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Robles-Lecompte A, Cheng J, McKenna AM, Chang NB. Linking pattern shifts of dissolved organic nitrogen fractional removal with microbial species richness in a cascade upflow biofiltration process. WATER RESEARCH 2024; 264:122130. [PMID: 39146847 DOI: 10.1016/j.watres.2024.122130] [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: 11/15/2023] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 08/17/2024]
Abstract
Nutrient pollution has become an important issue to solve in stormwater runoff due to the fast population growth and urbanization that impacts water quality and triggers harmful algal blooms. There is an acute need to link the dissolved organic nitrogen (DON) decomposition with the coupled nitrification and denitrification pathways to realize the pattern shifts in the nitrogen cycle. This paper presented a lab-scale cascade upflow biofiltration system for comparison of nitrate and phosphate removal from stormwater matrices through two specialty adsorbents at three influent conditions. The two specialty adsorbents are denoted as biochar iron and perlite integrated green environmental media (BIPGEM) and zero-valent iron and perlite-based green environmental media (ZIPGEM). An initial condition with stormwater runoff, a second condition with spiked nitrate, and a third condition with spiked nitrate and phosphate were used in this study. To differentiate nitrifier and denitrifier population dynamics associated with the decomposition of DON, integrative analysis of quantitative polymerase chain reaction (qPCR) and 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were performed in association with nitrate removal efficiencies for both media with or without the presence of phosphate. While the qPCR may detect one gene for a single microbe or pathogen and realize the microbial population dynamics in the bioreactors, the 21 T FT-ICR MS can separate and assign elemental compositions to identify organic compounds of DON. Results indicated that ZIPGEM obtained a higher potential for nutrient removal than BIPGEM when the influent was spiked with nitrate and phosphate simultaneously. The sustainable, scalable, and adaptable upflow bioreactors operated in sequence (in a cascade mode) can be expanded flexibly on an as-needed basis to meet the local water quality standards showing process reliability, resilience, and sustainability simultaneously.
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Affiliation(s)
- Alejandra Robles-Lecompte
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Jinxiang Cheng
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
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Zhu J, Chen G, Tang S, Cheng K, Wu K, Cai Z, Zhou J. The micro-ecological feature of colonies is a potential strategy for Phaeocystis globosa bloom formation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174134. [PMID: 38909792 DOI: 10.1016/j.scitotenv.2024.174134] [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: 01/31/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Phaeocystis globosa is among the dominant microalgae associated with harmful algal blooms. P. globosa has a polymorphic life cycle and its ecological success has been attributed to algal colony formation, however, few studies have assessed differences in microbial communities and their functional profiles between intra- and extra-colonies during P. globosa blooms. To address this, environmental and metagenomics tools were used to conduct a time-series analysis of the bacterial composition and metabolic characteristics of intra- and extra-colonies during a natural P. globosa bloom. The results show that bacterial composition, biodiversity, and network interactions differed significantly between intra- and extra-colonies. Dominant extra-colonial bacteria were Bacteroidia and Saccharimonadis, while dominant intra-colonial bacteria included Alphaproteobacteria and Gammaproteobacteria. Despite the lower richness and diversity observed in the intra-colonial bacterial community, relative to extra-colonies, the complexity and interconnectedness of the intra-colonial networks were higher. Regarding bacterial function, more functional genes were enriched in substance metabolism (polysaccharides, iron element and dimethylsulfoniopropionate) and signal communication (quorum sensing, indoleacetic acid-IAA) pathways in intra- than in extra-colonies. Conceptual model construction showed that microbial cooperative synthesis of ammonium, vitamin B12, IAA, and siderophores were strongly related to the P. globosa bloom, particularly in the intra-colonial environment. Overall, our data highlight the differences in bacterial structure and functions within and outside the colony during P. globosa blooms. These findings represent fundamental information indicating that phenotypic heterogeneity is a selective strategy that improves microbial population competitiveness and environmental adaptation, benefiting P. globosa bloom formation and persistence.
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Affiliation(s)
- Jianming Zhu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong Province, PR China
| | - Si Tang
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Keke Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Kebi Wu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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3
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Li LP, Jiao XY, Peng S, Wei DB, Jin YC, Wang CS, Pan D, Liu P, Wang XR, Tang YP, Ren D, Liu XH. Exploring the variations in molecular characteristics of dissolved organic matter driven by aquaculture types. WATER RESEARCH 2024; 266:122355. [PMID: 39226743 DOI: 10.1016/j.watres.2024.122355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/10/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
In recent decades, global aquaculture has expanded rapidly, raising concerns about coastal environmental degradation due to unregulated or poorly regulated discharge of aquaculture tailwater. Despite the crucial role of dissolved organic matter (DOM) in biogeochemical processes and aquatic biodiversity, the influence of aquaculture type on the molecular characteristics of DOM remains largely unexplored. Herein, this study investigated the variations in chemical and spectroscopic properties as well as molecular characteristics and composition of DOM across different aquaculture types including crustacean, fish and shellfish. Our findings revealed notable differences in DOM quantities among different aquaculture types, with crustacean and fish aquaculture water containing higher DOM amount compared to shellfish aquaculture water. This disparity can be attributed to the more frequent formulated feeds of crustacean and fish in contrast to shellfish aquaculture. Furthermore, distinct differences were also observed in the characteristics and composition of DOM among the different aquaculture waters. Specifically, DOM in shellfish aquaculture water exhibited a higher abundance of unsaturated and reduced molecules as well as increased aromaticity compared to the other two aquaculture waters. Conversely, DOM from fish aquaculture water showed a greater contribution from terrestrial origin characterized by elevated levels of plant-based components such as lignin-like and tannin-like compounds. Interestingly, DOM from shellfish aquaculture water contained lower levels of microbial-derived components such as lipid-like and protein-like compounds, likely due to reduced microorganism populations resulting from lower nutrients availability and higher salinity. Overall, these significant variations in characteristics and composition of DOM underscore the potential impacts of aquaculture type on the DOM biogeochemical cycle and the environmental quality in aquatic ecosystems.
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Affiliation(s)
- Li-Ping Li
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xin-Yi Jiao
- College of Environmental Science and Engineering, China West Normal University, NO.1 Shida Road, Shunqing District, Nanchong 637009, China
| | - Shuang Peng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dong-Bin Wei
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yan-Chao Jin
- Fujian Key Laboratory of Pollution Control & Resource Reuse, College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Cai-Shan Wang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Ding Pan
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Peng Liu
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xue-Rong Wang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Yu-Ping Tang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Dong Ren
- College of Environmental Science and Engineering, China West Normal University, NO.1 Shida Road, Shunqing District, Nanchong 637009, China.
| | - Xin-Hui Liu
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Environment, Beijing Normal University, Beijing 100875, China.
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4
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Liddicoat C, Edwards RA, Roach M, Robinson JM, Wallace KJ, Barnes AD, Brame J, Heintz-Buschart A, Cavagnaro TR, Dinsdale EA, Doane MP, Eisenhauer N, Mitchell G, Rai B, Ramesh SA, Breed MF. Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173543. [PMID: 38821286 DOI: 10.1016/j.scitotenv.2024.173543] [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: 03/27/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.
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Affiliation(s)
- Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Michael Roach
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Kiri Joy Wallace
- Environmental Research Institute, University of Waikato, Hamilton, Aotearoa, New Zealand
| | - Andrew D Barnes
- Environmental Research Institute, University of Waikato, Hamilton, Aotearoa, New Zealand
| | - Joel Brame
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Timothy R Cavagnaro
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Elizabeth A Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), 04103 Leipzig, Germany; Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Grace Mitchell
- Environmental Research Institute, University of Waikato, Hamilton, Aotearoa, New Zealand; Manaaki Whenua - Landcare Research, Hamilton, Aotearoa, New Zealand
| | - Bibishan Rai
- Environmental Research Institute, University of Waikato, Hamilton, Aotearoa, New Zealand
| | - Sunita A Ramesh
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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5
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Han D, Yang Y, Guo Z, Dai S, Jiang M, Zhu Y, Wang Y, Yu Z, Wang K, Rong C, Yu Y. A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective. Foods 2024; 13:2534. [PMID: 39200461 PMCID: PMC11353490 DOI: 10.3390/foods13162534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.
