1
|
Oshiki M, Saito T, Nakaya Y, Satoh H, Okabe S. Growth of the Nitrosomonas europaea cells in the biofilm and planktonic growth mode: Responses of extracellular polymeric substances production and transcriptome. J Biosci Bioeng 2023; 136:430-437. [PMID: 37925312 DOI: 10.1016/j.jbiosc.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Nitrosomonas europaea, an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode.
Collapse
Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Takahiro Saito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yuki Nakaya
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| |
Collapse
|
2
|
Yuan Q, Jia Z, Roots P, Wells G. A strategy for fast anammox biofilm formation under mainstream conditions. CHEMOSPHERE 2023; 318:137955. [PMID: 36702412 DOI: 10.1016/j.chemosphere.2023.137955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
One of the bottlenecks to applying anaerobic ammonium oxidation (Anammox) is the long start-up time, especially under mainstream conditions. This study proposed a strategy for fast anammox biofilm formation under mainstream conditions. By first cultivating an aerobic heterotrophic biofilm, and then transferring to anoxic conditions, a pre-cultivated heterotrophic biofilm can be formed in 12 days. The pre-cultivated heterotrophic biofilm then functions as a "glue" to accelerate anammox bacteria adhesion and biofilm formation. Secondary settled effluent with externally added 15-30 mg-N·L-1 ammonium and nitrite was applied as reactor influent. With a single inoculation of suspended growth anammox-laden biomass and no bioaugmentation, an anammox-enriched biofilm formed after 5 months of operation under uncontrolled temperature of 15-20 °C. Both the nitrogen removal rate and specific anammox activity exponentially increased over the course of study, corresponding to an estimated anammox doubling time of 10.8 days. The biofilm thickness on primed carriers was 2-3 times higher than on the non-primed carriers over the first 5 months of operation, and the hszA gene copy number in primed biofilms revealed was consistently 1 to 2 times higher than the non-primed carrier biofilm, indicating that biofil m carrier priming via selection for a pre-cultivated heterotrophic biofilm base can effectively improve the anammox enrichment rate at early stages of reactor operation. Time, rather than the type of biofilm (primed versus non-primed), had a stronger influence on microbial community structure over the full 230 days of reactor operation. Candidatus Brocadia was the only detected anammox bacteria genus. Overall, pre-cultivation of heterotrophs on biofilm carriers provides a simple route to accelerate anammox-enriched biofilm formation under mainstream conditions.
Collapse
Affiliation(s)
- Quan Yuan
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, China; Department of Civil & Environmental Engineering, Northwestern University, Evanston, USA
| | - Zhen Jia
- Department of Civil & Environmental Engineering, Northwestern University, Evanston, USA
| | - Paul Roots
- Department of Civil & Environmental Engineering, Northwestern University, Evanston, USA
| | - George Wells
- Department of Civil & Environmental Engineering, Northwestern University, Evanston, USA.
| |
Collapse
|
3
|
Ramos P, Honda R, Hoek EMV, Mahendra S. Carbon/nitrogen ratios determine biofilm formation and characteristics in model microbial cultures. CHEMOSPHERE 2023; 313:137628. [PMID: 36565767 DOI: 10.1016/j.chemosphere.2022.137628] [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: 11/02/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The influence of growth medium water chemistry, specifically carbon/nitrogen (C/N) molar ratios, on the characteristics and development of biofilms of the model microorganism Pseudomonas aeruginosa was investigated. C/N = 9 had a unique effect on biofilm composition as well as quorum sensing (QS) pathways, with higher concentrations of carbohydrates and proteins in the biofilm and a significant upregulation of the QS gene lasI in planktonic cells. The effect of C/N ratio on total attached biomass was negligible. Principal component analysis revealed a different behavior of most outputs such as carbohydrates and QS chemicals at C/N = 9, and pointed to correlations between parameters of biofilm formation and steady state distribution of cells and extracellular components. C/N ratio was also shown to influence organic compound utilization by both planktonic and sessile organisms, with a maximum chemical oxygen demand (COD) removal of 83% achieved by biofilms at C/N = 21. Planktonic cells achieved higher COD removal rates, but greater overall rates after six days occurred in biofilms. The development of a dual-species biofilm of P. aeruginosa and Nitrobacter winogradskyi was also influenced by C/N, with increase in the relative abundance of the slower-growing N. winogradskyi above C/N = 9. These results indicate that altering operational parameters related to C/N would be relevant for mitigating or promoting biofilm formation and function depending on the desired industrial application or treatment configuration.
