1
|
Zhang L, Zhao X, Wang J, He L, Ren C, Wang J, Guo Y, Wang N, Zhao F. Antarctic Soils Select Copiotroph-Dominated Bacteria. Microorganisms 2024; 12:1689. [PMID: 39203535 PMCID: PMC11357078 DOI: 10.3390/microorganisms12081689] [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: 08/04/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
The life strategies of bacterial communities determine their structure and function and are an important driver of biogeochemical cycling. However, the variations in these strategies under different soil resource conditions remain largely unknown. We explored the bacterial life strategies and changes in structure and functions between Antarctic soils and forest (temperate, subtropical, and tropical) soils. The results showed that the weighted mean rRNA operon copy number in temperate soils was 19.5% lower than that in Antarctic soils, whereas no significant differences were observed among Antarctic, subtropical, and tropical soils. An unexpected result was that bacterial communities in Antarctic soils tended to be copiotrophs, such as Actinobacteriota and Bacteroidota, whereas those in temperate soils tended to be oligotrophs, such as Acidobacteriota and Chloroflexi. Functional predictions showed that in comparison to copiotrophs in Antarctic soils, temperate-inhabiting oligotrophic bacteria exhibited an 84.2-91.1% lower abundance of labile C decomposition genes (hemicellulose, cellulose, monosaccharides, and disaccharides), whereas a 74.4% higher abundance of stable C decomposition (lignin). Genes involved in N cycling (nitrogen fixation, assimilatory nitrate reduction, and denitrification) were 24.3-64.4% lower in temperate soils than in Antarctic soils. Collectively, our study provides a framework for describing the life strategies of soil bacteria, which are crucial to global biogeochemical cycles.
Collapse
Affiliation(s)
- Lujie Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
| | - Xue Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
| | - Jieying Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
| | - Liyuan He
- Oak Ridge National Laboratory, Environmental Sciences Division and Climate Change Science Institute, Oak Ridge, TN 37831, USA
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Jun Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi’an 710127, China
| | - Yaoxin Guo
- The College of Life Sciences, Northwest University, Xi’an 710072, China
| | - Ninglian Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
| | - Fazhu Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi’an 710127, China
| |
Collapse
|
2
|
Meshram S, Adhikari TB. Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:364. [PMID: 38337897 PMCID: PMC10856849 DOI: 10.3390/plants13030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.
Collapse
Affiliation(s)
- Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara 144402, India;
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
3
|
Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023; 18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.
Collapse
Affiliation(s)
- Osiel S Gonçalves
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Mateus F Santana
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
4
|
Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
Collapse
Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
| |
Collapse
|
5
|
Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
Collapse
Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| |
Collapse
|