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Wang HY, Yu ZG, Zhou FW, Hernandez JC, Grandjean A, Biester H, Xiao KQ, Knorr KH. Microbial communities and functions are structured by vertical geochemical zones in a northern peatland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175273. [PMID: 39111416 DOI: 10.1016/j.scitotenv.2024.175273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.
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Affiliation(s)
- Hong-Yan Wang
- Key Laboratory of Hydrometeorological Disaster Mechanism and Warning, Ministry of Water Resources, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhi-Guo Yu
- Key Laboratory of Hydrometeorological Disaster Mechanism and Warning, Ministry of Water Resources, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Feng-Wu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Julio-Castillo Hernandez
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - Annkathrin Grandjean
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster 48149, Germany
| | - Harald Biester
- Institut für Geoökologie, Technische Universitat Braunschweig, Langer Kamp 19C, Braunschweig 38106, Germany
| | - Ke-Qing Xiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Klaus-Holger Knorr
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster 48149, Germany.
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Sennett LB, Roco CA, Lim NYN, Yavitt JB, Dörsch P, Bakken LR, Shapleigh JP, Frostegård Å. Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N 2O emissions. Nat Commun 2024; 15:7298. [PMID: 39181870 PMCID: PMC11344836 DOI: 10.1038/s41467-024-51688-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.
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Affiliation(s)
- Louise B Sennett
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Constance A Roco
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
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Quinteros-Urquieta C, Francois JP, Aguilar-Muñoz P, Orellana R, Villaseñor R, Moreira-Muñoz A, Molina V. Microbial Diversity of Soil in a Mediterranean Biodiversity Hotspot: Parque Nacional La Campana, Chile. Microorganisms 2024; 12:1569. [PMID: 39203411 PMCID: PMC11356564 DOI: 10.3390/microorganisms12081569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC's vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.
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Affiliation(s)
- Carolina Quinteros-Urquieta
- Programa de Doctorado Interdisciplinario en Ciencias Ambientales, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Jean-Pierre Francois
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Polette Aguilar-Muñoz
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción 4070386, Chile
| | - Roberto Orellana
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Rodrigo Villaseñor
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Andres Moreira-Muñoz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso 2362807, Chile;
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción 4070386, Chile
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Chen M, Grégoire DS, Bain JG, Blowes DW, Hug LA. Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities. Appl Environ Microbiol 2024; 90:e0014324. [PMID: 38814057 PMCID: PMC11218620 DOI: 10.1128/aem.00143-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.
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Affiliation(s)
- Molly Chen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Daniel S. Grégoire
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Jeffrey G. Bain
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - David W. Blowes
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Kimura ZI, Kuriyama H, Iwasaki Y. Exploring Acetogenesis in Firmicutes: From Phylogenetic Analysis to Solid Medium Cultivation with Solid-Phase Electrochemical Isolation Equipments. Microorganisms 2023; 11:2976. [PMID: 38138120 PMCID: PMC10746088 DOI: 10.3390/microorganisms11122976] [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: 09/05/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
This study introduces a groundbreaking approach for the exploration and utilization of electrotrophic acetogens, essential for advancing microbial electrosynthesis systems (MES). Our initial focus was the development of Solid-Phase Electrochemical Isolation Equipment (SPECIEs), a novel cultivation method for isolating electrotrophic acetogens directly from environmental samples on a solid medium. SPECIEs uses electrotrophy as a selection pressure, successfully overcoming the traditional cultivation method limitations and enabling the cultivation of diverse microbial communities with enhanced specificity towards acetogens. Following the establishment of SPECIEs, we conducted a genome-based phylogenetic analysis using the Genome Taxonomy Database (GTDB) to identify potential electrotrophic acetogens within the Firmicutes phylum and its related lineages. Subsequently, we validated the electrotrophic capabilities of selected strains under electrode-oxidizing conditions in a liquid medium. This sequential approach, integrating innovative cultivation techniques with detailed phylogenetic analysis, paves the way for further advances in microbial cultivation and the identification of new biocatalysts for sustainable energy applications.
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Affiliation(s)
- Zen-ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506, Japan; (H.K.); (Y.I.)
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Taraboletti A, King A, Dixon Y, Orr O, Parnell C, Watson Y, Nash B, Esimai C, Ude G. Assessing microbial diversity in soil samples along the Potomac River: implications for environmental health. Microbiol Spectr 2023; 11:e0254023. [PMID: 37874137 PMCID: PMC10714937 DOI: 10.1128/spectrum.02540-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE This study integrates microbial analysis into an undergraduate chemistry class, offering students a hands-on approach to environmental research. We examined the soil along the urbanized Potomac River, discovering a mix of common marine microbes and others that are indicators of urban waste and pollution. Our findings provide valuable insights into the environmental impacts of urbanization on soil health and reveal the effectiveness of using modern genetic tools to teach students about real-world issues. This innovative educational approach not only deepens students' understanding of chemistry and ecology but also prepares them to be thoughtful, informed participants in addressing contemporary environmental challenges while shedding light on the state of the soil microbiome near and around the DC metro area.
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Affiliation(s)
- Alexandra Taraboletti
- Chemistry Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Alexus King
- Biology Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Yasheka Dixon
- Biology Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Oshane Orr
- Biology Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Chevell Parnell
- Biology Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Yasheika Watson
- Biology Program, Division of Sciences and Mathematics, University of the District of Columbia, Washington, DC, USA
| | - Bruce Nash
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Chimdimnma Esimai
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, USA
| | - George Ude
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, USA
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Soares MB, Duckworth OW, Stýblo M, Cable PH, Alleoni LRF. Pyrolysis temperature and biochar redox activity on arsenic availability and speciation in a sediment. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132308. [PMID: 37639794 PMCID: PMC10528781 DOI: 10.1016/j.jhazmat.2023.132308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
Biochar is widely used for water and soil remediation in part because of its local availability and low production cost. However, its effectiveness depends on physicochemical properties related to its feedstock and pyrolysis temperature, as well as the environmental conditions of its use site. Furthermore, biochar is susceptible to natural aging caused by changes in soil or sediment moisture, which can alter its redox properties and interactions with contaminants such as arsenic (As). In this study, we investigated the effect of pyrolysis temperature and biochar application on the release and transformations of As in contaminated sediments subjected to redox fluctuations. Biochar application and pyrolysis temperature played an important role in As species availability, As methylation, and dissolved organic carbon concentration. Furthermore, successive flooding cycles that induced reductive conditions in sediments increased the As content in the solution by up to seven times. In the solid phase, the application of biochar and the flooding cycle altered the spatial distribution and speciation of carbon, iron (Fe) and As. In general, the application of biochar decreased the reduction of Fe(III) and As(V) after the first cycle of flooding. Our results demonstrate that the flooding cycle plays an important role in the reoxidation of biochar to the point of enhancing the immobilization of As.
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Affiliation(s)
- Matheus B Soares
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil; Department of Crop and Soil Sciences, North Carolina State University, 27695 Raleigh, NC, USA.
| | - Owen W Duckworth
- Department of Crop and Soil Sciences, North Carolina State University, 27695 Raleigh, NC, USA
| | - Miroslav Stýblo
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 27599-7461 Chapel Hill, NC, USA
| | - Peter H Cable
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 27599-7461 Chapel Hill, NC, USA
| | - Luís R F Alleoni
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil
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Marcos P, Whyte P, Burgess C, Bolton D. A Small Study on Clostridioides difficile in Spinach Field Soil and the Chemical and Microbial Factors that may Influence Prevalence. Curr Microbiol 2023; 80:236. [PMID: 37286880 DOI: 10.1007/s00284-023-03328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/09/2023] [Indexed: 06/09/2023]
Abstract
Clostridioides difficile is a human pathogen that is ubiquitous in soil. Despite increasing infection rates and evidence of foodborne transmission, there is limited data on prevalence in soil or which factors influence persistence. The aim of this study was to investigate the prevalence of these bacteria in soil from three different spinach fields and to examine the chemical composition (carbon, organic carbon, nitrogen, organic matter, minerals and pH) and microbiota to gain insight into the factors that may promote/inhibit C. difficile. The overall C. difficile prevalence (10%) was lower than expected (based on international studies) and a significantly (P < 0.05) higher prevalence was obtained in Field 3 (20%) as compared to Fields 1 and 2 (5% each). Analysis of the soil suggested that the pH as well as organic matter, calcium and phosphorus content directly and indirectly (via the microbiota) influenced the prevalence of C. difficile in adjacent fields, where other factors (eg. climate) are similar. Although further studies are required to validate our findings, the data provides the first step in developing potential soil based control strategies.
