scholarly journals Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 244 ◽  
Author(s):  
Mohammad Murtaza Alami ◽  
Jinqi Xue ◽  
Yutao Ma ◽  
Dengyan Zhu ◽  
Aqleem Abbas ◽  
...  
Keyword(s):  
Cropping Systems ◽  
Cropping System ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Soil Samples ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Coptis Chinensis ◽  
The Sustainable Development ◽  
Fungal Community Structure

Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. Coptis chinensis Franch is one of the most important medicinal plants in China. In the current study, we provide detailed information regarding the diversity and composition of rhizospheric fungal communities of the C. chinensis plants in continuous cropping fields and fallow fields in two seasons (winter and summer), using next-generation sequencing. Alpha diversity was higher in the five-year C. chinensis field and lower in fallow fields. Significant differences analysis confirmed more fungi in the cultivated field soil than in fallow fields. Additionally, PCoA of beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Five fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycota) were identified from the soil samples in addition to the unclassified fungal taxa and Cryptomycota, and among these phyla, Ascomycota was predominantly found. FUNGuild fungal functional prediction revealed that saprotroph was the dominant trophic type in all two time-series soil samples. Redundancy analysis (RDA) of the dominant phyla data and soil physiochemical properties revealed the variations in fungal community structure in the soil samples. Knowledge from the present study could provide a valuable reference for solving the continuous cropping problems and promote the sustainable development of the C. chinensis industry.

scholarly journals Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 57 ◽  
Author(s):  
Mohammad Murtaza Alami ◽  
Jinqi Xue ◽  
Yutao Ma ◽  
Dengyan Zhu ◽  
Zedan Gong ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Cropping Systems ◽  
Alpha Diversity ◽  
Terrestrial Ecosystems ◽  
Soil Samples ◽  
Principal Coordinate Analysis ◽  
Continuous Cropping ◽  
Coptis Chinensis ◽  
Bacterial Phyla ◽  
Significant Difference

Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.

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 fungal communities to continuous cropping of flue-cured tobacco

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shengnan Wang ◽  
Jiangke Cheng ◽  
Tong Li ◽  
Yuncheng Liao
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Cropping Systems ◽  
Quantitative Polymerase Chain Reaction ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Fungal Community Structure ◽  
Soil Variables ◽  
Fungal Abundance

AbstractFungal communities are considered to be critically important for crop health and soil fertility. However, our knowledge of the response of fungal community structure to the continuous cropping of flue-cured tobacco is limited, and the interaction of soil fungal communities under different cropping systems remains unclear. In this study, we comparatively investigated the fungal abundance, diversity, and community composition in the soils in which continuous cropping of flue-cured tobacco for 3 years (3ys), 5 years (5ys), and cropping for 1 year (CK) using quantitative polymerase chain reaction and high-throughput sequencing technology. The results revealed that continuous cropping of flue-cured tobacco changed the abundance of soil fungi, and caused a significant variation in fungal diversity. In particular, continuous cropping increased the relative abundance of Mortierellales, which can dissolve mineral phosphorus in soil. Unfortunately, continuous cropping also increased the risk of potential pathogens. Moreover, long-term continuous cropping had more complex and stabilize network. This study also indicated that available potassium and available phosphorous were the primary soil factors shifting the fungal community structure. These results suggested that several soil variables may affect fungal community structure. The continuous cropping of flue-cured tobacco significantly increased the abundance and diversity of soil fungal communities.

scholarly journals The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingjing Chang ◽  
Yu Sun ◽  
Lei Tian ◽  
Li Ji ◽  
Shasha Luo ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Wild Rice ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogen Invasion ◽  
Rice Rhizosphere ◽  
Soilborne Fungi

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.

scholarly journals Long-term cropping system studies support intensive and responsive cropping systems in the low-rainfall Australian Mallee

2015 ◽  
Vol 66 (6) ◽  
pp. 553 ◽  
Author(s):  
A. M. Whitbread ◽  
C. W. Davoren ◽  
V. V. S. R. Gupta ◽  
R. Llewellyn ◽  
the late D. Roget
Keyword(s):  
Crop Residue ◽  
Field Experiments ◽  
Cropping Systems ◽  
Cropping System ◽  
Continuous Cropping ◽  
Gross Margin ◽  
No Till ◽  
Residue Retention ◽  
Term Field

