scholarly journals The fungal community in non-rhizosphere soil of Panax ginseng are driven by different cultivation modes and increased cultivation periods

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9930
Author(s):  
Yu Bao ◽  
Bao Qi ◽  
Wei Huang ◽  
Bao Liu ◽  
Yu Li
Keyword(s):  
Fungal Community ◽  
Rhizosphere Soil ◽  
Amplicon Sequencing ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Fungal Community Composition ◽  
Sustained Development ◽  
Sequencing Method ◽  
Ginseng Cultivation ◽  
Wild Ginseng

Continuous cropping obstacles severely hindered the sustained development of the ginseng industry. Among the obstacles, an imbalance of soil microbiome community was considered one of the major culprits. The fungal community is an essential part of the soil microbiome community. Extensive characterization of the fungal community composition and variation during ginseng cultivation will help us understand the mechanism underlying continuous cropping obstacles. By using a high-throughput amplicon sequencing method, the non-rhizospheric fungal community of farmland cultivated ginseng of 2 years old (C2) and 5 years old (C5), understory wild ginseng of 15 years old (W15) and 35 years old (W35), fallow fields which have been abandoned for 10 (F10) years were characterized. Farmland cultivated ginseng and understory wild ginseng harbored distinct non-rhizospheric fungal communities, and extension of cultivation periods enlarged the fungal community difference between two cultivation modes. Extended cultivation periods significantly decreased the OTU richness and PD whole tree indices, and OTU number and cultivation periods were negatively correlated. Extension of cultivation periods led to an increased abundance of pathotrophs. Still, the increased abundance of pathotrophs may not be the leading cause of severe continuous cropping obstacles in farmland cultivated ginseng. Compared with understory wild ginseng, farmland cultivated ginseng had a lower abundance of symbiotrophs and a higher abundance of saprotrophs. This changed symbiotrophs/saprotrophs ratio may have some correlation with the severe continuous cropping obstacles that occurred in farmland cultivated ginseng. Fallowing on the fungal community of the non-rhizosphere soil was generally opposite of that of extension of ginseng cultivation periods. The impacts of farmland cultivation on the fungal community of the non-rhizosphere soil can last for decades, even if the following is practiced.

scholarly journals Long-Term Monoculture Negatively Regulates Fungal Community Composition and Abundance of Tea Orchards

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 466 ◽  
Author(s):  
Yasir Arafat ◽  
Muhammad Tayyab ◽  
Muhammad Umar Khan ◽  
Ting Chen ◽  
Hira Amjad ◽  
...  
Keyword(s):  
Soil Ph ◽  
Fungal Community ◽  
Cropping System ◽  
Alpha Diversity ◽  
Fungal Species ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Fungal Community Composition ◽  
Continuous Cropping System ◽  
Tea Plants

Continuous cropping frequently leads to soil acidification and major soil-borne diseases in tea plants, resulting in low tea yield. We have limited knowledge about the effects of continuous tea monoculture on soil properties and the fungal community. Here, we selected three replanted tea fields with 2, 15, and 30 years of monoculture history to assess the influence of continuous cropping on fungal communities and soil physiochemical attributes. The results showed that continuous tea monoculture significantly reduced soil pH and tea yield. Alpha diversity analysis showed that species richness declined significantly as the tea planting years increased and the results based on diversity indicated inconsistency. Principal coordinate analysis (PCoA) revealed that monoculture duration had the highest loading in structuring fungal communities. The relative abundance of Ascomycota, Glomeromycota, and Chytridiomycota decreased and Zygomycota and Basidiomycota increased with increasing cropping time. Continuous tea cropping not only decreased some beneficial fungal species such as Mortierella alpina and Mortierella elongatula, but also promoted potentially pathogenic fungal species such as Fusarium oxysporum, Fusarium solani, and Microidium phyllanthi over time. Overall, continuous tea cropping decreased soil pH and potentially beneficial microbes and increased soil pathogenic microbes, which could be the reason for reducing tea yield. Thus, developing sustainable tea farming to improve soil pH, microbial activity, and enhanced beneficial soil microbes under a continuous cropping system is vital for tea production.

scholarly journals Response of Soil Microbiome Structure to Biological Control Agents (BCAs) in Strawberry Greenhouse