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Affiliation(s)
- Pilar Marcos
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Declan Bolton
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.
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Tang Q, Wang P, Liu H, Jin D, Chen X, Zhu L. Effect of chlorantraniliprole on soil bacterial and fungal diversity and community structure. Heliyon 2023; 9:e13668. [PMID: 36852024 PMCID: PMC9957708 DOI: 10.1016/j.heliyon.2023.e13668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Chlorantraniliprole (CAP) is an insecticide with low toxicity and high efficiency, which is widely used in agriculture in China. However, its potential ecological risks remain unknown. In this study, we investigated the impact of different CAP concentrations on bacterial and fungal communities in soil based on high-throughput sequencing. The results showed that CAP application had no significant effect on soil bacterial and fungal diversity, but altered the bacterial and fungal community structure. In particular, the soil bacterial and fungal community structure in the low CAP concentration treatment group exhibited large variability. Compared with 0 day, the phylum level of bacteria changed at 115 days, and fungi changed at 175 days, indicating that soil microbial community might have significant correlation with CAP degradation in soil. Correlation analysis between soil properties and microbial communities showed that TN, TP, and NO3-N were three key factors that significantly influenced microbial community structure. These results provide basic data for studying the effects of pesticides on ecosystem and potential remediation strategies of polluted soil.
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Affiliation(s)
- Qian Tang
- Key Laboratory ofAgricultural Product Processing and Quality Control(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs; Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
| | - Pingping Wang
- Key Laboratory ofAgricultural Product Processing and Quality Control(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs; Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
| | - Huijun Liu
- Key Laboratory ofAgricultural Product Processing and Quality Control(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs; Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
- Corresponding author.
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiangning Chen
- Key Laboratory ofAgricultural Product Processing and Quality Control(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs; Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
- Corresponding author.
| | - Lifei Zhu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
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The metamicrobiome: key determinant of the homeostasis of nutrient recycling. Trends Ecol Evol 2023; 38:183-195. [PMID: 36328807 DOI: 10.1016/j.tree.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
The metamicrobiome is an integrated concept to study carbon and nutrient recycling in ecosystems. Decomposition of plant-derived matter by free-living microbes and fire - two key recycling pathways - are highly sensitive to global change. Mutualistic associations of microbes with plants and animals strongly reduce this sensitivity. By solving a fundamental allometric trade-off between metabolic and homeostatic capacity, these mutualisms enable continued recycling of plant matter where and when conditions are unfavourable for the free-living microbiome. A diverse metamicrobiome - where multiple plant- and animal-associated microbiomes complement the free-living microbiome - thus enhances homeostasis of ecosystem recycling rates in variable environments. Research into metamicrobiome structure and functioning in ecosystems is therefore important for progress towards understanding environmental change.
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Martínez‐Arias C, Witzell J, Solla A, Martin JA, Rodríguez‐Calcerrada J. Beneficial and pathogenic plant-microbe interactions during flooding stress. PLANT, CELL & ENVIRONMENT 2022; 45:2875-2897. [PMID: 35864739 PMCID: PMC9543564 DOI: 10.1111/pce.14403] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 05/29/2023]
Abstract
The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.
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Affiliation(s)
- Clara Martínez‐Arias
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Johanna Witzell
- Department of Forestry and Wood TechnologyLinnaeus UniversityVäxjöSweden
| | - Alejandro Solla
- Faculty of Forestry, Institute for Dehesa Research (INDEHESA)Universidad de ExtremaduraPlasenciaSpain
| | - Juan Antonio Martin
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Jesús Rodríguez‐Calcerrada
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
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Li N, Wang B, Huang Y, Huang Q, Jiao F, An S. Response of cbbL-harboring microorganisms to precipitation changes in a naturally-restored grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156191. [PMID: 35618124 DOI: 10.1016/j.scitotenv.2022.156191] [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: 03/09/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The impact of the long-term uneven precipitation distribution model on the diversity and community composition of soil C-fixing microorganisms in arid and semiarid grasslands remains unclear. In 2015, we randomly set up five experimental plots with precipitation gradients on the natural restoration grassland of the Loess Plateau (natural precipitation, NP; ± 40% natural precipitation: decreased precipitation (DP), DP40; increased precipitation (IP), IP40; ± 80% natural precipitation: DP80; IP80). In the third and fifth years after the experimental layout (spanned two years), we explored the cbbL-genes, which are functional genes in the Calvin cycle, harboring microbial diversity and community composition under different precipitation treatments. The results showed that the increase in mean annual precipitation significantly changed the cbbL-harboring microbial alpha diversity, especially when controlling for 40% natural precipitation. The response of the dominant microbial communities to interannual increased precipitation variation shifted from Gammaproteobacteria (Bradyrhizobium) to Betaproteobacteria (Variovorax). The structural equation model showed that precipitation directly affected the cbbL-harboring microbial diversity and community composition and indirectly by affecting soil NO3- (mg N kg -1), soil organic matter, dissolved organic N content, and above- and underground biomass. In conclusion, studying how cbbL-harboring microbial diversity and community composition respond to uneven precipitation variability provides new insights into the ecological processes of C-fixing microbes in semi-arid naturally-restored grasslands dominated by the Calvin cycle.
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Affiliation(s)
- Na Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qian Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Jiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China.
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13
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Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland. Microorganisms 2022; 10:microorganisms10081653. [PMID: 36014071 PMCID: PMC9416152 DOI: 10.3390/microorganisms10081653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.
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14
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Hall SJ, Huang W, Napieralski SA, Roden E. Shared Microbial Taxa Respond Predictably to Cyclic Time-Varying Oxygen Limitation in Two Disparate Soils. Front Microbiol 2022; 13:866828. [PMID: 35722278 PMCID: PMC9203030 DOI: 10.3389/fmicb.2022.866828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022] Open
Abstract
Periodic oxygen (O2) limitation in humid terrestrial soils likely influences microbial composition, but whether communities share similar responses in disparate environments remains unclear. To test if specific microbial taxa share consistent responses to anoxia in radically different soils, we incubated a rainforest Oxisol and cropland Mollisol under cyclic, time-varying anoxic/oxic cycles in the laboratory. Both soils are known to experience anoxic periods of days to weeks under field conditions; our incubation treatments consisted of anoxic periods of 0, 2, 4, 8, or 12 d followed by 4 d of oxic conditions, repeated for a total of 384 d. Taxa measured by 16S rRNA gene sequences after 48 d and 384 d of experimental treatments varied strongly with increasing anoxic period duration, and responses to anoxia often differed between soils at multiple taxonomic levels. Only 19% of the 30,356 operational taxonomic units (OTUs) occurred in both soils, and most OTUs did not respond consistently to O2 treatments. However, the OTUs present in both soils were disproportionally abundant, comprising 50% of sequences, and they often had a similar response to anoxic period duration in both soils (p < 0.0001). Overall, 67 OTUs, 36 families, 15 orders, 10 classes, and two phyla had significant and directionally consistent (positive or negative) responses to anoxic period duration in both soils. Prominent OTUs and taxonomic groups increasing with anoxic period duration in both soils included actinomycetes (Micromonosporaceae), numerous Ruminococcaceae, possible metal reducers (Anaeromyxobacter) or oxidizers (Candidatus Koribacter), methanogens (Methanomicrobia), and methanotrophs (Methylocystaceae). OTUs decreasing with anoxic duration in both soils included nitrifiers (Nitrospira) and ubiquitous unidentified Bradyrhizobiaceae and Micromonosporaceae. Even within the same genus, different OTUs occasionally showed strong positive or negative responses to anoxic duration (e.g., Dactylosporangium in the Actinobacteria), highlighting a potential for adaptation or niche partitioning in variable-O2 environments. Overall, brief anoxic periods impacted the abundance of certain microbial taxa in predictable ways, suggesting that microbial community data may partially reflect and integrate spatiotemporal differences in O2 availability within and among soils.
