Core microbiota drive functional stability of soil microbiome in reforestation ecosystems

Background: Nε-acetyl L-α lysine is an unusual acetylated di-amino acid synthesized and accumulated by certain halophiles under osmotic stress. Osmolytes are generally known to protect proteins and other cellular components under various stress conditions. Objective: The structural and functional stability imparted by Nε-acetyl L-lysine on proteins were unknown and hence was studied and compared to other commonly known bacterial osmolytes - ectoine, proline, glycine betaine, trehalose and sucrose. Methods: Effects of osmolytes on the temperature and pH profiles, pH stability and thermodynamic stability of the model enzyme, α-amylase were analyzed. Results: At physiological pH, all the osmolytes under study increased the optimal temperature for enzyme activity and improved the thermodynamic stability of the enzyme. At acidic conditions (pH 3.0), Nε-acetyl L-α lysine and ectoine improved both the catalytic and thermodynamic stability of the enzyme; it was reflected in the increase in residual enzyme activity after incubation of the enzyme at pH 3.0 for 15 min by 60% and 63.5% and the midpoint temperature of unfolding transition by 11°C and 10°C respectively. Conclusion: Such significant protective effects on both activity and stability of α-amylase imparted by addition of Nε-acetyl L-α lysine and ectoine at acidic conditions make these osmolytes interesting candidates for biotechnological applications.

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Soil microbiome response to land application of wastewater treatment biosolids

Proceedings of the Water Environment Federation ◽

10.2175/193864718824828920 ◽

2018 ◽

Vol 2018 (4) ◽

pp. 850-863

Author(s):

Kevin Lambirth ◽

Jean Creech ◽

Cynthia Gibas

Keyword(s):

Wastewater Treatment ◽

Land Application ◽

Soil Microbiome

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Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab031 ◽

2021 ◽

Author(s):

Alicia Balbín-Suárez ◽

Samuel Jacquiod ◽

Annmarie-Deetja Rohr ◽

Benye Liu ◽

Henryk Flachowsky ◽

...

Keyword(s):

Gene Expression ◽

Plant Defense ◽

Defense Response ◽

Soil Column ◽

Soil Layer ◽

Soil Microbiome ◽

Control Soil ◽

Apple Rootstocks ◽

Apple Replant Disease ◽

Replant Disease

Abstract A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD) causing agents to spread in soil. ‘M26’ apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of OTUs affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production, and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.

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Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

Microorganisms ◽

10.3390/microorganisms9081638 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1638

Author(s):

Shashika S. Hewavitharana ◽

Emmi Klarer ◽

Joji Muramoto ◽

Carol Shennan ◽

Mark Mazzola

Keyword(s):

Disease Control ◽

Fusarium Wilt ◽

Environmental Variables ◽

Incubation Temperature ◽

Soil Microbiome ◽

Charcoal Rot ◽

Soil Disinfestation ◽

Anaerobic Soil Disinfestation ◽

Input Type ◽

Incubation Duration

Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using ‘low rate’ amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha−1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols.

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Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils

Microorganisms ◽

10.3390/microorganisms9061273 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1273

Author(s):

Nazareth Torres ◽

Runze Yu ◽

S. Kaan Kurtural

Keyword(s):

Mycorrhizal Fungi ◽

Time Course ◽

Management Practices ◽

Irrigation Management ◽

Fungal Communities ◽

Soil Microbiome ◽

Wine Quality ◽

Network Analyses ◽

Vineyard Soil ◽

Vineyard Soils

Vineyard-living microbiota affect grapevine health and adaptation to changing environments and determine the biological quality of soils that strongly influence wine quality. However, their abundance and interactions may be affected by vineyard management. The present study was conducted to assess whether the vineyard soil microbiome was altered by the use of biostimulants (arbuscular mycorrhizal fungi (AMF) inoculation vs. non-inoculated) and/or irrigation management (fully irrigated vs. half irrigated). Bacterial and fungal communities in vineyard soils were shaped by both time course and soil management (i.e., the use of biostimulants and irrigation). Regarding alpha diversity, fungal communities were more responsive to treatments, whereas changes in beta diversity were mainly recorded in the bacterial communities. Edaphic factors rarely influence bacterial and fungal communities. Microbial network analyses suggested that the bacterial associations were weaker than the fungal ones under half irrigation and that the inoculation with AMF led to the increase in positive associations between vineyard-soil-living microbes. Altogether, the results highlight the need for more studies on the effect of management practices, especially the addition of AMF on cropping systems, to fully understand the factors that drive their variability, strengthen beneficial microbial networks, and achieve better soil quality, which will improve crop performance.

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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

Microorganisms ◽

10.3390/microorganisms9071400 ◽

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.

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Cooperation among phosphate-solubilizing bacteria, humic acids and arbuscular mycorrhizal fungi induces soil microbiome shifts and enhances plant nutrient uptake

Chemical and Biological Technologies in Agriculture ◽

10.1186/s40538-021-00230-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Vincenza Cozzolino ◽

Hiarhi Monda ◽

Davide Savy ◽

Vincenzo Di Meo ◽

Giovanni Vinci ◽

...

