Continuous cropping of cut chrysanthemum reduces rhizospheric soil microbial populations, diversity and network complexity

Abstract Continuous cropping of cut chrysanthemum causes soil degradation and chrysanthemum quality decline, but the biotic and abiotic mechanisms behind it remain unclear. This impedes our ability to assess the true effects of continuous cropping on agricultural soil functions and our ability to repair impaired soils. Here we examined the impact of different replanting years on microbial communities and enzyme activities in rhizosphere soil of cut chrysanthemum (Chrysanthemum morifolium). Our results showed that soil total nitrogen (TN) and organic carbon (SOC) contents were significantly lower in the soil with 12 years of continuous cropping (Y12) than that in the soil with 1 year of cropping (Y1). Compared with Y1, Y12 treatment decreased alkaline phosphatase and β -glucosidase by 12.1 and 24.4%, but increased the activities of soil urease and catalase by 98.2 and 34.8%, respectively. Soil bacterial populations in Y6 (continuous cropping for 6 years) and Y12 treatments decreased by 52.3 and 87.5% compared with that in Y1 treatment. Moreover, the bacterial α-diversity (Shannon index) significantly decreased by 37.3 and 57.6% over 6 and 12 years of continuous cropping, respectively. Long-term monoculture cropping shifted the bacterial community composition, with decreased abundances of dominant phyla such as Proteobacteria and Acidobacteria, but with an increase in the relative abundances of Actinobacteria and Chloroflexi, and Gemmatimonadetes. Moreover, Y6 and Y12 treatments harbored less microbial network complexity, lower bacterial taxa, and fewer linkages among bacterial taxa, relative to Y1. Soil pH, SOC, and TN were the main edaphic factors affecting soil bacterial community compositions and diversity. Overall, our results demonstrate that continuous cropping has a significant negative impact on soil microbial diversity and complexity.

Download Full-text

Organic Amendments and Sampling Date Influences on Soil Bacterial Community Composition and Their PredictiveFunctional Profiles in an Olive Grove Ecosystem

Agriculture ◽

10.3390/agriculture11111178 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1178

Author(s):

Laura L. de Sosa ◽

Beatriz Moreno ◽

Rafael Alcalá Alcalá Herrera ◽

Marco Panettieri ◽

Engracia Madejón ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Agricultural Soils ◽

Soil Microbial Communities ◽

Soil Bacterial Community ◽

Olive Grove ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Soil Bacterial ◽

The Impact

A collapse of soil microbial diversity, mainly due to chemical inputs, has been reported to lead to the degradation of conventional agroecosystems. The use of compost from urban and agricultural waste management, in order to achieve a net gain in the storage of C, is an adequate management of agricultural soils, especially in rainfed conditions. However, the great variability of composts of different maturity and origins and of the soils to which they are added limits the ability to predict the impact of these amendments on the dynamics of soil microbial communities. This study was designed to gain insights on the effect of exogenous organic matter management on the soil bacterial community and its contribution to key functions relevant to agricultural soils. To achieve this, two different types of compost (alperujo or biosolids composts) at two doses were used as soil amendments twice for 3 years in a rainfed olive grove ecosystem. A metagenomic analysis was carried out to assess the abundance and composition of the soil bacterial communities and predicted functions. We only detected a minor and transitory effect on the bacterial abundance of the soil, the structure of the community and the potential functions, less related to the dose or the type of compost than to seasonal variations. Although the result suggests that the soil bacteria were highly resilient, promoting community stability and functional resilience after the addition of the two composts, more efforts are necessary to assess not only the resulting soil microbial community after organic fertilization but the intrinsic microbial community within the organic amendment that acts as an inoculum, and to what extent the changes in its dose could lead to the functionality of the soil.