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Affiliation(s)
- Steven J. Hall
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Steven J. Hall,
| | - Wenjuan Huang
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | | | - Eric Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
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15
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Xia X, Stewart DI, Cheng L, Liu Y, Wang Y, Ding A. Variation of bacterial community and alkane monooxygenase gene abundance in diesel n-alkane contaminated subsurface environment under seasonal water table fluctuation. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 248:104017. [PMID: 35523047 DOI: 10.1016/j.jconhyd.2022.104017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/26/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
n-Alkanes, the main component of diesel fuel, are common light non-aqueous phase liquids (LNAPLs) that threaten ecological security. The subsurface from vadose zone, through fluctuating zone, to saturated zone, is a critical multi-interface earth layer which significantly affects the biodegradation processes of n-alkanes. A pilot-scale diesel contaminated aquifer column experiment has been undertaken to investigate the variations of bacterial community and alkane monooxygenase (alkB) gene abundance in these zones due to water-table fluctuations. The n-alkanes formed a layer immediately above the water table, and when this was raised, they were carried upwards through the fluctuating zone into the vadose zone. Water content and n-alkanes component C10-C12 are main factors influencing bacterial community variation in the vadose zone, while C10-C12 is a key driving factor shaping bacterial community in the fluctuating zone. The most abundant bacterial phyla at all three zones were Proteobacteria, Firmicutes and Actinobacteria, but moisture-niche selection determined their relative abundance. The intermittent wetting cycle resulted in higher abundance of Proteobacteria, and lower abundance of Actinobacteria in the vadose and fluctuating zones in comparison to the control column with a static water-table. The abundances of the alkB gene variants were relatively uniform in different zones, probably because the bacterial populations harboring alkB gene are habituated to biogenic n-alkanes rather than responding to diesel fuel contamination. The variation in the bacterial populations with height due to moisture-niche selection had very little effect on the alkB gene abundance, possibly because numerous species in both phyla (Proteobacteria and Actinobacteria) carry an alkB gene variant. Nevertheless, the drop in the water table caused a short-term spike in alkB gene abundance in the saturated zone, which is most likely associated with transport of solutes or colloids from the fluctuating zone to bacteria species in the saturated zone, so a fluctuating water table could potentially increase n-alkane biodegradation function.
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Affiliation(s)
- Xuefeng Xia
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | | | - Lirong Cheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Yueqiao Liu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Yingying Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China.
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16
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Zhu SC, Zheng HX, Liu WS, Liu C, Guo MN, Huot H, Morel JL, Qiu RL, Chao Y, Tang YT. Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review. Front Microbiol 2022; 12:751794. [PMID: 35087482 PMCID: PMC8787142 DOI: 10.3389/fmicb.2021.751794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.
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Affiliation(s)
- Shi-Chen Zhu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China
| | - Hong-Xiang Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China.,Laboratoire Sols et Environnement, INRAE-Universiteì de Lorraine, Vandoeuvre-leÌs-Nancy, France
| | - Mei-Na Guo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China.,Laboratoire Sols et Environnement, INRAE-Universiteì de Lorraine, Vandoeuvre-leÌs-Nancy, France
| | - Hermine Huot
- CNRS, LIEC, Université de Lorraine, Nancy, France
| | - Jean Louis Morel
- Laboratoire Sols et Environnement, INRAE-Universiteì de Lorraine, Vandoeuvre-leÌs-Nancy, France
| | - Rong-Liang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, China
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17
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Huang W, Wang K, Ye C, Hockaday WC, Wang G, Hall SJ. High carbon losses from oxygen-limited soils challenge biogeochemical theory and model assumptions. GLOBAL CHANGE BIOLOGY 2021; 27:6166-6180. [PMID: 34464997 DOI: 10.1111/gcb.15867] [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: 07/28/2021] [Revised: 07/28/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Oxygen (O2 ) limitation contributes to persistence of large carbon (C) stocks in saturated soils. However, many soils experience spatiotemporal O2 fluctuations impacted by climate and land-use change, and O2 -mediated climate feedbacks from soil greenhouse gas emissions remain poorly constrained. Current theory and models posit that anoxia uniformly suppresses carbon (C) decomposition. Here we show that periodic anoxia may sustain or even stimulate decomposition over weeks to months in two disparate soils by increasing turnover and/or size of fast-cycling C pools relative to static oxic conditions, and by sustaining decomposition of reduced organic molecules. Cumulative C losses did not decrease consistently as cumulative O2 exposure decreased. After >1 year, soils anoxic for 75% of the time had similar C losses as the oxic control but nearly threefold greater climate impact on a CO2 -equivalent basis (20-year timescale) due to high methane (CH4 ) emission. A mechanistic model incorporating current theory closely reproduced oxic control results but systematically underestimated C losses under O2 fluctuations. Using a model-experiment integration (ModEx) approach, we found that models were improved by varying microbial maintenance respiration and the fraction of CH4 production in total C mineralization as a function of O2 availability. Consistent with thermodynamic expectations, the calibrated models predicted lower microbial C-use efficiency with increasing anoxic duration in one soil; in the other soil, dynamic organo-mineral interactions implied by our empirical data but not represented in the model may have obscured this relationship. In both soils, the updated model was better able to capture transient spikes in C mineralization that occurred following anoxic-oxic transitions, where decomposition from the fluctuating-O2 treatments greatly exceeded the control. Overall, our data-model comparison indicates that incorporating emergent biogeochemical properties of soil O2 variability will be critical for effectively modeling C-climate feedbacks in humid ecosystems.
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Affiliation(s)
- Wenjuan Huang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Kefeng Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Chenglong Ye
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | | | - Gangsheng Wang
- Institute for Water-Carbon Cycles and Carbon Neutrality, and State Key Laboratory of Water Resources and Hydropower Engineering Sciences, Wuhan University, Wuhan, China
| | - Steven J Hall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
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18
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Francioli D, Cid G, Kanukollu S, Ulrich A, Hajirezaei MR, Kolb S. Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota. Front Microbiol 2021; 12:773116. [PMID: 34803993 PMCID: PMC8602104 DOI: 10.3389/fmicb.2021.773116] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 01/04/2023] Open
Abstract
Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany.,Faculty of Life Sciences, Thaer Institute, Humboldt University of Berlin, Berlin, Germany
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19
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Ramdass AC, Rampersad SN. Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism. BMC Microbiol 2021; 21:287. [PMID: 34670489 PMCID: PMC8527658 DOI: 10.1186/s12866-021-02346-4] [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: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Background Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment. Methods Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria. Results 16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch. Conclusions The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02346-4.