Collapse
Affiliation(s)
- Pia Ramos
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA
| | - Ryo Honda
- Faculty of Geoscience and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Eric M V Hoek
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA; UCLA California NanoSystems Institute, Los Angeles, CA, 90095, USA; UCLA Institute of the Environment & Sustainability, Los Angeles, CA, 90095, USA
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA; UCLA California NanoSystems Institute, Los Angeles, CA, 90095, USA; UCLA Institute of the Environment & Sustainability, Los Angeles, CA, 90095, USA.
| |
Collapse
|
4
|
Liu B, Lin W, Huang S, Sun Q, Yin H, Luo J. Removal of Mg 2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155923. [PMID: 35577082 DOI: 10.1016/j.scitotenv.2022.155923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg2+) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg2+ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO3), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.
Collapse
Affiliation(s)
- Buchan Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China
| | - Shenxi Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Qiuyun Sun
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Hao Yin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
| |
Collapse
|
5
|
Chun SJ, Kim YJ, Cui Y, Nam KH. Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117851. [PMID: 34358869 DOI: 10.1016/j.envpol.2021.117851] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/13/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.
Collapse
Affiliation(s)
- Seong-Jun Chun
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea
| | - Young-Joong Kim
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea
| | - Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyong-Hee Nam
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea.
| |
Collapse
|
6
|
Ericsson AC, Busi SB, Davis DJ, Nabli H, Eckhoff DC, Dorfmeyer RA, Turner G, Oswalt PS, Crim MJ, Bryda EC. Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration. Anim Microbiome 2021; 3:55. [PMID: 34353374 PMCID: PMC8340428 DOI: 10.1186/s42523-021-00116-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general. METHODS A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data. RESULTS The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data. CONCLUSIONS The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.
Collapse
Affiliation(s)
- Aaron C. Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Susheel B. Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel J. Davis
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- Animal Modeling Core, University of Missouri, Columbia, MO USA
| | - Henda Nabli
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
| | | | - Rebecca A. Dorfmeyer
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Giedre Turner
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Payton S. Oswalt
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
| | | | - Elizabeth C. Bryda
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- Animal Modeling Core, University of Missouri, Columbia, MO USA
| |
Collapse
|
7
|
Keshvardoust P, Huron VAA, Clemson M, Barraud N, Rice SA. Nitrite production by ammonia-oxidizing bacteria mediates chloramine decay and resistance in a mixed-species community. Microb Biotechnol 2020; 13:1847-1859. [PMID: 32729670 PMCID: PMC7533321 DOI: 10.1111/1751-7915.13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/14/2020] [Accepted: 06/24/2020] [Indexed: 12/02/2022] Open
Abstract
As water distribution centres increasingly switch to using chloramine to disinfect drinking water, it is of paramount importance to determine the interactions of chloramine with potential biological contaminants, such as bacterial biofilms, that are found in these systems. For example, ammonia-oxidizing bacteria (AOB) are known to accelerate the decay of chloramine in drinking water systems, but it is also known that organic compounds can increase the chloramine demand. This study expanded upon our previously published model to compare the decay of chloramine in response to alginate, Pseudomonas aeruginosa, Nitrosomonas europaea and a mixed-species nitrifying culture, exploring the contributions of microbial by-products, heterotrophic bacteria and AOBs to chloramine decay. Furthermore, the contribution of AOBs to biofilm stability during chloramination was investigated. The results demonstrate that the biofilm matrix or extracellular polymeric substances (EPS), represented by alginate in these experiments, as well as high concentrations of dead or inactive cells, can drive chloramine decay rather than any specific biochemical activity of P. aeruginosa cells. Alginate was shown to reduce chloramine concentrations in a dose-dependent manner at an average rate of 0.003 mg l-1 h-1 per mg l-1 of alginate. Additionally, metabolically active AOBs mediated the decay of chloramine, which protected members of mixed-species biofilms from chloramine-mediated disinfection. Under these conditions, nitrite produced by AOBs directly reacted with chloramine to drive its decay. In contrast, biofilms of mixed-species communities that were dominated by heterotrophic bacteria due to either the absence of ammonia, or the addition of nitrification inhibitors and glucose, were highly sensitive to chloramine. These results suggest that mixed-species biofilms are protected by a combination of biofilm matrix-mediated inactivation of chloramine as well as the conversion of ammonia to nitrite through the activity of AOBs present in the community.
