scholarly journals Study on the Diversity of Fungal and Bacterial Communities in Continuous Cropping Fields of Chinese Chives (Allium tuberosum)

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Yizhu Gu ◽  
Yuxin Wang ◽  
Pingzhi Wang ◽  
Chaonan Wang ◽  
Jinhai Ma ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Nutrient Content ◽  
Scientific Management ◽  
Continuous Cropping ◽  
Potassium Fertilizer ◽  
Beneficial Bacteria ◽  
Bacterial Phyla ◽  
Chinese Chives

In this study, high-throughput sequencing technology was used to analyse the diversity and composition of fungal and bacterial communities in continuous cropping soil of Chinese chives. The soil nutrient was also measured to explore the rationality of current fertilization management. These results can provide a basis for the prevention and control of the continuous cropping obstacles of Chinese chives and further scientific management. Soil samples from fields continuously cropped with Chinese chives for one year, three years, and five years were collected and analysed. The results showed that the nutrient content of TP, AP, AK and TK increased significantly with increasing continuous cropping years. Short-term continuous cropping soil nutrients have not deteriorated. Alpha-diversity analysis showed that significant differences were not found in the diversity of the fungal and bacterial community among different years. Ascomycota, Basidiomycota and Mortierellomycota were the three most dominant fungal phyla. Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria were the dominant bacterial phyla. Continuous cropping makes Fusarium increase, and the beneficial bacteria Pseudomonas decreased significantly. According to the correlation heat map analysis of environmental factors, excessive phosphorus may lead to the increase of Fusarium, potassium may promote the proliferation of beneficial bacteria in the continuous cropping process, and it is necessary to regulate the application of phosphate and potassium fertilizer.

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 Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2015 ◽  
Vol 12 (13) ◽  
pp. 10233-10269 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Keystone Species ◽  
Small World ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

scholarly journals Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hui Xi ◽  
Jili Shen ◽  
Zheng Qu ◽  
Dingyi Yang ◽  
Shiming Liu ◽  
...  
Keyword(s):  
Severe Disease ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Microbial Groups

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2016 ◽  
Vol 13 (1) ◽  
pp. 175-190 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Food Web Structure ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

scholarly journals Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hanan R. Shehata ◽  
Subramanyam Ragupathy ◽  
Thomas A. Henry ◽  
Steven G. Newmaster
Keyword(s):  
Functional Diversity ◽  
Ginkgo Biloba ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Panax Quinquefolius ◽  
Tissue Type ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

scholarly journals Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

2022 ◽  
Vol 9 ◽  
Author(s):  
Min-Chong Shen ◽  
Yu-Zhen Zhang ◽  
Guo-Dong Bo ◽  
Bin Yang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Agricultural Soil ◽  
Rhizosphere Soil ◽  
Alpha Diversity ◽  
Low Fertility ◽  
Control Group ◽  
Beneficial Bacteria ◽  
Chemical Fertilizers ◽  
Agricultural Resources ◽  
Microbial Responses

The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.

scholarly journals Variation of Soil Bacterial Communities during Lettuce Continuous Cropping

2019 ◽  
Vol 131 ◽  
pp. 01091
Author(s):  
Jie Hong ◽  
Yue Yang ◽  
Yi Gao ◽  
LianQuan Zhong ◽  
QuanMing Xu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Continuous Cropping ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Lettuce Yield

The variation of bacterial community in lettuce continuous cropping was determined by high throughput sequencing. During the continuous planting of lettuce, the richness and diversity of bacterial communities in the soil increased, and the ACE index and Chao index increased by 40.21 % and 36.91 %, respectively. The proportion of Actinobacteria, Chloroflexi, Firmicutes and Nitrospirae in the soil increased, while the abundance of Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes and Proteobacteria gradually declined. And the abundance in the soil accounting for 1 % of the dominant bacterial genera increased to 11, among them, Anaerolinea, Bacillus, Nitrosomonas, and Xanthomonas etc became the dominant bacterium genus in the soil after lettuce continuous cropping. After the lettuce had been planted 8 times, the yield decreased by 21.20 % compared to the first harvest. Lettuce continuous cropping had an effect on bacterial community and lettuce yield to some extent.

scholarly journals Changes in the Soil Bacterial Community in a Chronosequence of Temperate Walnut-Based Intercropping Systems

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 299 ◽  
Author(s):  
Pengxiang Gao ◽  
Xiaofeng Zheng ◽  
Lai Wang ◽  
Bin Liu ◽  
Shuoxin Zhang
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Agroforestry System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Phyla ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Agroforestry (tree-based intercropping) is regarded as a promising practice in sustainable agricultural management. However, the impacts of converting cropland to an agroforestry system on microbial communities remain poorly understood. In this study, we assessed the soil bacterial communities in conventional wheat monoculture systems and a chronosequence (5–14 years) walnut-wheat agroforestry system through the high-throughput sequencing of 16S rRNA genes to investigate the effect of agroforestry age on soil bacterial communities and the correlation between soil properties and bacterial communities in the agroecosystem. Our results demonstrate that establishing and developing walnut tree-based agroforestry increased soil bacterial diversity and changed bacterial community structure. Firmicutes, Proteobacteria, Actinobacteria and Acidobacteria were the dominant soil bacterial phyla and Bacillus was the dominant genus. Crop monoculture systems were characterized by the Bacillus (Firmicutes)-dominated microbial community. The relative abundance of Bacillus decreased with agroforestry age; however, subgroups of Proteobacteria and Actinobacteria increased. Of the selected soil physicochemical properties, soil pH and bulk density were significantly correlated with bacterial alpha diversity, and soil pH and organic carbon were the principal drivers in shaping the soil microbial structure as revealed by redundancy analysis (RDA).

scholarly journals Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Vaso Taleski ◽  
Ivica Dimkić ◽  
Blazo Boev ◽  
Ivan Boev ◽  
Sanja Živković ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Optical Emission ◽  
Diversity Indices ◽  
Emission Spectrometry ◽  
High Concentration ◽  
Bacterial Phyla ◽  
The Republic

ABSTRACT The Allchar mineral mine is one of the oldest arsenic–antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

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