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Affiliation(s)
- Amanda C Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sephra N Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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20
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Gao Y, Song X, Liu K, Li T, Zheng W, Wang Y, Liu Z, Zhang M, Chen Q, Li Z, Li R, Zheng L, Liu W, Miao T. Mixture of controlled-release and conventional urea fertilizer application changed soil aggregate stability, humic acid molecular composition, and maize nitrogen uptake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147778. [PMID: 34051498 DOI: 10.1016/j.scitotenv.2021.147778] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/20/2021] [Accepted: 05/11/2021] [Indexed: 05/27/2023]
Abstract
Controlled-release urea (CRU) fertilizer application has been shown to improve crop yield and nitrogen (N) use efficiency. However, its effects when mixed with conventional urea fertilizer on soil aggregate stability, humic acid (HA) molecular composition and crop N uptake remain unclear. Soil and plant samples were collected from a long-term (2008-2019) experiment on field maize (Zea mays L., 'Zhengdan 958') which included two types of fertilizers [conventional urea fertilizer (CUF), blended CUF with CRU fertilizer (CRF)], four N application rates (0, 150, 300 and 450 kg ha-1), each in three replicates. The results showed that at 300 kg N ha-1, compared to CUF treatment, the CRF treatment significantly improved soil aggregate characteristics [aggregate content with particle size larger than 0.25 mm (R0.25) by 9.6%, mean weight diameter by 19.8%, and geometric mean diameter by 21.7%]. CRF treatment also increased HA content by 5.5%, fulvic acid (FA) by 5.5%, lignin-like molecules by 0.94 times, and protein-like molecules by 3.69 times. At grain-filling stage, CRF treatments significantly increased the sum of soil NH4+-N and NO3--N content by 23.3-24.5%, sap bleeding rate by 12.8-18.2% and N delivery rate through bleeding sap by 60.6-87.7% compared to CUF treatments at the same N application rate. At the same rate of N application, the CRF treatments significantly improved the average yield during three growing seasons by 9.4-14.0% in contrast with CUF treatments. The regression equations showed that the maximum yield was 8294 kg ha-1 for CUF at the application rate of 312 kg N ha-1 while it was 9890 kg ha-1 for CRF at the application rate of 286 kg N ha-1. We conclude that the long-term application of CRF changed the HA molecular structure, enhanced the water stable aggregates, improved crop N uptake, and increased economically viable maize yield.
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Affiliation(s)
- Yongxiang Gao
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xue Song
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Kexin Liu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, United States
| | - Taige Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Wenkui Zheng
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Zhiguang Liu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China; State Key Laboratory of Nutrition Resources Integrated Utilization, Kingenta Ecological Engineering Group Co., Linshu, Shandong 276700, China.
| | - Min Zhang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China; State Key Laboratory of Nutrition Resources Integrated Utilization, Kingenta Ecological Engineering Group Co., Linshu, Shandong 276700, China.
| | - Qi Chen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Zeli Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ruochen Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lei Zheng
- State Key Laboratory of Nutrition Resources Integrated Utilization, Kingenta Ecological Engineering Group Co., Linshu, Shandong 276700, China
| | - Wenlong Liu
- State Key Laboratory of Nutrition Resources Integrated Utilization, Kingenta Ecological Engineering Group Co., Linshu, Shandong 276700, China
| | - Tianyu Miao
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Recourses and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
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21
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Towards sustainable agriculture: rhizosphere microbiome engineering. Appl Microbiol Biotechnol 2021; 105:7141-7160. [PMID: 34508284 DOI: 10.1007/s00253-021-11555-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.
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22
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Lin Y, Gross A, Silver WL. Low Redox Decreases Potential Phosphorus Limitation on Soil Biogeochemical Cycling Along a Tropical Rainfall Gradient. Ecosystems 2021. [DOI: 10.1007/s10021-021-00662-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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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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24
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Zhang Z, Furman A. Soil redox dynamics under dynamic hydrologic regimes - A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143026. [PMID: 33143917 DOI: 10.1016/j.scitotenv.2020.143026] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Electron transfer (redox) reactions, mediated by soil microbiota, modulate elemental cycling and, in part, establish the redox poise of soil systems. Understanding soil redox processes significantly improves our ability to characterize coupled biogeochemical cycling in soils and aids in soil health management. Redox-sensitive species exhibit different reactivity, mobility, and toxicity subjected to their redox state. Thus, it is crucial to quantify the redox potential (Eh) in soils and to characterize the dominant redox couples therein. Several, often coupled, external drivers, can influence Eh. Among these factors, soil hydrology dominates. It controls soil physical properties that in turn further regulates Eh. Soil spatial heterogeneity and temporally dynamic hydrologic regimes yield complex distributions of Eh. Soil redox processes have been studied under various environmental conditions, including relatively static and dynamic hydrologic regimes. Our focus here is on dynamic, variably water-saturated environments. Herein, we review previous studies on soil redox dynamics, with a specific focus on dynamic hydrologic regimes, provide recommendations on knowledge gaps, and targeted future research needs and directions. We review (1) the role of soil redox conditions on the soil chemical-species cycling of organic carbon, nitrogen, phosphorus, redox-active metals, and organic contaminants; (2) interactions between microbial activity and redox state in the near-surface and deep subsurface soil, and biomolecular methods to reveal the role of microbes in the redox processes; (3) the effects of dynamic hydrologic regimes on chemical-species cycling and microbial dynamics; (4) the experimental setups for mimicking different hydrologic regimes at both laboratory and field scales. Finally, we identify the current knowledge gaps related to the study of soil redox dynamics under different hydrologic regimes: (1) fluctuating conditions in the deep subsurface; (2) the use of biomolecular tools to understand soil biogeochemical processes beyond nitrogen; (3) limited current field measurements and potential alternative experimental setups.
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Affiliation(s)
- Zengyu Zhang
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Alex Furman
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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25
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Shen R, Lan Z, Rinklebe J, Nie M, Hu Q, Yan Z, Fang C, Jin B, Chen J. Flooding variations affect soil bacterial communities at the spatial and inter-annual scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143471. [PMID: 33213905 DOI: 10.1016/j.scitotenv.2020.143471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Hydrological variations have substantial effects on the diversity and composition of soil bacterial communities in wetlands. At the spatial scale, the responses of soil bacterial diversity and composition to hydrological variations in wetlands have been extensively investigated. However, at the temporal scale, especially at the inter-annual scale, the corresponding bacterial responses are rarely reported. Therefore, we explored the effects of flooding variations on the diversity and composition of soil bacterial communities at a lakeshore wetland in two hydrological contrasting years. Three flooding variables, i.e. flooding duration (FD), total duration of the growing season (TGD), and exposure duration of the growing season (EGD), were used to characterize flooding regime. Soil bacterial communities were determined using 16S rRNA gene sequencing method. We found a very high soil bacterial diversity at the lakeshore wetland. The Shannon's indexes of soil bacterial communities varied from 5.61 to 7.11 in two years. Soil bacterial α-diversity followed a unimodal curve along the elevation gradient, and was significantly lower in the flooding year than in the drought year. Principal coordinate analysis demonstrated that the compositions of soil bacterial communities were separated in order of elevation and year along the first and second axes, respectively. The apparent habitat preferences of soil bacterial families were closely connected with their respiratory traits, and this trend was stronger at the inter-annual scale than at the spatial scale. Soil bacterial compositions were predominantly determined by the direct (by changing respiratory traits) and indirect (by changing soil pH) effects of TGD at the spatial scale, while they were simultaneously regulated by the direct effects of three flooding variables at the inter-annual scale. Our results enhance the understanding of soil microbial communities in wetlands and have large implications for developing general theories to predicting soil microbial functions.