2020 ◽  
Author(s):  
Senlin Liu ◽  
Muzammil Hassan Khan ◽  
Zhongyuan Yuan ◽  
Sarfraz Hussain ◽  
Hui Cao ◽  
...  
Keyword(s):  
Biological Control ◽  
Microbial Community ◽  
Fungal Pathogens ◽  
Soil Health ◽  
Amplicon Sequencing ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Biological Control Agents ◽  
Land Utilization ◽  
Effective Microorganisms

AbstractContinuous cropping always leads to severe abiotic and biotic problems, especially the high-intensity land utilization in greenhouses, which causes widespread concern. Effective Microorganisms (EM) and Bacillus subtilis (BS) have been widely used to promote plant growth and increase yields as biological control agents (BCAs). However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments by combining EM and BS with compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after the addition of EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Interestingly, both the relative abundance and FUNGuild predictions was consistent in revealing that BCAs may inhibit fungal pathogens in soils. Correlation analysis indicated that soil microbial community was indirectly driven by soil properties. Co-occurrence networks demonstrated that BCAs could be microecologically homogeneous through enhancing bacterial network complexity and modularity. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.

scholarly journals Dynamics of soil properties and fungal community structure in continuous-cropped alfalfa fields in Northeast China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7127 ◽  
Author(s):  
Qin Yao ◽  
Yanxia Xu ◽  
Xuefeng Liu ◽  
Junjie Liu ◽  
Xinyu Huang ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Properties ◽  
Fungal Community ◽  
Continuous Cropping ◽  
Fungal Community Composition ◽  
Fungal Community Structure ◽  
P Content ◽  
Soil Fungal Community ◽  
Relative Abundances ◽  
Total P

To compensate for the seasonal imbalance between livestock and forage yield in the cold region of Northeast China, alfalfa (Medicago sativa L.) continuous cropping has been widely employed in animal husbandry. However, the effects of continuous cropping of alfalfa on soil properties, including physical, chemical and biological properties, are poorly understood. In this study, we investigated the soil properties and fungal community composition of alfalfa fields under continuous cropping for different time periods (i.e., 1, 2, 6, 9, 12, 13 and 35 years). The results showed that soil moisture, total C, total N, NO3−-N and available K content decreased at less than 10 years of continuous cropping and then increased at more than 10 years of continuous cropping, but soil total P and available P content showed the opposite tendency. The soil fungal community composition determined using Illumina Miseq sequencing showed that continuous cropping increased the fungal alpha diversity and changed the fungal community structure. The relative abundances of Guehomyces and Chaetomium decreased, but the relative abundances of Phaeomycocentrospora and Paecilomyces increased with continuous cropping time. In addition, continuous cropping of alfalfa increased the relative abundances of some plant pathogens, such as Haematonectria haematococca and Cyphellophora sp. Soil total P and available P content were important soil factors affecting the soil fungal community diversity, fungal community structure and the relative abundances of specific fungi in this alfalfa continuous cropping system.

Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China

2020 ◽  
Vol 66 (5) ◽  
pp. 359-367
Author(s):  
Arslan Jamil ◽  
Jun-Yu Yang ◽  
Dai-Fa Su ◽  
Jiang-Yun Tong ◽  
Shan-Yan Chen ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Altitudinal Gradient ◽  
Rhizosphere Soil ◽  
Fungal Community Composition ◽  
Altitude Gradient ◽  
Community Patterns ◽  
Composition And Structure ◽  
Soil Fungal Community ◽  
Duchesnea Indica

The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.

scholarly journals Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0245180
Author(s):  
Senlin Liu ◽  
Muzammil Hassan Khan ◽  
Zhongyuan Yuan ◽  
Sarfraz Hussain ◽  
Hui Cao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Plant Pathogens ◽  
Soil Amendments ◽  
Amplicon Sequencing ◽  
Growth And Yield ◽  
Yield Enhancement ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Effective Microorganisms ◽  
Fungal Plant Pathogens

With the constant surge of strawberry cultivation and human demand, widespread concern has been expressed about the severe soil and plant health problems caused by continuous strawberry cropping, particularly monocropping in greenhouses. Effective microorganisms (EM) and Bacillus subtilis (BS) have been extensively commercialized as biological control agents (BCAs) to promote plant growth and yield enhancement. However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments based on these two BCAs by adding low and high contents of compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after adding EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Through taxonomic classification and FUNGuild analysis, we found that the application of soil amendments resulted in a significant decline in the relative abundance of fungal plant pathogens (Rhizopus, Penicillium and Fusarium) in the soils; accordingly, the metabolic functions of a range of detrimental fungi were inhibited. Correlation analysis indicated that soil microbial community was indirectly driven by soil physicochemical properties. Co-occurrence networks revealed that soil amendments contributed to the connectivity of bacterial network, and EM-treated with high compost was the most complex and balanced. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.

