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Xu M, Ren M, Yao Y, Liu Q, Che J, Wang X, Xu Q. Biochar decreases cadmium uptake in indica and japonica rice (Oryza sativa L.): Roles of soil properties, iron plaque, cadmium transporter genes and rhizobacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135402. [PMID: 39096632 DOI: 10.1016/j.jhazmat.2024.135402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Biochar is an effective and economical strategy for in situ soil cadmium (Cd) remediation. It is essential to comprehensively investigate how biochar mitigates Cd uptake of the main rice subspecies. A pot experiment was established via adding corn stalk biochar into Cd-contaminated soil growing indica Yangdao 6 (YD) and japonica Nangeng 9108 (9108). 9108 had lower shoot biomass (-17.9%) but higher root biomass (+14.4%) and shoot Cd concentration (+29.4%) than YD. Biochar decreased soil available Cd by 25.2% and shoot Cd concentration by 13.6% through the liming and passivation effects. Biochar also favored Cd mitigation by recruiting Fe reducer, Cd remover and plant growth-promoting rhizobacteria (e.g. Bacteroides, Deferrisomatota, Bacillus and Allorhizobium). Besides, biochar reduced Cd uptake by stimulating iron plaques formation for 9108. Moreover, biochar did not reduce Cd uptake by inhibiting Cd transporter genes' expressions and it increased OsHMA2 expression in YD. In conclusion, biochar had great capacity in mitigating Cd pollution and rice subspecies responded differently to biochar in iron plaque formation and Cd transporter genes. The research established a comprehensive understanding of the mechanisms underlying Cd mitigation by biochar and helped to breed low Cd-accumulated rice cultivars to safeguard rice production.
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Affiliation(s)
- Meiling Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Meiling Ren
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Yu Yao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Qi Liu
- College of Forestry, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jing Che
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaozhi Wang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Qiao Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne, VIC 3086, Australia.
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Momper L, Casar CP, Osburn MR. A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA. Environ Microbiol 2023; 25:3719-3737. [PMID: 37964716 DOI: 10.1111/1462-2920.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.
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Affiliation(s)
- Lily Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
- Exponent, Inc, Menlo Park, California, USA
| | - Caitlin P Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
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Vigderovich H, Eckert W, Elvert M, Gafni A, Rubin-Blum M, Bergman O, Sivan O. Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments. Front Microbiol 2023; 14:1206414. [PMID: 37577416 PMCID: PMC10415106 DOI: 10.3389/fmicb.2023.1206414] [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: 04/15/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.
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Affiliation(s)
- Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Marcus Elvert
- MARUM—Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Almog Gafni
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Oded Bergman
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Escudero C, Amils R. Dark biosphere: Just at the very tip of the iceberg. Environ Microbiol 2023; 25:147-149. [PMID: 36307896 PMCID: PMC10100182 DOI: 10.1111/1462-2920.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Cristina Escudero
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.,Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.,Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
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Meyer-Dombard DR, Malas J. Advances in Defining Ecosystem Functions of the Terrestrial Subsurface Biosphere. Front Microbiol 2022; 13:891528. [PMID: 35722320 PMCID: PMC9201636 DOI: 10.3389/fmicb.2022.891528] [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: 03/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
The subsurface is one of the last remaining 'uncharted territories' of Earth and is now accepted as a biosphere in its own right, at least as critical to Earth systems as the surface biosphere. The terrestrial deep biosphere is connected through a thin veneer of Earth's crust to the surface biosphere, and many subsurface biosphere ecosystems are impacted by surface topography, climate, and near surface groundwater movement and represent a transition zone (at least ephemerally). Delving below this transition zone, we can examine how microbial metabolic functions define a deep terrestrial subsurface. This review provides a survey of the most recent advances in discovering the functional and genomic diversity of the terrestrial subsurface biosphere, how microbes interact with minerals and obtain energy and carbon in the subsurface, and considers adaptations to the presented environmental extremes. We highlight the deepest subsurface studies in deep mines, deep laboratories, and boreholes in crystalline and altered host rock lithologies, with a focus on advances in understanding ecosystem functions in a holistic manner.
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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