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Affiliation(s)
- Ruichang Shen
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecosystem, Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China; Institute of Biodiversity Science, Fudan University, Shanghai 200433, China; Jiangxi Poyang Lake Wetland Conservation and Restoration National Permanent Scientific Research Base, National Ecosystem Research Station of Jiangxi Poyang Lake Wetland, Nanchang 330031, China; Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China; Jiangxi Institute of Ecological Civilization, Nanchang University, Nanchang 330031, China.
| | - Zhichun Lan
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecosystem, Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China; Institute of Biodiversity Science, Fudan University, Shanghai 200433, China; Jiangxi Poyang Lake Wetland Conservation and Restoration National Permanent Scientific Research Base, National Ecosystem Research Station of Jiangxi Poyang Lake Wetland, Nanchang 330031, China; Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China; Jiangxi Institute of Ecological Civilization, Nanchang University, Nanchang 330031, China
| | - Jörg Rinklebe
- School of Architecture and Civil Engineering, Laboratory of Soil- and Groundwater-Management, University of Wuppertal, Pauluskirchstraße 7, 42285 Wuppertal, Germany; Department of Environment, Energy, and Geoinformatics, Sejong University, Seoul 05006, Republic of Korea
| | - Ming Nie
- Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
| | - Qiwu Hu
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, China
| | - Zhifeng Yan
- Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Changming Fang
- Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
| | - Bingsong Jin
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecosystem, Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China; Jiangxi Poyang Lake Wetland Conservation and Restoration National Permanent Scientific Research Base, National Ecosystem Research Station of Jiangxi Poyang Lake Wetland, Nanchang 330031, China; Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China; Jiangxi Institute of Ecological Civilization, Nanchang University, Nanchang 330031, China
| | - Jiakuan Chen
- Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
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26
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Saia SM, Carrick HJ, Buda AR, Regan JM, Walter MT. Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2722-2742. [PMID: 33559467 DOI: 10.1021/acs.est.0c03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.
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Affiliation(s)
- Sheila M Saia
- Depatment of Biological and Agricultural Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hunter J Carrick
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Anthony R Buda
- Pasture Systems and Watershed Management Research Unit, Agricultural Research Service, United States Department of Agriculture, University Park, Pennsylvania 16802, United States
| | - John M Regan
- Department of Civil and Environmental Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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27
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Gustave W, Yuan Z, Liu F, Chen Z. Mechanisms and challenges of microbial fuel cells for soil heavy metal(loid)s remediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143865. [PMID: 33293085 DOI: 10.1016/j.scitotenv.2020.143865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/24/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
Bioelectrochemical approaches offer a simple, effective, and environmentally friendly solution to pollutant remediation. As a versatile technology, although many studies have shown its potential in soil heavy metal(loid) remediation, the mechanism behind this process is not simple or well-reviewed. Thus, in this review we summarized the impacts of the microbial fuel cells (MFCs) on metal (loids) movement and transformation in the soil environment in terms of changes in soil pH, electromigration, and substrate competition between anode-respiring bacteria and the soil microbial community. Furthermore, the progress of MFCs in the fixation/removal of different elements from the soil environment is described. Hence, this review provides critical insight into the use of the MFC for soil metal(loid) bioremediation.
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Affiliation(s)
- Williamson Gustave
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China; Department of Environmental Science, University of Liverpool, Brownlow Hill, Liverpool, L69 7ZX, United Kingdom; The School of Chemistry, Environmental & Life Sciences, University of the Bahamas, New Providence, Nassau, Bahamas
| | - Zhaofeng Yuan
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China; Department of Environmental Science, University of Liverpool, Brownlow Hill, Liverpool, L69 7ZX, United Kingdom
| | - Fuyuan Liu
- Department of Electric and Electronic Engineering, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
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28
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Gao GF, Peng D, Zhang Y, Li Y, Fan K, Tripathi BM, Adams JM, Chu H. Dramatic change of bacterial assembly process and co-occurrence pattern in Spartina alterniflora salt marsh along an inundation frequency gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142546. [PMID: 33035970 DOI: 10.1016/j.scitotenv.2020.142546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/02/2020] [Accepted: 09/19/2020] [Indexed: 05/20/2023]
Abstract
Exotic Spartina alterniflora has become widely distributed along most of the coastlines in China in a wide range of inundation frequencies. However, the assembly processes and co-occurrence patterns of the bacterial community in S. alterniflora wetlands under different inundation frequencies remain elusive. In this study, an in-situ mesocosm was established to investigate the changes in soil bacterial community. We found that soil water content was the most decisive factor in influencing the bacterial community. Balanced variation, rather than abundance gradients, accounted for the major shifts in bacterial communities and was significantly and positively correlated with the changes in water content, suggesting that species substitution was facilitated by the increased water content. Deterministic processes were dominant in community assembly, and a large degree of change in water content increased variable selection. Co-occurrence network revealed that increasing water content significantly decreased the average degree and the relative abundance of keystone species, resulting in a network with less complexity. Structural equation modelling suggests that increasing inundation frequency has strong impacts on bacterial community, primarily by altering water content, network degree, and the relative abundance of keystone species. Overall, our results illustrate that increasing inundation frequency significantly influences the bacterial community assembly processes and co-occurrence patterns.
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Affiliation(s)
- Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Dan Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binu M Tripathi
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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29
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Yan S, Cheng KY, Ginige MP, Zheng G, Zhou L, Kaksonen AH. Optimization of nitrate and selenate reduction in an ethanol-fed fluidized bed reactor via redox potential feedback control. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123770. [PMID: 33254781 DOI: 10.1016/j.jhazmat.2020.123770] [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: 06/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 06/12/2023]
Abstract
Electron donors are a major cost-factor in biological removal of oxyanions, such as nitrate and selenate from wastewater. In this study, an online ethanol dosing strategy based on feedback control of oxidation-reduction potential (ORP) was designed to optimize the performance of a lab-scale fluidized bed reactor (FBR) in treating selenate and nitrate (5 mM each) containing wastewater. The FBR performance was evaluated at various ORP setpoints ranging between -520 mV and -240 mV (vs. Ag/AgCl). Results suggested that both nitrate and selenate were completely removed at ORPs between -520 mV and -360 mV, with methylseleninic acid, selenocyanate, selenosulfate and ammonia being produced at low ORPs between -520 mV and -480 mV, likely due to overdosing of ethanol. At ORPs between -300 mV and -240 mV, limited ethanol dosing resulted in an apparent decline in selenate removal whereas nitrate removal remained stable. Resuming the ORP to -520 mV successfully restored complete selenate reduction. An optimal ORP of -400 mV was identified for the FBR, whereby selenate and nitrate were nearly completely removed with a minimal ethanol consumption. Overall, controlling ORP via feedback-dosing of the electron donor was an effective strategy to optimize FBR performance for reducing selenate and nitrate in wastewater.
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Affiliation(s)
- Su Yan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Land and Water, 147 Underwood Avenue, Floreat WA, 6014, Australia; Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ka Yu Cheng
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Land and Water, 147 Underwood Avenue, Floreat WA, 6014, Australia; School of Engineering and Information Technology, Murdoch University, Perth WA, Australia
| | - Maneesha P Ginige
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Land and Water, 147 Underwood Avenue, Floreat WA, 6014, Australia
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Land and Water, 147 Underwood Avenue, Floreat WA, 6014, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia.
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30
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Nguyen J, Lara-Gutiérrez J, Stocker R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol Rev 2020; 45:6041721. [PMID: 33338228 PMCID: PMC8371271 DOI: 10.1093/femsre/fuaa068] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
From the homeostasis of human health to the cycling of Earth's elements, microbial activities underlie environmental, medical and industrial processes. These activities occur in chemical and physical landscapes that are highly dynamic and experienced by bacteria as fluctuations. In this review, we first discuss how bacteria can experience both spatial and temporal heterogeneity in their environments as temporal fluctuations of various timescales (seconds to seasons) and types (nutrient, sunlight, fluid flow, etc.). We then focus primarily on nutrient fluctuations to discuss how bacterial communities, populations and single cells respond to environmental fluctuations. Overall, we find that environmental fluctuations are ubiquitous and diverse, and strongly shape microbial behavior, ecology and evolution when compared with environments in which conditions remain constant over time. We hope this review may serve as a guide toward understanding the significance of environmental fluctuations in microbial life, such that their contributions and implications can be better assessed and exploited.