scholarly journals Continuous Cropping Regulates Fungal Community Structures and Functional Groups in Rhizosphere Soil of Tibet Barley

2020 ◽  
Author(s):  
Youhua Yao ◽  
Yuan Zhao ◽  
Xiaohua Yao ◽  
Yixiong Bai ◽  
Likun An ◽  
...  
Keyword(s):  
Community Structure ◽  
High Altitude ◽  
Fungal Community ◽  
Plant Pathogens ◽  
Rhizosphere Soil ◽  
Rrna Gene ◽  
Continuous Cropping ◽  
Ecological Groups ◽  
Fungal Plant Pathogens ◽  
Endophyte Fungi

Abstract Continuous cropping regulates the community structure of rhizosphere soil microbes; however, the effects of continuous cropping on the community structure and function of rhizosphere fungal communities of plants cultivated in high-altitude regions are not well understood. In this study, 18S rRNA gene high-throughput sequencing was applied to examine the rhizosphere fungal community structure during continuous cropping of Tibet barley (a principal cereal cultivated on the Qinghai-Tibetan Plateau). The results showed that the Chao1 and phylogenetic diversity (PD) indices declined as cropping years increased. Additionally, relative abundance of the genera Cystofilobasidium, Mucor, and Ustilago increased, whereas the abundance of Fusarium decreased during continuous cropping. Furthermore, identification of ecological groups using FUNGuild revealed that saprotrophs, pathogens, and symbiotrophs were the dominant groups in rhizosphere soil, and these three trophic modes all increased significantly with continuous cropping. During continuous cropping, the fungal plant-pathogens Parastagonospora and Ustilago also increased remarkably, as did the endophyte fungi Verticillium. Collectively, continuous cropping of Tibet barely increased the potential for plant-pathogenic and endophyte fungi in rhizosphere soil. Thus, the development of sustainable farming practices to reduce the abundance of harmful fungi is vital to Tibet barley growth and production during continuous cropping of plants cultivated in high-altitude regions.

scholarly journals Inducing Banana Fusarium Wilt Disease Suppression through Soil Microbiome Reshaping by Pineapple-Banana Rotation Combined with Biofertilizer Application

2021 ◽  
Author(s):  
Beibei Wang ◽  
Jinming Yang ◽  
Zongzhuan Shen ◽  
Yannan Ou ◽  
Lin Fu ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Fungal Community ◽  
Organic Fertilizer ◽  
Fertilizer Application ◽  
Wilt Disease ◽  
Disease Suppression ◽  
Fungal Communities ◽  
Soil Microbiome ◽  
Fungal Community Composition ◽  
Fusarium Wilt Disease

Abstract. Crop rotation and bio-organic fertilizer application have historically been employed as efficient management strategies for soil-borne disease suppression through soil microbiome manipulation. However, details of how this occurs, and to what extent the combination of methods affects soil microbiota reconstruction from diseased soils lacks investigation. In this study, pineapple-banana rotation combined with biofertilizer application was used to suppress banana Fusarium wilt disease, and effects on both bacterial and fungal communities were investigated using the Miseq Illumine sequencing platform. Our results show that pineapple-banana rotation significantly reduces Fusarium wilt disease incidence, and that the application of bio-organic fertilizer causes additional suppression. Bacterial and fungal communities thrive using rotation in combination with bio-organic fertilizer application: taxonomic and phylogenetic α-diversity in both bacteria and fungi increase along with disease suppression. Between the two strategies, bio-organic fertilizer application affects both bacterial and fungal community composition most predominantly, followed by rotation. Large-scale changes in the fungal community composition and special Burkholderia-related network functions contribute to the observed soil borne-disease suppression. Our results indicate that pineapple-banana rotation combined with bio-organic fertilizer application has strong potential for the sustainable management of banana Fusarium wilt disease.

