1
|
Liu J, Wang C, Zhou J, Dong K, Elsamadony M, Xu Y, Fujii M, Wei Y, Wang D. Thermodynamics and explainable machine learning assist in interpreting biodegradability of dissolved organic matter in sludge anaerobic digestion with thermal hydrolysis. BIORESOURCE TECHNOLOGY 2024; 412:131382. [PMID: 39214181 DOI: 10.1016/j.biortech.2024.131382] [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: 07/07/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Dissolved organic matter (DOM) is essential in biological treatment, yet its specific roles remain incompletely understood. This study introduces a machine learning (ML) framework to interpret DOM biodegradability in the anaerobic digestion (AD) of sludge, incorporating a thermodynamic indicator (λ). Ensemble models such as Xgboost and LightGBM achieved high accuracy (training: 0.90-0.98; testing: 0.75-0.85). The explainability of the ML models revealed that the features λ, measured m/z, nitrogen to carbon ratio (N/C), hydrogen to carbon ratio (H/C), and nominal oxidation state of carbon (NOSC) were significant formula features determining biodegradability. Shapley values further indicated that the biodegradable DOM were mostly formulas with λ lower than 0.03, measured m/z value higher than 600 Da, and N/C ratios higher than 0.2. This study suggests that a strategy based on ML and its explainability, considering formula features, particularly thermodynamic indicators, provides a novel approach for understanding and estimating the biodegradation of DOM.
Collapse
Affiliation(s)
- Jibao Liu
- Department of Civil and Environmental Engineering, School of Environment and Society, Tokyo Institute of Technology, 2-12-1-M1-22 Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Chenlu Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiahui Zhou
- Department of Civil and Environmental Engineering, School of Environment and Society, Tokyo Institute of Technology, 2-12-1-M1-22 Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kun Dong
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541006, China
| | - Mohamed Elsamadony
- Department of Mechanical Engineering, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia; Center for Refining and Advanced Chemicals, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Yufeng Xu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541006, China.
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, School of Environment and Society, Tokyo Institute of Technology, 2-12-1-M1-22 Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yuansong Wei
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dunqiu Wang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541006, China
| |
Collapse
|
2
|
Yang X, Feng K, Wang S, Yuan MM, Peng X, He Q, Wang D, Shen W, Zhao B, Du X, Wang Y, Wang L, Cao D, Liu W, Wang J, Deng Y. Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation. MICROBIOME 2024; 12:166. [PMID: 39244624 PMCID: PMC11380791 DOI: 10.1186/s40168-024-01890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment. RESULTS During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions. CONCLUSIONS All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.
Collapse
Affiliation(s)
- Xingsheng Yang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94704, USA
| | - Xi Peng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Danrui Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Bo Zhao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingcheng Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Linlin Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Dong Cao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenzong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Jianjun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
3
|
Song Y, Cao X, Li SA, Li Z, Grossart HP, Ma H. Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 367:122011. [PMID: 39094415 DOI: 10.1016/j.jenvman.2024.122011] [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: 01/25/2024] [Revised: 07/13/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.
Collapse
Affiliation(s)
- Yingyue Song
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Zhe Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 16775, Neuglobsow, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
| |
Collapse
|
4
|
Cao X, Li SA, Huang H, Ma H. Wildfire Impacts on Molecular Changes of Dissolved Organic Matter during Its Passage through Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38904350 DOI: 10.1021/acs.est.3c11056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The frequency and intensity of global wildfires are escalating, leading to an increase in derived pyrogenic dissolved organic matter (pyDOM), which potentially influences the riverine carbon reservoir and poses risks to drinking water safety. However, changes in pyDOM properties as it traverses through soil to water bodies are highly understudied due to the challenges of simulating such processes under laboratory conditions. In this study, we extracted soil DOM along hillslope gradients and soil depths in both burned and unburned catchments post wildfire. Using high-resolution mass spectrometry and a substrate-explicit model, we observed significant increases in the relative abundance of condensed aromatics (ConAC) and tannins in wildfire-affected soil DOM. Wildfire-affected soil DOM also displayed a broader spectrum of molecular and thermodynamic properties, indicative of its diverse composition and reactivity. Furthermore, as the fire-induced weakening of topsoil microbial reprocessing abilities hindered the transformation of plant-derived DOM, the relative abundance of lignin-like compounds increased with soil depth in the fire regions. Meanwhile, the distribution of shared molecular formulas along the hillslope gradient (from shoulder to toeslope) exhibited analogous patterns in both burned and unburned catchments. Although there was an increased prevalence of ConAC and tannin in the burned catchments, the relative abundance of these fractions diminished along the hillslope in all three catchments. Based on the substrate-explicit model, the biodegradability exhibited by wildfire-affected DOM fractions offers the possibility of its conversion along hillslopes. Our findings reveal the spatial distribution of DOM properties after a wildfire, facilitating accurate evaluation of dissolved organic carbon composition involved in the watershed-scale carbon cycle.
