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Hindi SS, Albureikan MOI. Fabrication, Characterization, and Microbial Biodegradation of Transparent Nanodehydrated Bioplastic (NDB) Membranes Using Novel Casting, Dehydration, and Peeling Techniques. Polymers (Basel) 2023; 15:3303. [PMID: 37571197 PMCID: PMC10422282 DOI: 10.3390/polym15153303] [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: 05/21/2023] [Revised: 07/15/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
NDBs were fabricated from gum Arabic (GA) and polyvinyl alcohol (PVA) in different ratios using novel techniques (casting, dehydration, and peeling). The GA/PVA blends were cast with a novel vibration-free horizontal flow (VFHF) technique, producing membranes free of air bubble defects with a homogenous texture, smooth surface, and constant thickness. The casting process was achieved on a self-electrostatic template (SET) made of poly-(methyl methacrylate), which made peeling the final product membranes easy due to its non-stick behavior. After settling the casting of the membranous, while blind, the sheets were dried using nanometric dehydration under a mild vacuum stream using a novel stratified nano-dehydrator (SND) loaded with P2O5. After drying the NDB, the dry, smooth membranes were peeled easily without scratching defects. The physicochemical properties of the NDBs were investigated using FTIR, XRD, TGA, DTA, and AFM to ensure that the novel techniques did not distort the product quality. The NDBs retained their virgin characteristics, namely, their chemical functional groups (FTIR results), crystallinity index (XRD data), thermal stability (TGA and DTA), and ultrastructural features (surface roughness and permeability), as well as their microbial biodegradation ability. Adding PVA enhanced the membrane's properties except for mass loss, whereby increasing the GA allocation in the NDB blend reduces its mass loss at elevated temperatures. The produced bioplastic membranes showed suitable mechanical properties for food packaging applications and in the pharmaceutical industry for the controlled release of drugs. In comparison to control samples, the separated bacteria and fungi destroyed the bioplastic membranes. Pseudomonas spp. and Bacillus spp. were the two main strains of isolated bacteria, and Rhizobus spp. was the main fungus. The nano-dehydration method gave the best solution for the prompt drying of water-based biopolymers free of manufacturing defects, with simple and easily acquired machinery required for the casting and peeling tasks, in addition to its wonderful biodegradation behavior when buried in wet soil.
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Affiliation(s)
- Sherif S. Hindi
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University (KAU), P.O. Box 80208, Jeddah 21589, Saudi Arabia
| | - Mona Othman I. Albureikan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80208, Jeddah 21589, Saudi Arabia;
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He L, Sun X, Li S, Zhou W, Chen Z, Bai X. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161754. [PMID: 36709888 DOI: 10.1016/j.scitotenv.2023.161754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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3
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Zhang W, Wang J, Zhu L, Wang J, Mao S, Yan X, Wen S, Wang L, Dong Z, Kim YM. New insights into the effects of antibiotics and copper on microbial community diversity and carbon source utilization. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023:10.1007/s10653-023-01491-1. [PMID: 36939996 DOI: 10.1007/s10653-023-01491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Residual antibiotics (ABs) and heavy metals (HMs) are continuously released from soil, reflecting their intensive use and contamination of water and soil, posing an environmental problem of great concern. Relatively few studies exist of the functional diversity of soil microorganisms under the combined action of ABs and HMs. To address this deficiency, BIOLOG ECO microplates and the Integrated Biological Responses version 2 (IBRv2) method were used to comprehensively explore the effects of single and combined actions of copper (Cu) and enrofloxacin (ENR), oxytetracycline (OTC), and sulfadimidine (SM2) on the soil microbial community. The results showed that the high concentration (0.80 mmol/kg) compound group had a significant effect on average well color development (AWCD) and OTC showed a dose-response relationship. The results of IBRv2 analysis showed that the single treatment group of ENR or SM2 had a significant effect on soil microbial communities, and the IBRv2 of E1 was 5.432. Microbes under ENR, SM2, and Cu stress had more types of available carbon sources, and all treatment groups were significantly more enriched with microorganisms having D-mannitol and L-asparagine as carbon sources. This study confirms that the combined effects of ABs and HMs can inhibit or promote the function of soil microbial communities. In addition, this paper will provide new insights into IBRv2 as an effective method to evaluate the impacts of contaminants on soil health.
