scholarly journals Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol

2019 ◽  
Vol 6 (1) ◽  
pp. 181054
Author(s):  
Zhenhua Yu ◽  
Jian Jin ◽  
Yansheng Li ◽  
Yue Yang ◽  
Yue Zhao ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Crop Productivity ◽  
Soya Bean ◽  
Soil Microbial ◽  
Topsoil Layer

Eroded black soils (classified as Mollisols) lead to a thinner topsoil layer, reduced organic carbon storage and declined crop productivity. Understanding the changes in soil microbial communities owing to soil erosion is of vital importance as soil microbial communities are sensitive indicators of soil condition and are essential in soil nutrient cycling. This study used the reconstructed facility with 10, 20 and 30 cm topsoil thickness under no-till soya bean–corn rotation in black soil region of Northeast China. Illumina MiSeq sequencing targeting 16S rRNA, q PCR and soil respiration measurement were performed to assess the changes in soya bean and corn rhizosphere bacterial communities, as well as their abundance and activities due to the topsoil thickness. The results showed that soil bacterial communities from both soya bean and corn were more sensitive to topsoil removal than to soil biogeochemical characteristics. Topsoil depths significantly influenced both soya bean and corn bacterial communities, while they only significantly influenced the bacterial abundance and respiration in corn. We also found that the topsoil depths significantly induced the changes in phyla and genera from both soya bean and corn rhizosphere bacterial community, which aid further understandings on how topsoil layer influences the global nutrient cycling of Mollisols by influencing the change in microbial communities.

Alleviating Continuous Monocropping Obstacle in Melon: Biological Elimination of Phenolic Acid

2020 ◽  
Author(s):  
Huiqin Xie ◽  
Yongli Ku ◽  
Xiangna Yang ◽  
Le Cao ◽  
Xueli Mei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Phenolic Acids ◽  
Fruit Quality ◽  
High Performance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Soil Microbial

Abstract Background: Melon (Cucumis melo L.) is one of the most important fruit crops grown in China. However, the yield and quality of melon have significantly declined under continuous cropping. Phenolic acids are believed to be associated with the continuous monocropping obstacle (CMO) and can influence plant microbe interactions. Coumaric acid (CA) is one of the major phenolic acids found in melon root exudates. The objectives of this study were to estimate the elimination of CA by the soil bacterium K3 as well as its effects on mitigating melon CMO. CA degradation was investigated by monitoring the CA retained in the growth medium using high performance liquid chromatography (HPLC). The effects of CA and K3 on rhizosphere soil microbial communities were investigated by the spread plate method and Illumina MiSeq sequencing. Furthermore, the effects of CA and K3 on melon seedling growth were measured under potted conditions. The changes in soil enzymes and fruit quality under K3 amendment were examined in a greenhouse experiment. Result:The results suggest that the addition of CA had the same result as the CMO, such as deterioration of the microbial community and slower growth of melon plants. HPLC and microbial analysis showed that K3 had a pronounced ability to decompose CA and could improve the soil microbial community environment. Soil inoculation with K3 agent could significantly improve the fruit quality of melon.Conclusion: Our results show that the effects of K3 in the soil are reflected by changes in populations and diversity of soil microbes and suggest that deterioration of microbial communities in soil might be associated with the growth constraint of melon in continuous monoculture systems.

scholarly journals The relative importance of rapid evolution for plant-microbe interactions depends on ecological context

2014 ◽  
Vol 281 (1785) ◽  
pp. 20140028 ◽  
Author(s):  
Casey P. terHorst ◽  
Jay T. Lennon ◽  
Jennifer A. Lau
Keyword(s):  
Microbial Communities ◽  
Bacterial Abundance ◽  
Rapid Evolution ◽  
Soil Microbial Communities ◽  
Ecological Effect ◽  
Ecological Context ◽  
Ecological Processes ◽  
Soil Microbial ◽  
Long Term Experiment ◽  
Microbe Interactions

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant–microbe interactions.

scholarly journals Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

2021 ◽  
Author(s):  
Jing Zhang ◽  
Peter G.L. Klinkhamer ◽  
Klaas Vrieling ◽  
T. Martijn Bezemer
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Signaling Pathway ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Core Microbiome ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

scholarly journals Extreme drought triggers transition to an alternative soil microbial state

2021 ◽  
Author(s):  
Irene Cordero ◽  
Ainara Leizeaga ◽  
Lettice C Hicks ◽  
Johannes Rousk ◽  
Richard D Bardgett
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Climate Extremes ◽  
Extreme Drought ◽  
Alternative States ◽  
Soil Microbial ◽  
Fungal Community Structure ◽  
Functional States