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Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Mingchao Jiang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
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Ma K, Li Y, Song W, Zhou J, Liu X, Wang M, Gong X, Wang L, Tu Q. Disentangling drivers of mudflat intertidal DOM chemodiversity using ecological models. Nat Commun 2024; 15:6620. [PMID: 39103321 DOI: 10.1038/s41467-024-50841-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
Microorganisms consume and transform dissolved organic matter (DOM) into various forms. However, it remains unclear whether the ecological patterns and drivers of DOM chemodiversity are analogous to those of microbial communities. Here, a large-scale investigation is conducted along the Chinese coasts to resolve the intrinsic linkages among the complex intertidal DOM pools, microbial communities and environmental heterogeneity. The abundance of DOM molecular formulae best fits log-normal distribution and follows Taylor's Law. Distance-decay relationships are observed for labile molecular formulae, while latitudinal diversity gradients are noted for recalcitrant molecular formulae. Latitudinal patterns are also observed for DOM molecular features. Negative cohesion, bacterial diversity, and molecular traits are the main drivers of DOM chemodiversity. Stochasticity analyses demonstrate that determinism dominantly shapes the DOM compositional variations. This study unveils the intrinsic mechanisms underlying the intertidal DOM chemodiversity and microbial communities from ecological perspectives, deepening our understanding of microbially driven chemical ecology.
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Affiliation(s)
- Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaofan Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China.
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7
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Xiao R, Huang D, Du L, Tang X, Song B, Yin L, Chen Y, Zhou W, Gao L, Li R, Huang H, Zeng G. Molecular insights into linkages among free-floating macrophyte-derived organic matter, the fate of antibiotic residues, and antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134351. [PMID: 38653136 DOI: 10.1016/j.jhazmat.2024.134351] [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: 11/27/2023] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Macrophyte rhizospheric dissolved organic matter (ROM) served as widespread abiotic components in aquatic ecosystems, and its effects on antibiotic residues and antibiotic resistance genes (ARGs) could not be ignored. However, specific influencing mechanisms for ROM on the fate of antibiotic residues and expression of ARGs still remained unclear. Herein, laboratory hydroponic experiments for water lettuce (Pistia stratiotes) were carried out to explore mutual interactions among ROM, sulfamethoxazole (SMX), bacterial community, and ARGs expression. Results showed ROM directly affect SMX concentrations through the binding process, while CO and N-H groups were main binding sites for ROM. Dynamic changes of ROM molecular composition diversified the DOM pool due to microbe-mediated oxidoreduction, with enrichment of heteroatoms (N, S, P) and decreased aromaticity. Microbial community analysis showed SMX pressure significantly stimulated the succession of bacterial structure in both bulk water and rhizospheric biofilms. Furthermore, network analysis further confirmed ROM bio-labile compositions as energy sources and electron shuttles directly influenced microbial structure, thereby facilitating proliferation of antibiotic resistant bacteria (Methylotenera, Sphingobium, Az spirillum) and ARGs (sul1, sul2, intl1). This investigation will provide scientific supports for the control of antibiotic residues and corresponding ARGs in aquatic ecosystems.
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Affiliation(s)
- Ruihao Xiao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Li Du
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Xiang Tang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lingshi Yin
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yashi Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Wei Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lan Gao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Ruijin Li
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Hai Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
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8
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Yang R, Ji M, Zhang X, He F, Yu Z, Zeng J, Zhao D. Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake. ENVIRONMENTAL RESEARCH 2024; 250:118390. [PMID: 38331139 DOI: 10.1016/j.envres.2024.118390] [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: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.
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Affiliation(s)
- Runhan Yang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Mengting Ji
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Xiaomin Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fei He
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; Ministry of Ecology and Environment, Nanjing Institute of Environment Sciences, Nanjing, 210042, China
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang, 332899, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China.
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9
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Dang C, Morrissey EM. The size and diversity of microbes determine carbon use efficiency in soil. Environ Microbiol 2024; 26:e16633. [PMID: 38733078 DOI: 10.1111/1462-2920.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.
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Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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10
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Xu H, Xiao Q, Dai Y, Chen D, Zhang C, Jiang Y, Xie J. Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data. MICROBIAL ECOLOGY 2023; 86:3043-3056. [PMID: 37831075 DOI: 10.1007/s00248-023-02307-6] [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: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.
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Affiliation(s)
- Hongxiang Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiong Xiao
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Dexin Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Cheng Zhang
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China.
| | - Yongjun Jiang
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
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11
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Wang S, Heal KV, Zhang Q, Yu Y, Tigabu M, Huang S, Zhou C. Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118793. [PMID: 37619380 DOI: 10.1016/j.jenvman.2023.118793] [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: 02/10/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.
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Affiliation(s)
- Shuzhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Qin Zhang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yuanchun Yu
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Mulualem Tigabu
- Swedish University of Agricultural Sciences, Faculty of Forest Science, Southern Swedish Forest Research Centre, P.O. Box 190, SE-234 22, Lomma, Sweden
| | - Shide Huang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354315, Fujian Province, China
| | - Chuifan Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
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12
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Zhang C, Mo S, Liu Z, Chen B, Korshin G, Hertkorn N, Ni J, Yan M. Interpreting pH-Dependent Differential UV/VIS Absorbance Spectra to Characterize Carboxylic and Phenolic Chromophores in Natural Organic Matter. WATER RESEARCH 2023; 244:120522. [PMID: 37660469 DOI: 10.1016/j.watres.2023.120522] [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: 05/12/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Natural organic matter (NOM) is critical for the biogeochemical cycles of energy and many elements in terrestrial and aquatic ecosystems, and protonation-active functional groups in NOM molecules, notably carboxylic and phenolic groups often mediate these critical environmental functions. Molecular heterogeneity, polydispersity and dynamic behavior of NOM complicate achieving an unambiguous description of its molecular properties and reactivity. This study demonstrates that differential ultraviolet-visible (UV/VIS) absorbance spectra (DAS) of NOM acquired at varying pH values exhibit several distinct features associated with the deprotonation of NOM molecules, independent of the environmental provenance of NOM (e.g., surface water, seawater, sediment, and wastewater). The protonation-active functionalities that contribute to the Gaussian distribution bands present in the DAS were identified here by comparing characteristic properties of the bands with the stoichiometries of NOM molecules ascertained by Ultrahigh-Resolution Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS). The protonation-active individual chromophores universally present in NOM molecules were identified by a genetic molecular network analysis. The observed DAS features were closely modeled via superimposing DAS spectra of 51 individual protonation-active chromophores. Molecular orbital theory was applied to further interpret the deprotonation of these chromophores, their molecular structure, electron distribution, and electron transitions measured using DAS. The high sensitivity and easy implementation of the DAS approach allows using it as a powerful tool to quantify the molecular properties and reactivity of NOM at environmental concentrations.
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Affiliation(s)
- Chenyang Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shansheng Mo
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Zhongli Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Bingya Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98195-2700, United States
| | - Norbert Hertkorn
- Helmholtz-Centre Munich, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Mingquan Yan
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China..