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Affiliation(s)
- Wenjie Zhang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China.
| | - Lusheng Zhu
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Shushuai Mao
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Xiaojing Yan
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Shengfang Wen
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Lanjun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Zikun Dong
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-Gu, Seoul, 04763, Republic of Korea
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Zhang Y, Wu X, Chen C, Xu J, Dong F, Liu X, Li X, Zheng Y. Application of thifluzamide alters microbial network structure and affects methane cycle genes in rice-paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155769. [PMID: 35526624 DOI: 10.1016/j.scitotenv.2022.155769] [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: 12/24/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Thifluzamide is an effective agent for controlling rice sheath blight and has a long half-life in soil. However, the effects of thifluzamide on the abundance of microbes harboring methane-cycle genes and soil microbial community assembly patterns are not well known. Thus, we conducted a three-month indoor mesocosm experiment to ascertain the effects of thifluzamide (0.05, 0.5, and 5 mg kg-1 soil; 0.05 mg kg-1 soil being recommended) on bacterial and archaeal community structure and on the abundance of methanogen genes using two typical paddy soils: sandy soil from Hangzhou (HZ) and loam sandy soil from Jiansanjiang (JSJ). The effects of thifluzamide on soil microorganisms were related to soil type. In JSJ loam sandy soil, thifluzamide significantly increased bacterial α diversity after 7-30 d and archaeal α diversity at 30 and 60 d. In HZ sandy soil, however, α diversity did not change significantly. Network analysis showed that thifluzamide-treated soils possessed more complex networks with more total nodes and links, a higher average degree of connectivity, and more keystone species. Thifluzamide application increased the number of keystone species associated with methane production in both types of paddy soil. A relatively greater number of modules were significantly negatively correlated with mcrA abundance in the HZ T10 network, but more modules were positively correlated with mcrA abundance in the JSJ T100 network. The half-life of thifluzamide varied for the different doses, i.e., from 152.0 to 419.6 d. The results reveal that methane-cycle genes, soil microbiome assembly, and interactions among microbial species all change in response to thifluzamide stress.
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Affiliation(s)
- Ying Zhang
- College of Plant Protection, Hunan Agricultural University, Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Changsha 410128, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China; Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Xiaohu Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Caijun Chen
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Jun Xu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Fengshou Dong
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Xingang Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Xiaogang Li
- College of Plant Protection, Hunan Agricultural University, Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Changsha 410128, China.
| | - Yongquan Zheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
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Li Y, Wang T, Camps-Arbestain M, Whitby CP. The regulators of soil organic carbon mineralization upon lime and/or phosphate addition vary with depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154378. [PMID: 35276156 DOI: 10.1016/j.scitotenv.2022.154378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Knowledge of the key factors regulating soil organic carbon (OC) mineralization in response to fertilizers and lime application is essential to understanding the effects of agricultural land management on soil OC preservation. Microbial community composition and OC availability to microorganisms have been proposed as the two most imperative factors controlling soil OC mineralization, although their relative importance is still under debate. Here we performed a laboratory incubation in combination with high-throughput sequencing and structural equation modeling to examine the mechanisms underlying the responses of OC mineralization in the topsoil and the subsoil of a volcanic soil (an Andosol) to the additions of lime and/or phosphate. Results showed that lime and/or phosphate additions induced distinct shifts in the microbial community composition and functional profiles in the topsoil and the subsoil. We found that OC mineralization relied on microbial community composition and functionality in the topsoil but was strongly related to the quality and quantity of the water-extractable OC (indicative of the OC availability) in the subsoil. These data suggest that the key regulator controlling the response of OC mineralization to lime and/or P additions shifts from microbial community composition to OC availability as soil depth increases in the Andosol. Our findings highlight the central role of mechanisms controlling soil OC mineralization in regulating the responses of mineralization to intensive agricultural management practices.
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Affiliation(s)
- Yang Li
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Tao Wang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Marta Camps-Arbestain
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Catherine P Whitby
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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7
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Koner S, Chen JS, Hsu BM, Rathod J, Huang SW, Chien HY, Hussain B, Chan MWY. Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127266. [PMID: 34600373 DOI: 10.1016/j.jhazmat.2021.127266] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.
