- Universidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, San Lorenzo, Paraguay
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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11
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Liu Y, Zhu Y, Wu D, Wang Z, Wang Y, Wang G, Zhou X, Sun H. Effect of free nitrous acid on nitritation process: Microbial community, inhibitory kinetics, and functional biomarker. BIORESOURCE TECHNOLOGY 2023; 371:128595. [PMID: 36634879 DOI: 10.1016/j.biortech.2023.128595] [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: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
This work comprehensively deciphered the effect of free nitrous acid (FNA) on the microbial community, inhibitory kinetics, and nitrifiers in nitritation process. Nitritation was first successfully achieved through selective inhibition of free ammonia (FA) on nitrite oxidizers (NOB). Then, batch tests clearly showed that FNA significantly inhibits the ammonia oxidation rate (rsu) and the growth rate (μ) of ammonia oxidizers (AOB), which was well described by the Hellinga model (KI = 0.222 mg·L-1). The structural equation model indicated that FNA was significantly and negatively associated with rsu, μ, Nitrosomonas, Commamons, Nitrospira, and Nitrotoga and positively correlated with Paracoccus. Furthermore, Nitrosomonas significantly drove the ammonia utilization and growth of AOB and was identified as the most important functional biomarker indicating the nitritation in response to FNA levels using random forest model. This study provides helpful information on the kinetics of the mechanism underlying the FNA inhibition on nitrification.
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Affiliation(s)
- Yucan Liu
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China; School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Yuliang Zhu
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China; School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Daishun Wu
- Fujian Provincial Key Laboratory of Coastal Basin Environment, School of Marine and Biochemical Engineering, Fujian Polytechnic Normal University, Fuqing 350300, China
| | - Zhaoyang Wang
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yajun Wang
- School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Gang Wang
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Xin Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China.
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12
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Bayer B, McBeain K, Carlson CA, Santoro AE. Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers. LIMNOLOGY AND OCEANOGRAPHY 2023; 68:84-96. [PMID: 37064272 PMCID: PMC10092583 DOI: 10.1002/lno.12252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Nitrifying microorganisms, including ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and nitrite-oxidizing bacteria, are the most abundant chemoautotrophs in the ocean and play an important role in the global carbon cycle by fixing dissolved inorganic carbon (DIC) into biomass. The release of organic compounds by these microbes is not well quantified, but may represent an as-yet unaccounted source of dissolved organic carbon (DOC) available to marine food webs. Here, we provide measurements of cellular carbon and nitrogen quotas, DIC fixation yields and DOC release of 10 phylogenetically diverse marine nitrifiers. All investigated strains released DOC during growth, representing on average 5-15% of the fixed DIC. Changes in substrate concentration and temperature did not affect the proportion of fixed DIC released as DOC, but release rates varied between closely related species. Our results also indicate previous studies may have underestimated DIC fixation yields of marine nitrite oxidizers due to partial decoupling of nitrite oxidation from CO2 fixation, and due to lower observed yields in artificial compared to natural seawater medium. The results of this study provide critical values for biogeochemical models of the global carbon cycle, and help to further constrain the implications of nitrification-fueled chemoautotrophy for marine food-web functioning and the biological sequestration of carbon in the ocean.
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Affiliation(s)
- Barbara Bayer
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
- Present address:
Department of Microbiology and Ecosystem ScienceUniversity of ViennaViennaAustria
| | - Kelsey McBeain
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
- Present address:
Department of OceanographyUniversity of Hawai'i at ManoaHonoluluHawaii
| | - Craig A. Carlson
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Alyson E. Santoro
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
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13
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Woo Y, Cruz MC, Wuertz S. Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms. Microbiol Spectr 2022; 10:e0184522. [PMID: 36445127 PMCID: PMC9769795 DOI: 10.1128/spectrum.01845-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.
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Affiliation(s)
- Yissue Woo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mercedes Cecilia Cruz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
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14
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Whangchai N, Klahan R, Balakrishnan D, Unpaprom Y, Ramaraj R, Pimpimol T. Development of aeration devices and feeding frequencies for oxygen concentration improvement in 60-tones freshwater recirculating aquaculture and biofloc ponds of Asian seabass (Lates calcarifer) rearing. CHEMOSPHERE 2022; 307:135761. [PMID: 35931264 DOI: 10.1016/j.chemosphere.2022.135761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
This research aimed to improve the technique to maintain the oxygen content of two freshwater Asian sea bass (Lates calcarifer) culture systems (recirculating aquaculture system; RAS; and biofloc system; Floc). The dissolved oxygen content was increased by using a blower with flexible rubber hose aerators. For the first study, the effectiveness of oxygenation was investigated. As a result, the aerator and flexible rubber hose are appropriate for increasing oxygen levels in the fish pond. An air pump with a flexible aeration tube (400 W), one set of ejector aerators (250 W), and two sets of ejector aerators (250 × 2 W) were used to test the efficiency of oxygenation. In addition, the performance of the RAS and Floc systems, off-flavor (geosmin and MIB) in taints, and economic returns were assessed. This study found that after monitoring two 60-tonne concrete ponds with one set of blowers (RAS1) and two sets of blowers (RAS2) connected by a flexible rubber tube; feeding frequency (2 and 6 times/day). However, daily dissolved oxygen fluctuated in the RAS, and this value went to its lowest after post-feeding. Dissolved oxygen was higher than the two-meal pack per day when the feeding was expanded to six meals. This aeration device could provide dissolved oxygen enough for 900 kg fish/400 W. Seabass raised in the freshwater RAS system had higher yields and growth rates than those raised in the biofloc pond systems. In addition, low off-flavors trained was observed. Therefore, this research could improve aeration management by aeration devices and increase feeding frequency while developing freshwater-adapted Asian seabass production.
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Affiliation(s)
- Niwooti Whangchai
- Faculty of Fisheries Technology and Aquatic Resources, Maejo University, Chiang Mai, 50290, Thailand
| | - Rungkan Klahan
- Faculty of Agricultural Technology, Phetchaburi Rajabhat University, Phetchaburi, 76000, Thailand
| | - Deepanraj Balakrishnan
- College of Engineering, Prince Mohammad Bin Fahd University, Al Khobar, 31952, Saudi Arabia
| | - Yuwalee Unpaprom
- Program in Biotechnology, Faculty of Science, Maejo University, Chiang Mai, 50290, Thailand
| | | | - Tipsukhon Pimpimol
- Faculty of Fisheries Technology and Aquatic Resources, Maejo University, Chiang Mai, 50290, Thailand.