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13
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White AM, Van Frost SR, Jauquet JM, Magness AM, McMahon KD, Remucal CK. Quantifying the Role of Simultaneous Transformation Pathways in the Fate of the Novel Aquatic Herbicide Florpyrauxifen-Benzyl. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12421-12430. [PMID: 37552855 DOI: 10.1021/acs.est.3c03343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Predicting the fate of organic compounds in the environment is challenging due to the inability of laboratory studies to replicate field conditions. We used the intentionally applied aquatic herbicide florpyrauxifen-benzyl (FPB) as a model compound to investigate the contribution of multiple transformation pathways to organic compound fate in lakes. FPB persisted in five Wisconsin lakes for 5-7 days with an in-lake half-life of <2 days. FPB formed four transformation products, with the bioactive product florpyrauxifen persisting up to 30 days post-treatment. Parallel laboratory experiments showed that FPB degrades to florpyrauxifen via base-promoted hydrolysis. Hydroxy-FPB and hydroxy-florpyrauxifen were identified as biodegradation products, while dechloro-FPB was identified as a photoproduct. Material balance calculations using both laboratory rates and field product concentrations demonstrated that hydrolysis (∼47% of loss), biodegradation (∼20%), sorption (∼13%), and photodegradation (∼4%) occurred on similar timescales. Furthermore, the combined results demonstrated that abiotic and plant-catalyzed hydrolysis of FPB to florpyrauxifen, followed by biodegradation of florpyrauxifen to hydroxy-florpyrauxifen, was the dominant transformation pathway in lakes. This study demonstrates how combined field and laboratory studies can be used to elucidate the role of simultaneous and interacting pathways in the fate of organic compounds in aquatic environments.
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Affiliation(s)
- Amber M White
- Environmental Chemistry and Technology Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Sydney R Van Frost
- Department of Civil and Environmental Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Josie M Jauquet
- Department of Civil and Environmental Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Angela M Magness
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Christina K Remucal
- Environmental Chemistry and Technology Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Civil and Environmental Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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14
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He Y, Luo Y, Wei C, Long L, Wang C, Wu Y. Effects of dissolved organic matter derived from cow manure on heavy metal(loid)s and bacterial community dynamics in mercury-thallium mining waste slag. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:5857-5877. [PMID: 37178440 DOI: 10.1007/s10653-023-01607-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Organic amendments in aided phytostabilization of waste slag containing high levels of heavy metal (loid)s (HMs) are an important way to control the release of HMs in situ. However, the effects of dissolved organic matter (DOM) derived from organic amendments on HMs and microbial community dynamics in waste slag are still unclear. Here, the effect of DOM derived from organic amendments (cow manure) on the geochemical behaviour of HMs and the bacterial community dynamics in mercury (Hg)-thallium (Tl) mining waste slag were investigated. The results showed that the Hg-Tl mining waste slag without the addition of DOM continuously decreased the pH and increased the EC, Eh, SO42-, Hg, and Tl levels in the leachate with increasing incubation time. The addition of DOM significantly increased the pH, EC, SO42-, and arsenic (As) levels but decreased the Eh, Hg, and Tl levels. The addition of DOM significantly increased the diversity and richness of the bacterial community. The dominant bacterial phyla (Proteobacteria, Firmicutes, Acidobacteriota, Actinobacteriota, and Bacteroidota) and genera (Bacillus, Acinetobacter, Delftia, Sphingomonas, and Enterobacter) were changed in association with increases in DOM content and incubation time. The DOM components in the leachate were humic-like substances (C1 and C2), and the DOC content and maximum fluorescence intensity (FMax) values of C1 and C2 in the leachate decreased and first increased and then decreased with increasing incubation time. The correlations between HMs and DOM and the bacterial community showed that the geochemical behaviours of HMs in Hg-Tl mining waste slag were directly influenced by DOM-mediated properties and indirectly influenced by DOM regulation of bacterial community changes. Overall, these results indicated that DOM properties associated with bacterial community changes increased As mobilization but decreased Hg and Tl mobilization from Hg-Tl mining waste slag.
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Affiliation(s)
- Yu He
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Youfa Luo
- Key Laboratory of Kast Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Hostile Environment Ecological Restoration Technology Engineering Research Centre, Guizhou University, Guiyang, 550025, China.
| | - Chaoxiao Wei
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Licui Long
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Chi Wang
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Yonggui Wu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Hostile Environment Ecological Restoration Technology Engineering Research Centre, Guizhou University, Guiyang, 550025, China
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15
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Ishaq SE, Ahmad T, Liang L, Hou J, Dong Y, Yu T, Wang F. Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486324 DOI: 10.1099/ijsem.0.005972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).
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Affiliation(s)
- Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, PR China
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16
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Shen J, Liang Z, Kuzyakov Y, Li W, He Y, Wang C, Xiao Y, Chen K, Sun G, Lei Y. Dissolved organic matter defines microbial communities during initial soil formation after deglaciation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163171. [PMID: 37001675 DOI: 10.1016/j.scitotenv.2023.163171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/13/2023]
Abstract
Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.
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Affiliation(s)
- Jie Shen
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ziyan Liang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yakov Kuzyakov
- Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049 Kazan, Russia
| | - Weitao Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Xiao
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ke Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Geng Sun
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Yanbao Lei
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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17
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Huang J, Yang J, Han M, Wang B, Sun X, Jiang H. Microbial carbon fixation and its influencing factors in saline lake water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162922. [PMID: 36933719 DOI: 10.1016/j.scitotenv.2023.162922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (14C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L-1 h-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L-1 h-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China.
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18
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Lin J, Zhou X, Lu X, Xu Y, Wei Z, Ruan A. Grain size distribution drives microbial communities vertically assemble in nascent lake sediments. ENVIRONMENTAL RESEARCH 2023; 227:115828. [PMID: 37011792 DOI: 10.1016/j.envres.2023.115828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/08/2023]
Abstract
Sediment microbes are crucial for maintaining biogeochemical cycles in aquatic ecosystems, yet the influence of sediment geophysical structure on microbial communities remains unclear. In this study, we collected sediment cores from a nascent reservoir in its initial stage of deposition and utilized the multifractal model to comprehensively characterize the heterogeneity of sediment grain size and pore space. Our results demonstrate that both environmental physiochemistry and microbial community structures varied significantly with depth, with the grain size distribution (GSD) being the key driver of sediment microbial diversity, as revealed by the partial least squares path model (PLS-PM) method. GSD can potentially impact microbial communities and biomass by controlling pore space and organic matter. Overall, this study represents the first attempt to apply soil multifractal models into the integrated description of physical structure in sediment. Our findings provide valuable insights into the vertical distribution of microbial communities.
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Affiliation(s)
- Jie Lin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiaotian Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiang Lu
- Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316 Oslo, Norway
| | - Yaofei Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Zhipeng Wei
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Aidong Ruan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.
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19
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Xue W, Zhang C, Zhou D. Positive and negative effects of recirculating aquaculture water advanced oxidation: O 3 and O 3/UV treatments improved water quality but increased antibiotic resistance genes. WATER RESEARCH 2023; 235:119835. [PMID: 36905731 DOI: 10.1016/j.watres.2023.119835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Recirculating aquaculture systems (RASs) can be efficiently used for aquaculture, and oxidation treatment is commonly used to improve water quality. However, the effects of oxidation treatments on aquaculture water safety and fish yield in RASs are poorly understood. In this study, we tested the effects of O3 and O3/UV treatments on aquaculture water quality and safety during culture of crucian carp. O3 and O3/UV treatments reduced the dissolved organic carbon (DOC) concentration by ∼40% and destroyed the refractory organic lignin-like features. There was enrichment of ammonia oxidizing (Nitrospira, Nitrosomonas, and Nitrosospira) and denitrifying (Pelomonas, Methyloversatilis, and Sphingomonas) bacteria, and N-cycling functional genes were enriched by 23% and 48%, respectively, after O3 and O3/UV treatments. Treatment with O3 and O3/UV reduced NH4+-N and NO2--N in RASs. O3/UV treatment increased fish length and weight as well as probiotics in fish intestine. However, high saturated intermediates and tannin-like features induced antibiotic resistance genes (ARGs) in O3 and O3/UV treatments, by 52% and ∼28%, respectively, and also enhanced horizontal transfer of ARGs. Overall, the application of O3/UV achieved better effects. However, understanding the potential biological risks posed by ARGs in RASs and determining the most efficient water treatment strategies to mitigate these risks should be goals of future work.
