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Qin W, Wei SP, Zheng Y, Choi E, Li X, Johnston J, Wan X, Abrahamson B, Flinkstrom Z, Wang B, Li H, Hou L, Tao Q, Chlouber WW, Sun X, Wells M, Ngo L, Hunt KA, Urakawa H, Tao X, Wang D, Yan X, Wang D, Pan C, Weber PK, Jiang J, Zhou J, Zhang Y, Stahl DA, Ward BB, Mayali X, Martens-Habbena W, Winkler MKH. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat Microbiol 2024; 9:524-536. [PMID: 38297167 DOI: 10.1038/s41564-023-01593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.
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Affiliation(s)
- Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Stephany P Wei
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Eunkyung Choi
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - Xiangpeng Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | | | - Xianhui Wan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Baozhan Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hanyan Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Lei Hou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wyatt W Chlouber
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xin Sun
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Michael Wells
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Long Ngo
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Xuanyu Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Dongyu Wang
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Chongle Pan
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
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Godfrey B, Li B, Gottshall E, Brysons S, Abrahamson B, Winkler M. Co-immobilization of AOA strains with anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions. Chemosphere 2023; 342:140192. [PMID: 37722534 DOI: 10.1016/j.chemosphere.2023.140192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Hydrogel encapsulation of ammonium oxidizing archaea (AOA) along with anammox bacteria holds potential to enable mainstream partial nitritation (PN)-anammox process attributing to AOA's high affinity to ammonia and oxygen. This study explored the growth of AOA and anammox in hydrogel-based synthetic biogranules by testing two AOA strains, three types of hydrogel beads and two substrate levels, to identify the optimal combination favoring the concomitant growth of AOA and anammox. The AOA Nitrososphaera viennensis (AOA-NV) exhibited higher abundance (10-2.3±0.6 AOA/16S) than the AOA-DW (10-4.7±0.8 AOA/16S) during the entire experimental period. Amongst the three types of hydrogel beads, the PVA-SA-BaCl2 (140 days) and PVA-SA-H3BO3 beads (>180 days) exhibited better long-term structural stability than the PEGDMA-SA-CaCl2 beads. The PVA-SA-H3BO3 beads exhibited the best long-term stability and both the PVA/SA BaCl2 and PVA-SA-H3BO3 beads had comparable ability to retain AOA, anammox and the overall microbial community. Substrate conditions rather than the bead type primarily controlled the microbial community structure. Modest substrate concentrations (1 mM NH4+-N in the feed and 0.8 mg/L dissolved oxygen (DO) in the reactor during aeration phase) followed by low substrate conditions (0.1 mM NH4+-N and 0.2 mg DO/L) both supported the growth of AOA and anammox, while the low substrate condition also suppressed the growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), with AOA /AOB and anammox/NOB ratio of 0.7 and 0.4 at moderate substrate condition and 16.5 and 2.6 at low substrate condition.
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Affiliation(s)
- Bruce Godfrey
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Bo Li
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA.
| | - Ekaterina Gottshall
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Samuel Brysons
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Britt Abrahamson
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Mari Winkler
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
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Candry P, Abrahamson B, Stahl DA, Winkler MKH. Microbially mediated climate feedbacks from wetland ecosystems. Glob Chang Biol 2023; 29:5169-5183. [PMID: 37386740 DOI: 10.1111/gcb.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%-30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change.
