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DeFord L, Yoon JY. Soil microbiome characterization and its future directions with biosensing. J Biol Eng 2024; 18:50. [PMID: 39256848 PMCID: PMC11389470 DOI: 10.1186/s13036-024-00444-1] [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: 04/23/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
Soil microbiome characterization is typically achieved with next-generation sequencing (NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity. These techniques have been instrumental in microbiology, but they have limitations. They require extensive time, funding, expertise, and computing power to be effective. Moreover, these techniques are restricted to controlled laboratory conditions; they are not applicable in field settings, nor can they rapidly generate data. This hinders using NGS as an environmental monitoring tool or an in-situ checking device. Biosensing technology can be applied to soil microbiome characterization to overcome these limitations and to complement NGS techniques. Biosensing has been used in biomedical applications for decades, and many successful commercial products are on the market. Given its previous success, biosensing has much to offer soil microbiome characterization. There is a great variety of biosensors and biosensing techniques, and a few in particular are better suited for soil field studies. Aptamers are more stable than enzymes or antibodies and are more ready for field-use biosensors. Given that any microbiome is complex, a multiplex sensor will be needed, and with large, complicated datasets, machine learning might benefit these analyses. If the signals from the biosensors are optical, a smartphone can be used as a portable optical reader and potential data-analyzing device. Biosensing is a rich field that couples engineering and biology, and applying its toolset to help advance soil microbiome characterization would be a boon to microbiology more broadly.
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Affiliation(s)
- Lexi DeFord
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jeong-Yeol Yoon
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA.
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA.
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Lepinay C, Větrovský T, Chytrý M, Dřevojan P, Fajmon K, Cajthaml T, Kohout P, Baldrian P. Effect of plant communities on bacterial and fungal communities in a Central European grassland. ENVIRONMENTAL MICROBIOME 2024; 19:42. [PMID: 38902816 PMCID: PMC11188233 DOI: 10.1186/s40793-024-00583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Čertoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity. RESULTS High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition. CONCLUSIONS The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.
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Affiliation(s)
- Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Pavel Dřevojan
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Karel Fajmon
- Regional Office Protected Landscape Area Bílé Karpaty, Nature Conservation Agency of the Czech Republic, Nádražní 318, 763 26, Luhačovice, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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Zhang J, Li X, Qian A, Xu X, Lv Y, Zhou X, Yang X, Zhu W, Zhang H, Ding Y. Effects of operating conditions on the in situ control of sulfur-containing odors by using a novel alternative landfill cover and its transformation mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7959-7976. [PMID: 38175505 DOI: 10.1007/s11356-023-31721-z] [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: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Sulfur-containing gases are main sources of landfill odors, which has become a big issue for pollution to environment and human health. Biocover is promising for treating landfill odors, with advantages of durability and environmental friendliness. In this study, charcoal sludge compost was utilized as the main effective component of a novel alternative landfill cover and the in situ control of sulfur-containing odors from municipal solid waste landfilling process was simulated under nine different operating conditions. Results showed that five sulfur-containing odors (hydrogen sulfide, H2S; methyl mercaptan, CH3SH; dimethyl sulfide, CH3SCH3; ethylmercaptan, CH3CH2SH; carbon disulfide, CS2) were monitored and removed by the biocover, with the highest removal efficiencies of 77.18% for H2S, 87.36% for CH3SH, and 92.19% for CH3SCH3 in reactor 8#, and 95.94% for CH3CH2SH and 94.44% for CS2 in reactor 3#. The orthogonal experiment showed that the factors influencing the removal efficiencies of sulfur-containing odors were ranked from high to low as follows: temperature > weight ratio > humidity content. The combination of parameters of 20% weight ratio, 25°C temperature, and 30% water content was more recommended based on the consideration of the removal efficiencies and economic benefits. The mechanisms of sulfur conversion inside biocover were analyzed. Most organic sulfur was firstly degraded to reduced sulfides or element sulfur, and then oxidized to sulfate which could be stable in the layer as the final state. In this process, sulfur-oxidizing bacteria play a great role, and the distribution of them in reactor 1#, 5#, and 8# was specifically monitored. Bradyrhizobiaceae and Rhodospirillaceae were the dominant species which can utilize sulfide as substance to produce sulfate and element sulfur, respectively. Based on the results of OUTs, the biodiversity of these sulfur-oxidizing bacteria, these microorganisms, was demonstrated to be affected by the different parameters. These results indicate that the novel alternative landfill cover modified with bamboo charcoal compost is effective in removing sulfur odors from landfills. Meanwhile, the findings have direct implications for addressing landfill odor problems through parameter adjustment.