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Affiliation(s)
- Jen Nguyen
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juanita Lara-Gutiérrez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
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31
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Zhao P, Wang W, Whalen JK, Zhang S, Ye Q. Transportation and degradation of decabrominated diphenyl ether in sequential anoxic and oxic crop rotation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115082. [PMID: 32629310 DOI: 10.1016/j.envpol.2020.115082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
This work evaluated the debromination and uptake of 14C-labeled BDE-209 in rice cultivars grown in anoxic soil for 120 days (d) followed by cultivation of vegetables (peanut, eggplant and pepper) in oxic soil (120 d). Degradation of BDE-209 to lower polybrominated diphenyl ethers (PBDEs) occurred in cultivated soils, and more metabolites were released in oxic soil than in anoxic soil. The crop rotation from anoxic to oxic greatly enhanced the dissipation of BDE-209 in the soil (P < 0.05), in which the dissipation in anoxic soil planted with Huanghuazhan (HHZ, indica) and Yudao 1 (YD1, indica) were 6.8% and 2.4%, respectively, while in oxic soil with peanut and pepper were increased to 25.8% and 21.7%, respectively. The crop rotation also enhanced the degradation of BDE-209 in the soil, the recovered BDE-209 in soil after 120 d anoxic incubation with YD1 was 81.1%, but it decreased to 47.8% and 45.8% after another 120 d oxic incubation. Bioconcentration factors were between 0.23 and 0.36 for rice, eggplant and pepper but reached to 0.5 in peanut, which contains more lipids in the edible portion than the other test crops. The estimated daily intake for vegetables was 0.01-0.07 μg BDE-209-equivalent kg-1 bw day-1, which is at least two orders of magnitude below the maximum acceptable oral dose (7 μg kg-1 bw day-1). Our work confirms that crop rotation from rice to vegetable enhanced the dissipation and debromination of BDE-209 in the soil, and indicate that sequential anoxic-oxic rotation practice is considered to be effective in remediation of environmental pollutants.
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Affiliation(s)
- Pengfei Zhao
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China; Department of Natural Resource Science, Macdonald Campus, McGill University, Ste Anne de Bellevue, QC, H9X 3V9, Canada
| | - Wei Wang
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China
| | - Joann K Whalen
- Department of Natural Resource Science, Macdonald Campus, McGill University, Ste Anne de Bellevue, QC, H9X 3V9, Canada
| | - Sufen Zhang
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China
| | - Qingfu Ye
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China.
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32
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Baltsavias S, Van Treuren W, Weber MJ, Charthad J, Baker S, Sonnenburg JL, Arbabian A. In Vivo Wireless Sensors for Gut Microbiome Redox Monitoring. IEEE Trans Biomed Eng 2020; 67:1821-1830. [PMID: 31634824 PMCID: PMC7170758 DOI: 10.1109/tbme.2019.2948575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A perturbed gut microbiome has recently been linked with multiple disease processes, yet researchers currently lack tools that can provide in vivo, quantitative, and real-time insight into these processes and associated host-microbe interactions. We propose an in vivo wireless implant for monitoring gastrointestinal tract redox states using oxidation-reduction potentials (ORP). The implant is powered and conveniently interrogated via ultrasonic waves. We engineer the sensor electronics, electrodes, and encapsulation materials for robustness in vivo, and integrate them into an implant that endures autoclave sterilization and measures ORP for 12 days implanted in the cecum of a live rat. The presented implant platform paves the way for long-term experimental testing of biological hypotheses, offering new opportunities for understanding gut redox pathophysiology mechanisms, and facilitating translation to disease diagnosis and treatment applications.
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Han YS, Park JH. Effect of redox variation on the geochemical behavior of Sb in a vegetated Sb(V)-contaminated soil column. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122112. [PMID: 32311915 DOI: 10.1016/j.jhazmat.2020.122112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/27/2019] [Accepted: 01/13/2020] [Indexed: 06/11/2023]
Abstract
This study examined the geochemical behavior of antimony (Sb) in a vegetated contaminated soil column consisting of unsaturated rhizosphere and a waterlogging layer. The results showed a reducing condition (Oxidation-Reduction Potential (ORP) of -171 mV) was formed in about 5 days in the waterlogging zone. The amount of Sb released was higher under the oxidizing unsaturated-rhizosphere compared to that in the waterlogging zone possibly because of the weaker affinity of Sb(V) to Mn- and/or Fe-oxides in soil. The fraction of Sb(III) in the dissolved total Sb increased with time when soil redox states were subjected to a further reduction. Solid phase Sb K-edge X-ray absorption spectroscopy (XAS) of soils showed that Sb(III) fraction of the deeper layer soil increased while the unsaturated upper soil solely composed Sb(V). In this study, 250 mg/kg of Sb pollution did not significantly affect plant growth and no significant transport of Sb occurred from the soil to plant. However, changes in redox conditions within the soil column induced a shift in soil microbial communities. Consequently, the importance of redox states of soil on geochemical behavior of Sb and the effects of soil flooding or waterlogging deserve attention in the management of Sb-contaminated soil.
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Affiliation(s)
- Young-Soo Han
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Jin Hee Park
- Department of Environmental & Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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Zolti A, Green SJ, Sela N, Hadar Y, Minz D. The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts. MICROBIOME 2020; 8:71. [PMID: 32438915 PMCID: PMC7243336 DOI: 10.1186/s40168-020-00850-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/28/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. RESULTS Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. CONCLUSIONS We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.
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Affiliation(s)
- Avihai Zolti
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
| | - Stefan J. Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - Noa Sela
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
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König S, Vogel HJ, Harms H, Worrich A. Physical, Chemical and Biological Effects on Soil Bacterial Dynamics in Microscale Models. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Kivlin SN, Hawkes CV. Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest. Ecology 2020; 101:e02985. [PMID: 31958139 DOI: 10.1002/ecy.2985] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/21/2019] [Accepted: 12/20/2019] [Indexed: 11/06/2022]
Abstract
The spatial and temporal linkages between turnover of soil microbial communities and their associated functions remain largely unexplored in terrestrial ecosystems. Yet defining these relationships and how they vary across ecosystems and microbial lineages is key to incorporating microbial communities into ecological forecasts and ecosystem models. To define linkages between turnover of soil bacterial and fungal communities and their function we sampled fungal and bacterial composition, abundance, and enzyme activities across a 3-ha area of wet tropical primary forest over 2 yr. We show that fungal and bacterial communities both exhibited temporal turnover, but turnover of both groups was much lower than in temperate ecosystems. Turnover over time was driven by gain and loss of microbial taxa and not changes in abundance of individual species present in multiple samples. Only fungi varied over space with idiosyncratic variation that did not increase linearly with distance among sampling locations. Only phosphorus-acquiring enzyme activities were linked to shifts in septate, decomposer fungal abundance; no enzymes were affected by composition or diversity of fungi or bacteria. Although temporal and spatial variation in composition was appreciable, because turnover of microbial communities did not alter the functional repertoire of decomposing enzymes, functional redundancy among taxa may be high in this ecosystem. Slow temporal turnover of tropical soil microbial communities and large functional redundancy suggests that shifts in abundance of particular functional groups may capture ecosystem function more accurately than composition in these heterogeneous ecosystems.
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Affiliation(s)
- Stephanie N Kivlin
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712, USA
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Abstract
Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved. Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.