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Affiliation(s)
- Suprokash Koner
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
| | - Jagat Rathod
- Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Wei Huang
- Center for environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan; Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung, Taiwan
| | - Hua-Yi Chien
- Environmental Technology Development Department, Taiwan VCM Corporation, Kaohsiung, Taiwan; Department of Environmental Sciences and Engineering, Fooyin University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
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Alves RJE, Callejas IA, Marschmann GL, Mooshammer M, Singh HW, Whitney B, Torn MS, Brodie EL. Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Front Microbiol 2021; 12:735282. [PMID: 34917043 PMCID: PMC8669745 DOI: 10.3389/fmicb.2021.735282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Vmax and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.
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Affiliation(s)
- Ricardo J Eloy Alves
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ileana A Callejas
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gianna L Marschmann
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maria Mooshammer
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans W Singh
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Bizuayehu Whitney
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Margaret S Torn
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Energy and Resources Group, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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Salwan R, Sharma V, Saini R, Pandey M. Identification of plant beneficial Bacillus spp. for Resilient agricultural ecosystem. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100046. [PMID: 34841337 PMCID: PMC8610352 DOI: 10.1016/j.crmicr.2021.100046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
The plant beneficial microbes from rhizosphere soils in cauliflower fields were characterized for plants beneficial attributes such as phosphorus solubilization, siderophore, chitinase and protease activity, and indole acetic acid type of growth regulator. The antagonistic behavior of these isolates against fusarium oxysporum and sclerotinia sclerotiorum revealed their potential in combating the biotic stresses.
The use of synthetic pesticides and chemicals to continuously increase agricultural productivity is causing severe damage to our ecosystem. Therefore, there is need to enhance our understanding about the factors which can contribute to soil processes and play key role in developing sustainable agricultural ecosystem. In this context, the bacteria from cauliflower rhizosphere were isolated and characterized for different plants beneficial attributes. The relationship of soil bacteria and its elemental composition was examined using canonical correspondence analysis. The elemental composition analysis of soil samples revealed presence of Mg, Al, Si, P, K, Ca, Fe and their oxides. In addition, the isolates were found positive for phosphorus solubilization, siderophore, chitinase and protease activity, and indole acetic acid type of growth regulator. The direct confrontation assay revealed antagonistic behavior of these isolates against Fusarium oxysporum and Sclerotinia sclerotiorum. The promising isolates were identified and affiliated to closely related species of genus Bacillus in phylogenetic relationship. The canonical correspondence analysis revealed distribution of elements and their relationship with the identified species in particular area. The characteristics of these isolates revealed their potential in alleviating the biotic and abiotic stresses and hence enhancing crops yield without the usage of synthetic fertilizers and pesticides. The present study is first of its kind and will open new avenues to explore microbial community structure across different farmlands soils to develop resilience agricultural ecosystem.
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Affiliation(s)
- R. Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture & Forestry, Neri, 177 001 HP, India
- Corresponding author.
| | - V. Sharma
- University Centre for Research and Development, Chandigarh University, 140 413, India
- Corresponding author.
| | - R. Saini
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture & Forestry, Neri, 177 001 HP, India
| | - M. Pandey
- University Centre for Research and Development, Chandigarh University, 140 413, India
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10
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Wang X, Sale P, Franks A, Jin J, Krohn C, Armstrong R, Tang C. An Insight Into the Effect of Organic Amendments on the Transpiration Efficiency of Wheat Plant in a Sodic Duplex Soil. FRONTIERS IN PLANT SCIENCE 2021; 12:722000. [PMID: 34745159 PMCID: PMC8563830 DOI: 10.3389/fpls.2021.722000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Transpiration efficiency, the shoot biomass produced per unit of transpired water, is generally considered to be a constant property for a given crop in a given environment. To determine whether deep-banded organic amendments affect the transpiration efficiency (TE) of wheat plants and to provide a possible explanation for any changes in the TE, two-column experiments were carried out under controlled environment conditions. A Sodosol soil with physically constrained subsoils and a well-structured Vertosol were subjected to treatments including a control, fertilizer nutrients alone, and fertilizer-enriched organic amendments. The addition of fertilizer-enriched organic amendments in Sodosol consistently increased the canopy TE compared to the control and inorganic fertilizer treatments. The instantaneous TE, at the leaf level, was also increased by the organic-based amendments due to greater reductions in stomatal conductance and transpiration rates during periods of moderate water-deficit stress and the subsequent recovery from this stress. Shoot nitrogen (N) status could not explain the increases in TE following the addition of organic amendments relative to inorganic amendments. The increases in canopy TE were directly associated with increases in the absolute abundance of indigenous Bacillus (R 2 = 0.92, p <0), a well-known genus comprising many strains of plant beneficial rhizobacteria, in subsoil below the amendment band. In contrast, there were no differences in the canopy TE and instantaneous leaf TE between the organic and fertilizer amendments in the Vertosol with a well-structured subsoil. The positive effect of organic amendments on TE in the Sodosol should be attributed to their direct or indirect effect on improving the physical structure or biological properties of the subsoil.