Keyword(s):

Microbial Community ◽

Arbuscular Mycorrhizal Fungi ◽

Humic Acids ◽

Mycorrhizal Fungi ◽

Soil Microorganisms ◽

Microbial Community Composition ◽

Arbuscular Mycorrhizal ◽

Soil Microbiome ◽

Phosphate Solubilizing Bacteria ◽

Saprotrophic Fungi

Abstract Background Increasing the presence of beneficial soil microorganisms is a promising sustainable alternative to support conventional and organic fertilization and may help to improve crop health and productivity. If the application of single bioeffectors has shown satisfactory results, further improvements may arise by combining multiple beneficial soil microorganisms with natural bioactive molecules. Methods In the present work, we investigated in a pot experiment under greenhouse conditions whether inoculation of two phosphate-solubilizing bacteria, Pseudomonas spp. (B2) and Bacillus amyloliquefaciens (B3), alone or in combination with a humic acids (HA) extracted from green compost and/or a commercial inoculum (M) of arbuscular mycorrhizal fungi (AMF), may affect maize growth and soil microbial community. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis were performed to detect changes in the microbial community composition. Results Plant growth, N and P uptake, and mycorrhizal root colonization were found to be larger in all inoculated treatments than in the uninoculated control. The greatest P uptake was found when B. amyloliquefaciens was applied in combination with both HA and arbuscular mycorrhizal fungi (B3HAM), and when Pseudomonas was combined with HA (B2HA). The PLFA-based community profile revealed that inoculation changed the microbial community composition. Gram+/Gram− bacteria, AMF/saprotrophic fungi and bacteria/fungi ratios increased in all inoculated treatments. The greatest values for the AMF PLFA marker (C16:1ω5) and AMF/saprotrophic fungi ratio were found for the B3HAM treatment. Permutation test based on DGGE data confirmed a similar trend, with most significant variations in both bacterial and fungal community structures induced by inoculation of B2 or B3 in combination with HA and M, especially in B3HAM. Conclusions The two community-based datasets indicated changes in the soil microbiome of maize induced by inoculation of B2 or B3 alone or when combined with humic acids and mycorrhizal inoculum, leading to positive effects on plant growth and improved nutrient uptake. Our study implies that appropriate and innovative agricultural management, enhancing the potential contribution of beneficial soil microorganisms as AMF, may result in an improved nutrient use efficiency in plants.

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Assessing Soil Health: Measuring the Soil Microbiome

Crops & Soils ◽

10.1002/crso.20099 ◽

2021 ◽

Vol 54 (2) ◽

pp. 32-35

Author(s):

Elizabeth Rieke ◽

Shannon Cappellazzi

Keyword(s):

Soil Health ◽

Soil Microbiome

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Soil gas probes for monitoring trace gas messengers of microbial activity

Scientific Reports ◽

10.1038/s41598-021-86930-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Joseph R. Roscioli ◽

Laura K. Meredith ◽

Joanne H. Shorter ◽

Juliana Gil-Loaiza ◽

Till H. M. Volkmann

Keyword(s):

Microbial Activity ◽

Soil Heterogeneity ◽

Soil Gas ◽

Microbial Processes ◽

Trace Gas ◽

Soil Microbiome ◽

Sampling System ◽

Site Specific ◽

Gas Measurements ◽

Subsurface Monitoring

AbstractSoil microbes vigorously produce and consume gases that reflect active soil biogeochemical processes. Soil gas measurements are therefore a powerful tool to monitor microbial activity. Yet, the majority of soil gases lack non-disruptive subsurface measurement methods at spatiotemporal scales relevant to microbial processes and soil structure. To address this need, we developed a soil gas sampling system that uses novel diffusive soil probes and sample transfer approaches for high-resolution sampling from discrete subsurface regions. Probe sampling requires transferring soil gas samples to above-ground gas analyzers where concentrations and isotopologues are measured. Obtaining representative soil gas samples has historically required balancing disruption to soil gas composition with measurement frequency and analyzer volume demand. These considerations have limited attempts to quantify trace gas spatial concentration gradients and heterogeneity at scales relevant to the soil microbiome. Here, we describe our new flexible diffusive probe sampling system integrated with a modified, reduced volume trace gas analyzer and demonstrate its application for subsurface monitoring of biogeochemical cycling of nitrous oxide (N2O) and its site-specific isotopologues, methane, carbon dioxide, and nitric oxide in controlled soil columns. The sampling system observed reproducible responses of soil gas concentrations to manipulations of soil nutrients and redox state, providing a new window into the microbial response to these key environmental forcings. Using site-specific N2O isotopologues as indicators of microbial processes, we constrain the dynamics of in situ microbial activity. Unlocking trace gas messengers of microbial activity will complement -omics approaches, challenge subsurface models, and improve understanding of soil heterogeneity to disentangle interactive processes in the subsurface biome.

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