scholarly journals Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

2021 ◽  
Author(s):  
Annelein Meisner ◽  
Basten L. Snoek ◽  
Joseph Nesme ◽  
Elizabeth Dent ◽  
Samuel Jacquiod ◽  
...  
Keyword(s):  
Water Availability ◽  
Phase 1 ◽  
Soil Microbial Communities ◽  
Soil Microbial Activity ◽  
Community Response ◽  
Soil Microbiome ◽  
Cycle Phase ◽  
Thawing Cycle ◽  
Soil Microbial ◽  
Microbial Response

AbstractClimate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

scholarly journals Effects of Monoculture, Crop Rotation, and Soil Moisture Content on Selected Soil Physicochemical and Microbial Parameters in Wheat Fields

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
A. Marais ◽  
M. Hardy ◽  
M. Booyse ◽  
A. Botha
Keyword(s):  
Soil Moisture ◽  
Microbial Communities ◽  
Crop Rotation ◽  
Management Practices ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Soil Microbial Activity ◽  
Most Probable Number ◽  
Probable Number ◽  
Soil Microbial

Different plants are known to have different soil microbial communities associated with them. Agricultural management practices such as fertiliser and pesticide addition, crop rotation, and grazing animals can lead to different microbial communities in the associated agricultural soils. Soil dilution plates, most-probable-number (MPN), community level physiological profiling (CLPP), and buried slide technique as well as some measured soil physicochemical parameters were used to determine changes during the growing season in the ecosystem profile in wheat fields subjected to wheat monoculture or wheat in annual rotation with medic/clover pasture. Statistical analyses showed that soil moisture had an over-riding effect on seasonal fluctuations in soil physicochemical and microbial populations. While within season soil microbial activity could be differentiated between wheat fields under rotational and monoculture management, these differences were not significant.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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 The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus

2020 ◽  
Author(s):  
Lanying Ma ◽  
Fernando Igne Rocha ◽  
Jaejin Lee ◽  
Jinlyung Choi ◽  
Mauricio Tejera ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
N Fertilizer ◽  
Soil Microbiome ◽  
Stand Age ◽  
Soil Microbial ◽  
Miscanthus Giganteus

Yield of the perennial grass Miscanthus × giganteus has shown an inconsistent and unpredictable response to nitrogen (N) fertilizer, yet fertilization underpins the crop’s environmental and economic sustainability. The interactions among soil microbial communities, N availability, and M. × giganteus and management may explain changes in plant productivity. In this study, soil samples from different stand ages of M. × giganteus in a replicated chronosequence field trial were used to investigate the effects of stand age and N fertilizer rates on microbial community structure. We hypothesized that there is a definable M. × giganteus soil microbiome and that this community varies significantly with stand age and fertilization. Our results showed that the main phyla in soil microbial communities, regardless of plant age, are similar but microbial community structures are significantly different. The variation in observed microbial communities generally decreases in older stand ages. The amount of N fertilizer applied also affected the microbial community structure associated with different aged M. × giganteus. Specifically, the relative abundance of Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Acidobacteria (Subgroup Gp1) increased shortly after fertilization and were more associated with younger M. × giganteus. Further, our results show a significant relationship between bacterial alpha diversity and fertilization rates and that this response is also impacted by stand age. Overall, our results emphasize linkages between microbial community structure, plant age, and fertilization in M. × giganteus.

scholarly journals Soil Microbial Activity and Diversity in Response to Soil Chemical Factors in Agricultural Soils

2019 ◽  
Vol 24 (1) ◽  
pp. 43
Author(s):  
Lily Ishak ◽  
Philip Hugh Brown
Keyword(s):  
Microbial Communities ◽  
Agricultural Soils ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbial Activity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Microbial Responses ◽  
Chemical Factors ◽  
Microbial Groups

The role of microbial communities in maintaining soil health is mostly influenced by chemical condition of soil. Microbial communities vary in response to soil chemical factors. The contradictive results from previous findings emphasise that it is difficult to define a pattern of the influence of soil chemical factors on soil microbial diversity and activity. The aim of the study was to assess soil microbial responses to soil chemical factors in agricultural soils. Composite soil (Dermosol order) samples taken from 16 commercial crop sites in Bundaberg, Queensland, Australia, were chemically and biologically analysed. It was found that bacterial and fungal activity and diversity were significantly affected by soil EC, SOM and NO3-N content, but were not influenced by soil pH, CEC, and Ca:Mg ratio. The diversity of bacterial and fungal communities displayed a positive linear relationship with soil EC, whereas the activity and diversity of these two microbial groups and SOM displayed a significant quadratic relationship. The finding suggested that microbial community was predominantly influenced by SOM content.

scholarly journals Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills

2021 ◽  
Author(s):  
Eden Zhang ◽  
Paul Czechowski ◽  
Aleks Terauds ◽  
Sin Yin Wong ◽  
Devan S. Chelliah ◽  
...  
Keyword(s):  
Rank Order ◽  
Soil Microbial Communities ◽  
Biodiversity Loss ◽  
Ecosystem Dynamics ◽  
Soil Microbiome ◽  
Successful Implementation ◽  
Predictive Capacity ◽  
Forest Modelling ◽  
Soil Microbial ◽  
Vestfold Hills

AbstractMicroorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing >17, 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial diversity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or “splits” occurring within the 10 – 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of biodiversity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.

scholarly journals Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Taniya Roy Chowdhury ◽  
Joon-Yong Lee ◽  
Eric M. Bottos ◽  
Colin J. Brislawn ◽  
Richard Allen White ◽  
...  
Keyword(s):  
Climate Change ◽  
United States ◽  
Soil Moisture ◽  
Metabolic Pathways ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Microbiome ◽  
Soil Drying ◽  
Soil Microbial ◽  
And Function

ABSTRACT Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies. IMPORTANCE Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community’s metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.

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.

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