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

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.

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The Effect of Leonardite-Derived Amendments on Soil Microbiome Structure and Potato Yield

Agriculture ◽

10.3390/agriculture10050147 ◽

2020 ◽

Vol 10 (5) ◽

pp. 147

Author(s):

Nuraly Akimbekov ◽

Xiaohui Qiao ◽

Ilya Digel ◽

Gulzhamal Abdieva ◽

Perizat Ualieva ◽

...

Keyword(s):

Microbial Community ◽

Humic Substances ◽

Tuber Yield ◽

Soil Amendments ◽

Microbial Community Composition ◽

Growth And Yield ◽

Soil Microbiome ◽

High Yield ◽

Mature Stage ◽

Potato Growth

Humic substances originating from various organic matters can ameliorate soil properties, stimulate plant growth, and improve nutrient uptake. Due to the low calorific heating value, leonardite is rather unsuitable as fuel. However, it may serve as a potential source of humic substances. This study was aimed at characterizing the leonardite-based soil amendments and examining the effect of their application on the soil microbial community, as well as on potato growth and tuber yield. A high yield (71.1%) of humic acid (LHA) from leonardite has been demonstrated. Parental leonardite (PL) and LHA were applied to soil prior to potato cultivation. The 16S rRNA sequencing of soil samples revealed distinct relationships between microbial community composition and the application of leonardite-based soil amendments. Potato tubers were planted in pots in greenhouse conditions. The tubers were harvested at the mature stage for the determination of growth and yield parameters. The results demonstrated that the LHA treatments had a significant effect on increasing potato growth (54.9%) and tuber yield (66.4%) when compared to the control. The findings highlight the importance of amending leonardite-based humic products for maintaining the biogeochemical stability of soils, for keeping their healthy microbial community structure, and for increasing the agronomic productivity of potato plants.

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

10.21203/rs.3.rs-109459/v1 ◽

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.

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Farm Level Evaluation of Trichoderma Enriched Organic Substrates for Improved Field Establishment and Yield Enhancement in Chillies (Capsicum annuum L.)

Current Journal of Applied Science and Technology ◽

10.9734/cjast/2020/v39i1930788 ◽

2020 ◽

pp. 30-37

Author(s):

S. Kalavathi ◽

Merin Babu ◽

Jeena Mathew ◽

S. Indhuja

Keyword(s):

Plant Pathogens ◽

Poultry Manure ◽

Growth And Yield ◽

Yield Enhancement ◽

Organic Substrates ◽

Neem Cake ◽

Trichoderma Sp ◽

Efficient Delivery ◽

Proper Formulation ◽

Field Efficacy

Trichoderma sp. is extensively used for controlling several soil and seed bornefungal plant pathogens and for enhancing crop growth and yield. But the field efficacy depends on several factors viz., proper formulation, an efficient delivery system, methods of applicationand environmental conditions. The performance and persistence in field to a greater extent is decided by the carriers or substrates used for mass multiplication. In a field trial undertaken on the varied performance of Trichoderma sp. involving different substrate combinations on the yield of chillies by ICAR-CPCRI for the period, April, 2014 to June 2016 two combinations, viz., Cowdung + Neem cake (4:1) and Coir pith compost + Neem cake + Poultry Manure + Cowdung (2:1:1:1) were found to be superior when enriched with Trichodermaharzianum (CPTD 28) as well as native isolate, Trichoderma sp. KKTD 6.

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Isolation of Cultivation-Resistant Oomycetes, First Detected as Amplicon Sequences, from Roots of Herbicide-Terminated Winter Rye

Phytobiomes Journal ◽

10.1094/pbiomes-10-16-0011-r ◽

2017 ◽

Vol 1 (1) ◽

pp. 24-35 ◽

Cited By ~ 19

Author(s):

Matthew G. Bakker ◽

Thomas B. Moorman ◽

Thomas C. Kaspar ◽

Daniel K. Manter

Keyword(s):

Microbial Community ◽

Cover Crops ◽

Cover Crop ◽

Plant Pathogens ◽

Community Dynamics ◽

Disease Risk ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Winter Rye ◽

Cereal Rye

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. We used high throughput amplicon sequencing to characterize the composition and structure of oomycete and fungal communities associated with a rye cover crop, and to track their community dynamics in the first several weeks after herbicide was applied to terminate the cover crop. The dominant oomycetes associated with cereal rye roots were Pythium volutum, Pythium sp. F86 (an unknown species within clade B), and Lagena radicicola. Because P. volutum is sensitive to common additives in isolation media, and L. radicicola is an obligate intracellular parasite, a unique aspect of this work is to reveal the dominance of oomycete taxa that would have been missed entirely under a traditional cultivation-based approach. Based on first detection in an amplicon sequencing survey, we were able to isolate P. volutum and Pythium sp. F86. We demonstrate that both species are pathogenic on corn, and that corn seedlings grown in the field following a rye cover crop show elevated rates of infection by P. volutum, highlighting a potential disease risk associated with cover cropping. P. volutum and Pythium sp. F86 exhibited contrasting spatial patterns of abundance, with nearly complete turnover of the dominant species across the field site. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with a cereal rye cover crop were more diverse and dynamic, with some displacement of basidiomycetes by ascomycetes over time. Several plant pathogens, as well as putative beneficial organisms, were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, highlights the power of culture-independent microbial community assessment to yield new insights, and suggests the need for informed management to reduce seedling disease risk in corn following rye cover crops.

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

10.7287/peerj.preprints.27600v1 ◽

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

10.7287/peerj.preprints.27600 ◽

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

PeerJ ◽

10.7717/peerj.9930 ◽

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.

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Morphological, biochemical and molecular identification of rhizobacteria isolates with potential for biocontrol of fungal plant pathogens

Archives of Phytopathology and Plant Protection ◽

10.1080/03235408.2021.1909370 ◽

2021 ◽

pp. 1-14

Author(s):

Stephen Larbi-Koranteng ◽

Richard Tuyee Awuah ◽

Fredrick Kankam ◽

Muntala Abdulai ◽

Marian Dorcas Quain ◽

...

Keyword(s):

Molecular Identification ◽

Plant Pathogens ◽

Fungal Plant Pathogens

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Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽

10.1186/s40168-021-01072-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Benjamin J. Callahan ◽

Dmitry Grinevich ◽

Siddhartha Thakur ◽

Michael A. Balamotis ◽

Tuval Ben Yehezkel

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Amplicon Sequencing ◽

Species Level ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Strain Identification ◽

Long Reads ◽

Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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