scholarly journals Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

2020 ◽  
Vol 8 (9) ◽  
pp. 1385
Author(s):  
Jun Li ◽  
Ziqiong Luo ◽  
Chenhui Zhang ◽  
Xinjing Qu ◽  
Ming Chen ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Pathogen Resistance ◽  
High Yield ◽  
Glutathione Metabolism ◽  
Oilseed Crop ◽  
Soil Microbial ◽  
Bacteria And Fungi

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.

scholarly journals Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 809
Author(s):  
Sen Wang ◽  
Wanyu Liu ◽  
Jun Li ◽  
Haotian Sun ◽  
Yali Qian ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Relative Abundance ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Fine Particulate Matter ◽  
Ecological Functions ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Variation Characteristics ◽  
Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

scholarly journals Effects of Short-Term Rice Straw Return on the Soil Microbial Community

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 561
Author(s):  
Enze Wang ◽  
Xiaolong Lin ◽  
Lei Tian ◽  
Xinguang Wang ◽  
Li Ji ◽  
...  
Keyword(s):  
Microbial Community ◽  
Rice Straw ◽  
Paddy Soil ◽  
Soil Microbial Community ◽  
Short Term ◽  
Soil Microbial ◽  
Microbial Network ◽  
Straw Return ◽  
Bacteria And Fungi ◽  
Main Factor

Rice straw is a byproduct of agricultural production and an important agricultural resource. However, rice straw has not yet been effectively used, and incorrect treatment methods (such as burning in the field) can cause serious damage to the environment. Studies have shown that straw returning is beneficial to soil, but there have been few studies focused on the effect of the amount of short-term straw returned on the soil microbial community. This study evaluates 0%, 50%, 75%, and 100% rice straw returned to the field on whether returning different amounts of straw in the short term would affect the diversity and composition of the soil microbial community and the correlation between bacteria and fungi. The results show that the amount of straw returned to the field is the main factor that triggers the changes in the abundance and composition of the microbial community in the paddy soil. A small amount of added straw (≤ 50% straw added) mainly affects the composition of the bacterial community, while a larger amount of added straw (> 50% straw added) mainly affects the composition of the fungal community. Returning a large amount of straw increases the microbial abundance related to carbon and iron cycles in the paddy soil, thus promoting the carbon and iron cycle processes to a certain extent. In addition, network analysis shows that returning a large amount of straw also increases the complexity of the microbial network, which may encourage more microbes to be niche-sharing and comprehensively improve the ecological environment of paddy soil. This study may provide some useful guidance for rice straw returning in northeast China.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Kaoping Zhang ◽  
Manuel Delgado-Baquerizo ◽  
Yong-Guan Zhu ◽  
Haiyan Chu
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
Spatial Scale ◽  
Environmental Variables ◽  
Soil Microbial Communities ◽  
Spatiotemporal Variation ◽  
Relative Importance ◽  
Large Spatial Scale ◽  
Environmental Covariates ◽  
Soil Microbial

ABSTRACT The relative importance of spatial and temporal variability in shaping the distribution of soil microbial communities at a large spatial scale remains poorly understood. Here, we explored the relative importance of space versus time when predicting the distribution of soil bacterial and fungal communities across North China Plain in two contrasting seasons (summer versus winter). Although we found that microbial alpha (number of phylotypes) and beta (changes in community composition) diversities differed significantly between summer and winter, space rather than season explained more of the spatiotemporal variation of soil microbial alpha and beta diversities. Environmental covariates explained some of microbial spatiotemporal variation observed, with fast-changing environmental covariates—climate variables, soil moisture, and available nutrient—likely being the main factors that drove the seasonal variation found in bacterial and fungal beta diversities. Using random forest modeling, we further identified a group of microbial exact sequence variants (ESVs) as indicators of summer and winter seasons and for which relative abundance was associated with fast-changing environmental variables (e.g., soil moisture and dissolved organic nitrogen). Together, our empirical field study’s results suggest soil microbial seasonal variation could arise from the changes of fast-changing environmental variables, thus providing integral support to the large emerging body of snapshot studies related to microbial biogeography. IMPORTANCE Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms

2019 ◽  
Vol 95 (6) ◽  
Author(s):  
Anders Bjørnsgaard Aas ◽  
Carrie J Andrew ◽  
Rakel Blaalid ◽  
Unni Vik ◽  
Håvard Kauserud ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Structure ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Diversity Patterns ◽  
Bistorta Vivipara ◽  
Adjacent Soil ◽  
Bacteria And Fungi