Download Full-text

Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

Microbiology Research ◽

10.3390/microbiolres12010012 ◽

2021 ◽

Vol 12 (1) ◽

pp. 157-172

Author(s):

Shankar G. Shanmugam ◽

Normie W. Buehring ◽

Jon D. Prevost ◽

William L. Kingery

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Production System ◽

Soil Microbial Community ◽

Production Systems ◽

Bacterial Community Composition ◽

Soybean Production ◽

Soil Microbial ◽

Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

Download Full-text

Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

Applied Sciences ◽

10.3390/app11030918 ◽

2021 ◽

Vol 11 (3) ◽

pp. 918

Author(s):

Lingzi Mo ◽

Augusto Zanella ◽

Xiaohua Chen ◽

Bin Peng ◽

Jiahui Lin ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Negative Impact ◽

Bacterial Community Composition ◽

N Deposition ◽

Soil Bacterial Community ◽

Rrna Gene ◽

Soil Dna ◽

Urban Green ◽

Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

Download Full-text

Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.16025/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

Rhizosphere Soil ◽

Photosynthetic Capacity ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

Download Full-text

Erosion reduces soil microbial diversity, network complexity and multifunctionality

The ISME Journal ◽

10.1038/s41396-021-00913-1 ◽

2021 ◽

Author(s):

Liping Qiu ◽

Qian Zhang ◽

Hansong Zhu ◽

Peter B. Reich ◽

Samiran Banerjee ◽

...

Keyword(s):

Soil Erosion ◽

Microbial Diversity ◽

Microbial Communities ◽

Negative Impact ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Relative Abundances ◽

The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

Download Full-text

Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

Environmental Research Letters ◽

10.1088/1748-9326/ac444f ◽

2021 ◽

Author(s):

Xinyu Yi ◽

Chen Ning ◽

Shuailong Feng ◽

Haiqiang Gao ◽

Jianlun Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Environmental Changes ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Environmental Drivers ◽

Wetland Soil ◽

Rrna Gene ◽

Soil Microbial ◽

Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

Download Full-text

Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest

PeerJ ◽

10.7717/peerj.7631 ◽

2019 ◽

Vol 7 ◽

pp. e7631 ◽

Cited By ~ 3

Author(s):

Yong Li ◽

Dashuan Tian ◽

Jinsong Wang ◽

Shuli Niu ◽

Jing Tian ◽

...

Keyword(s):

Species Richness ◽

Bacterial Community ◽

Community Composition ◽

Fungal Community ◽

Bacterial Community Composition ◽

Shannon Index ◽

Subtropical Forest ◽

Fungal Community Composition ◽

Soil Bacterial ◽

P Addition

Atmospheric nitrogen (N) deposition and phosphorus (P) addition both can change soil bacterial and fungal community structure with a consequent impact on ecosystem functions. However, which factor plays an important role in regulating responses of bacterial and fungal community to N and P enrichments remains unclear. We conducted a manipulative experiment to simulate N and P inputs (10 g N · m−2 · yr−1 NH4NO3 or 10 g P · m−2 · yr−1 NaH2PO4) and compared their effects on soil bacterial and fungal species richness and community composition. The results showed that the addition of N significantly increased NH4+ and Al3+ by 99.6% and 57.4%, respectively, and consequently led to a decline in soil pH from 4.18 to 3.75 after a 5-year treatment. P addition increased Al3+ and available P by 27.0% and 10-fold, respectively, but had no effect on soil pH. N addition significantly decreased bacterial species richness and Shannon index and resulted in a substantial shift of bacterial community composition, whereas P addition did not. Neither N nor P addition changed fungal species richness, Shannon index, and fungal community composition. A structural equation model showed that the shift in bacterial community composition was related to an increase in soil acid cations. The principal component scores of soil nutrients showed a significantly positive relationship with fungal community composition. Our results suggest that N and P additions affect soil bacterial and fungal communities in different ways in subtropical forest. These findings highlight how the diversity of microbial communities of subtropical forest soil will depend on future scenarios of anthropogenic N deposition and P enrichment, with a particular sensitivity of bacterial community to N addition.