Continuous-cropping systems based on no-till and crop residue retention have been widely adopted across the low-rainfall cereal belt in southern Australia in the last decade to manage climate risk and wind erosion. This paper reports on two long-term field experiments that were established in the late 1990s on texturally different soil types at a time of uncertainty about the profitability of continuous-cropping rotations in low-rainfall environments. Continuous-cereal systems significantly outyielded the traditional pasture–wheat systems in five of the 11 seasons at Waikerie (light-textured soil), resulting in a cumulative gross margin of AU$1600 ha–1 after the initial eight seasons, almost double that of the other treatments. All rotation systems at Kerribee (loam-textured soil) performed poorly, with only the 2003 season producing yields close to 3 t ha–1 and no profit achieved in the years 2004–08. For low-rainfall environments, the success of a higher input cropping system largely depends on the ability to offset the losses in poor seasons by capturing greater benefits from good seasons; therefore, strategies to manage climatic risk are paramount. Fallow efficiency, or the efficiency with which rainfall was stored during the period between crops, averaged 17% at Kerribee and 30% at Waikerie, also indicating that soil texture strongly influences soil evaporation. A ‘responsive’ strategy of continuous cereal with the occasional, high-value ‘break crop’ when seasonal conditions are optimal is considered superior to fixed or pasture–fallow rotations for controlling grass, disease or nutritional issues.

scholarly journals Status of Available Phosphorus and Forms of Phosphorus in Soil under Major Cropping Systems of Y.S.R. Kadapa District, A.P.

2019 ◽  
pp. 1-7
Author(s):  
G. K. Surya Krishna ◽  
T. Giridhara Krishna ◽  
V. Munaswamy ◽  
Y. Reddi Ramu
Keyword(s):  
Physicochemical Properties ◽  
Andhra Pradesh ◽  
Cropping Systems ◽  
Cropping System ◽  
Soil Samples ◽  
Available Phosphorus ◽  
Free Lime ◽  
Mean Values ◽  
Southern Zone ◽  
Total P

An investigation was carried out to study different forms of phosphorus under major cropping systems in Y.S.R. Kadapa district of Southern Zone of Andhra Pradesh. Five soil samples from each cropping system at 0-15 cm depth collected from each cropping system to study their physicochemical properties, status of available P2O5 and different forms of P. Majority of the soils were moderately alkaline in reaction, non-saline, free lime content indicating that these soils are moderately calcareous, medium to high in available P2O5. Highest mean values for available P2O5 (182.41 kg ha-1), Al-P (80.82 mg kg-1), Ca-P (118.55 mg kg-1) and total-P (434.35 mg kg-1) were recorded in groundnut monocropping system whereas for saloid P (23.01 mg kg-1), Fe-P (69.82 mg kg-1) and other forms of P (228.35 mg kg-1) highest mean values were recorded under sunflower-sesame, groundnut-groundnut and fallow-bengal gram cropping systems, respectively.

scholarly journals Impact of Intercropping on the Diazotrophic Community in the Soils of Continuous Cucumber Cropping Systems

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Gao ◽  
Sen Li ◽  
Fengzhi Wu
Keyword(s):  
Cropping Systems ◽  
Regression Tree ◽  
Cropping System ◽  
Community Diversity ◽  
Scaling Analysis ◽  
N Fixation ◽  
Continuous Cropping ◽  
Available Nitrogen ◽  
Multivariate Regression Tree ◽  
Diazotrophic Community

Diazotrophs are important soil components that help replenish biologically available nitrogen (N) in the soil and contribute to minimizing the use of inorganic N fertilizers in agricultural ecosystems. However, there is little understanding of how diazotrophs respond to intercropping and soil physicochemical properties in cucumber continuous cropping systems. In this study, using the nifH gene as a marker, we have examined the impacts of seven intercropping plants on diazotrophic community diversity and composition compared to a cucumber continuous cropping system during two cropping seasons. The results showed that intercropping increased the abundance of the nifH gene, which was negatively correlated with available phosphorous in the fall. Diazotrophic diversity and richness were higher in the rape–cucumber system than in the monoculture. Multivariate regression tree analysis revealed that the diversity of the diazotrophic communties was shaped mainly by soil moisture and available phosphorous. Skermanella were the dominant genera in all of the samples, which increased significantly in the mustard–cucumber system in the fall. There was no effect of intercropping on the structure of the diazotrophic community in this case. Non-metric multidimensional scaling analysis showed that cropping season had a greater effect than intercropping on the community structure of the diazotrophs. Overall, our results suggest that intercropping altered the abundance and diversity rather than the structure of the diazotrophic community, which may potentially affect the N fixation ability of continuous cropping systems.