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Affiliation(s)
- Pieter Candry
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Britt Abrahamson
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - David Allan Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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Li B, Godfrey BJ, RedCorn R, Candry P, Abrahamson B, Wang Z, Goel R, Winkler MKH. Mainstream nitrogen removal from low temperature and low ammonium strength municipal wastewater using hydrogel-encapsulated comammox and anammox. Water Res 2023; 242:120303. [PMID: 37419028 DOI: 10.1016/j.watres.2023.120303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Application of partial nitritation (PN)-anammox to mainstream wastewater treatment faces challenges in low water temperature and low ammonium strength. In this study, a continuous flow PN-anammox reactor with hydrogel-encapsulated comammox and anammox was designed and operated for nitrogen removal from mainstream wastewater with low temperature. Long-term operation with synthetic and real wastewater as the feed demonstrated nearly complete ammonium and total inorganic nitrogen (TIN) removal by the reactor at temperatures as low as 10 °C. A significantly decreased nitrogen removal performance and biomass activity was observed in the reactor at 4 °C before a selective heating strategy was employed. A novel heating technology using radiation to heat carbon black co-encapsulated in the hydrogel matrix with biomass was used to selectively heat biomass but not water in the treatment system. This selective heating technology enabled nearly complete ammonium removal and 89.4 ± 4.3 % TIN removal at influent temperature of 4 °C and reactor temperature 5 °C. Activity tests suggested selective heating brought the biomass activity at influent temperatures of 4 °C and reactor temperature 5 °C to a level comparable to that at 10 °C. Comammox and anammox were consistently present in the system and spatially organized in the hydrogel beads as revealed by qPCR and fluorescence in-situ hybridization (FISH). The abundance of comammox largely decreased by 3 orders of magnitude during the operation at 4 °C, and rapidly recovered after the application of selective heating. The anammox-comammox technology tested in this study essentially enabled mainstream shortcut nitrogen removal, and the selective heating ensured good performance of the technology at temperature as low as 5 °C.
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Affiliation(s)
- Bo Li
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA.
| | - Bruce J Godfrey
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - Raymond RedCorn
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - Pieter Candry
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - Britt Abrahamson
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
| | - Zhiwu Wang
- Virginia Polytechnic Institute and State University, Department of Biological Systems Engineering, 1230 Washington St. SW, Blacksburg VA 24061, VA 20147, USA
| | - Ramesh Goel
- The University of Utah, Department of Civil & Environmental Engineering, 110 S. Central Campus Drive, 2000MCE, Salt Lake City, UT 84112, USA
| | - Mari-K H Winkler
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA 98195, USA
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Gottshall EY, Godfrey B, Li B, Abrahamson B, Qin W, Winkler M. Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner. Front Microbiol 2022; 13:1022899. [PMID: 36590435 PMCID: PMC9797979 DOI: 10.3389/fmicb.2022.1022899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Apparent contribution of complete ammonia-oxidizing organisms (comammox) to the global nitrogen cycle highlights the necessity for understanding niche differentiation of comammox bacteria among other ammonia oxidizers. While the high affinity for ammonia of the comammox species Nitrospira inopinata suggests their niche partitioning is expected to be centered in oligotrophic environments, their absence in nutrient-depleted environments (such as the oceans) suggests that other (abiotic) factors might control their distribution and spatial localization within microbial communities. Many ammonia- and nitrite-oxidizing organisms are sensitive to light; however, the photosensitivity of comammox has not been explored. Since comammox bacteria encode enzymatic machinery homologous to canonical ammonia-and nitrite-oxidizers, we hypothesized that comammox N. inopinata, the only available pure culture of this group of microorganisms, may be inhibited by illumination in a similar manner. We evaluated the impact of light intensity, wavelength, and duration on the degree of photoinhibition for cultures of the comammox species N. inopinata and the soil ammonia-oxidizing archaea Nitrososphaera viennensis. Both species were highly sensitive to light. Interestingly, mimicking diurnal light exposure caused an uncoupling of ammonia and nitrite oxidation in N. inopinata, indicating nitrite oxidation might be more sensitive to light exposure than ammonia oxidation. It is likely that light influences comammox spatial distribution in natural environments such as surface fresh waters according to diurnal cycles, light attenuation coefficients, and the light penetration depths. Our findings therefore provide ecophysiological insights for further studies on comammox both in field and laboratory settings.
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Affiliation(s)
- Ekaterina Y. Gottshall
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States,*Correspondence: Ekaterina Y. Gottshall,
| | - Bruce Godfrey
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Wei Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Mari Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
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