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Gross A, Lin Y, Weber PK, Pett‐Ridge J, Silver WL. The role of soil redox conditions in microbial phosphorus cycling in humid tropical forests. Ecology 2019; 101:e02928. [DOI: 10.1002/ecy.2928] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/16/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Avner Gross
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
- Department of Geography and Environmental Development Ben Gurion University of the Negev Beer Sheva Israel
| | - Yang Lin
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
| | - Peter K. Weber
- Lawrence Livermore National Laboratory Physical and Life Science Directorate Livermore California 94550 USA
| | - Jennifer Pett‐Ridge
- Lawrence Livermore National Laboratory Physical and Life Science Directorate Livermore California 94550 USA
| | - Whendee L. Silver
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
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Yang L, Li Y, Su F, Li H. Metabolomics Study of Subsurface Wastewater Infiltration System Under Fluctuation of Organic Load. Curr Microbiol 2019; 77:261-272. [PMID: 31828380 DOI: 10.1007/s00284-019-01830-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/29/2019] [Indexed: 11/26/2022]
Abstract
Subsurface Wastewater Infiltration System (SWIS) is a sewage ecological treatment technology with low investment, energy consumption, and operating cost. SWIS soil contains a large variety of microorganisms. The metabolic process and production of microorganisms are an important basis for qualitatively describing the process of pollutant removal. In order to discover the microbial decontamination pathways in SWIS, the metabolic profiles of soil microorganisms in SWIS were analyzed by UPLC-MS. Partial least squares-discriminant analysis (PLS-DA)and principal component analysis (PCA) pattern recognition methods were used to classify the samples. According to the model's variable importance factor (VIP value), potential biomarkers were screened and biological information contained in the metabolites was also analyzed. The correlation between metabolites and environmental factors was explored by RDA analysis. In total, 230 differential metabolites with VIP value greater than 1.5 were screened out when the influent organic load fluctuated at 250 mg L-1, 400 mg L-1, and 500 mg L-1. After identifying and screening, 35 differential metabolites were identified and used to further analyze the metabolic pathway. It turns out that microbial metabolites in SWIS were mainly glycosides, fatty acids, amino acids, pigments, diterpenoids, and some polymers under medium and high organic loading conditions. At low organic load, the microbial metabolites in SWIS were mainly ketones, alcohols, and esters.
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Affiliation(s)
- Lei Yang
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China
| | - Yinghua Li
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China.
| | - Fei Su
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China
| | - Haibo Li
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China
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40
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Jin X, Kengara FO, Yue X, Wang F, Schroll R, Munch JC, Gu C, Jiang X. Shorter interval and multiple flooding-drying cycling enhanced the mineralization of 14C-DDT in a paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 676:420-428. [PMID: 31048172 DOI: 10.1016/j.scitotenv.2019.04.284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
DDT and its main metabolites (DDTs) are still the residual contaminants in soil. Sequential anaerobic-aerobic cycling has long been approved for enhancing the degradation of DDTs in soil. However, there is a lack of study investigating whether anaerobic-aerobic cycling would enhance the mineralization of DDT, and what a kind of anaerobic-aerobic management regimes would be optimal. To fill these gaps, the fate of 14C-DDT under different flooding-drying cycles was examined in a paddy soil by monitoring its mineralization and bioavailability. The results show the total mineralization of 14C-DDT in 314 days accounted for 1.01%, 1.30%, and 1.41%, individually for the treatments subjected to one, two, and three flooding-drying cycles. By comparison, the treatment subjected to the permanently aerobic phase had only 0.12% cumulative mineralization. Shorter intervals and multiple flooding-drying cycles enhanced the mineralization of 14C-DDT, however, reduced its bioavailability. Therefore, the enhanced mineralization was explained from an abiotic pathway as predicted by the one-electron reduction potential (E1), the Fukui function for nucleophilic attack (f+) and the steps for anaerobic decarboxylation. From a practical view, it is important to investigate how the anaerobic-aerobic interval and frequency would affect the degradation and mineralization of DDT, which is very essential in developing remediation strategies.
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Affiliation(s)
- Xin Jin
- School of the Environment Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Microbe-Plant Interactions, Neuherberg 85764, Germany.
| | - Fredrick O Kengara
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Microbe-Plant Interactions, Neuherberg 85764, Germany; Department of Chemistry, Maseno University, Maseno 40105, Kenya
| | - Xianhui Yue
- School of the Environment Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210008, China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Reiner Schroll
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Microbe-Plant Interactions, Neuherberg 85764, Germany
| | - Jean C Munch
- Lehrstuhl für Grünlandlehre, Technische Universität München, Fresing D-85350, Germany
| | - Cheng Gu
- School of the Environment Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210008, China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Wu JH, Chen WY, Kuo HC, Li YM. Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin- and dibenzofuran-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:506-515. [PMID: 30831347 DOI: 10.1016/j.envpol.2019.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/16/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ± 68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ± 118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 109 copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.
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Affiliation(s)
- Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan.
| | - Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Hung-Chih Kuo
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Yun-Ming Li
- Mass Laboratory, National Chiao-Tung University, Hsinchu, Taiwan
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Yang F, Zhang D, Wu J, Chen Q, Long C, Li Y, Cheng X. Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 663:662-672. [PMID: 30731412 DOI: 10.1016/j.scitotenv.2019.01.357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/25/2019] [Accepted: 01/27/2019] [Indexed: 06/09/2023]
Abstract
Since the completion of Three Gorges Dam in 2008, a large water-level fluctuation zone with anti-seasonal submergence has formed between the elevations of 145 m and 175 m in the Three Gorges Reservoir in China. In addition to hydrological regime, revegetation has also occurred in this water-level fluctuation zone. However, how the hydrological regime and revegetation regulate soil prokaryotic community remains unclear. Here, we investigated soil prokaryotic community structure, diversity and environmental parameters in different flooding zones from two soil layers (0-10 cm and 10-30 cm) at 6 locations along the water-level fluctuation zone from upstream to downstream. The soil prokaryotic diversity tended to decrease from upstream to downstream, and the alpha diversity was higher in the topsoil than in the deep soil at all sites. Flooding significantly enhanced the prokaryotic diversity compared to the control (i.e., permanent dry zone). The soil prokaryotic composition underwent deterministic processes in the upstream sites and stochastic processes in the downstream sites, with stronger stochastic processes in the topsoil than in the deep soil across all sites and elevations. As expected, the soil pH, moisture, NH4+-N, organic carbon and nitrogen were proven to be determinants of the prokaryotic community composition. Changes in plant traits (plant biomass, richness, and carbon content) after revegetation induced by submergence also played an important role in structuring the prokaryotic community. The prokaryotic community exhibited a shorter average path distance (GD) in the flooding zones compared to the control, with the shortest average degree (avgK) and the lowest levels of stability in the longer periodic inundation zones. Overall, our results suggest that soil properties and plant functional traits are critical controls of the prokaryotic community's ability to develop at regional scales and water submergence can likewise be an important factor for variations in the prokaryotic community composition in riparian zones.
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Affiliation(s)
- Fan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Dandan Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Junjun Wu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Qiong Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Chunyan Long
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Yongheng Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing, PR China; College of Science, University of Tibet, Lhasa, PR China
| | - Xiaoli Cheng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, PR China.
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Barba C, Folch A, Sanchez-Vila X, Martínez-Alonso M, Gaju N. Are dominant microbial sub-surface communities affected by water quality and soil characteristics? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:332-343. [PMID: 30818236 DOI: 10.1016/j.jenvman.2019.02.079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO3 and SO4, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.
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Affiliation(s)
- Carme Barba
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Albert Folch
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Xavier Sanchez-Vila
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Maira Martínez-Alonso
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
| | - Núria Gaju
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
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Hunting ER, Harrison RG, Bruder A, van Bodegom PM, van der Geest HG, Kampfraath AA, Vorenhout M, Admiraal W, Cusell C, Gessner MO. Atmospheric Electricity Influencing Biogeochemical Processes in Soils and Sediments. Front Physiol 2019; 10:378. [PMID: 31040789 PMCID: PMC6477044 DOI: 10.3389/fphys.2019.00378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/19/2019] [Indexed: 11/16/2022] Open
Abstract
The Earth’s subsurface represents a complex electrochemical environment that contains many electro-active chemical compounds that are relevant for a wide array of biologically driven ecosystem processes. Concentrations of many of these electro-active compounds within Earth’s subsurface environments fluctuate during the day and over seasons. This has been observed for surface waters, sediments and continental soils. This variability can affect particularly small, relatively immobile organisms living in these environments. While various drivers have been identified, a comprehensive understanding of the causes and consequences of spatio-temporal variability in subsurface electrochemistry is still lacking. Here we propose that variations in atmospheric electricity (AE) can influence the electrochemical environments of soils, water bodies and their sediments, with implications that are likely relevant for a wide range of organisms and ecosystem processes. We tested this hypothesis in field and laboratory case studies. Based on measurements of subsurface redox conditions in soils and sediment, we found evidence for both local and global variation in AE with corresponding patterns in subsurface redox conditions. In the laboratory, bacterial respiratory responses, electron transport activity and H2S production were observed to be causally linked to changes in atmospheric cation concentrations. We argue that such patterns are part of an overlooked phenomenon. This recognition widens our conceptual understanding of chemical and biological processes in the Earth’s subsurface and their interactions with the atmosphere and the physical environment.