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15
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Monteiro GGTN, Barros DJ, Gabriel GVM, Venturini AM, Veloso TGR, Vazquez GH, Oliveira LC, Neu V, Bodelier PLE, Mansano CFM, Tsai SM, Navarrete AA. Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities. Front Microbiol 2022; 13:913453. [PMID: 35979497 PMCID: PMC9376453 DOI: 10.3389/fmicb.2022.913453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 -), which can be further oxidized to nitrate (NO3 -). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 - and NO3 -, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 +) and NO3 --and NO2 --dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.
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Affiliation(s)
| | - Dayane J. Barros
- Graduate Program in Biodiversity and Biotechnology (BIONORTE), Federal University of Tocantins (UFT), Palmas, Brazil
| | - Gabriele V. M. Gabriel
- Graduate Program in Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Andressa M. Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, United States
| | - Tomás G. R. Veloso
- Graduate Program in Agricultural Microbiology, Federal University of Viçosa, Viçosa, Brazil
| | - Gisele H. Vazquez
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
| | - Luciana C. Oliveira
- Department of Physics, Chemistry, and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Vania Neu
- Federal Rural University of Amazonia (UFRA), Belém, Brazil
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | - Acacio A. Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
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16
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Mohapatra M, Manu S, Dash SP, Rastogi G. Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 314:115013. [PMID: 35447445 DOI: 10.1016/j.jenvman.2022.115013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/16/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Seagrasses are complex benthic coastal ecosystems that play a crucial role in organic matter cycling and carbon sequestration. However, little is known about how seagrasses influence the structure and carbon utilization potential of benthic bacterial communities. This study examined the bacterial communities in monospecific and mixed meadows of seagrasses and compared with bulk (unvegetated) sediments from Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes revealed a vegetation effect in terms of differences in benthic bacterial community diversity, composition, and abundances in comparison with bulk sediments. Desulfobacterales, Chromatiales, Enterobacteriales, Clostridiales, Vibrionales, and Acidimicrobiales were major taxa that contributed to differences between seagrass and bulk sediments. Seagrasses supported ∼5.94 fold higher bacterial abundances than the bulk due to rich organic carbon stock in their sediments. Co-occurrence network demonstrated much stronger potential interactions and connectedness in seagrass bacterial communities compared to bulk. Chromatiales and Acidimicrobiales were identified as the top two keystone taxa in seagrass bacterial communities, whereas, Dehalococcoidales and Rhizobiales were in bulk communities. Seagrasses and local environmental factors, namely, water depth, water pH, sediment salinity, redox potential, total organic carbon, available nitrogen, sediment texture, sediment pH, and sediment core depth were the major drivers of benthic bacterial community composition. Carbon metabolic profiling revealed that heterotrophic bacteria in seagrass sediments were much more metabolically diverse and active than bulk. The utilization of carbon substrate guilds, namely, amino acids, amines, carboxylic acids, carbohydrates, polymers, and phenolic compounds was enhanced in seagrass sediments. Metabolic mapping predicted higher prevalence of sulfate-reducer and N2 fixation metabolic functions in seagrass sediments. Overall, this study showed that seagrasses control benthic bacterial community composition and diversity, enhance heterotrophic carbon substrate utilization, and play crucial roles in organic matter cycling including degradation of hydrocarbon and xenobiotics in coastal sediments.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500048, India
| | - Stiti Prangya Dash
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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17
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Neissi A, Rafiee G, Rahimi S, Farahmand H, Pandit S, Mijakovic I. Enriched microbial communities for ammonium and nitrite removal from recirculating aquaculture systems. CHEMOSPHERE 2022; 295:133811. [PMID: 35124092 DOI: 10.1016/j.chemosphere.2022.133811] [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: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The aim of this study was the enrichment of high-performance microbial communities in biofilters for removal of ammonium and nitrite from aquaculture water. Ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were enriched from different environmental water samples. The microbial communities with higher ammonium and nitrite removal activity were selected and adapted to different temperatures [9 °C, 15 °C, room temperature (25 °C), and 30 °C]. The expression of genes involved in nitrification including ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) were measured in temperature-adapted AOB and NOB microbiomes. The microbial species present in the selected microbiomes were identified via 16s rRNA sequencing. The microbial communities containing Nitrosomonas oligotropha and Nitrobacter winogradskyi showed the highest ammonium and nitrite removal activity at all temperatures used for adaptation. Furthermore, the microbial communities do not contain any pathogenic bacteria. They also exhibited the highest expression of AMO and NXR genes. Using the enriched microbial communities, we achieved a 288% and 181% improvement in ammonium and nitrite removal over the commonly used communities in biofilters at 9 °C, respectively. These results suggest that the selected microbiomes allowed for a significant improvement of water quality in a recirculating aquaculture system (RAS).
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Affiliation(s)
- Alireza Neissi
- Nuclear Agricultural School, Nuclear Science and Technology Research Institute, 31465/1498, Karaj, Iran
| | - Gholamreza Rafiee
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, 331585-4314, Karaj, Iran.
| | - Shadi Rahimi
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden.
| | - Hamid Farahmand
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, 331585-4314, Karaj, Iran
| | - Santosh Pandit
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Ivan Mijakovic
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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18
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Hossain S, Chow CWK, Cook D, Sawade E, Hewa GA. Review of Nitrification Monitoring and Control Strategies in Drinking Water System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074003. [PMID: 35409686 PMCID: PMC8997939 DOI: 10.3390/ijerph19074003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Nitrification is a major challenge in chloraminated drinking water systems, resulting in undesirable loss of disinfectant residual. Consequently, heterotrophic bacteria growth is increased, which adversely affects the water quality, causing taste, odour, and health issues. Regular monitoring of various water quality parameters at susceptible areas of the water distribution system (WDS) helps to detect nitrification at an earlier stage and allows sufficient time to take corrective actions to control it. Strategies to monitor nitrification in a WDS require conducting various microbiological tests or assessing surrogate parameters that are affected by microbiological activities. Additionally, microbial decay factor (Fm) is used by water utilities to monitor the status of nitrification. In contrast, approaches to manage nitrification in a WDS include controlling various factors that affect monochloramine decay rate and ammonium substrate availability, and that can inhibit nitrification. However, some of these control strategies may increase the regulated disinfection-by-products level, which may be a potential health concern. In this paper, various strategies to monitor and control nitrification in a WDS are critically examined. The key findings are: (i) the applicability of some methods require further validation using real WDS, as the original studies were conducted on laboratory or pilot systems; (ii) there is no linkage/formula found to relate the surrogate parameters to the concentration of nitrifying bacteria, which possibly improve nitrification monitoring performance; (iii) improved methods/monitoring tools are required to detect nitrification at an earlier stage; (iv) further studies are required to understand the effect of soluble microbial products on the change of surrogate parameters. Based on the current review, we recommend that the successful outcome using many of these methods is often site-specific, hence, water utilities should decide based on their regular experiences when considering economic and sustainability aspects.
