scholarly journals SOILomics; where Microbiome Genetics meets Precision Agriculture

2021 ◽  
Vol 26 ◽  
pp. e940
Author(s):  
Dimitrios Vlachakis ◽  
Aspasia Efthimiadou
Keyword(s):  
Climate Change ◽  
Precision Agriculture ◽  
Management Practices ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
New Techniques ◽  
New Era ◽  
Soil Microbial ◽  
Soil Biochemistry

Advances in genetics, soil biochemistry and microbiome analysis are opening up a new era in Precision Agriculture. In this direction, new techniques bring groundbreaking changes in land management practices through direct or indirect management of soil microbial communities. There is huge demand for the protection and enhancement of soil health and climate change resilience of crops. The increase in population, food consumption and fast approaching climate change pose a new threat to mankind that only by being proactive and highly prepared to deploy all novel and innovative stratagems in state-of-the-art soil microbiome precision agriculture can be avoided.

scholarly journals SOILomics; where Microbiome Genetics meets Precision Agriculture

2021 ◽  
Vol 26 (1) ◽  
pp. e943
Author(s):  
Dimitrios Vlachakis ◽  
Aspasia Efthimiadou
Keyword(s):  
Climate Change ◽  
Precision Agriculture ◽  
Management Practices ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
New Techniques ◽  
New Era ◽  
Soil Microbial ◽  
Soil Biochemistry

Advances in genetics, soil biochemistry and microbiome analysis are opening up a new era in Precision Agriculture. In this direction, new techniques bring groundbreaking changes in land management practices through direct or indirect management of soil microbial communities. There is huge demand for the protection and enhancement of soil health and climate change resilience of crops. The increase in population, food consumption and fast approaching climate change pose a new threat to mankind that only by being proactive and highly prepared to deploy all novel and innovative stratagems in state-of-the-art soil microbiome precision agriculture can be avoided.

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 Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7839 ◽  
Author(s):  
Yichao Yang ◽  
Amanda J. Ashworth ◽  
Jennifer M. DeBruyn ◽  
Cammy Willett ◽  
Lisa M. Durso ◽  
...  
Keyword(s):  
Poultry Litter ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Cattle Manure ◽  
Soil Microbiome ◽  
Pasture Management ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.

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 Continuous monocropping highly affect the composition and diversity of microbial communities in peanut (Arachis hypogaea L.)

2021 ◽  
Vol 49 (4) ◽  
pp. 12532
Author(s):  
Ali I. MALLANO ◽  
Xianli ZHAO ◽  
Yanling SUN ◽  
Guangpin JIANG ◽  
Huang CHAO
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Rhizosphere Soil ◽  
Diversity Index ◽  
Cropping Systems ◽  
Soil Microbial Communities ◽  
Pathogenic Fungi ◽  
Continuous Cropping ◽  
Bacterial Phyla ◽  
Soil Microbial

Continuous cropping systems are the leading cause of decreased soil biological environments in terms of unstable microbial population and diversity index. Nonetheless, their responses to consecutive peanut monocropping cycles have not been thoroughly investigated. In this study, the structure and abundance of microbial communities were characterized using pyrosequencing-based approach in peanut monocropping cycles for three consecutive years. The results showed that continuous peanut cultivation led to a substantial decrease in soil microbial abundance and diversity from initial cropping cycle (T1) to later cropping cycle (T3). Peanut rhizosphere soil had Actinobacteria, Protobacteria, and Gemmatimonadetes as the major bacterial phyla. Ascomycota, Basidiomycota were the major fungal phylum, while Crenarchaeota and Euryarchaeota were the most dominant phyla of archaea. Several bacterial, fungal and archaeal taxa were significantly changed in abundance under continuous peanut cultivation. Bacterial orders, Actinomycetales, Rhodospirillales and Sphingomonadales showed decreasing trends from T1>T2>T3. While, pathogenic fungi Phoma was increased and beneficial fungal taxa Glomeraceae decreased under continuous monocropping. Moreover, Archaeal order Nitrososphaerales observed less abundant in first two cycles (T1&T2), however, it increased in third cycle (T3), whereas, Thermoplasmata exhibit decreased trends throughout consecutive monocropping. Taken together, we have shown the taxonomic profiles of peanut rhizosphere communities that were affected by continuous peanut monocropping. The results obtained from this study pave ways towards a better understanding of the peanut rhizosphere soil microbial communities in response to continuous cropping cycles, which could be used as bioindicator to monitor soil quality, plant health and land management practices.

scholarly journals Identification and characterization of proteins, lipids, and metabolites in two organic fertilizer products derived from different nutrient sources

2021 ◽  
Vol 64 (1) ◽  
Author(s):  
Jianyu Li ◽  
Xin Zhao ◽  
Laura S. Bailey ◽  
Manasi N. Kamat ◽  
Kari B. Basso
Keyword(s):  
Biochemical Composition ◽  
Organic Fertilizer ◽  
Saturated Fatty Acids ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Organic Fertilizers ◽  
Vegetable Production ◽  
Limited Information ◽  
Nutrient Sources ◽  
Soil Microbial

AbstractThe biochemical composition of organic fertilizers largely determines their nutrient supply characteristics following soil application as well as their potential impact on soil microbial communities. Yet, limited information is available regarding the biochemical composition of organic fertilizers derived from different nutrient sources. Here, we qualitatively analyzed the presence and abundance of proteins, lipids, and metabolites in a liquid fish fertilizer (LFF) product and a type of granular organic fertilizer (GOF) commonly used in organic vegetable production, using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Our results suggest that the presence and abundance of proteins, lipids, and metabolites differ greatly between GOF and LFF. The qualitative analysis shows LFF as a rich source of metabolites, while complex proteins and long-chain saturated fatty acids are dominant in GOF. The degree of biochemical composition complexity may help explain the varying impacts of different types of organic fertilizers on nutrient availability, soil health, and environmental quality.

scholarly journals Plant genotype controls wetland soil microbial functioning in response to sea-level rise

2021 ◽  
Vol 18 (23) ◽  
pp. 6133-6146
Author(s):  
Hao Tang ◽  
Susanne Liebner ◽  
Svenja Reents ◽  
Stefanie Nolte ◽  
Kai Jensen ◽  
...  
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Microbial Community ◽  
Sea Level Rise ◽  
Sea Level ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
Litter Breakdown ◽  
Plant Genotype ◽  
Soil Microbial

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

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