Collapse
Affiliation(s)
- Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hai Huang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| |
Collapse
|
5
|
Li SA, Wang Q, Ma H, Cao X, Song Y, Cui F, Tanentzap AJ. Photochemical processes transform dissolved organic matter differently depending on its initial composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171465. [PMID: 38453086 DOI: 10.1016/j.scitotenv.2024.171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
Dissolved organic matter (DOM) is one of the most important fluxes in the global carbon cycle but its response to light exposure remains unclear at a molecular-level. The chemical response of DOM to light should vary with its molecular composition and environmental conditions while some basic hypotheses are still unclear, such as the balance between photobleaching and photo-humification and the question of oxidative properties. Here we exposed aquatic DOM from diverse freshwaters impacted by different levels of anthropogenic activity and algal exudates to environmentally-realistic light conditions. We found that photobleaching occurred in DOM with relatively high initial humic content producing low H/C molecules, whereas DOM with low initial humic content was humified. DOM pools with relatively high initial saturation and low aromaticity were prone to transform towards more unsaturated molecular formulae and high H/C molecules with a distinct decrease of bioavailability. Photo-transformation was mainly influenced by reactive intermediates, with reactive oxygen species (ROS) playing a dominant role in humification when the initial humus content of DOM was high. In contrast, for algal DOM with high protein content, it was likely that the autoxidation of excited state DOM was more important than indirect oxidation involving ROS. Our results reveal how photo-transformation patterns depend on the initial composition of DOM and provide new insights into the role of photochemical processes in biogeochemical cycling of DOM.
Collapse
Affiliation(s)
- Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qianru Wang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yingyue Song
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Fuyi Cui
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
| |
Collapse
|
6
|
Hu A, Jang KS, Tanentzap AJ, Zhao W, Lennon JT, Liu J, Li M, Stegen J, Choi M, Lu Y, Feng X, Wang J. Thermal responses of dissolved organic matter under global change. Nat Commun 2024; 15:576. [PMID: 38233386 PMCID: PMC10794202 DOI: 10.1038/s41467-024-44813-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The diversity of intrinsic traits of different organic matter molecules makes it challenging to predict how they, and therefore the global carbon cycle, will respond to climate change. Here we develop an indicator of compositional-level environmental response for dissolved organic matter to quantify the aggregated response of individual molecules that positively and negatively associate with warming. We apply the indicator to assess the thermal response of sediment dissolved organic matter in 480 aquatic microcosms along nutrient gradients on three Eurasian mountainsides. Organic molecules consistently respond to temperature change within and across contrasting climate zones. At a compositional level, dissolved organic matter in warmer sites has a stronger thermal response and shows functional reorganization towards molecules with lower thermodynamic favorability for microbial decomposition. The thermal response is more sensitive to warming at higher nutrients, with increased sensitivity of up to 22% for each additional 1 mg L-1 of nitrogen loading. The utility of the thermal response indicator is further confirmed by laboratory experiments and reveals its positive links to greenhouse gas emissions.
Collapse
Affiliation(s)
- Ang Hu
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Wenqian Zhao
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Jinfu Liu
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Mingjia Li
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - James Stegen
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Mira Choi
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianjun Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
7
|
Tureţcaia AB, Garayburu-Caruso VA, Kaufman MH, Danczak RE, Stegen JC, Chu RK, Toyoda JG, Cardenas MB, Graham EB. Rethinking Aerobic Respiration in the Hyporheic Zone under Variation in Carbon and Nitrogen Stoichiometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15499-15510. [PMID: 37795960 PMCID: PMC10586321 DOI: 10.1021/acs.est.3c04765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Hyporheic zones (HZs)─zones of groundwater-surface water mixing─are hotspots for dissolved organic matter (DOM) and nutrient cycling that can disproportionately impact aquatic ecosystem functions. However, the mechanisms affecting DOM metabolism through space and time in HZs remain poorly understood. To resolve this gap, we investigate a recently proposed theory describing trade-offs between carbon (C) and nitrogen (N) limitations as a key regulator of HZ metabolism. We propose that throughout the extent of the HZ, a single process like aerobic respiration (AR) can be limited by both DOM thermodynamics and N content due to highly variable C/N ratios over short distances (centimeter scale). To investigate this theory, we used a large flume, continuous optode measurements of dissolved oxygen (DO), and spatially and temporally resolved molecular analysis of DOM. Carbon and N limitations were inferred from changes in the elemental stoichiometric ratio. We show sequential, depth-stratified relationships of DO with DOM thermodynamics and organic N that change across centimeter scales. In the shallow HZ with low C/N, DO was associated with the thermodynamics of DOM, while deeper in the HZ with higher C/N, DO was associated with inferred biochemical reactions involving organic N. Collectively, our results suggest that there are multiple competing processes that limit AR in the HZ. Resolving this spatiotemporal variation could improve predictions from mechanistic models, either via more highly resolved grid cells or by representing AR colimitation by DOM thermodynamics and organic N.