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Affiliation(s)
- Sharif Hossain
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Correspondence:
| | - Christopher W. K. Chow
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - David Cook
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Emma Sawade
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Guna A. Hewa
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
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19
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Effects of soil texture and nitrogen fertilisation on soil bacterial community structure and nitrogen uptake in flue-cured tobacco. Sci Rep 2021; 11:22643. [PMID: 34811391 PMCID: PMC8608801 DOI: 10.1038/s41598-021-01957-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/08/2021] [Indexed: 12/05/2022] Open
Abstract
We tested the hypothesis that soil texture and nitrogen (N) fertilisation are the primary factors regulating the N cycle and soil bacterial community structure. The response of soil bacterial communities to N fertilisation in different textured soils might help in identifying the specific underlying mechanism and hence management of N fertiliser application in fields. We examined how N fertiliser accumulates in flue-cured tobacco and influences soil bacterial community structure in different textured soils. We conducted plot and micro-plot experimental measurements of N content in soil and tobacco samples using the KNO315N isotope technique. Soil bacterial community structure was determined using high-throughput sequencing of 16S rRNA. Nitrogen absorption and utilisation by tobacco plants were highest in sandy loam soils, followed by loam soil and clay loam. The ability of clay loam to supply N was weak during the plant growth period. Absence of fertilisation could reduce bacterial abundance in soils to various degrees. Bacterial diversity was higher in sandy loam soil than in loam soil and clay loam. Soil texture and N fertilisation significantly affected soil bacterial community structure and diversity. Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Chloroflexi were the dominant bacterial phyla, while Bacillus, Nitrobacter, Nitrosospira, Nitrospira, and Rhizobium were the primary N transformation bacteria at the genus level in all treatments. However, relative abundances differed with N fertiliser application, which could lead to differential N availability and N use efficiency of tobacco among soil types. We conclude that both soil texture and N fertilisation influence N accumulation and distribution in flue-cured tobacco and thus regulate soil bacterial communities. N fertiliser application in sandy loam soil should be strictly controlled for its higher N use efficiency, soil bacterial abundance, and diversity.
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20
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Zhang D, Cheng H, Hao B, Li Q, Wu J, Zhang Y, Fang W, Yan D, Li Y, Wang Q, Jin X, He L, Cao A. Fresh chicken manure fumigation reduces the inhibition time of chloropicrin on soil bacteria and fungi and increases beneficial microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117460. [PMID: 34438480 DOI: 10.1016/j.envpol.2021.117460] [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: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Chloropicrin (CP) controls soil-borne plant diseases caused by pathogenic microbes, increases crop yield, but has a long-term inhibitory effect on beneficial soil microorganisms. Therefore, we evaluated the effects of biofumigation material fresh chicken manure (FCM) on soil microorganisms, and the duration of those effects in this experiment. Our results showed that in the laboratory, FCM significantly increased substrate-induced respiration (SIR) of soil microorganisms by 2.2-3.2 times at 80 d compared to the control, however, CP significantly inhibited the SIR of soil microorganisms. FCM and CP increased NH4+-N concentration within 40 days which then returned to the control level. FCM increased NO3--N by 2.82-5.78 times by 80 days, compared with the control, while the concentration of NO3--N in the CP treatment was not significantly different from the control at the 80 day. Although in the laboratory FCM inhibited the relative abundance of 16 S rRNA and the nitrogen cycle functional genes AOA amoA, AOB amoA, nirK and nosZ over a 40-day period, the taxonomic diversity of soil bacteria and fungi in the FCM treatment were restored to unfumigated level within 90 days in the field. However, CP treatment has a strong inhibitory effect on soil microorganisms after 90 days. Importantly, the relative abundance of some beneficial microorganisms that control soil-borne pathogenic microbes or degrade pollutants increased significantly in FCM, including Bacillus, Pseudomonas and Streptomyces bacterial genera and Chaetomium and Mycothermus fungal genera. Noteworthy, like CP, FCM still had a strong inhibitory effect on Fusarium at 90 d. Our results indicated that FCM not only increased the content of inorganic nitrogen and improved the respiration rate of soil microorganisms, but it also shortened the recovery time of beneficial soil microorganisms and increased taxonomic diversity. Our previous reports showed that FCM and CP treatments had the same effect in disease control and crop growth. Combined with the results of this experiment, we believe that FCM has the potential to replace CP, which would eliminate CP's detrimental environmental impact, improve farmer safety and promote sustainable crop production.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Baoqiang Hao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingjie Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiajia Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China.
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21
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Liu F, Hu X, Zhao X, Gao Y. Effect of carrier particle size on enrichment and shift in nitrifier community behaviors for treating increased strength wastewater. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1959-1968. [PMID: 33797157 DOI: 10.1002/wer.1567] [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: 11/28/2020] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
In activated sludge systems, adding carriers can improve nitrifier enrichment. Different attachment area induced by different particle sizes of carriers may result in different nitrifier community. This research investigated the effect of different particle sizes of coal ash on nitrifier enrichment treating increased strength wastewater. Results indicated efficient nitrifying coal ash was obtained with smaller coal ash. The ammonia removal rates reached over 98%, which outclassed that in negative control (63.28%), and no nitrite accumulated in these systems under high nitrogen concentration of 1123.35 mg N/L. The high-throughput sequencing assays indicated carriers changed the microbial community structure significantly, thus facilitated the nitrification capacity. Increase abundance of nitrifier has a negative correlation with particle size of carriers. Nitrosomonas became the biggest beneficiary, which maximum composed 50.29% in fillers system and only 13.69% in negative control, whereas the number of Nitrobacter (less than 3.04%) became much lower than ammonia-oxidizing bacteria (AOB). However, the shift of microbial structures, large number of Dokdonella for instance, may guarantee the complete nitrification in systems with smaller carriers. Batch experiments showed a high dissolved oxygen (DO) concentration (4 mg/L) and slightly alkaline condition (pH 8.0) had a positive effect on nitrifying coal ash. PRACTITIONER POINTS: The increase size of nitrifier has a negative correlation with particle size of coal ash. The smaller coal ash reduces the adverse effect of high nitrogen on nitrification. The ammonia removal rate reached 99.82% with influent of 1123.35 mg NH 4 + - N /L in the smallest carriers system.
