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Tian S, Xia Y, Yu Z, Zhou H, Wu S, Zhang N, Yue X, Deng Y, Xia Y. Improvement and the relationship between chemical properties and microbial communities in secondary salinization of soils induced by rotating vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171019. [PMID: 38382605 DOI: 10.1016/j.scitotenv.2024.171019] [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: 10/11/2023] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.
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Affiliation(s)
- Shihan Tian
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Xia
- College of Tropical Crops, Yunnan Agricultural University, Pu'er 665099, China
| | - Zhong Yu
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Huazhi Biotechnology Co. Ltd, Changsha 410000, China
| | - Hongyin Zhou
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Sirui Wu
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Naiming Zhang
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Xianrong Yue
- Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Yishu Deng
- Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China
| | - Yunsheng Xia
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; Yunnan Engineering Research Center of Soil Fertility and Pollution Remediation,Kunming 650201, China.
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Sun L, Wang S, Narsing Rao MP, Shi Y, Lian ZH, Jin PJ, Wang W, Li YM, Wang KK, Banerjee A, Cui XY, Wei D. The shift of soil microbial community induced by cropping sequence affect soil properties and crop yield. Front Microbiol 2023; 14:1095688. [PMID: 36910216 PMCID: PMC10004276 DOI: 10.3389/fmicb.2023.1095688] [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: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-producing regions of northeastern China. To evaluate the effects of different cropping sequences under conventional fertilization practices on soil properties, microbial communities, and crop yield, six types of plant cropping systems were performed, including soybean monoculture, wheat-soybean rotation, wheat-maize-soybean rotation, soybean-maize-maize rotation, maize-soybean-soybean rotation and maize monoculture. Our results showed that compared with the single cropping system, soybean and maize crop rotation in different combinations or sequences can increase soil total organic carbon and nutrients, and promote soybean and maize yield, especially using soybean-maize-maize and maize-soybean-soybean planting system. The 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing showed that different cropping systems had different effects on bacterial and fungal communities. The bacterial and fungal communities of soybean monoculture were less diverse when compared to the other crop rotation planting system. Among the different cropping sequences, the number of observed bacterial species was greater in soybean-maize-maize planting setup and fungal species in maize-soybean-soybean planting setup. Some dominant and functional bacterial and fungal taxa in the rotation soils were observed. Network-based analysis suggests that bacterial phyla Acidobacteria and Actinobacteria while fungal phylum Ascomycota showed a positive correlation with other microbial communities. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) result showed the presence of various metabolic pathways. Besides, the soybean-maize-maize significantly increased the proportion of some beneficial microorganisms in the soil and reduced the soil-borne animal and plant pathogens. These results warrant further investigation into the mechanisms driving responses of beneficial microbial communities and their capacity on improving soil fertility during legume cropping. The present study extends our understanding of how different crop rotations effect soil parameters, microbial diversity, and metabolic functions, and reveals the importance of crop rotation sequences. These findings could be used to guide decision-making from the microbial perspective for annual crop planting and soil management approaches.