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Affiliation(s)
- Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Peter Sale
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Ashley Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
- Center for Future Landscapes, La Trobe University, Bundoora, VIC, Australia
| | - Jian Jin
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Christian Krohn
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Roger Armstrong
- Department of Jobs, Precincts & Regions, Grains Innovation Center, Horsham, VIC, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
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11
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Chun SJ, Cui Y, Baek SH, Ahn CY, Oh HM. Seasonal succession of microbes in different size-fractions and their modular structures determined by both macro- and micro-environmental filtering in dynamic coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147046. [PMID: 33894601 DOI: 10.1016/j.scitotenv.2021.147046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 05/16/2023]
Abstract
Microbes interact with each other in response to various environmental changes in coastal marine ecosystems. To explore how the macroenvironment (environmental filtering) and species-engineered microenvironment (niche construction) affect the ecological network of the marine microbiome in the highly dynamic coastal waters of Korea, we analyzed the modular structures of the microbial community and identified microbial interconnections in different size fractions for a year. Fluctuations in the macroenvironment, such as temperature and nutrient concentrations driven by seasonal changes, are the major factors in determining successive microbial modules. Compared to particle-associated (PA) microbes, free-living (FL) microbes seemed to be more affected by macroenvironmental filtering. Modules related to nutrients were further divided into various modules according to different lifestyles. In addition, a large transient discharge of the Changjiang (Yangtze River) in summer also formed a distinct microbial module, which was related to the high ammonia concentration arising from phytoplankton degradation. Microbes belonging to the SAR11, SAR86, and SAR116 clades, Flavobacteriaceae, and MG IIa-L showed repeated interconnections in temperature-related modules, while the SAR202 clade, Marinimicrobia, DEV007 clade, and Arctic97B-4 and Sva0996 marine groups displayed repeated connections in nutrient-related modules. These 'skeleton'-forming microbes created species-engineered microenvironments, further fine-tuning microbial modular structures. Furthermore, they serve as keystone species for module stability by linking interdependent microbial partners within their own modules through universally beneficial metabolic activities. Therefore, they could reinforce the ecological resilience of microbial communities under abiotic and biotic perturbations in dynamic coastal waters. In conclusion, both macro- and micro-environmental filtering were important for determining the seasonal succession of microbial community structures.
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Affiliation(s)
- Seong-Jun Chun
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon 33657, Republic of Korea; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seung Ho Baek
- South Sea Institute, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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12
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Thiele-Bruhn S. The role of soils in provision of genetic, medicinal and biochemical resources. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200183. [PMID: 34365823 DOI: 10.1098/rstb.2020.0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intact, 'healthy' soils provide indispensable ecosystem services that largely depend on the biotic activity. Soil health is connected with human health, yet, knowledge of the underlying soil functioning remains incomplete. This review highlights selected services, i.e. (i) soil as a genetic resource and hotspot of biodiversity, forming the basis for providing (ii) biochemical resources and (iii) medicinal services and goods. Soils harbour an unrivalled biodiversity of organisms, especially microorganisms. Some of the abilities of autochthonous microorganisms and their relevant enzymes serve (i) to improve natural soil functions and in particular plant growth, e.g. through beneficial plant growth-promoting, symbiotic and mycorrhizal microorganisms, (ii) to act as biopesticides, (iii) to facilitate biodegradation of pollutants for soil bioremediation and (iv) to yield enzymes or chemicals for industrial use. Soils also exert direct effects on human health. Contact with soil enriches the human microbiome, affords protection against allergies and promotes emotional well-being. Medicinally relevant are soil substrates such as loams, clays and various minerals with curative effects as well as pharmaceutically active organic chemicals like antibiotics that are formed by soil microorganisms. By contrast, irritating minerals, soil dust inhalation and misguided soil ingestion may adversely affect humans. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People.