scholarly journals Diet Induces the Difference of Gut Fungal Communities between Anser erythropus Wintering at Shengjin and Caizi Lakes, China

2021 ◽  
Author(s):  
Gang Liu ◽  
Zhizhong Gong ◽  
Jiahui Feng ◽  
Na Xu
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogenic Species ◽  
Potential Pathogen ◽  
Host Nutrition ◽  
The Difference ◽  
Serious Disease ◽  
Anser Erythropus

Abstract The gut microbiota play major roles in host nutrition and metabolism, and even potential to cause serious disease for animals and human, however, the knowledge of waterbirds’ gut fungal communities are quite limited at present. In this paper, the gut fungal communities and infer the potential pathogens isolated from the feces of Anser erythropus wintering at Shengjin Lake (SJ) and Caizi Lake (CZ) were investigated based on ITS gene region by using high-throughput sequencing. 1,302,562 valid tags corresponding to 2,102 OTUs were retained from 20 fecal samples, including 10 samples per lake. The OTUs from SJ geese represented seven phyla and 27 classes, seven phyla and 28 classes were identified from CZ samples. Ascomycota, Basidiomycota, Zygomycota and Rozellomycota were the dominant gut fungal phyla in this study, accounted for 61.60%, 35.60%, 1.84%, and 0.30% of the OTUs, respectively. The alpha diversity indices showed significantly different between the geese from SJ and CZ. The Anser erythropus mainly ate Poaceae spp. at SJ, while Carex spp. component was identified at CZ, suggesting that the variations in fungal community between the two lake geese might be induced by different diets. We also observed a fungal pattern with a higher number of significant correlations to bacterial genus, and Ceratobasidium, Tomentella, Paurocotylis, Tuber, Podospora and Mortierella were core fungal genus in the two lake geese. Nine potential pathogenic species were identified in the guts across all samples of Anser erythropus at SJ and CZ, it also showed the relative abundance of potential pathogen was significantly higher from SJ samples than that from CZ samples. These findings expanded our knowledge on the gut fungi for waterbirds, indicating the fungi are highly sensitive to diet at two lakes and should pay more attention to the potential pathogenic species of Anser erythropus.

scholarly journals Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase GenenifH

2015 ◽  
Vol 81 (13) ◽  
pp. 4536-4545 ◽  
Author(s):  
Bangzhou Zhang ◽  
C. Ryan Penton ◽  
Chao Xue ◽  
Qiong Wang ◽  
Tianling Zheng ◽  
...  
Keyword(s):  
Cropping Systems ◽  
Cropping System ◽  
Diversity Indices ◽  
Error Rates ◽  
Personal Genome ◽  
Ion Torrent ◽  
Personal Genome Machine ◽  
Operational Taxonomic Units ◽  
Sequence Profiles ◽  
Diazotrophic Community

ABSTRACTThe sequencing chips and kits of the Ion Torrent Personal Genome Machine (PGM), which employs semiconductor technology to measure pH changes in polymerization events, have recently been upgraded. The quality of PGM sequences has not been reassessed, and results have not been compared in the context of a gene-targeted microbial ecology study. To address this, we compared sequence profiles across available PGM chips and chemistries and with 454 pyrosequencing data by determining error types and rates and diazotrophic community structures. The PGM was then used to assess differences innifH-harboring bacterial community structure among four corn-based cropping systems. Using our suggested filters from mock community analyses, the overall error rates were 0.62, 0.36, and 0.39% per base for chips 318 and 314 with the 400-bp kit and chip 318 with the Hi-Q chemistry, respectively. Compared with the 400-bp kit, the Hi-Q kit reduced indel rates by 28 to 59% and produced one to seven times more reads acceptable for downstream analyses. The PGM produced higher frameshift rates than pyrosequencing that were corrected by the RDP FrameBot tool. Significant differences among platforms were identified, although the diversity indices and overall site-based conclusions remained similar. For the cropping system analyses, a total of 6,182 unique NifH operational taxonomic units at 5% amino acid dissimilarity were obtained. The current crop type, as well as the crop rotation history, significantly influenced the composition of the soil diazotrophic community detected.

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