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Affiliation(s)
- Jiayi Zhang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xiaowen Li
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Aiai Qian
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xianwen Xu
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ya Lv
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xinrong Zhou
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xinrui Yang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Weiqin Zhu
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Hangjun Zhang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ying Ding
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
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Maoloni A, Cardinali F, Milanović V, Reale A, Boscaino F, Di Renzo T, Ferrocino I, Rampanti G, Garofalo C, Osimani A, Aquilanti L. Impact of Different Drying Methods on the Microbiota, Volatilome, Color, and Sensory Traits of Sea Fennel ( Crithmum maritimum L.) Leaves. Molecules 2023; 28:7207. [PMID: 37894688 PMCID: PMC10609079 DOI: 10.3390/molecules28207207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Sea fennel (Crithmum maritimum L.) is a strongly aromatic herb of the Apiaceae family, whose full exploitation by the modern food industry is of growing interest. This study aimed at investigating the microbiological quality, volatile profile, and sensory traits of sea fennel spices produced using room-temperature drying, oven drying, microwave drying, and freeze drying. All the assayed methods were able to remove moisture up until water activity values below 0.6 were reached; however, except for microwave drying, none of the assayed methods were effective in reducing the loads of contaminating microorganisms. The metataxonomic analysis highlighted the presence of phytopathogens and even human pathogens, including members of the genera Bacillus, Pseudomonas, Alternaria, and Cryptococcus. When compared to fresh leaves, dried leaves showed increased L* (lightness) and c* (chroma, saturation) values and reduced hue angle. Dried leaves were also characterized by decreased levels of terpene hydrocarbons and increased levels of aldehydes, alcohols, and esters. For the sensory test, the microwave-dried samples obtained the highest appreciation by the trained panel. Overall, the collected data indicated microwave drying as the best option for producing sea fennel spices with low microbial loads, brilliant green color, and high-quality sensory traits.
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Affiliation(s)
- Antonietta Maoloni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Federica Cardinali
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Anna Reale
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Floriana Boscaino
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Tiziana Di Renzo
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Ilario Ferrocino
- Department of Agricultural, Forest, and Food Science, University of Turin, Largo Paolo Braccini 2, Grugliasco, 10095 Turin, Italy;
| | - Giorgia Rampanti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
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Amon CER, Fossou RK, Ebou AET, Koua DK, Kouadjo CG, Brou YC, Voko Bi DRR, Cowan DA, Zézé A. The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones. Front Microbiol 2023; 14:1220655. [PMID: 37692382 PMCID: PMC10483230 DOI: 10.3389/fmicb.2023.1220655] [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: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.
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Affiliation(s)
- Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Anicet E. T. Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Dominiqueua K. Koua
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Claude Ghislaine Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, Abidjan, Côte d’Ivoire
| | - Yao Casimir Brou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Don Rodrigue Rosin Voko Bi
- Unité de Formation et de Recherche en Agroforesterie, Université Jean Lorougnon Guédé, Daloa, Côte d’Ivoire
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
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Peres FV, Paula FS, Bendia AG, Gontijo JB, de Mahiques MM, Pellizari VH. Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales. Sci Rep 2023; 13:12782. [PMID: 37550336 PMCID: PMC10406867 DOI: 10.1038/s41598-023-39415-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.