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Affiliation(s)
- Sören Thiele-Bruhn
- Soil Science, University of Trier, Behringstrasse 21, D-54286 Trier, Germany
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Hao J, Chai YN, Lopes LD, Ordóñez RA, Wright EE, Archontoulis S, Schachtman DP. The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA. Appl Environ Microbiol 2021; 87:AEM.02673-20. [PMID: 33310710 PMCID: PMC7851703 DOI: 10.1128/aem.02673-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 02/03/2023] Open
Abstract
This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.
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Affiliation(s)
- Jingjie Hao
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Yen Ning Chai
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Lucas Dantas Lopes
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Raziel A Ordóñez
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, Iowa, USA
- Department of Plant Science and Industries Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily E Wright
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, Iowa, USA
| | | | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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14
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Wood JR, Burge OR, Bolstridge N, Bonner K, Clarkson B, Cole TL, Davis C, Fergus A, King P, McKeown MM, Morse C, Richardson SJ, Robertson H, Wilmshurst JM. Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition. PLoS One 2021; 16:e0243363. [PMID: 33406114 PMCID: PMC7787371 DOI: 10.1371/journal.pone.0243363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.
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Affiliation(s)
- Jamie R. Wood
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | | | - Karen Bonner
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | - Theresa L. Cole
- Department of Biology, Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Carina Davis
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | - Alex Fergus
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | - Perēri King
- Maungaharuru-Tangitū Trust, Hawke's Bay Mail Centre, Napier, New Zealand
| | | | - Chris Morse
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | | | - Janet M. Wilmshurst
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
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Evidence for signatures of ancient microbial life in paleosols. Sci Rep 2020; 10:16830. [PMID: 33033361 PMCID: PMC7545160 DOI: 10.1038/s41598-020-73938-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Loess-paleosol sequences are terrestrial archives of past climate change. They may host traces of ancient microbial life, but little information is available on the recovery of microbial biomarkers from such deposits. We hypothesized that microbial communities in soil horizons up to an age of 127 kyr carry information related to past environments. We extracted DNA from a loess-paleosol sequence near Toshan, Northern Iran, with 26 m thick deposits showing different degrees of soil development, performed quantitative PCR and 16S rRNA gene amplicon sequencing. Periods of soil formation archived within the loess sediment led to higher diversity and bacterial abundance in the paleosol horizons. Community composition fluctuated over the loess-paleosol sequence and was mainly correlated with age and depth, (ADONIS R2 < 0.14, P ≤ 0.002), while responses to paleosol soil traits were weaker. Phyla like Bacteriodetes, Proteobacteria or Acidobacteria were more prevalent in paleosol horizons characterized by intense soil formation, while weakly developed paleosols or loess horizons hosted a higher percentage and diversity of Actinobacteria. Taken together, our findings indicate that the microbial community in loess-paleosol sequences carries signatures of earlier environmental conditions that are preserved until today.
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Banerjee S, Misra A, Sar A, Pal S, Chaudhury S, Dam B. Poor nutrient availability in opencast coalmine influences microbial community composition and diversity in exposed and underground soil profiles. APPLIED SOIL ECOLOGY 2020; 152:103544. [DOI: 10.1016/j.apsoil.2020.103544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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17
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Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession. Sci Rep 2020; 10:9864. [PMID: 32555419 PMCID: PMC7299987 DOI: 10.1038/s41598-020-66638-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/27/2020] [Indexed: 11/08/2022] Open
Abstract
This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.
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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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Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
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Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
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Abstract
While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.
