Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Lutz, Stefanie; Thuerig, Barbara; Oberhaensli, T.; Mayerhofer, Johanna; Fuchs, Jacques; Widmer, Franco; Freimoser, Florian M.; Ahrens, Christian H.

doi:10.3389/fmicb.2020.01810

Cited by 51 publications

(38 citation statements)

References 120 publications

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“…Moreover, compost batch was shown to be the most important to determine bacterial and fungal community composition. Lutz et al (2020) also state that microbial community composition is highly dependent on the initial characteristics of the composts, including the compost material. A previous study by Vandecasteele et al (2021) showed that optimizing chemical properties of composts for a better fit in growing media was only successful if composts initially had a good suitability score.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, composts are characterized by high microbial activity that may stimulate plant growth and disease suppression ( Hoitink et al, 1996 ; Noble and Coventry, 2005 ; Raviv, 2008 ). Diverse potential biocontrol agents present in composts, such as Trichoderma , Pseudomonas , Pantoea and Bacillus spp., are known to contribute to a biocontrol effect ( Dukare et al, 2011 ; Chen et al, 2012 ; Antoniou et al, 2017 ; Lutz et al, 2020 ). This is in contrast to peat, which is considered to be poor in microorganisms, either beneficial or neutral, as compared to alternative growing media containing composts or other renewable materials, due to the recalcitrant chemical composition of Sphagnum biomass ( Hoitink and Boehm, 1999 ).…”

Section: Introductionmentioning

confidence: 99%

“…The bacterial genera Bacillus , Flavobacterium , Pseudomonas , and Cellulomonas have been shown to be dominant in the maturation phase of composts, while Altamaria , Aspergillus , Bipolaris and Fusarium have been shown to be the dominant fungal genera ( Ryckeboer et al, 2003 ). Several studies have shown the presence of microorganisms that have the potential to suppress soil-borne diseases in mature composts, such as Pseudomonas , Trichoderma , and Bacillus ( Dukare et al, 2011 ; Chen et al, 2012 ; Antoniou et al, 2017 ; Lutz et al, 2020 ). Carrión et al (2008) studied the effect of acidification on the compost microbiome and reported a decrease in microbial activity and an increase in autotrophic bacteria upon the addition of elemental sulfur.…”

Section: Introductionmentioning

confidence: 99%

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Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Pot

Tender

Ommeslag³

et al. 2021

Front. Microbiol.

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Three characteristics are considered key for optimal use of composts in growing media: maturity, pH and organic matter content. Maturation is a critical step in the processing of composts contributing to compost quality. Blending of composts with chopped heath biomass, sieving out the larger fraction of composts and acidification of composts by adding elemental sulfur may be used either to increase organic matter content or to reduce pH for a better fit in growing media. While several studies have shown the effectiveness of these treatments to improve the use of composts in growing media, the effect of these treatments on the compost microbiome has merely been assessed before. In the present study, five immature composts were allowed to mature, and were subsequently acidified, blended or sieved. Bacterial and fungal communities of the composts were characterized and quantified using 16S rRNA and ITS2 gene metabarcoding and phospholipid fatty acid analysis. Metabolic biodiversity and activity were analyzed using Biolog EcoPlates. Compost batch was shown to be more important than maturation or optimization treatments to determine the compost microbiome. Compost maturation increased microbial diversity and favored beneficial microorganisms, which may be positive for the use of composts in growing media. Blending of composts increased microbial diversity, metabolic diversity, and metabolic activity, which may have a positive effect in growing media. Blending may be used to modify the microbiome to a certain degree in order to optimize microbiological characteristics. Acidification caused a decrease in bacterial diversity and microbial activity, which may be negative for the use in growing media, although the changes are limited. Sieving had limited effect on the microbiome of composts. Because of the limited effect on the microbiome, sieving of composts may be used flexible to improve (bio)chemical characteristics. This is the first study to assess the effects of maturation and optimization treatments to either increase organic matter content or lower pH in composts on the compost microbiome.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Pot

Tender

Ommeslag³

et al. 2021

Front. Microbiol.