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Affiliation(s)
- Wenqi Xue
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Chongjun Zhang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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20
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Ayala-Ortiz C, Graf-Grachet N, Freire-Zapata V, Fudyma J, Hildebrand G, AminiTabrizi R, Howard-Varona C, Corilo YE, Hess N, Duhaime MB, Sullivan MB, Tfaily MM. MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data. MICROBIOME 2023; 11:28. [PMID: 36803638 PMCID: PMC9936664 DOI: 10.1186/s40168-023-01476-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. RESULTS Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. CONCLUSION Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User's guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ), respectively. Video Abstract.
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Affiliation(s)
| | - Nathalia Graf-Grachet
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: Roche, Pleasanton, CA 94588 USA
| | | | - Jane Fudyma
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: University of California, Davis|Department of Plant Pathology, Davis, CA 95616-8751 USA
| | - Gina Hildebrand
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
| | - Roya AminiTabrizi
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: University of Chicago Biological Sciences Division, Metabolomics Platform, Chicago, IL 60637 USA
| | - Cristina Howard-Varona
- Department of Microbiology, Ohio State University, Columbus, OH 43210 USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210 USA
| | - Yuri E. Corilo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Nancy Hess
- Present address: University of California, Davis|Department of Plant Pathology, Davis, CA 95616-8751 USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210 USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210 USA
| | - Malak M. Tfaily
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
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21
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Liu C, Liao K, Wang J, Wu B, Hu H, Ren H. Microbial Transformation of Dissolved Organic Sulfur during the Oxic Process in 47 Full-Scale Municipal Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2118-2128. [PMID: 36608328 DOI: 10.1021/acs.est.2c06776] [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] [Indexed: 06/17/2023]
Abstract
Dissolved organic sulfur (DOS) is a significant part of effluent organic matter of wastewater treatment plants (WWTPs) and poses a potential ecological risk for receiving waters. However, the oxic process is a critical unit of biological wastewater treatment for microorganisms performing organic matter removal, wherein DOS transformation and its mechanism are poorly understood. This study investigated the transformation of DOS during the oxic process in 47 full-scale municipal WWTPs across China from molecular and microbial aspects. Surprisingly, evident differences in DOS variations (ΔDOS) separated sampled WWTPs into two groups: 28 WWTPs with decreased DOS concentrations in effluents (ΔDOS < 0) and 19 WWTPs with increased DOS (ΔDOS > 0). These two groups also presented differences in DOS molecular characteristics: higher nitrogen/carbon (N/C) ratios (0.030) and more peptide-like DOS (8.2%) occurred in WWTPs with ΔDOS > 0, implying that peptide-like DOS generated from microbes contributed to increased DOS in effluents. Specific microbe-DOS correlations (Spearman correlation, p < 0.05) indicated that increased effluent DOS might be explained by peptide-like DOS preferentially being produced during copiotrophic bacterial growth and accumulating due to less active cofactor metabolisms. Considering the potential environmental issues accompanying DOS discharge from WWTPs with ΔDOS > 0, our study highlights the importance of focusing on the transformation and control of DOS in the oxic process.
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Affiliation(s)
- Caifeng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Kewei Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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22
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Guan X, He R, Zhang B, Gao C, Liu F. Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river. Front Microbiol 2023; 14:1133938. [PMID: 37032860 PMCID: PMC10075313 DOI: 10.3389/fmicb.2023.1133938] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
The physicochemical properties and microbial communities have significant annual and seasonal changes in karst aquifers. To explore the changes of microbial community and their relationships with environmental factors, water samples were collected from a typical karst river. Microbial communities in winter (Jan-2017 and Jan-2019) were stable with high similarity in spite of the 2 years sampling interval, but the microbial communities in Aug-2017 was different from that in Aug-2018. In four sampling times, there were 275 shared genera, whose average relative abundance ranging from 89.04 to 96.27%. The winter and summer specific genera were mainly from the recharge of tributary site K6 and discharge of waste water treatment plant (K2 and K3), respectively. The deterministic processes had a more significant effect on the microbial community assembly in winter than that in summer, which was affected by environmental pressure from pollution. Furthermore, antibiotics and inorganic nitrogen pollution affected element cycles of nitrogen and sulfur indirectly through microbial ecological modules in karst river, and the denitrification and desulfurization processes were potentially inhibited. These findings contributed to understand the changes and its assembly mechanism of microbial community, as well as the feedback to environment in polluted karst river.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Ruoxue He
- School of Ocean Sciences, China University of Geosciences, Beijing, China
- Department of Discipline Construction and Technology Development, Chengdu Technological University, Chengdu, China
| | - Biao Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Chengjie Gao
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing, China
- *Correspondence: Fei Liu,
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23
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Gui JY, Rao S, Huang X, Liu X, Cheng S, Xu F. Interaction between selenium and essential micronutrient elements in plants: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158673. [PMID: 36096215 DOI: 10.1016/j.scitotenv.2022.158673] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Nutrient imbalance (i.e., deficiency and toxicity) of microelements is an outstanding environmental issue that influences each aspect of ecosystems. Although the crucial roles of microelements in entire lifecycle of plants have been widely acknowledged, the effective control of microelements is still neglected due to the narrow safe margins. Selenium (Se) is an essential element for humans and animals. Although it is not believed to be indispensable for plants, many literatures have reported the significance of Se in terms of the uptake, accumulation, and detoxification of essential microelements in plants. However, most papers only concerned on the antagonistic effect of Se on metal elements in plants and ignored the underlying mechanisms. There is still a lack of systematic review articles to summarize the comprehensive knowledge on the connections between Se and microelements in plants. In this review, we conclude the bidirectional effects of Se on micronutrients in plants, including iron, zinc, copper, manganese, nickel, molybdenum, sodium, chlorine, and boron. The regulatory mechanisms of Se on these micronutrients are also analyzed. Moreover, we further emphasize the role of Se in alleviating element toxicity and adjusting the concentration of micronutrients in plants by altering the soil conditions (e.g., adsorption, pH, and organic matter), promoting microbial activity, participating in vital physiological and metabolic processes, generating element competition, stimulating metal chelation, organelle compartmentalization, and sequestration, improving the antioxidant defense system, and controlling related genes involved in transportation and tolerance. Based on the current understanding of the interaction between Se and these essential elements, future directions for research are suggested.
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Affiliation(s)
- Jia-Ying Gui
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xinru Huang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Xiaomeng Liu
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China.
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24
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The Effects of Roundup™ on Benthic Microbial Assemblages. ECOLOGIES 2022. [DOI: 10.3390/ecologies3040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Given the wide usage of Roundup, a common herbicide, the impacts of its presence in ecological communities are of great interest. Many studies have investigated the effects of glyphosate, the active ingredient in Roundup, on different factions of an ecosystem including on animals, plants, microorganisms, and nutrients. The current study expanded upon these works using Roundup instead of glyphosate to provide a realistic application in which to observe the development of microbial assemblages and nutrient composition in two different habitats. Winogradsky columns were prepared using benthic material from a ditch and a pond. Varying concentrations of Roundup were introduced to the columns at the beginning of the study and microbial growth and nutrient compositions from each column were measured weekly. The results indicate that the presence of Roundup has varying effects on microorganisms and nutrients. While photosynthetic microbes were negatively impacted, a shift in the microbial composition to heterotrophic microbes indicates that these microorganisms were able to utilize some ingredients in Roundup as a nutrient source. Additionally, the temporal analysis of nutrient compositions indicated that microbes metabolize glyphosate starting with the phosphate moiety even when the other compounds in Roundup are present. While these trends were observed in both benthic habitats, the composition of the ecological community can affect its ability to utilize the ingredients in Roundup as a nutrient source.
