Metagenomic Bioprospecting of Uncultivable Microbial Flora in Soil Microbiome for Novel Enzymes

Various concentrations of hypochlorite (12.5 to 200 ppm) and sodium bisulfite (0.15 to 2.50%) applied singly and as successive dips were compared for their effect on the microbial flora of shrimp. It was found that sodium bisulfite exhibited antimicrobial activity at all concentrations tested, with a 50% reduction in bacterial numbers at a concentration of 2.5%. Hypochlorite reduced the bacterial load 75% at a concentration of 200 ppm. Under certain conditions a sequential treatment of shrimp with bisulfite, followed by a hypochlorite dip, significantly increased the antimicrobial effectiveness of the hypochlorite. This synergistic effect, however, was not apparent on shrimp following 24 h of iced storage.

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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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