Soil microbial communities play a pivotal role in regulating ecosystem functioning but they are increasingly threatened by human-driven perturbations, including climate extremes, which are predicted to increase in frequency and intensity with climate change. It has been demonstrated that soil microbial communities are sensitive to climate extremes, such as drought, and that effects can be long-lasting. However, considerable uncertainties remain concerning the response of soil microbial communities to increases in the intensity and frequency of climate extremes, and their potential to trigger transitions to alternative, and potentially deleterious, taxonomic and functional states. Here we demonstrate that extreme, frequent drought induces a shift to an alternative soil microbial state characterised by strongly altered bacterial and fungal community structure of reduced complexity and functionality. Moreover, we found that this drought-induced alternative microbial state persisted after returning soil to its previous moisture status. However, bacterial communities were able to adapt by increasing their growth capacity, despite being of reduced diversity. Abrupt transitions to alternative states are well documented in aquatic and terrestrial plant communities in response to human-induced perturbations, including climate extremes. Our results provide experimental evidence that such transitions also occur in soil microbial communities in response to extreme drought with potentially deleterious consequences for soil health.

Peanut/Cotton Intercropping Increases Productivity and Economic Returns by Regulating Nutrient Accumulation and Soil Microbial Communities Under both Normal and Saline Soil Conditions

2021 ◽  
Author(s):  
Wei Xie ◽  
Kai Zhang ◽  
Xiaoying Wang ◽  
Xiaoxia Zou ◽  
Xiaojun Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Crop Yield ◽  
Bacterial Abundance ◽  
Saline Soil ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Nutrient Accumulation ◽  
Economic Returns ◽  
Soil Microbial ◽  
Functional Features

Abstract Background Intercropping has been widely adopted by farmers for it often enhances crop productivity and economic returns; however, the underpinning mechanisms from the perspective of belowground interspecific interactions are only partly understood especially when intercropping under saline soil conditions. By using permeable (100 µm) and impermeable (solid) root barriers in a multi-site field experiment, we aimed to study the impact of root-root interactions on nutrient accumulation, soil microbial communities, crop yield, and economic returns in a peanut/cotton intercropping system under non-saline, secondary-saline, and coastal saline soil conditions. Results The results indicate that intercropping (IC) decreased the peanut pods yield while increased the seed cotton yield, and consequently enhanced the economic returns compared with monoculture of peanut (MP) and cotton (MC). The higher accumulations of nutrients such as nitrogen (N), phosphorus (P), and potassium (K) were also observed in IC not only in the soil but also in vegetative tissues and reproductive organs. Bacterial community structure analysis under normal growth conditions reveals that IC dramatically altered the soil bacterial abundance composition in both peanut and cotton strips of the top soil whereas the bacterial diversity was barely affected compared with MP and MC. At blossom-needling stage, the metabolic functional features of the bacterial communities such as fatty acid biosynthesis, lipoic acid metabolism, peptidoglycan biosynthesis, and biosynthesis of ansamycins were significantly enriched in MP compared with other treatments. Conversely, these metabolic functional features were dramatically depleted in MP while significantly enriched in IC at podding stage. Permeable root barrier treatments (NC-P and NC-C) counteracted the benefits of IC and the side effects were more pronounced in impermeable treatments (SC-P and SC-C). Conclusion Peanut/cotton intercropping increases crop yield as well as economic returns under non-saline, secondary-saline, and coastal saline soil conditions probably by modulating the soil bacterial abundance composition and accelerating nutrients accumulation.

scholarly journals Diversity and Structural Variability of Bacterial Microbial Communities in Rhizocompartments of Desert Leguminous Plants

2020 ◽  
Author(s):  
Ziyuan Zhou ◽  
Guodong Ding ◽  
Minghan Yu ◽  
Guanglei Gao ◽  
Genzhu Wang
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Plants ◽  
Soil Microbial Communities ◽  
Niche Differentiation ◽  
Leguminous Plant ◽  
Leguminous Plants ◽  
Soil Microbial ◽  
The Core ◽  
Structural Variability

ABSTRACTBy assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural variability of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants had significant effects on the enrichment and filtration of specific bacterial microbiomes across different rhizocompartments (P<0.05). The core bacterial microbiomes causing structure and composition variability of bacterial communities across different niches of desert leguminous plants are also identified. By investigating the influence of niches on the structural variability of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.IMPORTANCEColonization by plant communities make valued contribution to sand-fixing in poor ecological desert environments, thereby reducing the effects of wind erosion in these areas. Our study revealed that specific core bacterial microbiomes in under-shrub soil microbial communities had a significant hierarchical enrichment effect among rhizocompartments, and were filtered into roots. The root endophyte microbiomes thus formed had low abundance and diversity, but their structural variability was the highest. In addition, our data also verified that the rhizocompartments of under desert leguminous plant shrubs had a significant differentiation effect for the core bacterial microbiomes enriched and filtered by host plants, and that each rhizocompartment represented a unique niche of bacterial communities. Understanding the interactions between xeric shrubs and soil microbial communities is a fundamental step for describing desert soil ecosystems, which in turn can offer a microbe-associated reference for evaluating the restoration of desert vegetation.