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25
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Lv J, Huang Z, Luo L, Zhang S, Wang Y. Advances in Molecular and Microscale Characterization of Soil Organic Matter: Current Limitations and Future Prospects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12793-12810. [PMID: 36037253 DOI: 10.1021/acs.est.2c00421] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soil organic matter (SOM) comprises a continuum of organic materials from granular organic debris to small organic molecules and contains more organic carbon than global vegetation and the atmosphere combined. It has remarkable effects on soil ecological functions and the global carbon cycle as well as the fate of pollutants in the terrestrial ecosystem. Therefore, characterization of SOM is an important topic in soil science, ecology, and environmental science. Chemical complexity and spatial heterogeneity are by far the two biggest challenges to our understanding of SOM. Recent developments in analytical techniques and methods provide the opportunity to reveal SOM composition at the molecular level and to observe its distribution in soils at micro- and nanoscales, which have greatly improved our understanding of SOM. This paper reviews the outstanding advances in SOM characterization regarding these two issues from target and nontarget analyses comprising molecular marker analysis, ultrahigh-resolution mass spectrometry analysis, and in situ microscopic imaging techniques such as synchrotron-based spectromicroscopy, nanoscale secondary ion mass spectrometry, and emerging electron and optical microscopic imaging techniques. However, current techniques and methods remain far from unlocking the unknown properties of SOM. We systematically point out the limitations of the current technologies and outline the future prospects for comprehensive characterization of SOM at the molecular level and micro- and nanoscales, paying particular attention to issues of environmental concern.
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Affiliation(s)
- Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoquan Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Guangdong Key Laboratory of Contaminated Site Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, Guangdong 510045, China
| | - Lei Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Ye QH, Sun GD, Wang YH, Zhang S, Xu Y, Feng L, Simpson MJ, He C, Shi Q, Li LP, Wang JJ. Lake reclamation alters molecular-level characteristics of lacustrine dissolved organic matter - A study of nine lakes in the Yangtze Plain, China. WATER RESEARCH 2022; 222:118884. [PMID: 35905647 DOI: 10.1016/j.watres.2022.118884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
In recent decades, the reclamation of lakes has captured 42% of the total lake area of the Yangtze Plain in China and introduced additional pressure on lacustrine water quality. While lacustrine dissolved organic matter (DOM) is critical in regulating biogeochemical processing and aquatic biodiversity, the impact of reclamation on the molecular-level characteristics of lacustrine DOM remains unexplored. Here, the DOM characteristics altered by reclamation practices in the Yangtze Plain lakes were investigated using fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, and Fourier transform ion cyclotron resonance mass spectrometry. Results demonstrated that reclamation not only elevated the quantity (on average +32%) but also altered the characteristics and composition of lacustrine DOM. Compared to the natural water sites close by, reclamation sites did not significantly alter the DOM aromaticity but significantly lowered the average molecular weight and increased the biolability of DOM. The chromophoric DOM and humic-like fluorescent components were remarkably elevated, but not the protein-like fluorescent components. More lipid-like and condensed aromatic-like components were detected in the lacustrine DOM as compared to the lignin-like, carbohydrate-like, and protein-like components, which may be driven by the increased microbial processing. Overall, the significant alteration in characteristics and composition of lacustrine DOM highlights the potential impact of reclamation on the DOM biogeochemical cycle and the environmental quality in aquatic ecosystems.
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Affiliation(s)
- Quan-Hui Ye
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Guo-Dong Sun
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ying-Hui Wang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Song Zhang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yang Xu
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Lian Feng
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Li-Ping Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou District, Zhuhai, Guangdong 519087, China.
| | - Jun-Jian Wang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Xili, Nanshan, Shenzhen, Guangdong 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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Qi Y, Cao H, Pan W, Wang C, Liang Y. The role of dissolved organic matter during Per- and Polyfluorinated Substance (PFAS) adsorption, degradation, and plant uptake: A review. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129139. [PMID: 35605500 DOI: 10.1016/j.jhazmat.2022.129139] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The negative effects of polyfluoroalkyl substances (PFAS) on the environment and health have recently attracted much attention. This article reviews the influence of soil- and water-derived dissolved organic matter (DOM) on the environmental fate of PFAS. In addition to being co-adsorped with PFAS to increase the adsorption capacity, DOM competes with PFAS for adsorption sites on the surface of the material, thereby reducing the removal rate of PFAS or increasing water solubility, which facilitates desorption of PFAS in the soil. It can quench some active species and inhibit the degradation of PFAS. In contrast, before DOM in water self-degrades, DOM has a greater promoting effect on the degradation of PFAS because DOM can complex with iron, iodine, among others, and act as an electron shuttle to enhance electron transfer. In soil aggregates, DOM can prevent microorganisms from being poisoned by direct exposure to PFAS. In addition, DOM increases the desorption of PFAS in plant root soil, affecting its bioavailability. In general, DOM plays a bidirectional role in adsorption, degradation, and plant uptake of PFAS, which depends on the types and functional groups of DOM. It is necessary to enhance the positive role of DOM in reducing the environmental risks posed by PFAS. In future, attention should be paid to the DOM-induced reduction of PFAS and development of a green and efficient continuous defluorination technology.
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Affiliation(s)
- Yuwen Qi
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Huimin Cao
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Weijie Pan
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Cuiping Wang
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Yanna Liang
- Department of Environmental and Sustainable Engineering, University at Albany, SUNY, Albany, NY 12222, USA
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28
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He C, Liu J, Wang R, Li Y, Zheng Q, Jiao F, He C, Shi Q, Xu Y, Zhang R, Thomas H, Batt J, Hill P, Lewis M, Maclntyre H, Lu L, Zhang Q, Tu Q, Shi T, Chen F, Jiao N. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment. WATER RESEARCH 2022; 216:118281. [PMID: 35316680 DOI: 10.1016/j.watres.2022.118281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.
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Affiliation(s)
- Changfei He
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China.
| | - Rui Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Qiang Zheng
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Fanglue Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Rui Zhang
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Helmuth Thomas
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada; Helmholtz-Center Geesthacht, Institute for Coastal Research, Max-Planck-Strasse 1, Geesthacht d-21502, Germany
| | - John Batt
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Marlon Lewis
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hugh Maclntyre
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Longfei Lu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, Shandong, China
| | - Qinghua Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Marine Equipment Inspection & Testing Co. Ltd, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Tuo Shi
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Feng Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Environmental Research Center, University of Maryland at Baltimore, United States
| | - Nianzhi Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China
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Karwautz C, Zhou Y, Kerros ME, Weinbauer MG, Griebler C. Bottom-Up Control of the Groundwater Microbial Food-Web in an Alpine Aquifer. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.854228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.
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30
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Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
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Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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31
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She W, Yang J, Wu G, Jiang H. The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153446. [PMID: 35092771 DOI: 10.1016/j.scitotenv.2022.153446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/16/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH4 and CO2), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH4 and CO2, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH4 and CO2 fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH4 fluxes and spatial variations of CO2, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.
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Affiliation(s)
- Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
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32
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Microbial community functioning during plant litter decomposition. Sci Rep 2022; 12:7451. [PMID: 35523988 PMCID: PMC9076648 DOI: 10.1038/s41598-022-11485-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 11/08/2022] Open
Abstract
Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or synergistically address different litter types. Therefore, we decomposed beech, oak, pine and grass litter from two geologically distinct sites in a lab-scale decomposition experiment. We performed a correlative network analysis on the results of direct infusion HR-MS DOM analysis and cross-validated functional predictions from 16S rRNA gene amplicon sequencing and with DOM and metaproteomic analyses. Here we show that many functions are redundantly distributed within decomposer communities and that their relative expression is rapidly optimized to address litter-specific properties. However, community changes are likely forced by antagonistic mechanisms as we identified several natural antibiotics in DOM. As a consequence, the decomposer community is specializing towards the litter source and the state of decomposition (community divergence) but showing similar litter metabolomes (metabolome convergence). Our multi-omics-based results highlight that DOM not only fuels microbial life, but it additionally holds meta-metabolomic information on the functioning of ecosystems.