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Affiliation(s)
- Francielli V Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil.
| | - Amanda G Bendia
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Michel M de Mahiques
- Department of Physical, Chemical and Geological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Vivian H Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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9
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Peng M, He H, Wang X, Wang Z, Zhuang L. Comparison of network connectivity and environmental driving factors of root-associated fungal communities of desert ephemeral plants in two habitat soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117375. [PMID: 36716547 DOI: 10.1016/j.jenvman.2023.117375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/04/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Root-associated microorganisms regulate plant growth and development, and their distribution is likely influenced by habitat conditions. In this study, the responses of rhizosphere and root-endophytic fungi of dominant ephemeral plants to aeolian soil (AS) and grey desert soil (DS) in the Gurbantünggüt Desert were analyzed using high-throughput sequencing. This was done to understand the adaptation strategies of this vegetation in typical habitat soils from a microbial perspective. We found that the diversity of root-associated fungi of ephemeral plants differed in the two habitat soils. The diversity of rhizosphere fungi was relatively low in AS compared to DS, whereas the diversity of root-endophytic fungi was higher in AS. The community structure of root-associated fungi and relative abundances of some dominant taxa differed between the two soils. A co-occurrence network showed that the degree of coupling and interaction between root-associated fungal taxa were closer in AS than in DS and that most of the fungal taxa were cooperative in the two habitat soils. Additionally, the network properties of the root-endophytic fungi were apparent different between the two soils. Environmental factors, including electrical conductivity, soil organic carbon, carbon/nitrogen, and carbon/phosphorus ratios, were found to be key factors affecting rhizosphere fungi in DS, whereas soil available phosphorus was the main factor in AS. Several factors affect the root-endophytic fungal community and are more influential in DS than in AS. Overall, the root-associated fungal communities of ephemeral plants had different adaptation strategies to the two soils: increasing the diversity of rhizosphere fungi and their relationship with environmental factors in DS, and increasing the diversity and network relationships of root-endophytic fungi in AS. These findings provide insight into the assemblage of ephemeral plant root-associated microbial communities and the underlying environmental factors, which allows for a deeper understanding of how to construct an artificial core root microbiota to promote plant growth and resistance.
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Affiliation(s)
- Mengwen Peng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Hao He
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Xiushuang Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Zhongke Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Li Zhuang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China.
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10
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Carbon Emission and Biodiversity of Arctic Soil Microbial Communities of the Novaya Zemlya and Franz Josef Land Archipelagos. Microorganisms 2023; 11:microorganisms11020482. [PMID: 36838447 PMCID: PMC9962458 DOI: 10.3390/microorganisms11020482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Cryogenic soils are the most important terrestrial carbon reservoir on the planet. However, the relationship between soil microbial diversity and CO2 emission by cryogenic soils is poorly studied. This is especially important in the context of rising temperatures in the high Arctic which can lead to the activation of microbial processes in soils and an increase in carbon input from cryogenic soils into the atmosphere. Here, using high-throughput sequencing of 16S rRNA gene amplicons, we analyzed microbial community composition and diversity metrics in relation to soil carbon dioxide emission, water-extractable organic carbon and microbial biomass carbon in the soils of the Barents Sea archipelagos, Novaya Zemlya and Franz Josef Land. It was found that the highest diversity and CO2 emission were observed on the Hooker and Heiss Islands of the Franz Josef Land archipelago, while the diversity and CO2 emission levels were lower on Novaya Zemlya. Soil moisture and temperature were the main parameters influencing the composition of soil microbial communities on both archipelagos. The data obtained show that CO2 emission levels and community diversity on the studied islands are influenced mostly by a number of local factors, such as soil moisture, microclimatic conditions, different patterns of vegetation and fecal input from animals such as reindeer.
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11
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Navarrete AA, Aburto F, González-Rocha G, Guzmán CM, Schmidt R, Scow K. Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158508. [PMID: 36063938 DOI: 10.1016/j.scitotenv.2022.158508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.