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Affiliation(s)
- Fang Liu
- Department of Environmental Engineering, School of Chemical & Environmental Engineering, Jiangsu University of Technology, Changzhou, China
- Department of Environmental Engineering, School of Resource & Civil Engineering, Northeastern University, Shenyang, China
| | - Xiaomin Hu
- Department of Environmental Engineering, School of Resource & Civil Engineering, Northeastern University, Shenyang, China
| | - Xin Zhao
- Department of Environmental Engineering, School of Resource & Civil Engineering, Northeastern University, Shenyang, China
| | - Yong Gao
- Department of Environmental Engineering, School of Chemical & Environmental Engineering, Jiangsu University of Technology, Changzhou, China
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22
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Lantz MA, Boddicker AM, Kain MP, Berg OMC, Wham CD, Mosier AC. Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. Front Microbiol 2021; 12:709371. [PMID: 34484146 PMCID: PMC8415719 DOI: 10.3389/fmicb.2021.709371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Nitrogen cycling microbes, including nitrite-oxidizing bacteria (NOB), perform critical ecosystem functions that help mitigate anthropogenic stresses and maintain ecosystem health. Activity of these beneficial nitrogen cycling microbes is dictated in part by the microorganisms’ response to physicochemical conditions, such as temperature, pH, and nutrient availability. NOB from the newly described Candidatus Nitrotoga genus have been detected in a wide range of habitats across the globe, yet only a few organisms within the genus have been physiologically characterized. For freshwater systems where NOB are critical for supporting aquatic life, Ca. Nitrotoga have been previously detected but little is known about the physiological potential of these organisms or their response to changing environmental conditions. Here, we determined functional response to environmental change for a representative freshwater species of Ca. Nitrotoga (Ca. Nitrotoga sp. CP45, enriched from a Colorado river). The physiological findings demonstrated that CP45 maintained nitrite oxidation at pH levels of 5–8, at temperatures from 4 to 28°C, and when incubated in the dark. Light exposure and elevated temperature (30°C) completely halted nitrite oxidation. Ca. Nitrotoga sp. CP45 maintained nitrite oxidation upon exposure to four different antibiotics, and potential rates of nitrite oxidation by river sediment communities were also resilient to antibiotic stress. We explored the Ca. Nitrotoga sp. CP45 genome to make predictions about adaptations to enable survival under specific conditions. Overall, these results contribute to our understanding of the versatility of a representative freshwater Ca. Nitrotoga sp. Identifying the specific environmental conditions that maximize NOB metabolic rates may ultimately direct future management decisions aimed at restoring impacted systems.
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Affiliation(s)
- Munira A Lantz
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Michael P Kain
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Owen M C Berg
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Courtney D Wham
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
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23
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Rodriguez J, Chakrabarti S, Choi E, Shehadeh N, Sierra-Martinez S, Zhao J, Martens-Habbena W. Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB. Front Microbiol 2021; 12:671480. [PMID: 34322099 PMCID: PMC8312096 DOI: 10.3389/fmicb.2021.671480] [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: 02/23/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.
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Affiliation(s)
| | | | | | | | | | | | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, United States
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24
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Li H, Abbas T, Cai M, Zhang Q, Wang J, Li Y, Di H, Tahir M. Cd bioavailability and nitrogen cycling microbes interaction affected by mixed amendments under paddy-pak choi continued planting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116542. [PMID: 33582635 DOI: 10.1016/j.envpol.2021.116542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/19/2020] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) is the most concerning soil pollutant, and a threat to human health, especially in China. The in-situ immobilization of Cadmium by amendments is one of the most widely adopted methods to remedy soil contamination. The study was designed to evaluate the effect of organo-chemical amendments on soil Cd bioavailability and nitrogen cycling microbes under continuous planting of rice (Oryza sativa) and pak choi (Brassica chinensis L.). The experiment was carried out using four amendments, Lime, Zeolite, Superphosphate, and Biochar, at two different ratios; M1: at the ratio of 47:47:5:1, and M2 at the ratio of 71:23:5:1, respectively. Moreover, both M1 and M2 were enriched at four levels (T1: 0.5%; T2: 1%; T3: 2%; T4: 4%). Results showed that compared with CK (Cd enriched soils), the yield of rice under treatments of M1T1 and M2T1 increased by 8.93% and 8.36%, respectively. While the biomass (fresh weight) of pak choi under M1 and M2 amendments increased by 2.52-2.98 times and 0.76-2.89 times respectively, under enrichment treatments T1, T2, and T3. The total Cd concentrations in rice grains treated with M1T3 and M2T3 decreased by 89.25% and 93.16%, respectively, compared with CK. On the other hand, the total Cd concentrations in pak choi under M1T3 and M2T2 decreased by 92.86% and 90.23%, respectively. The results showed that soil pH was the main factor affecting Cd bioavailability in rice and pak choi. The Variance partitioning analysis (VPA) of rice and pak choi showed that soil pH was the most significant contributing factor. In the rice season, the contribution of soil pH (P) on Cd bioavailability was 10.14% (P = 0.102), and in the pak choi season, the contribution of soil pH was 8.38% (P = 0.133). Furthermore, the abundance of ammonia oxidation and denitrifying microorganisms had significantly correlation with soil pH and exchange Cd. In rice season, when the enrichment level of amendments increased from 0.5% (T1) to 2% (T3), the gene abundance of AOA, AOB, nirK, nirS and nosZ (І) tended to decrease. While in pak choi season, when the enrichment level increased at the level of 0.5% (T1), 1% (T2), and 2% (T3), the gene abundance of AOB, nirS, and nosZ (І) increased. Additionally, the gene abundance of AOA and nirK showed a reduction in the pak choi season contrasting to rice. And the mixed amendment M2 performed better at reducing Cd uptake than M1, which may have correlation with the ratio of lime and zeolite in them. Finally, we conclude that between these two amendments, when applied at a moderate level M2 type performed better than M1 in reducing Cd uptake, and also showed positive effects on both gene abundance and increase soil pH.