Effects of green manure of wild rocket (Diplotaxis tenuifolia L.) on cucumber rhizosphere fungal community

2021 ◽  
Vol 53 (1) ◽  
pp. 93-100
Author(s):  
X.H. Zhang ◽  
H.L Xie ◽  
Y.Y. Wang ◽  
X.G. Zhou
Keyword(s):  
Community Composition ◽  
Relative Abundance ◽  
Fungal Community ◽  
Green Manure ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Fungal Community Composition ◽  
Cucumis Sativus L ◽  
Manure Treatment ◽  
Wild Rocket

In pot culture, we evaluated the effects of green manure of wild rocket (Diplotaxis tenuifolia (L.) DC.) on cucumber (Cucumis sativus L.) rhizosphere fungal community composition. Cucumber rhizosphere fungal composition was analyzed by high-throughput amplicon sequencing of fungal ITS regions. Results showed that cucumber seedling rhizosphere fungal community composition was different between the fallow treatment and green manure treatment. However, green manure treatment did not affect the cucumber seedlings fungal community alpha diversity. Compared with the fallow treatment, cucumber grown in green manure of wild rocket had higher relative abundance of phylum Ascomycota but lower relative abundance of phylum Zygomycota. Moreover, green manure of wild rocket decreased operational taxonomic units (OTUs) classified as Pseudallescheria and Kernia spp. but increased OTUs classified as Humicola and Fusarium spp. in cucumber rhizosphere.

scholarly journals Dynamic succession of soil microbial community during continuous cropping of Astragalus membranaceus Bge. var. mongholicus (Bge.)

2019 ◽  
Author(s):  
Chuangshu Sun ◽  
Bingzhen Li ◽  
Youla Su ◽  
Xin Jia ◽  
Guilin Chen
Keyword(s):  
Microbial Community ◽  
Rhizosphere Soil ◽  
Negative Impact ◽  
Chinese Herb ◽  
Pathogenic Fungi ◽  
Dry Weight ◽  
Amplicon Sequencing ◽  
Bulk Soil ◽  
Astragalus Membranaceus ◽  
Continuous Cropping

Background. Continuous cropping disturbs the balance between the microbes beneficial to a plant and the pathogenic microorganisms in the rhizosphere soil, which has both a direct and indirect adverse effect on soil and plant health. It is highly significant to understand the mechanism of the obstacle found in continuous cropping and to search for a reasonable rotation model to solve the problem of continuous cropping. Astragalus membranaceus Bge. var. mongholicus (Bge.) (A. mongholicus) is a critical traditional Chinese herb, which is negatively affected by continuous cropping. Previous studies on the root rot pathogens of A. mongholicus have been conducted, while reports on the effects of A. mongholicus on the health of soil affected by continuous cropping are lacking. Methods. In this study, we observed the microbial community structure and the diversity of the rhizosphere soil under continuous cropping for 1, 3, and 6 years using the pyrosequencing approach, and compared this to bulk soil, using A. Mongholicus as the experimental material. The 16S rDNA and ITS amplicon sequencing techniques were used to detect the composition and diversity of bacteria and fungi in the rhizosphere soil and the bulk soil of A. Mongholicus. The diversity of the bacterial community and the structures of the rhizosphere and bulk soils were compared. The dynamics of the soil enzyme activity were also analyzed. Results. The results of this study illustrated that the continuous cropping of A. mongholicus caused a decline in the root dry weight, the ratio of root-top, and also influenced the growth of the root system of A. mongholicus. Continuous cropping and the sampling time shifts the diversity and structure of the microbial community in the rhizosphere soil of A. mongholicus, showing that the diversity of the microbial community in the A. mongholicus rhizosphere soil was decreased with an increase in the replanting years, while the structure of the microbial community deteriorated. The relative abundance of pathogenic fungi, Fusarium, Erysiphe, Rhizobiales, and Burkholderiales as well as bacteria related to nodulation were enriched in the A. mongholicus rhizosphere soil at different sampling stages. The beneficial bacteria decreased with the increasing years of continuous cropping during growth, which resulted in the microecological imbalance in the A. mongholicus rhizosphere, caused serious replanting diseases of continuous cropping. A decline in soil urease and invertase activities was observed after 6 years of continuous cropping. Our experimental results suggest that continuous cropping has a significant impact on soil bacterial and fungal community development, and that an increase in replanting years resulted in more negative impact on rhizosphere soil health and A. mongholicus growth.

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