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Affiliation(s)
- Lei Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China.,Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | | | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Zheng-Han 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, China
| | - Pin-Jiao Jin
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Wei Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Yu-Mei Li
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Kang-Kang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Aparna Banerjee
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM),Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | - Xiao-Yang Cui
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains. SUSTAINABILITY 2022. [DOI: 10.3390/su14159284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Climate warming is accelerating permafrost degradation. Soil microorganisms play key roles in the maintenance of high-latitude permafrost regions and forest ecosystems’ functioning and regulation of biogeochemical cycles. In this study, we used Illumina MiSeq high-throughput sequencing to investigate soil bacterial community composition at a primeval Larix gmelinii forest and a secondary Betula platyphylla forest in a permafrost region of the Greater Xing’an Mountains. The Shannon diversity index tended to decrease and then increase with increasing soil depth, which was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 40–60 cm. Proteobacteria (19.86–29.68%), Acidobacteria (13.59–31.44%), Chloroflexi (11.04–27.19%), Actinobacteria (7.05–25.57%), Gemmatimonadetes (1.76–9.18%), and Verrucomicrobia (2.03–7.00%) were the predominant phyla of the bacterial community in two forest types. The relative abundance of Proteobacteria showed a decreasing trend in the B. platyphylla forest and an increasing trend in the L. gmelinii forest, whereas that of Chloroflexi increased and then decreased in the B. platyphylla forest and decreased in the L. gmelinii forest with increasing soil depth. The relative abundance of Acidobacteria was significantly higher in the B. platyphylla forest than in the L. gmelinii forest at 0–20 cm depth, whereas that of Actinobacteria was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 0–20 cm and 40–60 cm depth. Principal coordinate analysis (PCoA) and two-way analysis of variance (ANOVA) indicated that microbial community composition was more significantly influenced by forest type than soil depth. Redundancy analysis (RDA) showed that microbial community structure was strongly affected by soil physicochemical properties such as nitrate nitrogen (NO3−-N), pH, and total organic carbon (TOC). These results offer insights into the potential relationship between soil microbial community and forest conversion in high latitude permafrost ecosystems.
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Wang J, Liao L, Wang G, Liu H, Wu Y, Liu G, Zhang C. N-induced root exudates mediate the rhizosphere fungal assembly and affect species coexistence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150148. [PMID: 34520919 DOI: 10.1016/j.scitotenv.2021.150148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Root exudates play essential roles in shaping root-associated microbial communities in plant-soil systems. However, knowledge regarding the influence of root exudates on soil communities, particularly concerning their assembly processes and species coexistence patterns, remains limited. In this study, we performed a 20-month pot experiment using a nitrogen (N) addition gradient (0, 2.5, 5, 7.5, 10, and 15 g N m-2 yr-1), amplicon sequencing, and metabolomics to investigate the effect of short-term N addition on the assembly process and species coexistence of fungal communities, as well as their association with root exudates in the rhizosphere and bulk soils around Bothriochloa ischaemum. The results demonstrated that short-term N addition led to distinct differences in the diversity, composition, assembly process, and co-occurrence networks of fungal communities in the rhizosphere and bulk soils. The diversity of fungal communities in the rhizosphere soil increased with the rate of N input and peaked at N10 treatment; this could be correlated with the increased abundance in long-chain organic acids (LCOAs). However, above the threshold N rate of 10 g N m-2 yr-1, diversity decreased probably because of the high N-induced inhibitory effect on root exudates (i.e., LCOAs). N addition increased the relative abundance of Sordariomycetes in the rhizosphere and decreased the relative abundance of Mortierellomycetes in the bulk soil, while enhancing the abundance of pathotrophs in both bulk and rhizosphere soils. The rhizosphere fungal community was dominated by a stochastic process at a low N input (N0 and N2.5) and by deterministic processes at a high N input (N10 and N15), which is opposite to the trends in the bulk soil. These fungal assembly processes determine the coexistence of fungal species; deterministic processes lead to less interconnected networks in rhizosphere soils that harbor a more complex network than the bulk soil. Associations between the assembly process and species coexistence in the rhizosphere of B. ischaemum were closely related to the changes in root exudates, such as amino acids, short-chain organic acids, and phenols, which were stimulated by N addition. Collectively, our study emphasizes the key roles of root exudates in the establishment of fungal communities in the plant-soil system and furthers our understanding of plant-microbe interactions.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China
| | - Lirong Liao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, PR China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China
| | - Hongfei Liu
- College of Forestry, Northwest A&F University, Yangling 712100, PR China; Department of Agroecology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Yang Wu
- College of Forestry, Northwest A&F University, Yangling 712100, PR China
| | - Guobin Liu
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, PR China
| | - Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China.
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