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Affiliation(s)
- Houfu Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China
| | - Touqeer Abbas
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China
| | - Mei Cai
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China
| | - Qichun Zhang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China.
| | - Jingwen Wang
- Hangzhou Plant Protection and Fertilizer Station Hangzhou, 310020, PR China
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, 311300, China
| | - Muhammad Tahir
- Department of Soil, Water, & Climate, Univ. of Minnesota, 1991 Upper Buford Cir, Falcon Heights, MN, 55108, USA
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25
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Differential Resilience of Soil Microbes and Ecosystem Functions Following Cessation of Long-Term Fertilization. Ecosystems 2021. [DOI: 10.1007/s10021-021-00633-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Picone N, Pol A, Mesman R, van Kessel MAHJ, Cremers G, van Gelder AH, van Alen TA, Jetten MSM, Lücker S, Op den Camp HJM. Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium. THE ISME JOURNAL 2021; 15:1150-1164. [PMID: 33303933 PMCID: PMC8115276 DOI: 10.1038/s41396-020-00840-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Ammonia oxidation was considered impossible under highly acidic conditions, as the protonation of ammonia leads to decreased substrate availability and formation of toxic nitrogenous compounds. Recently, some studies described archaeal and bacterial ammonia oxidizers growing at pH as low as 4, while environmental studies observed nitrification at even lower pH values. In this work, we report on the discovery, cultivation, and physiological, genomic, and transcriptomic characterization of a novel gammaproteobacterial ammonia-oxidizing bacterium enriched via continuous bioreactor cultivation from an acidic air biofilter that was able to grow and oxidize ammonia at pH 2.5. This microorganism has a chemolithoautotrophic lifestyle, using ammonia as energy source. The observed growth rate on ammonia was 0.196 day-1, with a doubling time of 3.5 days. The strain also displayed ureolytic activity and cultivation with urea as ammonia source resulted in a growth rate of 0.104 day-1 and a doubling time of 6.7 days. A high ammonia affinity (Km(app) = 147 ± 14 nM) and high tolerance to toxic nitric oxide could represent an adaptation to acidic environments. Electron microscopic analysis showed coccoid cell morphology with a large amount of intracytoplasmic membrane stacks, typical of gammaproteobacterial ammonia oxidizers. Furthermore, genome and transcriptome analysis showed the presence and expression of diagnostic genes for nitrifiers (amoCAB, hao, nor, ure, cbbLS), but no nirK was identified. Phylogenetic analysis revealed that this strain belonged to a novel bacterial genus, for which we propose the name "Candidatus Nitrosacidococcus tergens" sp. RJ19.
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Affiliation(s)
- Nunzia Picone
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Arjan Pol
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Rob Mesman
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Maartje A. H. J. van Kessel
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Geert Cremers
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Antonie H. van Gelder
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Theo A. van Alen
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Mike S. M. Jetten
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Huub J. M. Op den Camp
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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27
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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28
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Hosseinpour B, Saborimanesh N, Yerushalmi L, Walsh D, Mulligan CN. Start-up of oxygen-limited autotrophic partial nitrification-anammox process for treatment of nitrite-free wastewater in a single-stage hybrid bioreactor. ENVIRONMENTAL TECHNOLOGY 2021; 42:932-940. [PMID: 31378146 DOI: 10.1080/09593330.2019.1649467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
This study presents effective ammonium removal from nitrite-free ammonium-rich synthetic wastewater through combined partial nitrification (PN) and anammox processes in a multi-zone hybrid airlift bioreactor (BioCAST). Removal efficiencies of ammonia-nitrogen and total nitrogen up to 85.6% and 81.2%, respectively, were achieved shortly after the start-up of bioreactor treating the nitrite-free ammonium-rich synthetic wastewater with ammonium concentrations of 10-350 mg/L. The hybrid (containing suspended and attached biomass) and multi-zone design of the bioreactor with different dissolved oxygen levels, along with the inoculation with anammox-containing sludge were the main factors in the successful start-up of the bioreactor. Nitrate accumulation problem due to the fast growth of nitrite-oxidizing bacteria in the bioreactor was controlled by two operating strategies including lowering the HRT from 4 days to 2 days and controlling the dissolved oxygen concentration in the aerobic zone of the bioreactor between 0.9 and 1.2 mg/L. Moreover, the 16S rRNA gene analysis confirmed that the partial nitrification of ammonia to nitrite occurred by Nitrosomonas sp. primarily in the suspended biomass in the aerobic zone, while the conversion of nitrite to N2 occurred by Candidatus Brocadia species in the anoxic zone. This study showed the effective removal of ammonium from a nitrite-free wastewater by providing a proper HRT, controlling the DO concentration between 0.9 and 1.2 mg/L in the aerobic zone, and preventing biomass loss using both suspended and attached microbial cultures in different zones of the bioreactor.
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Affiliation(s)
- Bahareh Hosseinpour
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Canada
| | - Nayereh Saborimanesh
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Canada
| | - Laleh Yerushalmi
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Canada
| | - David Walsh
- Department of Biology, Centre for Structural and Functional Genomics, Montreal, Canada
| | - Catherine N Mulligan
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Canada
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29
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Growing Medium Type Affects Organic Fertilizer Mineralization and CNPS Microbial Enzyme Activities. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10121955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Managing plant fertilization is a major concern of greenhouse growers to achieve sustainable production with growing media (GM). Organic fertilization is popular but is more difficult to control, since organic compounds need first to be mineralized by microbes. After 7, 14, 28, and 56 days of incubation, we investigated the response of microbial activities and nutrient releases from three frequently used organic fertilizers (horn and two plant-based fertilizers) in three frequently employed GM types (peat, coir, and bark). We measured pH, electrical conductivity, nutrient contents (NH4+-N, NO3−-N, PO43−-P, SO42−-S), and enzyme activities (β-1.4-glucosidase, urease, acid phosphatase, arylsulfatase). After fertilization, microbes in coir expressed all the C, N, P, and S functions studied, making related nutrients available. In peat and bark, some C, N, P, and S-related pathways were locked. Peat presented high NH4+-N and PO43−-P releases linked to high acid phosphatase and β-glucosidase activities, while bark showed high nitrification rates but weak enzyme activities. Fertilizer types modulated these responses with lower activities and nutrient releases with horn. Our results contributed to better understanding mineralization processes in GM, showing different microbial responses to fertilization. This study pointed out the necessity to look deeper into microbial functions in GM optimizing biological and physicochemical properties.