scholarly journals Investigating the drought-prone biological interplay of soil microbial communities and Scots pine trees 

2021 ◽  
Author(s):  
Astrid Jäger ◽  
Martin Hartmann ◽  
Frank Hagedorn ◽  
Johan Six ◽  
Emily Solly
Keyword(s):  
Nutrient Cycling ◽  
Microbial Communities ◽  
Scots Pine ◽  
Tree Mortality ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Tree Vitality ◽  
Soil Microbial ◽  
Pine Trees ◽  
Effects Of Drought

&lt;p&gt;In forest ecosystems, microorganisms hold key functions as nutrient cyclers, decomposers, plant symbionts or pathogens and thereby regulate biogeochemical processes and forest health. These microbial dynamics are controlled by water availability in three fundamental ways: as resource, as solvent, and as transport medium. For one of the dominant tree species in Swiss forests - Scots pine (Pinus sylvestris L.) - high mortality rates have been observed in recent decades. In the Rhone valley of Switzerland, forest dieback appears to be primarily caused by direct effects of drought and an increasing susceptibility of trees to further constraints, such as pathogen attacks. Nonetheless, water limitation does not affect soil microbes and trees separately but rather induces a series of interconnected effects between trees and the associated soil microbiome, which could strongly alter carbon and nutrient cycling in forests. We conduct a study to investigate the effects of drought on the biological interplay between Scots pine trees and soil microbial communities. We aim to estimate how shifts in microbial community composition and functional capacity under drought may affect nutrient cycling and tree vitality potentially contributing to tree mortality. In order to understand these mechanisms, we perform greenhouse experiments with tree-soil mesocosms under controlled conditions. State-of-the art molecular methods such as metabarcoding of ribosomal markers, shotgun metagenome sequencing, and qPCR of key functional genes are used to unravel alterations in the soil microbiome and in the underlying functional metabolic potential related to drought and associated tree-mortality. Furthermore, to elucidate the impact of drought on microbial carbon dynamics, stable isotope labelling techniques have been applied to trace &lt;sup&gt;13&lt;/sup&gt;C labeled plant photosynthates into the soil microbial communities by analyzing &lt;sup&gt;13&lt;/sup&gt;C signatures of phospholipid fatty acids. Investigation of soil physicochemical properties and tree-vitality is done in parallel with the microbial assessments to understand the feedbacks on nutrient-cycling and the soil-tree continuum. The overarching aim of this study is to gain new insights into the complex relationships between soil, trees and microbes under drought.&lt;/p&gt;

scholarly journals Cover crop-driven shifts in soil microbial communities could modulate tomato early crop growth via plant-soil feedbacks

2021 ◽  
Author(s):  
Micaela Tosi ◽  
John Drummelsmith ◽  
Dasiel Obregón ◽  
Inderjot Chahal ◽  
Laura L. Van Eerd ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Cover Crops ◽  
Cover Crop ◽  
Crop Residues ◽  
Management Strategies ◽  
Soil Microbial Communities ◽  
Crop Productivity ◽  
Residue Management ◽  
Soil Microbial ◽  
Plant Soil

Abstract Sustainable agricultural practices such as crop diversification, cover crops and residue retention are increasingly applied to counteract detrimental effects of agriculture on natural resources. Since part of their effects occur via changes soil microbial communities, it is critical to understand how these respond to different practices. Our study analyzed five cover crop (cc) treatments (oat, rye, radish, rye-radish mixture and no-cc control) and two crop residue management strategies (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. Cc effects were small but stronger than those of residue management. Radish-based cover crops tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. Cc species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated cc effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features, some affected by cc, were correlated with early tomato growth in the following spring (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota). Our study suggests that, whereas mid-term cc effects were small, they need to be better understood as they could be influencing crop productivity via plant-soil feedbacks.

scholarly journals Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

2015 ◽  
Vol 112 (35) ◽  
pp. 10967-10972 ◽  
Author(s):  
Jonathan W. Leff ◽  
Stuart E. Jones ◽  
Suzanne M. Prober ◽  
Albert Barberán ◽  
Elizabeth T. Borer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Metagenomic Data ◽  
Life History Strategies ◽  
Marker Genes ◽  
Nutrient Inputs ◽  
Soil Microbial ◽  
Nutrient Additions ◽  
Relative Abundances

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.

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