ABSTRACT The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

scholarly journals Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays

2005 ◽  
Vol 71 (7) ◽  
pp. 4117-4120 ◽  
Author(s):  
Noah Fierer ◽  
Jason A. Jackson ◽  
Rytas Vilgalys ◽  
Robert B. Jackson
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Quantitative Pcr ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Pcr Assays ◽  
Bacteria And Fungi ◽  
Taxonomic Groups

ABSTRACT Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

2020 ◽  
Author(s):  
Yan Xu ◽  
Junfeng Niu ◽  
Lijun Chen ◽  
Xiaoqiang Wu ◽  
Zhongmin Dong ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Continuous Cropping ◽  
Pests And Diseases ◽  
Atractylodes Lancea ◽  
Bacteria And Fungi ◽  
The Relationship

Abstract Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

scholarly journals Soil Microbial Community Variation With Time and Soil Depth in Eurasian Steppe (Inner Mongolia, China)

2021 ◽  
Author(s):  
Hongbin Zhao ◽  
Wenling Zheng ◽  
Shengwei Zhang ◽  
Wenlong Gao ◽  
Yueyue Fan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Environmental Factors ◽  
Soil Microbial Community ◽  
Soil Depth ◽  
Microbial Community Composition ◽  
Spatial Transformation ◽  
Soil Microbial ◽  
Abundance And Diversity ◽  
Bacteria And Fungi

Abstract BackgroundSoil microorganisms play an indispensable role in the material and energy cycle of grassland ecosystem, and were affected by many environmental factors, such as time and space changes. However, there are few studies on the temporal and spatial transformation of soil microbial community in typical degraded steppe. We analyzed the community structure and diversity of soil bacteria and fungi and the effects of environmental factors on the community structure in Xilingol degraded steppe. ResultsThe abundance and diversity of bacteria and fungi were significantly affected by depth. Bacteria and fungi diversity of 10 cm was higher than that of 20 cm and 30 cm. The abundance of Acidobacteria, Proteobacteria, Actinomycetes, Ascomycetes and Basidiomycetes varies significantly with depth. What’s more, soil pH increased significantly with depth increasing, while SOM, AN, VWC and ST decreased significantly with increasing depth. In addition, Depth, TOC and AN had significant impact on the bacterial and fungi communities (p < 0.05). ConclusionsSpatial heterogeneity (depth) is more important than temporal (month) in predicting changes in microbial community composition and soil properties. And the abundance of Acidobacteria, Proteobacteria, Actinomycetes, Ascomycetes and Basidiomycetes varies significantly with depth. We speculate that SOM and VWC account for the abundance variations of Acidobacteria and Proteobacteria, and pH cause the abundance changes of Actinomycetes, Ascomycetes and Basidiomycota.

scholarly journals Impacts of Decaying Aromatic Plants on the Soil Microbial Community and on Tomato Seedling Growth and Metabolism: Suppression or Stimulation?

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1848
Author(s):  
Aggeliki Ainalidou ◽  
Foteini Bouzoukla ◽  
Urania Menkissoglu-Spiroudi ◽  
Despoina Vokou ◽  
Katerina Karamanoli
Keyword(s):  
Microbial Community ◽  
Microbial Biomass ◽  
Soil Microbial Community ◽  
Phospholipid Fatty Acid ◽  
Positive Control ◽  
Aromatic Plants ◽  
Tomato Seedling ◽  
Soil Microbial ◽  
Tomato Seedlings ◽  
Bacteria And Fungi

This study provides insight into changes in the features of tomato seedlings growing in soils enriched with spearmint, peppermint, or rosemary leaves and into changes in the microbial communities of these soils used as seedbeds; an organic amendment was also applied as a positive control. While the soil microbial community flourished in the presence of all three aromatic plants, tomato growth was inhibited or stimulated depending on the plant that was used. More specifically, phospholipid fatty acid (PLFA) analysis showed an increase in the total microbial biomass and in the biomass of all the groups examined, except for actinobacteria, and changes in the microbial community structure, with Gram-negative bacteria and fungi being favoured in the mint treatments, in which the microbial biomass was maximized. Seedlings from the rosemary treatment were entirely inhibited; they were at the open-cotyledon stage throughout the experiment. Seedlings from the mint treatments were the heaviest, longest, and had the highest chlorophyll content and photosynthetic yield. Metabolomic analysis showed metabolism enhancement associated with both growth and priming in seedlings from the mint treatments and disruption of metabolic pathways in those from the rosemary treatment. There is a great potential for applying these aromatic plants as soil amendments and as either biostimulants of plant growth or as herbicides.

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