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Affiliation(s)
- Ellard R Hunting
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States.,Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - R Giles Harrison
- Department of Meteorology, University of Reading, Reading, United Kingdom
| | - Andreas Bruder
- Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland, Bellinzona, Switzerland
| | | | - Harm G van der Geest
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Andries A Kampfraath
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Wim Admiraal
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Casper Cusell
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Mark O Gessner
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Department of Ecology, Berlin Institute of Technology, Berlin, Germany
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45
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Wang Y, Lin Z, Wang Y, Huang W, Wang J, Zhou J, He Q. Sulfur and iron cycles promoted nitrogen and phosphorus removal in electrochemically assisted vertical flow constructed wetland treating wastewater treatment plant effluent with high S/N ratio. WATER RESEARCH 2019; 151:20-30. [PMID: 30579051 DOI: 10.1016/j.watres.2018.12.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/24/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Phosphate (PO43--P) and nitrate (NO3--N) in the effluent of wastewater treatment plants are the predominant sources of eutrophication. In this study, a bench-scale electrochemically assisted vertical flow constructed wetland (E-VFCW) was developed, which exhibited favorable PO43--P (89.7-99.4%), NO3--N (82.7-99.6%), and TN (51.9-93.7%) removal efficiency in tertiary wastewater treatment. In addition, little N2O accumulation (0.32-2.19% of △NO3--N) was observed. The study further elucidated that PO43--P was removed mainly in the anode chamber by co-precipitation (Fe(n+)OH-PO4) and adsorption (FeOOH-PO4) pathways. Multi-pathway of NO3--N reduction was proposed, with 13.9-30.2% of NO3--N predominantly eliminated in the anode chamber by ferrous-dependent NO3--N reduction bacteria. In the cathode chamber, electrons storage and resupply modes during S cycle exerted crucial roles in NO3--N reduction, which enhanced the resilience capabilities of the E-VFCW to shock loadings. Stoichiometric analysis revealed that 3.3-6.6 mmol e-/cycle were stored in the form of S0, FeS, and FeS2 in the E-VFCW under longer HRT or higher current density. However, the deposited S resupplied 19.6% and 28.3% of electrons for NO3--N reduction under shorter HRT (1 h) or lower current density (0.01 mA cm-2). Moreover, ferrous-driven NO3--N-reducing or DNRA bacteria also promoted NO3--N elimination in the cathode chamber. These findings provide new insight into the coupling interactions among S, Fe and H cycles, as well as N and P transformations in electrochemically assisted NO3--N reduction systems.
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Affiliation(s)
- Yingmu Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Ziyuan Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Yue Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Wei Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Jiale Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Jian Zhou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
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46
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Gustave W, Yuan ZF, Sekar R, Toppin V, Liu JY, Ren YX, Zhang J, Chen Z. Relic DNA does not obscure the microbial community of paddy soil microbial fuel cells. Res Microbiol 2019; 170:97-104. [DOI: 10.1016/j.resmic.2018.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/11/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
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47
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Sims GK, Kanissery RG. Anaerobic Biodegradation of Pesticides. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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48
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Bhattacharyya A, Campbell AN, Tfaily MM, Lin Y, Kukkadapu RK, Silver WL, Nico PS, Pett-Ridge J. Redox Fluctuations Control the Coupled Cycling of Iron and Carbon in Tropical Forest Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:14129-14139. [PMID: 30451506 DOI: 10.1021/acs.est.8b03408] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Oscillating redox conditions are a common feature of humid tropical forest soils, driven by an ample supply and dynamics of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. However, the net result of variable soil redox regimes on iron (Fe) mineral dynamics and associated carbon (C) forms and fluxes is poorly understood in tropical soils. Using a 44-day redox incubation experiment with humid tropical forest soils from Puerto Rico, we examined patterns in Fe and C transformations under four redox regimes: static anoxic, "flux 4-day" (4d oxic, 4d anoxic), "flux 8-day" (8d oxic, 4d anoxic) and static oxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides, and led to an increase in soluble Fe(II) and amorphous Fe oxide pools. Preferential dissolution of the less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic C, presumably due to acidification or direct release of organic matter (OM) from dissolving Fe(III) mineral phases. The average nominal oxidation state of water-soluble C was lowest under persistent anoxic conditions, suggesting that more reduced organic compounds were metabolically unavailable for microbial consumption under reducing conditions. Anoxic soil compounds had high H/C values (and were similar to lignin-like compounds) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic C was highest in static oxic soils. These results show how Fe minerals and Fe-OM interactions in tropical soils are highly sensitive to variable redox effects. Shifting soil oxygen availability rapidly impacted exchanges between mineral-sorbed and aqueous C pools, increased the dissolved organic C pool under anoxic conditions implying that the periodicity of low-redox events may control the fate of C in wet tropical soils.
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Affiliation(s)
- Amrita Bhattacharyya
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
| | - Ashley N Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Lin
- Department of Environmental Science, Policy, and Management , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Ravi K Kukkadapu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Peter S Nico
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , 7000 East Avenue , Livermore , California 94550 , United States
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49
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Anderson CR, Peterson ME, Frampton RA, Bulman SR, Keenan S, Curtin D. Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum. PeerJ 2018; 6:e6090. [PMID: 30581677 PMCID: PMC6295159 DOI: 10.7717/peerj.6090] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/08/2018] [Indexed: 01/13/2023] Open
Abstract
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.
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Affiliation(s)
- Craig R Anderson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Michelle E Peterson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Rebekah A Frampton
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Simon R Bulman
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Sandi Keenan
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Denis Curtin
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
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50
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Soil Oxygen Limits Microbial Phosphorus Utilization in Humid Tropical Forest Soils. SOIL SYSTEMS 2018. [DOI: 10.3390/soilsystems2040065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil phosphorus (P) availability is of special interest in many humid tropical forests, especially those on highly weathered, iron (Fe)- and aluminum (Al)-rich soils where P often limits net primary productivity. Phosphorus cycling is partly dependent on the ability of microbes to compete for P with Fe and Al minerals, which strongly bind P. Soil P availability is also indirectly affected by soil redox conditions due to its effects on microbial activity and reductive dissolution of Fe oxides that may weaken Fe-O-P sorption strength. Here, we explored P sorption, soil Fe (II) concentrations, soil CO2 production, organic and inorganic P pools, and microbial biomass P in tropical soils that typically experience frequent low redox (valley soils), or fluctuating redox conditions (slope soils). Soils from both topographic positions were pre-incubated under oxic or anoxic headspaces and then amended with a mixture of P (as orthophosphate) and carbon (C, as acetate, to maintain microbial activity) and incubated in the dark for 24 h. Phosphorus sorption to the mineral phase occurred on a time scale of seconds to minutes in valley and slope soils, reflecting strong abiotic P sorption capacity. Valley soils were characterized by inherently higher Fe(II) concentrations and lower respiration rates. Under anoxic headspaces, Fe(II) concentrations increased 3-to 5-fold in the both soils. Soil respiration and microbial P utilization declined significantly in both soils under anoxic conditions, regardless of Fe(II) concentrations. Microbial P concentrations were highest when slope soils were incubated under an oxic headspace, despite the high P sorption under these conditions. Our results suggest that microbial P utilization is indirectly limited by low O2 availability and that microbes are able to effectively compete with minerals for P under Fe-oxidizing conditions. These results emphasize the central role of soil microorganisms in regulating P availability, even in the presence of strong abiotic sorption capacity.
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