Collapse
Affiliation(s)
- Anna B. Tureţcaia
- Department
of Earth and Planetary Sciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | | | - Matthew H. Kaufman
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Earth, Environment, and Physics, Worcester
State University, Worcester, Massachusetts 01602, United States
| | - Robert E. Danczak
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - James C. Stegen
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
- School
of the Environment, Washington State University, Pullman, Washington 99164, United States
| | - Rosalie K. Chu
- Environmental
Molecular Sciences Laboratory, Richland, Washington 99352, United States
| | - Jason G. Toyoda
- Environmental
Molecular Sciences Laboratory, Richland, Washington 99352, United States
| | - M. Bayani Cardenas
- Department
of Earth and Planetary Sciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Emily B. Graham
- Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
- School
of Biological Sciences, Washington State
University, Pullman, Washington 99164, United States
| |
Collapse
|
8
|
Yang Y, Wang Q, Xue J, Tian S, Du Y, Xie X, Gan Y, Deng Y, Wang Y. Organic matter degradation and arsenic enrichment in different floodplain aquifer systems along the middle reaches of Yangtze River: A thermodynamic analysis. WATER RESEARCH 2023; 239:120072. [PMID: 37207456 DOI: 10.1016/j.watres.2023.120072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Geogenic arsenic (As) contaminated groundwater has been widely accepted associating with dissolved organic matter (DOM) in aquifers, but the underlying enrichment mechanism at molecular-level from a thermodynamic perspective is poorly evidenced. To fill this gap, we contrasted the optical properties and molecular compositions of DOM coupled with hydrochemical and isotopic data in two floodplain aquifer systems with significant As variations along the middle reaches of Yangtze River. Optical properties of DOM indicate that groundwater As concentration is mainly associated with terrestrial humic-like components rather than protein-like components. Molecular signatures show that high As groundwater has lower H/C ratios, but greater DBE, AImod, and NOSC values. With the increase of groundwater As concentration, the relative abundance of CHON3 formulas gradually decreased while that of CHON2 and CHON1 increased, indicating the importance of N-containing organics in As mobility, which is also evidenced by nitrogen isotope and groundwater chemistry. Thermodynamic calculation demonstrated that organic matter with higher NOSC values preferentially favored the reductive dissolution of As-bearing Fe(III) (hydro)oxides minerals and thus promoted As mobility. These findings could provide new insights to decipher organic matter bioavailability in As mobilization from a thermodynamical perspective and are applicable to similar geogenic As-affected floodplain aquifer systems.
Collapse
Affiliation(s)
- Yijun Yang
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Qian Wang
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Jiangkai Xue
- Institute of Geological Survey, China University of Geosciences, Wuhan 430074, PR China
| | - Shuhang Tian
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Yao Du
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Xianjun Xie
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Yiqun Gan
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| | - Yamin Deng
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China.
