Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil

Bang‐Andreasen, Toke; Anwar, Muhammad Zohaib; Lanzén, Anders; Kjøller, Rasmus; Rønn, Regin; Jacobsen, Carsten Suhr

doi:10.1093/femsec/fiaa016

Cited by 42 publications

(34 citation statements)

References 87 publications

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“…The results showed that the effect of planting yellow horn on bacteria in y ash was much greater than that on fungi. Bang-Andreasen et al also found that the in uence of wood ash application on the abundance and diversity of bacteria in agricultural and forest soil was greater than that of fungi [35].…”

Section: Discussionmentioning

confidence: 96%

Influence of Planting Xanthoceras Sorbifolia Bunge on Bacteria and Fungi Diversity of Fly Ash

Liu¹,

Chen²,

Huo³

et al. 2021

Preprint

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Background: Fly ash is the product of coal combustion, and a large amount of fly ash accumulation is of great harm to the environment. The yellow horn (Xanthoceras sorbifolia Bunge) is a unique edible oil tree species in China. Yellow horn has developed root system and can survive in soil contaminated with heavy metals. Thus, it could be used for phytoremediation in fly ash. Results: In this study, high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing technology was used to analyze the microbial community diversity in fly ash before (CK group) and after (S group) planting yellow horn. The abundance and diversity of microorganisms in fly ash were changed by planting yellow horn. The dominant bacterial phyla: Proteobacteria (CK-24% vs S-42%), Firmicutes (CK-23% vs S-10%), Actinobacteria (CK-15% vs S-11%). The dominant phyla in fungi: Ascomycota (72% for CK, 69% for S), Mortierellomycota (4% for CK, 3% for S).Some beneficial bacteria that could degrade heavy metals increased in proportion, including Betaproteobacteriales (4% for CK vs 10% for S group), Burkholderiacae (1% for CK vs 6% for S groups), Nitrospirae (0.3% for CK vs 0.8% for S groups), Rhizobiales (3% for CK vs 6% for S groups) and Sphingomonadaceae (2% for CK vs 4% for S groups). Conclusion: These results indicate that the planting of yellow horn can increase the abundance of heavy metal-degrading bacteria in rhizosphere fly ash, which is of great significance for the biological remediation of fly ash.

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Section: Discussionmentioning

confidence: 96%

Influence of Planting Xanthoceras Sorbifolia Bunge on Bacteria and Fungi Diversity of Fly Ash

Liu¹,

Chen²,

Huo³

et al. 2021

Preprint

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“…Extracellular DNA is relatively stable and only slowly degrades in soils 62,63 and the inclusion of DNA from dead organisms will thus indicate slower community responses than what is actually true in the soil 64 . Total RNA-sequencing would circumvent the bias associated with relic DNA as RNA have much faster turnover time [65][66][67] . We therefore suggest that future studies should also consider RNA-based techniques when studying short-time reactions.…”

Section: Discussionmentioning

confidence: 99%

Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil

Bang‐Andreasen

Peltre

Ellegaard-Jensen

et al. 2021

Sci Rep

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Wood ash is alkaline and contains base-cations. Application of wood ash to forests therefore counteracts soil acidification and recycle nutrients removed during harvest. Wood ash application to soil leads to strong vertical gradients in physicochemical parameters. Consequently, we designed an experimental system where small-scale vertical changes in soil properties and prokaryotic community structure could be followed after wood ash application. A mixed fly and bottom ash was applied in dosages of 3 and 9 t ha−1 to the surface of soil mesocosms, simulating a typical coniferous podzol. Soil pH, exchangeable cations and 16S prokaryotic community was subsequently assessed at small depth intervals to 5 cm depth at regular intervals for one year. Wood ash significantly changed the prokaryotic community in the top of the soil column. Also, the largest increases in pH and concentrations of exchangeable cations was found here. The relative abundance of prokaryotic groups directionally changed, suggesting that wood ash favors copiotrophic prokaryotes at the expense of oligotrophic and acidophilic taxa. The effect of wood ash were negligible both in terms of pH- and biological changes in lower soil layers. Consequently, by micro-vertical profiling we showed that wood ash causes a steep gradient of abiotic factors driving biotic changes but only in the top-most soil layers.

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“…Wood ash amendment can affect soil physicochemical parameters and influence soil microbial community composition and functional expression, primarily related to soil chemical properties (increased pH, electrical conductivity, dissolved organic carbon, and phosphate) (Bang-Andreasen et al, 2020). Addition of the wood ash amendments caused an increase in genes associated with copiotrophic microbial subpopulations (rRNA); in general, more functional genes (mRNA) were observed to be upregulated than downregulated, with the majority originating from four functional categories: "post-translation modification, protein turnover and chaperones"; "transcription"; "replication, recombination, and repair"; and "carbohydrate transport and metabolism"-genes that are involved with carbon cycling (i.e., metabolism and cell growth) (Bang-Andreasen et al, 2020). The researchers concluded that increases in pH, bioavailable dissolved organic carbon, and nutrients (induced by the wood ash ammendments) allow copiotrophic groups to thrive at the expense of oligotrophic groups directly following amendment application.…”

Section: Metatranscriptomics-general Context and Current Applicationsmentioning

confidence: 99%

“Omics” Technologies for the Study of Soil Carbon Stabilization: A Review

Overy

Bell

Habtewold

et al. 2021

Front. Environ. Sci.

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Evidence-based decisions governing sustainable agricultural land management practices require a mechanistic understanding of soil organic matter (SOM) transformations and stabilization of carbon in soil. Large amounts of carbon from organic fertilizers, root exudates, and crop residues are input into agricultural soils. Microbes then catalyze soil biogeochemical processes including carbon extracellular transformation, mineralization, and assimilation of resources that are later returned to the soil as metabolites and necromass. A systems biology approach for a holistic study of the transformation of carbon inputs into stable SOM requires the use of soil “omics” platforms (metagenomics, metatranscriptomics, metaproteomics, and metabolomics). Linking the data derived from these various platforms will enhance our knowledge of structure and function of the microbial communities involved in soil carbon cycling and stabilization. In this review, we discuss the application, potential, and suitability of different “omics” approaches (independently and in combination) for elucidating processes involved in the transformation of stable carbon in soil. We highlight biases associated with these approaches including limitations of the methods, experimental design, and soil sampling, as well as those associated with data analysis and interpretation.

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Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil

Cited by 42 publications

References 87 publications

Influence of Planting Xanthoceras Sorbifolia Bunge on Bacteria and Fungi Diversity of Fly Ash

Influence of Planting Xanthoceras Sorbifolia Bunge on Bacteria and Fungi Diversity of Fly Ash

Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil

“Omics” Technologies for the Study of Soil Carbon Stabilization: A Review

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