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“…Furthermore, compost represents an important source of organic matter and nutrients for agriculture, playing a crucial role in sustaining soil biodiversity [ 16 ] and the production of horticultural species when used as a component in the preparation of pot substrates [ 17 ]. Moreover, the microflora of the compost have significant antagonistic effects against several soil-borne phytopathogenic microorganisms, and hence they can play a vital role in controlling them [ 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Physico-Chemical Characterization and Biological Activities of a Digestate and a More Stabilized Digestate-Derived Compost from Agro-Waste

Vitti

Elshafie

Logozzo

et al. 2021

Plants

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The excessive use of agricultural soils and the reduction in their organic matter, following circular economy and environmental sustainability concepts, determined a strong attention in considering composting as a preferred method for municipalities and industries to recycle organic by-products. Microorganisms degrade organic matter for producing CO2, water and energy, originating stable humus named compost. The current study analyzed the chemical composition of a cow slurry on-farm digestate and a more stabilized digestate-derived compost (DdC), along with their phytotoxic, genotoxic and antifungal activities. The chemical analysis showed that digestate cannot be an ideal amendment due to some non-acceptable characteristics. Biological assays showed that the digestate had phytotoxicity on the tested plants, whereas DdC did not induce a phytotoxic effect in both plants at the lowest dilution; hence, the latter was considered in subsequent analyses. The digestate and DdC induced significant antifungal activity against some tested fungi. DdC did not show genotoxic effect on Vicia faba using a micronuclei test. Soil treated with DdC (5 and 10%) induced damping-off suppression caused by Fusarium solani in tomato plants. The eco-physiological data indicated that DdC at 5–10% could increase the growth of tomato plants. In conclusion, DdC is eligible as a soil amendment and to strengthen the natural soil suppressiveness against F. solani.

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“…Recent advancements in high-throughput sequencing have revolutionized genomic discovery and unlocked new insights regarding the diversity and function of microbial communities (1)(2)(3)(4). For example, shotgun metagenomic sequencing has clarified how the functional capacity of the gut microbiome links to human health (5)(6)(7)(8), improved the efficacy of antibiotic resistance gene discovery (9)(10)(11)(12), identified beneficial soil microbes for agricultural use (13)(14)(15), and uncovered novel, medically relevant biosynthetic gene clusters in marine microbes (16)(17)(18). However, while metagenomes offer rich opportunity to transform discovery, the financial cost of producing metagenomic data limits their application.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles

Gaulke

Schmeltzer

Dasenko

et al. 2021

Preprint

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Shotgun metagenomic sequencing has transformed our understanding of microbial community ecology. However, preparing metagenomic libraries for high-throughput DNA sequencing remains a costly, labor-intensive, and time-consuming procedure, which in turn limits the utility of metagenomes. Several library preparation procedures have recently been developed to offset these costs, but it is unclear how these newer procedures compare to current standards in the field. In particular, it is not clear if all such procedures perform equally well across different types of microbial communities, or if features of the biological samples being processed (e.g., DNA amount) impact the accuracy of the approach. To address these questions, we assessed how five different shotgun DNA sequence library preparation methods, including the commonly used Nextera® Flex kit, perform when applied to metagenomic DNA. We measured each method's ability to produce metagenomic data that accurately represents the underlying taxonomic and genetic diversity of the community. We performed these analyses across a range of microbial community types (e.g., soil, coral-associated, mouse-gut-associated) and input DNA amounts. We find that the type of community and amount of input DNA influence each method’s performance, indicating that careful consideration may be needed when selecting between methods, especially for low complexity communities. However, cost-effective preparation methods we assessed are generally comparable to the current gold standard Nextera® DNA Flex kit for high-complexity communities. Overall, the results from this analysis will help expand and even facilitate access to metagenomic approaches in future studies.

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Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Cited by 51 publications

References 120 publications

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Physico-Chemical Characterization and Biological Activities of a Digestate and a More Stabilized Digestate-Derived Compost from Agro-Waste

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles

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