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30
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Landreau M, Byson SJ, You H, Stahl DA, Winkler MKH. Effective nitrogen removal from ammonium-depleted wastewater by partial nitritation and anammox immobilized in granular and thin layer gel carriers. WATER RESEARCH 2020; 183:116078. [PMID: 32623243 DOI: 10.1016/j.watres.2020.116078] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/24/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the effect of physicochemical conditions on the partial nitritation and anammox treatment by immobilized ammonia oxidizers under ammonium-deplete conditions. The impact of oxygen and temperature was studied by measuring the activity of immobilized aerobic and anaerobic ammonia-oxidizing organisms (Ammonia-oxidizing bacteria (AOB) and archaea (AOA), and Anammox bacteria) embedded in polyvinyl alcohol - sodium alginate (PVA-SA) beads and in thin layer poly-ethylene glycol hydrogels. Beads and flat hydrogels were incubated in a fluidized bed reactor (FBR) and in two flow cells, respectively. Both systems were fed with synthetic wastewater (15 mg N-NH4+/L) at different temperatures (20 °C and/or 30 °C) and different dissolved oxygen (DO) concentrations (0.1, 0.3, 0.5 and/or 1 mg/L) over 152 and 207 days, respectively. The FBR system had a maximum removal rate of 1.7 g-N/m3/d at 0.1 mg O2/L, corresponding to 80% removal efficiency, while a high aerobic ammonia-oxidizing activity but a partial oxygen inhibition of Anammox bacteria were observed at higher DO concentrations. In both flow cells, nitrogen removal efficiency was highest (80%) at 30 °C and 1 mg O2/L while removal was less favorable at lower DO and lower temperature. Our results indicate a potential use of hydrogel beads for an energy efficient technology with reduced aeration demand for treating low ammonia wastewater, while layered hydrogels are a possible first step for biological treatments of wastewater using tangential flow. In addition, we provide blueprint drawings of the flow cells, which may be used to 3D-print the apparatus for other applications.
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Affiliation(s)
- Matthieu Landreau
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA.
| | - Samuel J Byson
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - HeeJun You
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
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31
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Sedlacek CJ. It Takes a Village: Discovering and Isolating the Nitrifiers. Front Microbiol 2020; 11:1900. [PMID: 32849473 PMCID: PMC7431685 DOI: 10.3389/fmicb.2020.01900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.
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Affiliation(s)
- Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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32
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Nitrogen Removal Efficiency and Microbial Community Analysis of a High-Efficiency Honeycomb Fixed-Bed Bioreactor. WATER 2020. [DOI: 10.3390/w12061832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Based on the concept of microbial community multi-processing in integrated spatial bacterial succession (ISBS), this study constructs a highly efficient cellular fixed-bed bioreactor that follows the growth of biological flora in the wastewater treatment process. The reactor is organically partitioned based on synergistic laws and in accordance with environmental and microbial metabolic changes, and sewage is subjected to unitized and specialized biological treatment under direct current conditions. The results show that the ISBS reactor exhibits stable nitrogen removal performance under a low-carbon source. Compared with traditional sewage biochemical treatment technology, the microbial concentration is increased by 2–3 times and even up to 12 times, and the ammonia nitrogen removal rate is maintained at 99%. The removal rate reaches 90% (hydraulic retention time of 14 h). High-throughput sequencing analysis based on 16S rDNA reveals the microbial community structure succession at different depths of the same section of the reactor. The microbial community is rich under the influence of environmental factors and exhibits different responses. The intervals vary. An analysis of the microbial community function explains why the ISBS reactor has high nitrogen removal efficiency.
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33
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Jo Y, Cho K, Choi H, Lee C. Treatment of low-strength ammonia wastewater by single-stage partial nitritation and anammox using upflow dual-bed gel-carrier reactor (UDGR). BIORESOURCE TECHNOLOGY 2020; 304:123023. [PMID: 32088631 DOI: 10.1016/j.biortech.2020.123023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
This study investigated the single-stage partial nitritation and anammox (S-PNA) treatment of low-strength ammonia wastewater (≤140 mg NH4+-N/L). Upflow dual-bed gel-carrier reactor (UDGR) with polyvinyl alcohol cryogel biocarriers, developed in this study, was employed for the anammox biomass enrichment from conventional activated sludge and subsequent S-PNA experiments. Anammox biomass was successfully enriched from conventional activated sludge. The enriched anammox carriers were inoculated together with gel carriers containing nitrifying sludge into the S-PNA reactors. S-PNA activity developed rapidly, and the nitrogen removal efficiency and rate reached up to 90.1% (with complete ammonia removal) and 0.15 kg N/m3⋅d, respectively, under low nitrogen loading conditions (0.10-0.17 kg N/m3⋅d). The microbial community structure changed significantly while adapting to anammox and S-PNA conditions. Anammox was likely driven solely by a Candidatus Jettenia population accounting for ≤49.4% of bacterial 16S rRNA genes. The results demonstrate that the UDGR-based S-PNA is suitable for treating low-strength wastewater.
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Affiliation(s)
- Yeadam Jo
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hyungmin Choi
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea.
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34
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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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Yuan D, Wang W, Liu C, Xu L, Fei H, Wang X, Shen M, Wang S, Wang M, Zhu G. Source, contribution and microbial N-cycle of N-compounds in China fresh snow. ENVIRONMENTAL RESEARCH 2020; 183:109146. [PMID: 31991341 DOI: 10.1016/j.envres.2020.109146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO42- were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO42- and NO3- were from anthropogenic sources, and SO42- contributed (61%) more to the pollution load than NO3- (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 107 copies g-1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the 15N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.
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Affiliation(s)
- Dongdan Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chunlei Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hexin Fei
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaoling Wang
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Mengnan Shen
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Han S, Tan S, Wang A, Chen W, Huang Q. Deciphering belowground nitrifier assemblages with elevational soil sampling in a subtropical forest ecosystem (Mount Lu, China). FEMS Microbiol Ecol 2019; 96:5670618. [DOI: 10.1093/femsec/fiz197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/06/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTThe elevational distribution patterns of microbial functional groups have long been attracting scientific interest. Ammonia-oxidizers (ammonia-oxidizing archaea [AOA] and bacteria [AOB]), complete ammonia oxidation (comammox) Nitrospira and nitrite-oxidizers (e.g. Nitrobacter and Nitrospira) play crucial roles in the nitrogen cycle, yet their activities and abundances in response to elevational gradients in a subtropical forest ecosystem remain unclear. Here, we investigated the distribution of potential functions and abundances of these nitrifiers in forest soils along elevational gradients on Mount Lu, China. Our results showed that AOA and Nitrospira abundance was higher than that of their counterparts. Only AOA, Nitrobacter and comammox Nitrospira abundances followed a hump-backed-model with altitude. Soil potential ammonia-oxidation activity (PAO) and nitrite-oxidation activity (PNO) ranged from 0.003 to 0.084 and 0.34 to 0.53 μg NO2−-N g−1 dry soil h−1, respectively. The biotic (AOA, Nitrobacter, Nitrospira and comammox Nitrospira abundances) and abiotic factors (soil variables) jointly affected PAO, whereas the abiotic factors were mainly responsible for PNO. Variance partitioning analysis showed that contemporary environmental disturbance is the most important driver for the biogeography of nitrifier assemblages. Overall, our findings indicate that forest soil nitrifier assemblages exhibit a biogeographic pattern largely shaped by soil chemistry along an elevational gradient.
