scholarly journals Long-Term Amelioration Practices Reshape the Soil Microbiome in a Coastal Saline Soil and Alter the Richness and Vertical Distribution Differently Among Bacterial, Archaeal, and Fungal Communities

2022 ◽  
Vol 12 ◽  
Author(s):  
Ruibo Sun ◽  
Xiaogai Wang ◽  
Yinping Tian ◽  
Kai Guo ◽  
Xiaohui Feng ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Salinity ◽  
Saline Soil ◽  
Saline Water ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Economic Losses ◽  
Saline Water Irrigation ◽  
Coastal Saline Soil ◽  
Plastic Mulching

Globally soil salinity is one of the most devastating environmental stresses affecting agricultural systems and causes huge economic losses each year. High soil salinity causes osmotic stress, nutritional imbalance and ion toxicity to plants and severely affects crop productivity in farming systems. Freezing saline water irrigation and plastic mulching techniques were successfully developed in our previous study to desalinize costal saline soil. Understanding how microbial communities respond during saline soil amelioration is crucial, given the key roles soil microbes play in ecosystem succession. In the present study, the community composition, diversity, assembly and potential ecological functions of archaea, bacteria and fungi in coastal saline soil under amelioration practices of freezing saline water irrigation, plastic mulching and the combination of freezing saline water irrigation and plastic mulching were assessed through high-throughput sequencing. These amelioration practices decreased archaeal and increased bacterial richness while leaving fungal richness little changed in the surface soil. Functional prediction revealed that the amelioration practices, especially winter irrigation with saline water and film mulched in spring, promoted a community harboring heterotrophic features. β-null deviation analysis illustrated that amelioration practices weakened the deterministic processes in structuring coastal saline soil microbial communities. These results advanced our understanding of the responses of the soil microbiome to amelioration practices and provided useful information for developing microbe-based remediation approaches in coastal saline soils.

Diversity of Soil Microbial Communities under Different Soil Salinity Levels Analyzing by PLFA

2014 ◽  
Vol 955-959 ◽  
pp. 314-320 ◽  
Author(s):  
Xin Li ◽  
Yan Jiao ◽  
Ming De Yang
Keyword(s):  
Microbial Communities ◽  
Soil Salinity ◽  
Saline Soil ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Salinity Levels ◽  
Salinized Soil ◽  
Soil Microbial Composition

Under different soil salinity levels, diversity of soil microbial communities from Hetao irrigated land of Inner Mongolia was studied by phospholipid fatty acid (PLFA) analysis. The study found that PLFAs biomass in saline soil was significantly lower than those of strongly salinized soil and slight salinized soil. Microbes was bacteria-based from these soil. The bacterial PLFA loading in saline soil is significantly less than those of strongly salinized soil and slight salinized soil . Cluster analysis showed that changes had obviously taken place on soil microbial composition and quantity under different soil salinity levels.About 76.89% of variation in PLFA patterns explained by PC1(the first  principal components),and 17:1, 16:0, 18:1w9c, 18:1w9t, 18:2, 18:3w3c, 12:0 were strongly negatively correlated with PC1.However,soil salinity and pH were positively correlated with PC1.We conclude that soil salinity has  a profound affect on the microbial community structure.

scholarly journals Response of Symphyotrichum novi-belgii and Dianthus chinensis L. to saline water irrigation in a coastal saline soil

2016 ◽  
Vol 203 ◽  
pp. 32-37 ◽  
Author(s):  
Xiaobin Li ◽  
Yaohu Kang ◽  
Shuqin Wan ◽  
Xiulong Chen ◽  
Jiachong Xu
Keyword(s):  
Saline Soil ◽  
Saline Water ◽  
Saline Water Irrigation ◽  
Coastal Saline Soil

scholarly journals Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Chengyuan Tao ◽  
Rong Li ◽  
Wu Xiong ◽  
Zongzhuan Shen ◽  
Shanshan Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Pathogens ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Plant Diseases ◽  
Disease Suppression ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Soil Microbial ◽  
Bioorganic Fertilizer

Abstract Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

scholarly journals Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Shuo Jiao ◽  
Weimin Chen ◽  
Gehong Wei
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Chemical Contamination ◽  
Plant Interactions ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Microbial Responses ◽  
Legume Plants ◽  
Functional Profiles

ABSTRACT A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion. IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.

scholarly journals Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba

2020 ◽  
Vol 4 (2) ◽  
pp. 142-155 ◽  
Author(s):  
L. Mangeot-Peter ◽  
T. J. Tschaplinski ◽  
N. L. Engle ◽  
C. Veneault-Fourrey ◽  
F. Martin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mycorrhizal Fungi ◽  
Root Colonization ◽  
Soil Microbial Communities ◽  
Populus Tremula ◽  
Soil Microbiome ◽  
Gas Chromatography Mass Spectrometry ◽  
Natural Soil ◽  
Tree Roots ◽  
Natural Variations

Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × alba clone 717-1B4) in natural soil taken from a poplar stand under the same tree over two consecutive years and grew them in a greenhouse. We analyzed the soil and root microbiomes by high throughput Illumina MiSeq sequencing of fungal rDNA internal transcribed spacer and bacterial 16S rRNA amplicons and we characterized the root metabolome by gas chromatography-mass spectrometry. Soil and root microbial communities significantly shifted over the 2 years. A modification of the balance between endophytes, saprophytes, and mycorrhizal fungi occurred in the roots as well as a replacement of some dominant operational taxonomic units by others. These modifications were correlated with a significant alteration of the levels of about 10% of primary and secondary metabolites, suggesting that natural fluctuations in soil microbial communities can have a profound impact on tree root metabolism and physiology. Tree roots functioning may thus be indirectly strongly affected by the effects of future extreme climatic variations on the soil microbiome.

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