Collapse
Affiliation(s)
- Pejhman Keshvardoust
- The School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNSWAustralia
- The Centre for Marine Bio‐InnovationThe University of New South WalesSydneyNSWAustralia
| | - Vanessa A. A. Huron
- The School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNSWAustralia
- The Centre for Marine Bio‐InnovationThe University of New South WalesSydneyNSWAustralia
| | - Matthew Clemson
- The School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNSWAustralia
| | - Nicolas Barraud
- Genetics of Biofilms UnitDepartment of MicrobiologyInstitut PasteurParisFrance
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering and the School of Biological SciencesNanyang Technological UniversitySingapore
- Environmental SciencesThe University of New South WalesSydneyNSWAustralia
- ithree InstituteUniversity of Technology SydneySydneyNSWAustralia
| |
Collapse
|
8
|
Regularized S-Map Reveals Varying Bacterial Interactions. Appl Environ Microbiol 2020; 86:AEM.01615-20. [PMID: 32801185 DOI: 10.1128/aem.01615-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
There is a growing awareness that bacterial interactions follow a highly nonlinear pattern in reality. However, it is challenging to track the varying bacterial interactions using pairwise correlation analysis, which fails to explore their potential effects on the behavior of microbes. Here, we utilized a regularized sequential locally weighted global linear map (S-map) to capture the varying interspecific interactions from the time series data of a bacterial community under exposure to nitrite. Our results show that bacterial interactions are highly variable and that asymmetric interactions dominate the interaction pattern in a community. Furthermore, we propose a Jacobian coefficient-based statistical method to predict the harmony level of a bacterial community at each successive ecosystem state. The results show that the bacterial community exhibits a higher harmony level in nitrite-treated samples than in the control group. We show that the community harmony level is positively associated with the specific endogenous respiration rates and biofilm formation of the culture. In addition, the community tends to process lower diversity and structural stability under zero- and high-nitrite stresses. We demonstrate that the harmony level, rather than structural stability, is a useful index for unveiling the underlying mechanism of bacterial performance. Overall, the regularized S-map can help us to understand bacterial interactions in ecosystems more accurately than previous approaches.IMPORTANCE It has long been acknowledged that bacterial interactions play important roles in community structure and function. Revealing the interaction variability can allow an understanding of how bacteria respond to perturbation and why bacterial community performance changes. Such information should improve our skills in engineering bacterial communities (e.g., in a wastewater treatment plant) and achieve better removal performance and lower energy consumption.
Collapse
|
9
|
Tsuchiya Y, Nakagawa T, Takahashi R. Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant. Microbes Environ 2020; 35. [PMID: 32249239 PMCID: PMC7308565 DOI: 10.1264/jsme2.me19140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the amoA genes of ammonia-oxidizing bacteria and archaea (AOB and AOA) and a complete ammonia oxidizer (comammox) in the biofilm formed on the carriers in a full-scale WWTP. The quantification of amoA genes showed that the abundance of AOB and comammox was markedly greater in the biofilm than in the activated sludge suspended in a tank solution of the WWTP, while AOA was not detected in the biofilm or the activated sludge. A phylogenetic analysis of amoA genes revealed that as-yet-uncultivated comammox Nitrospira and uncultured AOB Nitrosomonas were predominant in the biofilm. The present results suggest that the biofilm formed on the surface of carriers enable comammox Nitrospira and AOB Nitrosomonas to co-exist and remain in the full-scale WWTP tank surveyed in this study.
