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E M, S U, R K, M W R, J P, F A, J H J L. Draft genome sequence of Collimonas sp. strain H4R21, an effective mineral-weathering bacterial strain isolated from the beech rhizosphere. Microbiol Resour Announc 2024:e0030824. [PMID: 39037313 DOI: 10.1128/mra.00308-24] [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: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
We present the draft genome sequence of Collimonas sp. strain H4R21, isolated from the rhizosphere of Fagus sylvatica in the forest experimental site of Montiers (France). This genome features coding capacity for plant growth promotion, such as the ability to solubilize minerals, to produce siderophores and antifungal secondary metabolites.
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Affiliation(s)
- Morin E
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
| | - Uroz S
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
- INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, France
| | - Kumar R
- Novozymes Inc., Davis, California, USA
| | - Rey M W
- Novozymes Inc., Davis, California, USA
| | - Pham J
- Novozymes Inc., Davis, California, USA
| | - Akum F
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Leveau J H J
- Department of Plant Pathology, University of California, Davis, California, USA
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2
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Philippot L, Chenu C, Kappler A, Rillig MC, Fierer N. The interplay between microbial communities and soil properties. Nat Rev Microbiol 2024; 22:226-239. [PMID: 37863969 DOI: 10.1038/s41579-023-00980-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/22/2023]
Abstract
In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.
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Affiliation(s)
- Laurent Philippot
- Université de Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroecology, Dijon, France.
| | - Claire Chenu
- University of Paris-Saclay, INRAE, AgroParisTech, Palaiseau, France
| | - Andreas Kappler
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA
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3
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Colautti A, Civilini M, Contin M, Celotti E, Iacumin L. Organic vs. conventional: impact of cultivation treatments on the soil microbiota in the vineyard. Front Microbiol 2023; 14:1242267. [PMID: 37901804 PMCID: PMC10602642 DOI: 10.3389/fmicb.2023.1242267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
The aim of this study was to compare the effects of two vineyard management practices on the soil and its associated microbiota. The experiments were conducted in two adjacent plots, one completely organically managed and the other conventionally managed in terms of phytosanitary treatments but fertilized with organic amendments. The chemical soil analyses were correlated to the prokaryotic and fungal communities, which were studied using the metabarcoding technique. The main difference between the two treatments was a significantly higher amount of Cu in the organic managed vineyard soil, while conventional managed soil presented higher concentration of Na and Mg and was also associated with higher pH values. Despite these differences, no significant diversities were observed on soil biodiversity and microbial composition considering alpha and beta diversity metrics. However, the percentages of some phyla analyzed individually differed significantly between the two managements. Analyzing the metabolisms of these phyla, it was discovered an increment of species correlated to soils with higher organic matter content or land not used for agricultural purposes in the organic treated soil. The findings indicate that, despite the use of copper-based phytosanitary products, there was no degradation and loss of biodiversity in the organic soil microbial population compared to conventional management with the same type of fertilization, and the observed microbial population was more similar to that of natural soils.
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Affiliation(s)
| | | | | | | | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
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Ndlovu S, Suinyuy TN, Pérez-Fernández MA, Magadlela A. Encephalartos natalensis, Their Nutrient-Cycling Microbes and Enzymes: A Story of Successful Trade-Offs. PLANTS (BASEL, SWITZERLAND) 2023; 12:1034. [PMID: 36903894 PMCID: PMC10005579 DOI: 10.3390/plants12051034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Encephalartos spp. establish symbioses with nitrogen (N)-fixing bacteria that contribute to soil nutrition and improve plant growth. Despite the Encephalartos mutualistic symbioses with N-fixing bacteria, the identity of other bacteria and their contribution to soil fertility and ecosystem functioning is not well understood. Due to Encephalartos spp. being threatened in the wild, this limited information presents a challenge in developing comprehensive conservation and management strategies for these cycad species. Therefore, this study identified the nutrient-cycling bacteria in Encephalartos natalensis coralloid roots, rhizosphere, and non-rhizosphere soils. Additionally, the soil characteristics and soil enzyme activities of the rhizosphere and non-rhizosphere soils were assayed. The coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis were collected from a population of >500 E. natalensis in a disturbed savanna woodland at Edendale in KwaZulu-Natal (South Africa) for nutrient analysis, bacterial identification, and enzyme activity assays. Nutrient-cycling bacteria such as Lysinibacillus xylanilyticus; Paraburkholderia sabiae, and Novosphingobium barchaimii were identified in the coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis. Phosphorus (P) cycling (alkaline and acid phosphatase) and N cycling (β-(D)-Glucosaminidase and nitrate reductase) enzyme activities showed a positive correlation with soil extractable P and total N concentrations in the rhizosphere and non-rhizosphere soils of E. natalensis. The positive correlation between soil enzymes and soil nutrients demonstrates that the identified nutrient-cycling bacteria in E. natalensis coralloid roots, rhizosphere, and non-rhizosphere soils and associated enzymes assayed may contribute to soil nutrient bioavailability of E. natalensis plants growing in acidic and nutrient-poor savanna woodland ecosystems.