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Affiliation(s)
- Alejandro Atenas Navarrete
- Postgrado Facultad de Ciencias Forestales, Universidad de Concepción, Chile; Laboratorio de Investigación en Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Chile; Iniciativa Foresta Nativa, Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Soil and Crop Sciences Department, Texas A&M University, 370 Olsen Blvd. Heep Center, TX 77845, USA; Departamento de Planificación Territorial y Sistemas Urbanos, Facultad de Ciencias Ambientales, Universidad de Concepción, Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Chile
| | - Radomir Schmidt
- Working Lands Innovation Center at the Institute of the Environment, University of California, Davis, USA
| | - Kate Scow
- Soil Microbial Ecology Lab, Department of Land, Air and Water Resources, University of California, Davis, USA
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12
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Liu H, Jiang S, Ou J, Tang J, Lu Y, Wei Y. Investigation of soil microbiota reveals variable dominant species at different land areas in China. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2071634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Hai Liu
- Criminal technology corps of Henan Provincial Public Security Bureau, Zhengzhou, Henan Province, China
| | - Shan Jiang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, PR China
| | - Jintao Ou
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Jinfeng Tang
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Key Laboratory for Water Quality and Conservation of Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Linköping University – Guangzhou University Research Center on Urban Sustainable Development, Guangzhou, People’s Republic of China
| | - Yang Lu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
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13
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Sierra MA, Ryon KA, Tierney BT, Foox J, Bhattacharya C, Afshin E, Butler D, Green SJ, Thomas WK, Ramsdell J, Bivens NJ, McGrath K, Mason CE, Tighe SW. Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations. ENVIRONMENTAL MICROBIOME 2022; 17:60. [PMID: 36544228 PMCID: PMC9768965 DOI: 10.1186/s40793-022-00455-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.
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Affiliation(s)
- Maria A Sierra
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Krista A Ryon
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Braden T Tierney
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jonathan Foox
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Evan Afshin
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, New York, IL, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | | | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, USA
| | | | - Christopher E Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Scott W Tighe
- Advanced Genomics Laboratory, University of Vermont Cancer Center, University of Vermont, Burlington, VT, USA.
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Impact of Physicochemical Parameters on the Diversity and Distribution of Microbial Communities Associated with Three South African Peatlands. Microorganisms 2022; 10:microorganisms10112103. [PMID: 36363695 PMCID: PMC9694404 DOI: 10.3390/microorganisms10112103] [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: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 01/21/2023] Open
Abstract
Peatlands are complex wetland-like ecosystems that harbor diverse microbial communities. In this study, the microbial communities (fungal and actinobacterial) associated with an unimpacted peatland (Vankervelsvlei; VV), an impacted peatland (Goukou River system; GK), and a developing peatland (Nuwejaars River system; NR) were determined through ITS and 16S rRNA metataxonomic analyses. Unidentified Acidimicrobiales dominated in GK and NR, unidentified Intrasporangiaceae and Solirubobacterales in NR, and Corynebacterium, Propionibacterium, and Streptomyces species in VV. The fungal phyla, Ascomycota and Basidiomycota, dominated all three sites, and harbored unique fungal taxa belonging to a wide range of fungal guilds. Physicochemical properties of the peat collected from the three sites were analyzed in association with microbial community structures in order to determine which parameters acted as the main drivers for microbial diversity. BEST analysis (linking microbial diversity patterns to environmental variables) showed that nitrogen (N), aluminum (Al), phosphorus (P), and potassium (K) were the most significant physicochemical drivers of actinobacterial community structure, while iron (Fe) and humification were the environmental parameters that affected the fungal communities the most. In conclusion, this study has provided some insight into the fungal and actinobacterial communities associated with three South African peatlands and the main environmental drivers that influence these communities.
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15
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Wang L, Zhang Q, Mei H, Cui X, Wang M, Zhu Y, Ji B, Wei Y. Different Distribution of Core Microbiota in Upper Soil Layer in Two Places of North China Plain. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2207220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Backgrounds:
Soils harbor diverse bacteria, and these bacteria play important roles in soil nutrition cycling and carbon storage. Numerous investigations of soil microbiota had been performed, and the core microbiota in different soil or vegetation soil types had been described. The upper layer of soil, as a source of organic matter, is important and affected by the habitats and dominant bacteria. However, the complexity of soil environments and relatively limited information of many geographic areas had attracted great attention on comprehensive exploration of soil microbes in enormous types of soil.
Methods:
To reveal the core upper layer soil microbiota, soil samples from metropolis and countryside regions in the North China Plain were investigated using high-throughput sequencing strategy.
Results:
The results showed that the most dominant bacteria are Proteobacteria (38.34%), Actinobacteria (20.56%), and Acidobacteria (15.18%). At the genus-level, the most abundant known genera are Gaiella (3.66%), Sphingomonas (3.6%), Acidobacteria Gp6 (3.52%), and Nocardioides (2.1%). Moreover, several dominant operational taxanomy units OTUs, such as OTU_3 and OTU_17, were identified to be associated with the soil environment. Microbial distributions of the metropolis samples were different from the countryside samples, which may reflect the environments in the countryside were more diverse than in the metropolis. Microbial diversity and evenness were higher in the metropolis than in the countryside, which might due to the fact that human activity increased the microbial diversity in the metropolis.