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33
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Alotaibi MO, Mohammed AE, Eltom KH. Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia. Saudi J Biol Sci 2022; 29:3749-3758. [PMID: 35844383 PMCID: PMC9280250 DOI: 10.1016/j.sjbs.2022.03.001] [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: 01/22/2022] [Revised: 02/08/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Wadi Namar lake is a new touristic attraction area in the south of Riyadh. Human activities around the lake may lead to changes in water quality with subsequent changes in microenvironment components including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water at Wadi Namar Lake. Therefore, water samples were collected from three different locations along the lake: L1 (no human activities, no plants), L2 (no human activity, some plants) and L3 (human activities, municipal wastes and some plants). The total DNA of the samples was extracted and subjected to 16S rDNA sequencing and metagenomic analysis; water pH, electrical conductivity (EC), total dissolved solids (TDS) as well as the concentration of Na+1, K+1, Cl-1 and total N were analysed. Metagenomic analysis showed variations in relative abundance of 17 phyla, 31 families, 43 genera and 19 species of bacteria between the locations. Proteobacteria was the most abundant phylum in all locations; however, its highest abundance was in L1. Planctomycete phylum was highly abundant in L1 and L3, while its abundance in L2 was low. The phyla Acidobacteria, Candidatus Saccharibacteria, Nitrospirae and Chloroflexi were associated with high TDS, EC, K+1 and Cl-1 concentrations in L3; various human activities around this location had possibly affected microbial diversity. Current study results help in recognising the structure of bacterial communities at Wadi Namar Lake in relation to their surroundings for planning to environment protection and future restoration of affected ecosystems.
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Affiliation(s)
- Modhi O. Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Afrah E. Mohammed
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Kamal H. Eltom
- Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat Postal Code 13314, Khartoum North, Sudan
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Zhu X, Wang Z, Luo Y, Ma Y, Xu Z, Wang L, Peng F, Pang Q, Li Y, He F, Xu B. Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 10:100163. [PMID: 36159732 PMCID: PMC9488004 DOI: 10.1016/j.ese.2022.100163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Fluoride (F-) is widespread in aquatic environments; however, it is not clear whether the fluctuation of F- concentrations in overlying lake water affects the composition and migration of dissolved organic matter (DOM) from sediment. A case study was presented in Sand Lake, China, and an experiment was conducted to analyze the influence of different F- concentrations in overlying water on DOM characteristics. Diffusion resulted in similarities in DOM components between overlying and pore waters, and bacterial activities and enzyme variation resulted in differences between them. Higher F- concentrations in overlying water resulted in a higher pH of pore water, which favored the enrichment of protein-like substances. Higher F- concentrations caused lower DOM concentrations and lower maximum fluorescence intensities (Fmax) of protein-like components in pore water. The F- concentrations had significantly negative correlations with Shannon indexes (P < 0.05). Thiobacillus influenced the migration of tyrosine-like substances by decreasing the pH of pore water. Trichococcus and Fusibacter altered the Fmax of protein-like, humic-like, and fulvic-like substances. The F- concentrations affected the DOM composition and migration due to the response of functional bacterial communities, which were positively correlated with the relative abundance of Thiobacillus and negatively correlated with the relative abundances of Trichococcus and Fusibacter. The high F- concentrations influenced the biosynthesis and degradation of protein-like substances by shifting the abundances of the relevant enzymes. The results of this study may provide ideas for investigating DOM cycling under the influence of F-, especially in lakes with fluctuations in F- concentrations.
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Affiliation(s)
- Xiang Zhu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Zibo Wang
- China National Environmental Monitoring Centre, No8-2 Anwai Dayangfang, Chaoyang District, Beijing, 100012, PR China
| | - Yidan Luo
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yushen Ma
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Zhipeng Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longmian Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Fuquan Peng
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Qingqing Pang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Yiping Li
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Fei He
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Bin Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
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35
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Gushgari-Doyle S, Lui LM, Nielsen TN, Wu X, Malana RG, Hendrickson AJ, Carion H, Poole FL, Adams MWW, Arkin AP, Chakraborty R. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions. ISME COMMUNICATIONS 2022; 2:32. [PMID: 37938300 PMCID: PMC9723602 DOI: 10.1038/s43705-022-00113-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 07/04/2023]
Abstract
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
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Affiliation(s)
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ria G Malana
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Heloise Carion
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
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36
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Gill JG, Hill-Spanik KM, Whittaker KA, Jones ML, Plante C. Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 2022; 10:e12835. [PMID: 35251777 PMCID: PMC8893026 DOI: 10.7717/peerj.12835] [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: 08/17/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
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Affiliation(s)
- John Geoffrey Gill
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | | | - Kerry A. Whittaker
- Sea Education Association, Woods Hole, MA, United States,Maine Maritime Academy, Castine, Maine, United States
| | - Martin L. Jones
- Department of Mathematics, College of Charleston, Charleston, SC, United States
| | - Craig Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
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Zhang L, Chen M, Chen X, Wang J, Zhang Y, Xiao X, Hu C, Liu J, Zhang R, Xu D, Jiao N, Zhang Y. Nitrifiers drive successions of particulate organic matter and microbial community composition in a starved macrocosm. ENVIRONMENT INTERNATIONAL 2021; 157:106776. [PMID: 34311224 DOI: 10.1016/j.envint.2021.106776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Organic carbon produced by nitrifiers plays an important role in maintaining the microbial metabolism in the aphotic ocean layer with carbon and energy scarcity. However, the contribution of nitrifiers to organic carbon processing remains unclear. To explore how nitrification impacts the material cycle in the starved ecosystem, we set up an ultra-large volume, long-term incubation experiment. Seawater collected from the Halifax coastal ocean was pumped into the Aquatron Tower Tank located at Dalhousie University, Canada, and was incubated under dark conditions for 73 days. The results indicated that the relative abundance of nitrifiers increased and nitrification was strengthened in the dark system where energy and organic carbon were scarce. The importance of nitrogenous compounds in particulate materials increased over the course of the incubation. Correlation analysis showed that the relative abundances of nitrifiers and particulate organic compounds containing nitrogen were significantly and positively correlated. Furthermore, network analysis suggested that metabolic processes related to nitrogenous and aromatic compounds are most important to particle associated bacteria. This study suggests that the nitrifiers could produce a series of organic compounds that result in the alteration of organic matter composition by promoting the degradation of recalcitrant aromatic compounds, which has important implications for organic matter processing in the starved dark ecosystem.
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Affiliation(s)
- Lianbao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Yu Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qinagdao 266237, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China.
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38
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Wang L, Lin Y, Ye L, Qian Y, Shi Y, Xu K, Ren H, Geng J. Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11294-11307. [PMID: 34338502 DOI: 10.1021/acs.est.1c02584] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.
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Affiliation(s)
- Liye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yuan Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yuli Qian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yufei Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Jinju Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
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Jayachandran S, Chakraborty P, Sarkar A, Kumar D, Babu PC. Post depositional changes of sedimentary organic matter influence chromium speciation in continental slope sediments - A case study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145783. [PMID: 33676215 DOI: 10.1016/j.scitotenv.2021.145783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Influences of post depositional changes of sedimentary organic matter (SOM) on chromium (Cr) speciation in continental slope sediments from the east and west coast of India are presented in this study. Average concentrations of total sedimentary Cr (CrT) in the slope areas of both the coasts were not elevated and ranged from 56.8 to 163 mg·kg-1 (avg. 97.3 ± 28.3 mg·kg-1). The geology of adjacent land masses influenced sedimentary Cr concentration in the slope areas. Geochemical fractionation study showed that a major fraction (51.6-159 mg·kg-1; avg. 89.6 ± 24.3 mg·kg-1) of the total sedimentary Cr was present in residual part of the sediments. Prime hosting phase for non-residual sedimentary Cr was oxidizable binding phase (SOM) (1.4-23.9 mg·kg-1; avg. 6.7 ± 6.3 mg·kg-1) followed by reducing binding phase (Fe/Mn-oxyhydroxide phase) (0.1-1.7 mg·kg-1; avg. 0.7 ± 0.3 mg·kg-1). Concentration of Cr (VI) in the slope sediments, varied from 0.2 to 8.3 mg·kg-1 (avg. 1.2 ± 1.0 mg·kg-1), was also predominantly associated with the SOM. The δ13Corg values of the SOM (ranged from -19.4 to -21.4‰; avg. -20.3 ± 0.5‰) suggests that they were derived from marine sources. Based on molar C/N ratio (ranged from 6.3-12.9; avg. 9.0 ± 2.0), the SOM were classified as labile organic matter. Increasing molar C/N ratio in the studied sediments was used as a proxy to reflect post depositional changes of the SOM. Association of normalized Cr (VI) (with respect to CrT) increased with increasing SOM concentration by 0.008 mg·kg-1. One unit increase of sedimentary molar C/N ratio was found to increase normalized Cr (VI) (w.r.t. CrT) by 0.003 mg·kg-1 in the sediments. This study suggests that post-depositional changes of SOM may increase Cr binding capacity and control its speciation and mobility in marine sediment system.