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Affiliation(s)
- Siphelele Ndlovu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Terence N. Suinyuy
- School of Biology and Environmental Sciences, University of Mpumalanga (Mbombela Campus), Private Bag X11283, Mbombela 1200, South Africa
| | - María A. Pérez-Fernández
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013 Seville, Spain
| | - Anathi Magadlela
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
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5
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Calabrese S, Wild B, Bertagni MB, Bourg IC, White C, Aburto F, Cipolla G, Noto LV, Porporato A. Nano- to Global-Scale Uncertainties in Terrestrial Enhanced Weathering. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15261-15272. [PMID: 36269897 DOI: 10.1021/acs.est.2c03163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Enhanced weathering (EW) is one of the most promising negative emissions technologies urgently needed to limit global warming to at least below 2 °C, a goal recently reaffirmed at the UN Global Climate Change conference (i.e., COP26). EW relies on the accelerated dissolution of crushed silicate rocks applied to soils and is considered a sustainable solution requiring limited technology. While EW has a high theoretical potential of sequestering CO2, research is still needed to provide accurate estimates of carbon (C) sequestration when applying different silicate materials across distinct climates and major soil types in combination with a variety of plants. Here we elaborate on fundamental advances that must be addressed before EW can be extensively adopted. These include identifying the most suitable environmental conditions, improving estimates of field dissolution rates and efficacy of CO2 removal, and identifying alternative sources of silicate materials to meet future EW demands. We conclude with considerations on the necessity of integrated modeling-experimental approaches to better coordinate future field experiments and measurements of CO2 removal, as well as on the importance of seamlessly coordinating EW with cropland and forest management.
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Affiliation(s)
- Salvatore Calabrese
- Biological and Agricultural Engineering, Texas A&M University, 333 Spence St., College Station, Texas77843, United States
| | - Bastien Wild
- Civil and Environmental Engineering, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
- Andlinger Center for Energy and the Environment, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
| | - Matteo B Bertagni
- High Meadows Environmental Institute, Guyot Hall, Princeton University, Princeton, New Jersey08544, United States
| | - Ian C Bourg
- Civil and Environmental Engineering, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
- High Meadows Environmental Institute, Guyot Hall, Princeton University, Princeton, New Jersey08544, United States
| | - Claire White
- Civil and Environmental Engineering, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
- Andlinger Center for Energy and the Environment, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
| | - Felipe Aburto
- Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd., College Station, Texas77843, United States
| | - Giuseppe Cipolla
- Dipartimento di Ingegneria, University of Palermo, Viale delle Scienze, 90128Palermo, PA, Italy
| | - Leonardo V Noto
- Dipartimento di Ingegneria, University of Palermo, Viale delle Scienze, 90128Palermo, PA, Italy
| | - Amilcare Porporato
- Civil and Environmental Engineering, Princeton University, 59 Olden St., Princeton, New Jersey08540, United States
- High Meadows Environmental Institute, Guyot Hall, Princeton University, Princeton, New Jersey08544, United States
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Sandhu M, Paul AT, Jha PN. Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil. PLoS One 2022; 17:e0266808. [PMID: 35486615 PMCID: PMC9053811 DOI: 10.1371/journal.pone.0266808] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/25/2022] [Indexed: 12/21/2022] Open
Abstract
Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.
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Affiliation(s)
- Monika Sandhu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Atish T. Paul
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Prabhat N. Jha
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
- * E-mail:
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7
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Ibrahim MM, Guo L, Wu F, Liu D, Zhang H, Zou S, Xing S, Mao Y. Field-applied biochar-based MgO and sepiolite composites possess CO 2 capture potential and alter organic C mineralization and C-cycling bacterial structure in fertilized soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152495. [PMID: 34968614 DOI: 10.1016/j.scitotenv.2021.152495] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Agricultural soils contribute a significant amount of anthropogenic CO2 emission, a greenhouse gas of global environmental concern. Hence, discovering sustainable materials that can capture CO2 in cultivated soils is paramount. Since the effect of biochar on C mineralization/retention in fertilized soils is unclear, we produced biochar-based MgO and sepiolite-nanocomposites with CO2 capture potential. The field-scale impacts of the modified-biochars were evaluated on net C exchange rate (NCER) periodically for 3 months in fertilized plots. The effects of the modified-biochar on organic-C mineralization, the activities, and dynamics of C-cycling-related 16S rRNA which are unknown, were investigated. Results revealed an initial rapid and higher cumulative CO2 emission from the sole fertilizer treatment (F). Unlike the biochar treatment (BF), the successful incorporation of MgO/Mg(OH)2 nanoparticles into the matrix and surface of biochar, and the potential formation of MgCO3 with soil CO2, mitigated CO2 emission, especially in the MgO-modified biochar (MgOBF), compared to the sepiolite-biochar treatment (SBF). Compared to F and BF, the higher C retention as MgCO3 in the modified biochar treatments led to an increase in cellulase activity, stimulation of key C-cycling-related bacteria, and the expression of genes associated with starch, sucrose, amino sugar, nucleotide sugar, ascorbate, aldarate, cellulose, and chitin degradation, thus, increasing organic C mineralization. Among the modified-biochar treatments, higher C mineralization was recorded in SBF, resulting in increased cumulative CO2 emission, despite its initial capture for up to 42 days. However, MgOBF was effective in capturing soil-derived CO2, despite the increased C mineralization compared to biochar. The changes in soil moisture and temperature significantly regulated NCER. Also, the modified biochars positively influenced the distribution of C-cycling-related bacteria by improving soil pH and available nutrients. Among the modified biochars, the observed higher mitigation effect of MgOBF on NCER indicated that it could be preferably applied in agricultural soils.