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Affiliation(s)
- Shun Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuang Tan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Achen Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Mampaey KE, Spérandio M, van Loosdrecht MC, Volcke EI. Dynamic simulation of N2O emissions from a full-scale partial nitritation reactor. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Lam WN, Chisholm RA. Resource conversion: a generalizable mechanism for resource‐mediated positive species interactions. OIKOS 2019. [DOI: 10.1111/oik.06672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Weng Ngai Lam
- Dept of Biological Sciences, National Univ. of Singapore 14 Science Drive 4 Singapore 117543 Republic of Singapore
| | - Ryan A. Chisholm
- Dept of Biological Sciences, National Univ. of Singapore 14 Science Drive 4 Singapore 117543 Republic of Singapore
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Trivedi C, Reich PB, Maestre FT, Hu HW, Singh BK, Delgado-Baquerizo M. Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands. THE ISME JOURNAL 2019; 13:2727-2736. [PMID: 31249390 PMCID: PMC6794256 DOI: 10.1038/s41396-019-0465-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022]
Abstract
Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.
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Affiliation(s)
- Chanda Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia
| | - Peter B Reich
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia
- Department of Forest Resources, University of Minnesota, St Paul, MN, 55108, USA
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, 28933, Spain
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Alicante, Spain
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
- Global Centre for Land Based Innovation, Western Sydney University, Building L9, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, 28933, Spain.
- Cooperative Institute for Research in Environmental Science, University of Colorado Boulder, Boulder, CO, USA.
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40
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Pan KL, Gao JF, Li DC, Fan XY. The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study. BIORESOURCE TECHNOLOGY 2019; 291:121914. [PMID: 31377507 DOI: 10.1016/j.biortech.2019.121914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L-1) and increased at high salinities (10, 15, 20 and 30 g L-1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while 13C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L-1 salinity, respectively.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
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41
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Martínez-Jardines M, Pérez-Alfaro E, González-Robles RO, Texier AC, Cuervo-López F. Decrease of inhibitory effect of 2-chlorophenol on nitrification in sequencing batch reactors. ENVIRONMENTAL TECHNOLOGY 2019; 40:3422-3433. [PMID: 29757088 DOI: 10.1080/09593330.2018.1476594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
The metabolic and kinetic behaviour of a nitrification process in the presence of 2-chlorophenol (2-CP) was evaluated in two sequencing batch reactors (SBR1, SBR2) inoculated with nitrifying sludge previously exposed to phenolic compounds. The SBR1 was inoculated with sludge previously exposed to 2-CP, while the SBR2 was inoculated with sludge previously exposed to p-cresol. An inhibitory effect of 20 mg 2-CP-C/L on both nitrification processes was observed, as specific rates decreased according to a control assay in the absence of 2-CP. However, the inhibitory effect decreased throughout the cycles. At the end of cycle 6, a stable nitrifying process was observed with the sludge previously exposed to 2-CP (SBR1), as an ammonium consumption efficiency and a nitrate production yield close to 99.6 ± 0.3% and 0.99 ± 0.02 were respectively achieved. Despite a complete ammonium consumption being achieved with the sludge previously exposed to p-cresol (SBR2), partial nitrification was observed as nitrate production yield accounted for 0.28 ± 0.08 and nitrite was accumulated within the culture. Nevertheless, both nitrifying sludges had the ability to completely consume 2-CP. The use of SBR systems with nitrifying sludge previously exposed to 2-CP resulted in a better nitrification performance, thus it may be a good alternative for achieving a stable nitrifying respiratory process where complete and simultaneous ammonium and 2-CP consumption can be acquired.
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Affiliation(s)
- Miguel Martínez-Jardines
- Department of Biotechnology CBS, Universidad Autónoma Metropolitana-Iztapalapa , Mexico City , Mexico
| | - Emmanuel Pérez-Alfaro
- Department of Basic Sciences, Universidad Tecnológica del Valle de Chalco , Valle de Chalco , Mexico
| | - R O González-Robles
- Department of Mathematics CBI, Universidad Autónoma Metropolitana-Iztapalapa , Mexico City , Mexico
| | - Anne-Claire Texier
- Department of Biotechnology CBS, Universidad Autónoma Metropolitana-Iztapalapa , Mexico City , Mexico
| | - Flor Cuervo-López
- Department of Biotechnology CBS, Universidad Autónoma Metropolitana-Iztapalapa , Mexico City , Mexico
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Rajta A, Bhatia R, Setia H, Pathania P. Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater. J Appl Microbiol 2019; 128:1261-1278. [PMID: 31587489 DOI: 10.1111/jam.14476] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Abstract
With the increase in industrial and agricultural activities, a large amount of nitrogenous compounds are released into the environment, leading to nitrate pollution. The perilous effects of nitrate present in the environment pose a major threat to human and animal health. Bioremediation provides a cost-effective and environmental friendly method to deal with this problem. The process of aerobic denitrification can reduce nitrate compounds to harmless dinitrogen gas. This review provides a brief view of the exhaustive role played by aerobic denitrifiers for tackling nitrate pollution under different ecological niches and their dependency on various environmental parameters. It also provides an understanding of the enzymes involved in aerobic denitrification. The role of aerobic denitrification to solve the issues faced by the conventional method (aerobic nitrification-anaerobic denitrification) in treating nitrogen-polluted wastewaters is elaborated.
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Affiliation(s)
- A Rajta
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - R Bhatia
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - H Setia
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - P Pathania
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
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González-Camejo J, Aparicio S, Ruano MV, Borrás L, Barat R, Ferrer J. Effect of ambient temperature variations on an indigenous microalgae-nitrifying bacteria culture dominated by Chlorella. BIORESOURCE TECHNOLOGY 2019; 290:121788. [PMID: 31326649 DOI: 10.1016/j.biortech.2019.121788] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Two outdoor photobioreactors were operated to evaluate the effect of variable ambient temperature on an indigenous microalgae-nitrifying bacteria culture dominated by Chlorella. Four experiments were carried out in different seasons, maintaining the temperature-controlled PBR at around 25 °C (by either heating or cooling), while the temperature in the non-temperature-controlled PBR was allowed to vary with the ambient conditions. Temperatures in the range of 15-30 °C had no significant effect on the microalgae cultivation performance. However, when the temperature rose to 30-35 °C microalgae viability was significantly reduced. Sudden temperature rises triggered AOB growth in the indigenous microalgae culture, which worsened microalgae performance, especially when AOB activity made the system ammonium-limited. Microalgae activity could be recovered after a short temperature peak over 30 °C once the temperature dropped, but stopped when the temperature was maintained around 28-30 °C for several days.