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Affiliation(s)
- Saranya Jayachandran
- Centre for Oceans, Rivers, Atmosphere and Land Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India; Geological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004, India
| | - Parthasarathi Chakraborty
- Centre for Oceans, Rivers, Atmosphere and Land Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India; Geological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004, India.
| | - Arindam Sarkar
- Regional Research Station (R & L Zone), Bidhan Chandra Krishi Viswavidyalaya, Jhargram, West Bengal 721507, India
| | - Deepak Kumar
- Geological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004, India
| | - Prakash C Babu
- Geological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004, India
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40
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Kinsela AS, Bligh MW, Vázquez-Campos X, Sun Y, Wilkins MR, Comarmond MJ, Rowling B, Payne TE, Waite TD. Biogeochemical Mobility of Contaminants from a Replica Radioactive Waste Trench in Response to Rainfall-Induced Redox Oscillations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8793-8805. [PMID: 34110792 DOI: 10.1021/acs.est.1c01604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Results of investigations into factors influencing contaminant mobility in a replica trench located adjacent to a legacy radioactive waste site are presented in this study. The trench was filled with nonhazardous iron- and organic matter (OM)-rich components, as well as three contaminant analogues strontium, cesium, and neodymium to examine contaminant behavior. Imposed redox/water-level oscillations, where oxygen-laden rainwater was added to the anoxic trench, resulted in marked biogeochemical changes including the removal of aqueous Fe(II) and circulation of dissolved carbon, along with shifts to microbial communities involved in cycling iron (Gallionella, Sideroxydans) and methane generation (Methylomonas, Methylococcaceae). Contaminant mobility depended upon element speciation and rainfall event intensity. Strontium remained mobile, being readily translocated under hydrological perturbations. Strong ion-exchange reactions and structural incorporation into double-layer clay minerals were likely responsible for greater retention of Cs, which, along with Sr, was unaffected by redox oscillations. Neodymium was initially immobilized within the anoxic trenches, due to either secondary mineral (phosphate) precipitation or via the chemisorption of organic- and carbonate-Nd complexes onto variably charged solid phases. Oxic rainwater intrusions altered Nd mobility via competing effects. Oxidation of Fe(II) led to partial retention of Nd within highly sorbing Fe(III)/OM phases, whereas pH decreases associated with rainwater influxes resulted in a release of adsorbed Nd to solution with both pH and OM presumed to be the key factors controlling Nd attenuation. Collectively, the behavior of simulated contaminants within this replica trench provided unique insights into trench water biogeochemistry and contaminant cycling in a redox oscillatory environment.
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Affiliation(s)
- Andrew S Kinsela
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Mark W Bligh
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
| | - Yingying Sun
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Marc R Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
| | - M Josick Comarmond
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Brett Rowling
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Timothy E Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - T David Waite
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
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41
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Mahmood M, Taki S, Nakai S, Gotoh T, Nishijima W, Umehara A, Aoyagi T, Sato Y, Hori T, Katayama Y, Hajdu-Rahkama R, Puhakka JA. Increase in sedimentary organic carbon with a change from hypoxic to oxic conditions. MARINE POLLUTION BULLETIN 2021; 168:112397. [PMID: 33962085 DOI: 10.1016/j.marpolbul.2021.112397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
In the Seto Inland Sea, Japan, chemical oxygen demand has increased over recent decades, while average dissolved oxygen concentrations in the bottom water have increased. In this study, we investigated responses of organic carbon (OC) in hypoxic sediment to changes of redox conditions using experimental columns containing sediment and overlying water. Surface sediment showed an increase in OC along with the change to an aerobic condition. Microbial community analysis showed a predominance of sulfur-oxidizing bacteria (SOB) such as Sulfurovum sp. in the sediment. This dominance could account for the increased OC. Additionally, the dissolved organic carbon (DOC) concentration in the overlying water increased. Further experiments using sandy sediment showed that biodegradation of Sulfurimonas denitrificans was associated with DOC release. These results show that a change in the sedimentary environment (increase in dissolved oxygen) increased the sedimentary OC and DOC of overlying water by stimulating certain autotrophic bacteria, especially the SOB.
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Affiliation(s)
- Mukseet Mahmood
- Graduate School of Engineering, Hiroshima University, Hiroshima, Japan
| | - Shunsuke Taki
- Graduate School of Engineering, Hiroshima University, Hiroshima, Japan
| | - Satoshi Nakai
- Graduate School of Engineering, Hiroshima University, Hiroshima, Japan.
| | - Takehiko Gotoh
- Graduate School of Engineering, Hiroshima University, Hiroshima, Japan
| | - Wataru Nishijima
- Environmental Research Management Center, Hiroshima University, Hiroshima, Japan
| | - Akira Umehara
- Environmental Research Management Center, Hiroshima University, Hiroshima, Japan
| | - Tomo Aoyagi
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Sato
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Tomoyuki Hori
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Yoko Katayama
- Center for Conservation Science, Tokyo National Research Institute for Cultural Properties, Tokyo, Japan
| | - Reka Hajdu-Rahkama
- Materials Science and Environmental Engineering, Tampere University, Tampere, Finland
| | - Jaakko A Puhakka
- Materials Science and Environmental Engineering, Tampere University, Tampere, Finland
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42
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Metze D, Popp D, Schwab L, Keller NS, da Rocha UN, Richnow HH, Vogt C. Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer. FEMS Microbiol Ecol 2021; 97:6055686. [PMID: 33378450 DOI: 10.1093/femsec/fiaa261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.
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Affiliation(s)
- Dennis Metze
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany.,Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Althanstraße 14, Austria
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Laura Schwab
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Nina-Sophie Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
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43
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Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
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Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
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44
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McKenna AM, Chen H, Weisbrod CR, Blakney GT. Molecular Comparison of Solid-Phase Extraction and Liquid/Liquid Extraction of Water-Soluble Petroleum Compounds Produced through Photodegradation and Biodegradation by FT-ICR Mass Spectrometry. Anal Chem 2021; 93:4611-4618. [PMID: 33660499 DOI: 10.1021/acs.analchem.0c05230] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We apply two widely used extraction techniques, liquid/liquid extraction and solid-phase extraction with styrene-divinylbenzene polymer with a proprietary nonpolar surface priority pollutant (PPL) to water-soluble compounds generated through photodegradation and biodegradation of petroleum. We compare the molecular composition of bio- and photodegraded water-soluble organic (WSO) acids by 21 T negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We highlight the compositional differences between the two extraction techniques for abiotic and biotic degradation processes and identify known toxic species (naphthenic acids) produced through hydrocarbon biodegradation identified by liquid/liquid extraction (LLE) that are not detected with solid-phase extraction (SPE) of the same sample. Photodegraded WSO compounds extracted by SPE-PPL correspond to species with higher O/C ratio and carbon number compared to LLE extracted compounds. Naphthenic acids, a recalcitrant class of nonaromatic carboxylic acids and known acute toxicants formed through biodegradation of oil, are detected in LLE extracts (up to C30 and double-bond equivalents, DBE < 3) but are not detected in SPE-PPL extracts. This suggests that LLE and SPE-PPL retain different water-soluble oil species based on the dominant type of oil weathering process.