Download Full-text

Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.10288/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Bacterial Community Composition ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress influences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: OJ was more shade-tolerant than LP. Shifts in rhizosphere soil bacterial community structure play a vital role in shade-tolerance of OJ plants.

Download Full-text

The Growth of Plants and Indigenous Bacterial Community Were Significantly Affected by Cadmium Contamination in Soil-Plant System

10.21203/rs.3.rs-181936/v1 ◽

2021 ◽

Author(s):

Yunyan Du ◽

Dawei Zhang ◽

Dinggang Zhou ◽

Lili Liu ◽

Jinfeng Wu ◽

...

Keyword(s):

Heavy Metals ◽

Bacterial Community ◽

Oilseed Rape ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Ecosystem Functions ◽

Plant System ◽

Α Diversity ◽

Soil Bacterial ◽

The Impact

Abstract Concentrations of heavy metals continue to increase in soil environments as a result of both anthropogenic activities and natural processes. Cadmium (Cd) is one of the most toxic heavy metals and poses health risks to both humans and the ecosystem. Herein, we explore the impacts of Cd on a soil-plant system composed of oilseed rape (Brassica napus and Brassica juncea) and bacteria. The two species of oilseed rape displayed a similar variation trend under Cd treatment. Cd accumulation within plant tissues enhanced with increasing concentrations of Cd in soils, and Cd treatment decreased chlorophyll content and suppressed plant growth. Meanwhile, Cd stress induced the changes of antioxidative enzymes activities including elevating SOD and POD activities and reducing CAT activity. The impact of Cd on the bacterial communities of soils was greater than bacterial communities of plants (phyllosphere and endophyte). The α-diversity of bacterial community in soils declined significantly under higher Cd concentration (30 mg/kg). In addition, soil bacterial communities composition and structure were altered in the presence of higher Cd concentration. Meanwhile, the bacterial community of bulk soil was significantly correlated with Cd, while the variation of rhizosphere soil bacterial community was markedly correlated with Cd and other environmental factors of both soils and plants. These results suggested that Cd could affect both the growth of plants and the indigenous bacterial community in soil-plant system, which might further change ecosystem functions in soils.

Download Full-text

The Effects of Pavement Types on Soil Bacterial Communities across Different Depths

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16101805 ◽

2019 ◽

Vol 16 (10) ◽

pp. 1805 ◽

Cited By ~ 1

Author(s):

Weiwei Yu ◽

Yinhong Hu ◽

Bowen Cui ◽

Yuanyuan Chen ◽

Xiaoke Wang

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Shannon Index ◽

Soil Bacterial Community ◽

Total Carbon ◽

Bacterial Composition ◽

Soil Bacterial ◽

Micro Organisms

Pavements have remarkable effects on topsoil micro-organisms, but it remains unclear how subsoil microbial communities respond to pavements. In this study, ash trees (Fraxinus Chinensis) were planted on pervious pavement (PP), impervious pavement (IPP), and non-pavement (NP) plots. After five years, we determined the soil bacterial community composition and diversity by high-throughput sequencing of the bacterial 16S rRNA gene. The results of our field experiment reveal that the presence of pavement changed soil bacterial community composition and decreased the Shannon index, but had no impact on the Chao 1 at the 0–20 cm layer. However, we achieved the opposite result at a depth of 20–80 cm. Furthermore, there was a significant difference in bacterial community composition using the Shannon index and the Chao 1 at the 80–100 cm layer. Soil total carbon (TC), total nitrogen (TN), available phosphorus (AP), NO3−-N, and available potassium (AK) were the main factors that influenced soil bacterial composition and diversity across different pavements. Soil bacterial composition and diversity had no notable difference between PP and IPPs at different soil layers. Our results strongly indicate that pavements have a greater impact on topsoil bacterial communities than do subsoils, and PPs did not provide a better habitat for micro-organisms when compared to IPPs in the short term.

Download Full-text