Collapse
|
10
|
Keshvardoust P, Huron VAA, Clemson M, Constancias F, Barraud N, Rice SA. Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria. NPJ Biofilms Microbiomes 2019; 5:22. [PMID: 31482007 PMCID: PMC6711990 DOI: 10.1038/s41522-019-0095-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/02/2019] [Indexed: 02/01/2023] Open
Abstract
Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.
Collapse
Affiliation(s)
- Pejhman Keshvardoust
- The School of Biotechnology and Biomolecular Sciences, UNSversatile open source tool for metagenomicsW Sydney, Sydney, NSW Australia
- The Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW Australia
| | - Vanessa A. A. Huron
- The School of Biotechnology and Biomolecular Sciences, UNSversatile open source tool for metagenomicsW Sydney, Sydney, NSW Australia
- The Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW Australia
| | - Matthew Clemson
- The School of Biotechnology and Biomolecular Sciences, UNSversatile open source tool for metagenomicsW Sydney, Sydney, NSW Australia
- Rural Clinical School, UNSW Sydney, Sydney, NSW Australia
| | - Florentin Constancias
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nicolas Barraud
- The Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW Australia
- Genetics of Biofilms Unit, Institut Pasteur, 25-28 Rue de Dr Roux, 75015 Paris, France
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Ithree Institute, University of Technology Sydney, UTS Faculty of Science Store, Building 1, Level 2, Thomas Street, Ultimo, NSW 2007 Australia
| |
Collapse
|
11
|
Wang B, Ni BJ, Yuan Z, Guo J. Cometabolic biodegradation of cephalexin by enriched nitrifying sludge: Process characteristics, gene expression and product biotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:275-282. [PMID: 30959294 DOI: 10.1016/j.scitotenv.2019.03.473] [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: 01/17/2019] [Revised: 03/14/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
The nitrifying systems have been reported to be able to biodegrade micropollutants, yet it is still unclear about the cometabolism of ammonia-oxidizing bacteria (AOB) towards micropollutants, in particular their enzyme and transcriptional responses under exposure of micropollutants. This study investigated cometabolic biodegradation of a selected antibiotic, cephalexin (CFX), by an enriched nitrifying culture through a series of batch experiments, together with the assessments of enzymatic activity, key gene expression, and biotoxicity of the degradation products. More than 99% CFX with an initial concentration of 50 μg/L could be removed with the presence of ammonium, while <44% of CFX removal was observed in the absence of ammonium, suggesting the cometabolic degradation of CFX by ammonia-oxidizing bacteria (AOB). After the addition of 50 μg/L CFX, the ammonia oxidizing rate (AOR) decreased from 36.6 to 11.0 mg N/(L·h·g VSS), followed by a slight recovery when CFX concentration decreased to below 8 μg/L. Ammonia monooxygenase (AMO) activity showed a similar trend with that of AOR. The quantitative reverse transcription PCR assay indicated that the expression level of amoA gene was significantly upregulated (up to 3-fold, p < 0.05) due to the addition of CFX, while decreased to the normal level once CFX was degraded, suggesting a mechanism of AOB to neutralize the toxicity of CFX by metabolizing ammonia more effectively. Meanwhile, the biotoxicity test showed the degradation products of CFX did not exhibit any antibacterial impacts in terms of cell viability, compared to the parent compounds. Our finding shed a light on AMO-mediated cometabolic biodegradation of antibiotics in nitrifying cultures.
Collapse
Affiliation(s)
- Bingzheng Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Bing-Jie Ni
- School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
| |
Collapse
|
12
|
Laloo AE, Wei J, Wang D, Narayanasamy S, Vanwonterghem I, Waite D, Steen J, Kaysen A, Heintz-Buschart A, Wang Q, Schulz B, Nouwens A, Wilmes P, Hugenholtz P, Yuan Z, Bond PL. Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5386-5397. [PMID: 29620869 DOI: 10.1021/acs.est.7b04273] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.
Collapse
Affiliation(s)
- Andrew E Laloo
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Justin Wei
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education , Hunan University , Changsa 410082 , China
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - David Waite
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Jason Steen
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Anne Kaysen
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Qilin Wang
- Griffith School of Engineering & Centre for Clean Environment and Energy , Griffith University , Nathan , QLD 4111 , Australia
| | - Benjamin Schulz
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Philip L Bond
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| |
Collapse
|