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Affiliation(s)
- Muhammed Mustapha Ibrahim
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China; Department of Soil Science, Joseph Sarwuan Tarka University, P.M.B, 2373 Makurdi, Nigeria
| | - Liming Guo
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Fengying Wu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Dongming Liu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Hongxue Zhang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Shuangquan Zou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Shihe Xing
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China
| | - Yanling Mao
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Key Research Laboratory of Soil Ecosystem Health and Regulation in Fujian Provincial University, Fuzhou 350002, Fujian Province, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China.
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8
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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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9
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Uroz S, Picard L, Turpault MP. Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria. Trends Microbiol 2022; 30:882-897. [PMID: 35181182 DOI: 10.1016/j.tim.2022.01.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Mineral weathering bacteria play essential roles in nutrient cycling and plant nutrition. However, we are far from having a comprehensive view of the factors regulating their distribution and the molecular mechanisms involved. In this review, we highlight the extrinsic factors (i.e., nutrient availability, carbon source) and the intrinsic properties of minerals explaining the distribution and functioning of these functional communities. We also present and discuss the progress made in understanding the molecular mechanisms and genes that are used by bacteria during the mineral weathering process, or regulated during their interaction with minerals, that have been recently unraveled by omics approaches.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France.
| | - Laura Picard
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France
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10
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Ogola HJO, Selvarajan R, Tekere M. Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome. Front Microbiol 2021; 12:592725. [PMID: 33716998 PMCID: PMC7943610 DOI: 10.3389/fmicb.2021.592725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30-55°; open canopy cover, <30%), mid (less steep, 15-30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20-65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent β-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.
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Affiliation(s)
- Henry Joseph Oduor Ogola
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Ramganesh Selvarajan
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Memory Tekere
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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11
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Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
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Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
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Pacwa-Płociniczak M, Biniecka P, Bondarczuk K, Piotrowska-Seget Z. Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil. Front Microbiol 2020; 11:2106. [PMID: 32983067 PMCID: PMC7487420 DOI: 10.3389/fmicb.2020.02106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 02/01/2023] Open
Abstract
Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.
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Affiliation(s)
- Magdalena Pacwa-Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paulina Biniecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Białystok, Poland
| | - Zofia Piotrowska-Seget
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Qu Z, Liu B, Ma Y, Xu J, Sun H. The response of the soil bacterial community and function to forest succession caused by forest disease. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13665] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhao‐Lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Jie Xu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
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Uroz S, Picard L, Turpault MP, Auer L, Armengaud J, Oger P. Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral. Environ Microbiol 2020; 22:3838-3862. [PMID: 32656915 DOI: 10.1111/1462-2920.15159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Minerals and rocks represent essential reservoirs of nutritive elements for the long-lasting functioning of forest ecosystems developed on nutrient-poor soils. While the presence of effective mineral weathering bacteria was evidenced in the rhizosphere of different plants, the molecular mechanisms involved remain uncharacterized. To fill this gap, we combined transcriptomic, proteomics, geo-chemical and physiological analyses to decipher the potential molecular mechanisms explaining the mineral weathering effectiveness of strain PML1(12) of Caballeronia mineralivorans. Considering the early-stage of the interaction between mineral and bacteria, we identified the genes and proteins differentially expressed when: (i) the environment is depleted of certain essential nutrients (i.e., Mg and Fe), (ii) a mineral is added and (iii) the carbon source (i.e., glucose vs mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of (i) mobilizing iron through the production of a non-ribosomal peptide synthetase-independent siderophore, (ii) inducing chemotaxis and motility in response to nutrient availability and (iii) strongly acidifying its environment in the presence of glucose using a suite of GMC oxidoreductases to weather mineral. These results provide new insights into the molecular mechanisms involved in mineral weathering and their regulation and highlight the complex sequence of events triggered by bacteria to weather minerals.
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Affiliation(s)
- Stéphane Uroz
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Laura Picard
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Marie-Pierre Turpault
- INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Lucas Auer
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France
| | - Jean Armengaud
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 30200 Bagnols-sur-Cèze, France
| | - Phil Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Lyon, France, Univ Lyon, Villeurbanne, F-69622, France
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Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil. Appl Environ Microbiol 2020; 86:AEM.02969-19. [PMID: 32144110 PMCID: PMC7205497 DOI: 10.1128/aem.02969-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil. This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens. Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling. IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.
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