| | - Yanxin Wang
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & School of Environmental Studies, China University of Geosciences, Wuhan 430078, PR China
| |
Collapse
|
9
|
Max BL, Angolile CM, Raymond VG, Mashauri HL. The dawn of repurposing vitamins as potential novel antimicrobial agents: A call for global emergency response amidst AMR crisis. Health Sci Rep 2023; 6:e1276. [PMID: 37216052 PMCID: PMC10199457 DOI: 10.1002/hsr2.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Amidst, the global pandemic of antimicrobial resistance (AMR), the rate at which AMR increases overwhelms the increased efforts to discover new effective antimicrobials. There is a persistent need for alternative treatment modalities so as to keep up with the pace. AMR is the leading cause of death in the world and its health and economic consequences suggest the urgent need for sustainable interventions. Vitamins have consistently proven to have antimicrobial activity as well as slowing down the AMR rate by influencing the AMR genes even towards extensive multidrug resistant strains. Evidences suggest that the use of some vitamins on their own or in combination with existing antimicrobial agents could be a breakthrough towards combating AMR. This will widen the antimicrobial agents' options in the treatment arena, preserve the antimicrobial agents susceptible to develop resistant so that they can be used in severe infections only, reduce the tension and burden of the AMR crisis significantly and give enough room for development of new antimicrobial agents. Moreover, almost all viral, fungal, parasitic and bacterial resistant strains of concern as listed by World Health Organization have been found to be sensitive to several vitamins either synergistically with other antimicrobials or independently. Considering their widened spectrum of immunomodulatory and antimicrobial effect, some vitamins can further be repositioned as prophylactic antimicrobial agents in clinical situations like in presurgeries prophylaxis so as to avoid unnecessary use of antimicrobials especially antibiotics. Various relevant AMR stakeholders should invest in clinical trials and systematic reviews with available data to enable quick repositioning of some potential vitamins as antimicrobial agents as an emergency rapid response towards AMR Crisis. This includes the preparation of guidelines containing specificity of which vitamin to be used for treatment of which type of infection.
Collapse
Affiliation(s)
- Baraka L. Max
- Department of Epidemiology and Biostatistics, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of Community Medicine, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
| | - Cornel M. Angolile
- Department of Epidemiology and Biostatistics, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of Community Medicine, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of PhysiologyKilimanjaro Christian Medical University CollegeMoshiTanzania
| | - Vicky G. Raymond
- Department of Epidemiology and Biostatistics, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of Internal MedicineKilimanjaro Christian Medical University CollegeMoshiTanzania
| | - Harold L. Mashauri
- Department of Epidemiology and Biostatistics, Institute of Public HealthKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of PhysiologyKilimanjaro Christian Medical University CollegeMoshiTanzania
- Department of Internal MedicineKilimanjaro Christian Medical University CollegeMoshiTanzania
| |
Collapse
|
10
|
Hu A, Jang KS, Meng F, Stegen J, Tanentzap AJ, Choi M, Lennon JT, Soininen J, Wang J. Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10504-10516. [PMID: 35737964 DOI: 10.1021/acs.est.2c01432] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels microbial metabolism and regulates biogeochemical cycles. Individual DOM molecules have unique functional traits, but how their assemblages vary deterministically under global change remains poorly understood. Here, we examine DOM and associated bacteria in 300 aquatic microcosms deployed on mountainsides that span contrasting temperatures and nutrient gradients. Based on molecular trait dimensions of reactivity and activity, we partition the DOM composition into labile-active, recalcitrant-active, recalcitrant-inactive, and labile-inactive fractions and quantify the relative influences of deterministic and stochastic processes governing the assembly of each. At both subtropical and subarctic study sites, the assembly of labile or recalcitrant molecules in active fractions is primarily governed by deterministic processes, while stochastic processes are more important for the assembly of molecules within inactive fractions. Surprisingly, the importance of deterministic selection increases with global change gradients for recalcitrant molecules in both active and inactive fractions, and this trend is paralleled by changes in the deterministic assembly of microbial communities and environmental filtering, respectively. Together, our results highlight the shift in focus from potential reactivity to realized activity and indicate that active and inactive fractions of DOM assemblages are structured by contrasting processes, and their recalcitrant components are consistently sensitive to global change. Our study partitions the DOM molecular composition across functional traits and links DOM with microbes via a shared ecological framework of assembly processes. This integrated approach opens new avenues to understand the assembly and turnover of organic carbon in a changing world.
Collapse
Affiliation(s)
- Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - James Stegen
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, U.K
| | - Mira Choi
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FIN 00014, Finland
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
11
|
Hu A, Choi M, Tanentzap AJ, Liu J, Jang KS, Lennon JT, Liu Y, Soininen J, Lu X, Zhang Y, Shen J, Wang J. Ecological networks of dissolved organic matter and microorganisms under global change. Nat Commun 2022; 13:3600. [PMID: 35739132 PMCID: PMC9226077 DOI: 10.1038/s41467-022-31251-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/09/2022] [Indexed: 12/13/2022] Open
Abstract
Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions. Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.