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Affiliation(s)
- Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Gregory T Blakney
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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45
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Guo F, Qin S, Xu L, Bai Y, Xing B. Thermal degradation features of soil humic acid sub-fractions in pyrolytic treatment and their relation to molecular signatures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:142318. [PMID: 33370911 DOI: 10.1016/j.scitotenv.2020.142318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 06/12/2023]
Abstract
Pyrolysis is a promising treatment for soil remediation for rapidity and fertility preservation. But it is difficult to establish the relationship between pyrolysis behaviors and soil organic matter (SOM) structures, for SOM is a mixture of heterogeneous compounds. HA sub-fractions from the same soil source may provide a series of promising objects to understand SOM at molecular level and the resulting patterns in SOM pyrolysis. We first propose a novel insight into pyrolysis mechanism response to molecular signatures using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with thermogravimetric analysis (TGA) to study six humic acid (HA) sub-fractions extracted from a forest soil. The findings indicate that decomposition of soil HA occurs systematically due to molecular signatures. The decomposition can be categorized as carboxyl controlled (below 280 °C), lipid-dominated (280-450 °C) and condensed aromatics-dominated processes (450-700 °C). Predominant reaction mechanism of all HA sub-fractions was random nucleation (α > 0.25). Lipid in HA tend to initiate multiple nuclei in thermal degradation, while condensed aromatics tend to initiate and grow centering single random point in higher conversion rate (α > 0.75). Bridging the molecular signature and thermogravimetry reveals that the pyrolysis stage below 350 °C should be divided into two distinct processes related to the carboxylic group and lipid compounds, although this stage has conventionally been considered as a single process. The N element of HA was mostly preserved in the condensed aromatics which was mainly pyrolyzed above 450 °C, suggesting that pyrolysis below 450 °C is a preferable remediation treatment considering nitrogen fertility preservation. The observed molecular-level pyrolysis patterns can be applied as a targeted remediation procedure for contaminated soils and can improve the understanding of SOM thermal behaviors at the molecular level.
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Affiliation(s)
- Fei Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Shuai Qin
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lei Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
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46
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Wu X, Spencer S, Gushgari-Doyle S, Yee MO, Voriskova J, Li Y, Alm EJ, Chakraborty R. Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater. Front Microbiol 2020; 11:610001. [PMID: 33391234 PMCID: PMC7773641 DOI: 10.3389/fmicb.2020.610001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.
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Affiliation(s)
- Xiaoqin Wu
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sarah Spencer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mon Oo Yee
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jana Voriskova
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan Li
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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47
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Zheng Y, He W, Li B, Hur J, Guo H, Li X. Refractory Humic-like Substances: Tracking Environmental Impacts of Anthropogenic Groundwater Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15778-15788. [PMID: 33216533 DOI: 10.1021/acs.est.0c04561] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To unravel the crucial components of natural organic matter that respond to the process of anthropogenic groundwater recharge (AGR) from different recharge water sources, dissolved organic matter (DOM) and base-extractable particulate organic matter (POM) in groundwater and surface water were analyzed using excitation-emission matrix spectroscopy coupled with parallel factor analysis (EEM-PARAFAC). The EEM and traditional spectral indices of samples show that the fluorescent intensity, molecular weight, and humification degree of the DOM were relatively higher than those of the POM, and the groundwater in the reclaimed water recharge area (RWRA) was more contaminated than in the south-to-north water recharge area (SNWRA). PARAFAC analysis indicates that the DOM was dominated by an allochthonous humic-like substance (C1), whereas the POM was dominated by tryptophan-like substances associated with microbial activity (C2). Partitioning of PARAFAC components between DOM and POM showed that the humic-like substances (C1 and C4) were more likely to be distributed into a dissolved phase compared to the protein-like substances (C2 and C3), which suggested the potential use of C1 and C4 as a tracking indicator. In particular, the clear gradient distributions along both the hydrogeological profile and different aquifer systems in terms of the concentration and composition of C1 also discriminated between the RWRA and SNWRA with regard to the effects of various AGRs on the groundwater. The association between C1 and water-quality indicators revealed by principal component analysis further indicated that refractory humic-like substances would track the environmental impacts of intentional AGR processes.
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Affiliation(s)
- Yaxin Zheng
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Wei He
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Binghua Li
- Department of Water Resources, Beijing Water Science and Technology Institute, Beijing 100048, China
| | - Jin Hur
- Department of Environment and Energy, Sejong University, Seoul 05006, South Korea
| | - Huaming Guo
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xiaomeng Li
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
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48
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Pagliaccia D, Bodaghi S, Chen X, Stevenson D, Deyett E, De Francesco A, Borneman J, Ruegger P, Peacock B, Ellstrand N, Rolshausen PE, Popa R, Ying S, Vidalakis G. Two Food Waste By-Products Selectively Stimulate Beneficial Resident Citrus Host-Associated Microbes in a Zero-Runoff Indoor Plant Production System. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.593568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The global production of food waste is a far-reaching problem with sizable financial, ethical, social, and environmental costs. Over 66 million tons of food waste is produced annually in the United States alone. This waste can be converted into valuable digestate by-products that promote a circular economy within agri-food systems. The present work investigated the use of two liquid digestates of microaerobic fermentation from mixed food waste and beer mash, respectively, as biostimulants for non-bearing citrus plants (nursery stock) grown in a zero-runoff greenhouse system with recirculating irrigation. The digestates' impact on the structure and diversity of the microbiota was determined on the irrigation water, soil, leaves, roots, and rhizosphere of citrus plants. A combination of culture-dependent (selective media) and culture-independent approaches (Next-Generation Sequencing) was used to assess the composition of the microbial communities and to single out the presence of foodborne pathogens. Our results suggest that the use of digestates is safe (i.e., no human or plant pathogens were present in the digestates or enriched in the plant production system following amendments). Digestates application to the irrigation water reduced the bacterial diversity within 24–48 h and selectively and significantly stimulated beneficial resident host-associated microorganisms (Pseudomonas putida) by two to three orders of magnitude. Carbon dynamics were analyzed in the nutrient solutions by measuring dissolved organic carbon and characterizing carbon species through gas chromatography-electron ionization-mass spectrometry. Our results indicate that dissolved organic carbon in the recirculating irrigation water spikes after each digestate amendment and it is quickly metabolized by bacteria, plateauing 24 h after application. Soil carbon, nitrogen, and nutrient dynamics were also analyzed, and results suggest that digestates increased the concentration of some plant nutrients in soils without causing a surge of potentially toxic elements. This study represents a proof-of-concept for the safe re-use of organic wastes, from farming and consumers, in agriculture. Implementing this type of integrated plant production system could reduce the environmental impact of food waste and benefit the public by improving soil health, reducing agricultural footprint, and increasing crop fitness by deploying a method based on a circular economy and sustainable food production approaches.
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49
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Hofmann R, Uhl J, Hertkorn N, Griebler C. Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments. Front Microbiol 2020; 11:543567. [PMID: 33250862 PMCID: PMC7674671 DOI: 10.3389/fmicb.2020.543567] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.
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Affiliation(s)
- Roland Hofmann
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany.,Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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50
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Wright RJ, Langille MGI, Walker TR. Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere. ISME JOURNAL 2020; 15:789-806. [PMID: 33139870 PMCID: PMC8027867 DOI: 10.1038/s41396-020-00814-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022]
Abstract
It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment—termed the “Plastisphere”—may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies, we have performed the first meta-analysis of the Plastisphere in marine, freshwater, other aquatic (e.g., brackish or aquaculture) and terrestrial environments. We show that random forest models can be trained to differentiate between groupings of environmental factors as well as aspects of study design, but—crucially—also between plastics when compared with control biofilms and between different plastic types and community successional stages. Our meta-analysis confirms that potentially biodegrading Plastisphere members, the hydrocarbonoclastic Oceanospirillales and Alteromonadales are consistently more abundant in plastic than control biofilm samples across multiple studies and environments. This indicates the predilection of these organisms for plastics and confirms the urgent need for their ability to biodegrade plastics to be comprehensively tested. We also identified key knowledge gaps that should be addressed by future studies.
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Affiliation(s)
- Robyn J Wright
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Canada. .,Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Morgan G I Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Tony R Walker
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Canada
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