Conclusion:
The upper layer soil core microbiota of the North China Plain were complex, and microbial distributions in these two places might be mainly affected by the human activity and environmental factors, not by the distance. Our data highlights the upper layer soil core microbiota in North China Plain, and provides insights for future soil microbial distribution studies in central China.
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16
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Li X, Kong P, Daughtrey M, Kosta K, Schirmer S, Howle M, Likins M, Hong C. Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States. Microorganisms 2022; 10:1514. [PMID: 35893572 PMCID: PMC9330173 DOI: 10.3390/microorganisms10081514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022] Open
Abstract
In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.
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Affiliation(s)
- Xiaoping Li
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA; (P.K.); (C.H.)
| | - Ping Kong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA; (P.K.); (C.H.)
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, NY 11901, USA;
| | - Kathleen Kosta
- California Department of Food and Agriculture, Sacramento, CA 95814, USA;
| | - Scott Schirmer
- Bureau of Environmental Programs, Illinois Department of Agriculture, Dekalb, IL 60115, USA;
| | - Matthew Howle
- Department of Plant Industry, Clemson University, Florence, SC 29506, USA;
| | - Michael Likins
- Chesterfield Cooperative Extension, Chesterfield County, VA 23832, USA;
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA; (P.K.); (C.H.)
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17
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Abstract
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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18
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Lindström S, Timonen S, Sundström L. The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae). Microbiologyopen 2021; 10:e1201. [PMID: 34459553 PMCID: PMC8289489 DOI: 10.1002/mbo3.1201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
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Affiliation(s)
- Stafva Lindström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Sari Timonen
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
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19
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de Souza AJ, Pereira APDA, Andreote FD, Tornisielo VL, Tizioto PC, Coutinho LL, Regitano JB. Sulfadiazine dissipation as a function of soil bacterial diversity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116374. [PMID: 33412451 DOI: 10.1016/j.envpol.2020.116374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Antibiotic residues in the environment are concerning since results in dispersion of resistance genes. Their degradation is often closely related to microbial metabolism. However, the impacts of soil bacterial community on sulfadiazine (SDZ) dissipation remains unclear, mainly in tropical soils. Our main goals were to evaluate effects of long-term swine manure application on soil bacterial structure as well as effects of soil microbial diversity depletion on SDZ dissipation, using "extinction dilution approach" and 14C-SDZ. Manure application affected several soil attributes, such as pH, organic carbon (OC), and macronutrient contents as well as bacterial community structure and diversity. Even minor bacterial diversity depletion impacted SDZ mineralization and non-extractible residue (NER) formation rates, but NER recovered along 42 d likely due to soil diversity recovery. However, this period may be enough to spread resistance genes into the environment. Surprisingly, the non-manured natural soil (NS-S1) showed faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a great number of bacterial families involved in major SDZ dissipation pathways (mineralization and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_(Subgroup_1), Micromonosporaceae, and Sphingobacteriaceae. This result is unique and contrasts our hypothesis that long-term manured soils would present adaptive advantages and, consequently, have higher SDZ dissipation rates. The literature suggests instantaneous chemical degradation of SDZ in acidic soils responsible to the fast formation of NER. Our results show that if chemical degradation happens, it is soon followed by microbial metabolism (biodegradation) performed by a pool of bacteria and the newly formed metabolites should favors NER formation since SDZ presented low sorption. It also showed that SDZ mineralization is a low redundancy function.
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Affiliation(s)
- Adijailton Jose de Souza
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Fernando Dini Andreote
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Valdemar Luiz Tornisielo
- Center of Nuclear Energy for Agriculture (CENA), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jussara Borges Regitano
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil.