Collapse
Affiliation(s)
- Ang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China.,College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Mira Choi
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jinfu Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China.,Nanchang Institute of Technology, Nanchang, 330099, China
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Xiancai Lu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yunlin Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ji Shen
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
12
|
Cyle KT, Klein AR, Aristilde L, Martínez CE. Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient. J Appl Microbiol 2022; 133:1479-1495. [PMID: 35665577 DOI: 10.1111/jam.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
Abstract
AIM Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. METHODS AND RESULTS In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE. CONCLUSION Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
Collapse
Affiliation(s)
- K Taylor Cyle
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC 3168, Australia
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Carmen Enid Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
13
|
Chakrawal A, Calabrese S, Herrmann AM, Manzoni S. Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth. Front Microbiol 2022; 13:859063. [PMID: 35656001 PMCID: PMC9152356 DOI: 10.3389/fmicb.2022.859063] [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: 01/20/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (NInorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and NInorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.
Collapse
Affiliation(s)
- Arjun Chakrawal
- Department of Physical Geography, Stockholm University, Stockholm, Sweden.,Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Salvatore Calabrese
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, United States
| | - Anke M Herrmann
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Stefano Manzoni
- Department of Physical Geography, Stockholm University, Stockholm, Sweden.,Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| |
Collapse
|
14
|
Little CJ, Rizzuto M, Luhring TM, Monk JD, Nowicki RJ, Paseka RE, Stegen JC, Symons CC, Taub FB, Yen JDL. Movement with meaning: integrating information into meta‐ecology. OIKOS 2022. [DOI: 10.1111/oik.08892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chelsea J. Little
- Biodiversity Research Centre, Univ. of British Columbia Vancouver BC Canada
- School of Environmental Science, Simon Fraser Univ. Burnaby BC Canada
| | - Matteo Rizzuto
- Dept of Biology, Memorial Univ. of Newfoundland St. John's NL Canada
| | | | - Julia D. Monk
- School of the Environment, Yale Univ. New Haven CT USA
| | - Robert J. Nowicki
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory Summerland Key FL USA
| | - Rachel E. Paseka
- Dept of Ecology, Evolution and Behavior, Univ. of Minnesota Saint Paul MN USA
| | | | - Celia C. Symons
- Dept of Ecology and Evolutionary Biology, Univ. of California Irvine CA USA
| | - Frieda B. Taub
- School of Aquatic and Fishery Sciences, Univ. of Washington Seattle WA USA
| | - Jian D. L. Yen
- School of BioSciences, Univ. of Melbourne, Melbourne, Australia, and Arthur Rylah Inst. for Environmental Reserach Heidelberg Victoria Australia
| |
Collapse
|
15
|
Abstract
Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law [Formula: see text] and to the growth yield by [Formula: see text] These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.
Collapse
|
16
|
Thermodynamics of Soil Microbial Metabolism: Applications and Functions. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11114962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The thermodynamic characterization of soils would help to study and to understand their strategies for survival, as well as defining their evolutionary state. It is still a challenging goal due to difficulties in calculating the thermodynamic state variables (enthalpy, Gibbs energy, and entropy) of the reactions taking place in, and by, soils. Advances in instrumentation and methodologies are bringing options for those calculations, boosting the interest in this subject. The thermodynamic state variables involve considering the soil microbial functions as key channels controlling the interchange of matter and energy between soil and the environment, through the concept of microbial energy use efficiency. The role of microbial diversity using the energy from the soil organic substrates, and, therefore, the who, where, with whom, and why of managing that energy is still unexplored. It could be achieved by unraveling the nature of the soil organic substrates and by monitoring the energy released by the soil microbial metabolism when decomposing and assimilating those substrates. This review shows the state of the art of these concepts and the future impact of thermodynamics on soil science and on soil ecology.
Collapse
|
17
|
Garayburu-Caruso VA, Danczak RE, Stegen JC, Renteria L, Mccall M, Goldman AE, Chu RK, Toyoda J, Resch CT, Torgeson JM, Wells J, Fansler S, Kumar S, Graham EB. Using Community Science to Reveal the Global Chemogeography of River Metabolomes. Metabolites 2020; 10:518. [PMID: 33419380 PMCID: PMC7767024 DOI: 10.3390/metabo10120518] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022] Open
Abstract
River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.
Collapse
Affiliation(s)
- Vanessa A. Garayburu-Caruso
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Robert E. Danczak
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - James C. Stegen
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Lupita Renteria
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Marcy Mccall
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Amy E. Goldman
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA; (R.K.C.); (J.T.)
| | - Jason Toyoda
- Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA; (R.K.C.); (J.T.)
| | - Charles T. Resch
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Joshua M. Torgeson
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Jacqueline Wells
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA;
| | - Sarah Fansler
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Swatantar Kumar
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; (V.A.G.-C.); (R.E.D.); (J.C.S.); (L.R.); (M.M.); (A.E.G.); (C.T.R.); (J.M.T.); (S.F.); (S.K.)
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| |
Collapse
|