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21
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Microbial and abiotic controls on mineral-associated organic matter in soil profiles along an ecosystem gradient. Sci Rep 2019; 9:10294. [PMID: 31312015 PMCID: PMC6635608 DOI: 10.1038/s41598-019-46501-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/28/2019] [Indexed: 11/23/2022] Open
Abstract
Formation of mineral-organic associations is a key process in the global carbon cycle. Recent concepts propose litter quality-controlled microbial assimilation and direct sorption processes as main factors in transferring carbon from plant litter into mineral-organic associations. We explored the pathways of the formation of mineral-associated organic matter (MOM) in soil profiles along a 120-ky ecosystem gradient that developed under humid climate from the retreating Franz Josef Glacier in New Zealand. We determined the stocks of particulate and mineral-associated carbon, the isotope signature and microbial decomposability of organic matter, and plant and microbial biomarkers (lignin phenols, amino sugars and acids) in MOM. Results revealed that litter quality had little effect on the accumulation of mineral-associated carbon and that plant-derived carbon bypassed microbial assimilation at all soil depths. Seemingly, MOM forms by sorption of microbial as well as plant-derived compounds to minerals. The MOM in carbon-saturated topsoil was characterized by the steady exchange of older for recent carbon, while subsoil MOM arises from retention of organic matter transported with percolating water. Overall, MOM formation is not monocausal but involves various mechanisms and processes, with reactive minerals being effective filters capable of erasing chemical differences in organic matter inputs.
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García-Gil A, Gasco-Cavero S, Garrido E, Mejías M, Epting J, Navarro-Elipe M, Alejandre C, Sevilla-Alcaine E. Decreased waterborne pathogenic bacteria in an urban aquifer related to intense shallow geothermal exploitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:765-775. [PMID: 29602115 DOI: 10.1016/j.scitotenv.2018.03.245] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
The implications of intensive use of shallow geothermal energy resources in shallow urban aquifers are still not known for waterborne pathogens relevant to human health. Firstly, we hypothesized that waterborne enteric pathogens would be relatively increased in heated groundwater plumes. To prove this, microbiological sampling of 31 piezometers covering the domain of an urban groundwater body affected by microbiological contamination and energetically exploited by 70 groundwater heat pump systems was performed. Mean differences of pathogenic bacteria contents between impacted and non-impacted monitoring points were assessed with a two-tailed independent Student's t-test or Mann-Whitney U and correlation coefficients were also calculated. Surprisingly, the results obtained revealed a significant and generalized decrease in waterborne pathogen contents in thermally impacted piezometers compared to that of non-impacted piezometers. This decrease is hypothesized to be caused by a heat shock to bacteria within the heat exchangers. The statistically significant negative correlations obtained between waterborne pathogen counts and temperature could be explained by the spatial distribution of the bacteria, finding that bacteria start to recover with increasing distance from the injection point. Also, different behavior groups fitting exponential regression models were found for the bacteria species studied, justified by the different presence and influence of several aquifer parameters and major, minor and trace elements studied, as well as the coexistence with other bacteria species. The results obtained from this work reinforce the concept of shallow geothermal resources as a clean energy source, as they could also provide the basis to control the pathogenic bacteria contents in groundwater bodies.
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Affiliation(s)
- Alejandro García-Gil
- Geological Survey of Spain (IGME), C/ Manuel Lasala n° 44, 9° B, 50006 Zaragoza, Spain.
| | - Samanta Gasco-Cavero
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Eduardo Garrido
- Geological Survey of Spain (IGME), C/ Manuel Lasala n° 44, 9° B, 50006 Zaragoza, Spain
| | - Miguel Mejías
- Geological Survey of Spain (IGME), C/ Ríos Rosas 23, 28003 Madrid, Spain
| | - Jannis Epting
- Department of Environmental Sciences, Applied and Environmental Geology, University of Basel, Bernoullistr. 32, 4056 Basel, Switzerland
| | - Mercedes Navarro-Elipe
- Municipal Institute of Public Health of Zaragoza (Zaragoza City Council), Ctra. Cogullada 28, 50059 Zaragoza, Spain
| | - Carmen Alejandre
- Municipal Institute of Public Health of Zaragoza (Zaragoza City Council), Ctra. Cogullada 28, 50059 Zaragoza, Spain
| | - Elena Sevilla-Alcaine
- Municipal Institute of Public Health of Zaragoza (Zaragoza City Council), Ctra. Cogullada 28, 50059 Zaragoza, Spain
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