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Affiliation(s)
- J González-Camejo
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain.
| | - S Aparicio
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - M V Ruano
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - L Borrás
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - R Barat
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain
| | - J Ferrer
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain
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Wang W, Su Y, Wang B, Wang Y, Zhuang L, Zhu G. Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:629-640. [PMID: 31170597 DOI: 10.1016/j.scitotenv.2019.04.415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.
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Affiliation(s)
- Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Baoling Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
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Mukhtar H, Lin YP, Lin CM, Petway JR. Assessing thermodynamic parameter sensitivity for simulating temperature responses of soil nitrification. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1596-1608. [PMID: 31414689 DOI: 10.1039/c9em00310j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Soil nitrification responses to temperature have major implications for the global nitrogen cycle. Temperature sensitivity of soil nitrification has been modeled using several mathematical models, yet the extent to which model-generated thermodynamic parameters are accurate and sensitive in describing temperature sensitivity is unclear. In this study, we performed global sensitivity analysis to identify the key thermodynamic parameters that are most influential when simulating the temperature response of the soil nitrification potential (NP) across two different temperature gradients (4-40 °C and 20-45 °C) which are imposed upon sixteen different soils with square root growth (SQRT) and macromolecular rate theory (MMRT) models. We found that two thermodynamic parameters stand out as moderately to highly sensitive, and are uniquely identifiable in each model, regardless of the temperature range. The minimum and maximum measured temperatures seem to have no impact on the list of sensitive parameters but do influence the parameter ranges, especially for the SQRT model. However, parameters that control the minimum temperature and curvature of the NP response curve (Tmin and ΔC‡P) were found to have little to no sensitivity to SQRT and MMRT model outputs, respectively. We show that the parameter sensitivity and range of measured temperatures influence the complementary model's ability to describe the temperature sensitivity of soil nitrification. Our proposed framework enhances the accurate interpretation of existing thermodynamic parameters that explain the temperature sensitivity of soil biochemical processes, and provides methodological recommendations for future temperature sensitivity studies.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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Petersen LAH, Lieven C, Nandy SK, Villadsen J, Jørgensen SB, Christensen I, Gernaey KV. Dynamic investigation and modeling of the nitrogen cometabolism in
Methylococcus capsulatus
(
Bath
). Biotechnol Bioeng 2019; 116:2884-2895. [DOI: 10.1002/bit.27113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Leander A. H. Petersen
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical EngineeringTechnical University of Denmark Lyngby Denmark
- Unibio A/S Odense Denmark
| | - Christian Lieven
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | | | - John Villadsen
- Center for Combustion and Harmful Emission Control (CHEC), Department of Chemical and Biochemical EngineeringTechnical University of Denmark Lyngby Denmark
| | - Sten B. Jørgensen
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical EngineeringTechnical University of Denmark Lyngby Denmark
| | | | - Krist V. Gernaey
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical EngineeringTechnical University of Denmark Lyngby Denmark
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De Tender C, Mesuere B, Van der Jeugt F, Haegeman A, Ruttink T, Vandecasteele B, Dawyndt P, Debode J, Kuramae EE. Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. Sci Rep 2019; 9:9890. [PMID: 31289280 PMCID: PMC6617458 DOI: 10.1038/s41598-019-46106-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 11/09/2022] Open
Abstract
Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.
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Affiliation(s)
- C De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium.
| | - B Mesuere
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000, Ghent, Belgium
| | - F Van der Jeugt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - A Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - T Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - B Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - P Dawyndt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - J Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - E E Kuramae
- Netherlands Institute of Ecology, department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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Nitrifier abundance and diversity peak at deep redox transition zones. Sci Rep 2019; 9:8633. [PMID: 31201353 PMCID: PMC6572806 DOI: 10.1038/s41598-019-44585-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/17/2019] [Indexed: 11/08/2022] Open
Abstract
More than half of the global ocean floor is draped by nutrient-starved sediments characterized by deep oxygen penetration and a prevalence of oxidized nitrogen. Despite low energy availability, this habitat hosts a vast microbial population, and geochemical characteristics suggest that nitrogen compounds are an energy source critical to sustaining this biomass. However, metabolic rates of nitrogen transformation and their link to microbial survival in this global-scale ecosystem remain virtually unknown. Here we provide quantitative constraints on microbial nitrogen cycling in open ocean oligotrophic sediments from seafloor to basement, spanning approximately 8 million years. We find active microbial nitrogen transformation throughout the sediment column but at very low rates. Local peaks in diversity and abundance of nitrifiers and denitrifiers occur at redox transition zones deep within the sediments, strongly indicating that these microbes are revived from their maintenance state and start growing again after millions of years of attrition.
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Su YC, Sathyamoorthy S, Chandran K. Bioaugmented methanol production using ammonia oxidizing bacteria in a continuous flow process. BIORESOURCE TECHNOLOGY 2019; 279:101-107. [PMID: 30711750 PMCID: PMC6395879 DOI: 10.1016/j.biortech.2019.01.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/22/2023]
Abstract
Organic compounds such as methanol are widely used for enhancing denitrification at wastewater treatment plants (WWTPs) to meet effluent water quality permits. On the other hand, methane, which is the main feedstock for industrial methanol production, is also generated during anaerobic digestion in WWTPs, but is often flared to mitigate its greenhouse impacts. The overarching goal herein was to develop a novel continuous process for methanol production from methane using nitrifying activated sludge. The maximum AOB specific methanol production rate using hydroxylamine as electron donor was 1.61 ± 0.15 and 1.27 ± 0.15 mg-COD-CH3OH/(mg-COD-AOB*d), for hydraulic retention times (HRTs) of 7.5 h and 2 h, respectively. The corresponding production rate using ammonia as electron donor was 0.31 ± 0.08 mg-COD-CH3OH/(mg-COD-AOB*d) at a HRT of 2 h. These results show that nitrifier-mediated methanol production in a continuous-flow system can enhance the efficiency of WWTPs through internal production of biomethanol for denitrification, while simultaneously minimizing wasteful biogas flaring.
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Affiliation(s)
- Yu-Chen Su
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States
| | - Sandeep Sathyamoorthy
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States
| | - Kartik Chandran
- Columbia University, Department of Earth and Environmental Engineering, 500 West 120th Street, Room 1045 Mudd Hall, New York, NY 10027, United States.
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Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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