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20
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Qiong W, Fengshan P, Xiaomeng X, Rafiq MT, Xiao'e Y, Bao C, Ying F. Cadmium level and soil type played a selective role in the endophytic bacterial community of hyperaccumulator Sedum alfredii Hance. CHEMOSPHERE 2021; 263:127986. [PMID: 33297030 DOI: 10.1016/j.chemosphere.2020.127986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/25/2020] [Accepted: 08/10/2020] [Indexed: 06/12/2023]
Abstract
Phytoremediation technology has been applied for heavy metal elimination for many years, however little research about the difference of remediation efficiency of hyperaccumulator in different soils was reported. Here, a pot experiment was conducted with a cadmium (Cd)/zinc hyperaccumulator Sedum alfredii Hance grown on different types of soils and the differences of its endophytic bacterial community were elucidated. The results showed that the biomass of S. alfredii grown on black soil under both low and high Cd treatment was much heavier than that grown on other soils, and Cd uptake and Cd accumulation of S. alfredii in paddy soil was the highest, suggesting that black soil was more suitable for S. alfredii growth while paddy soil was more efficient for Cd phytoextraction. Moreover, Cd treated level and soil type both affected the structure of plant endophytic bacterial community. The two shared genera in the four representative soils were Caulobacter and Acinetobacter under low Cd level, and Caulobacter and Lactobacillus under high Cd level. Cd treatment shifted the structure and abundance of plant endophytes in different types of soils, while black soil and paddy soil were more similar in the distribution and abundance of S. alfredii endophytic community. This study highlighted the understanding of response to Cd within S. alfredii endophytic community in different types of soils, which could be beneficial for enhanced phytoremediation efficiency and better S. alfredii cultivation.
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Affiliation(s)
- Wang Qiong
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Pan Fengshan
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China; Hailiang Group Co., Ltd., Hailiang Building, No.1508, Binsheng Road, Hangzhou City, 310052, Zhejiang, China
| | - Xu Xiaomeng
- Hangzhou Steam Turbine Co. Ltd., No. 357 Shiqiao Road, Hangzhou City, 310052, Zhejiang, China
| | - Muhammad Tariq Rafiq
- Centre for Interdisciplinary Research in Basic Sciences, International Islamic University, Islamabad, 44000, Pakistan
| | - Yang Xiao'e
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Chen Bao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China; Hangzhou Jinjiang Group Co., Ltd., Jinjiang Building, No. 111, South Hushu Road, Hangzhou City, 310005, Zhejiang, China.
| | - Feng Ying
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China.
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Gastélum G, Rocha J. La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.
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Khan AL, Asaf S, M. Abed RM, Ning Chai Y, N. Al-Rawahi A, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A. Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance. Microorganisms 2020; 8:microorganisms8020213. [PMID: 32033333 PMCID: PMC7074696 DOI: 10.3390/microorganisms8020213] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Raeid M. M. Abed
- Sultan Qaboos University, College of Science, Biology Department, Muscat 123, Sultanate of Oman;
| | - Yen Ning Chai
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed N. Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
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23
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Newitt JT, Prudence SMM, Hutchings MI, Worsley SF. Biocontrol of Cereal Crop Diseases Using Streptomycetes. Pathogens 2019; 8:pathogens8020078. [PMID: 31200493 PMCID: PMC6630304 DOI: 10.3390/pathogens8020078] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022] Open
Abstract
A growing world population and an increasing demand for greater food production requires that crop losses caused by pests and diseases are dramatically reduced. Concurrently, sustainability targets mean that alternatives to chemical pesticides are becoming increasingly desirable. Bacteria in the plant root microbiome can protect their plant host against pests and pathogenic infection. In particular, Streptomyces species are well-known to produce a range of secondary metabolites that can inhibit the growth of phytopathogens. Streptomyces are abundant in soils and are also enriched in the root microbiomes of many different plant species, including those grown as economically and nutritionally valuable cereal crops. In this review we discuss the potential of Streptomyces to protect against some of the most damaging cereal crop diseases, particularly those caused by fungal pathogens. We also explore factors that may improve the efficacy of these strains as biocontrol agents in situ, as well as the possibility of exploiting plant mechanisms, such as root exudation, that enable the recruitment of microbial species from the soil to the root microbiome. We argue that a greater understanding of these mechanisms may enable the development of protective plant root microbiomes with a greater abundance of beneficial bacteria, such as Streptomyces species.
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Affiliation(s)
- Jake T Newitt
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Samuel M M Prudence
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
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