Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Abstract

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

Cassava/peanut intercropping improves soil quality via rhizospheric microbes increased available nitrogen contents

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Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

“…Although all cultivated AOA strains grow chemolithoautotrophically through oxidation of ammonia, several studies have suggested that growth of at least some AOA predominant in soils and freshwater might not depend solely, or primarily, on ammonia oxidation (see for example Jia and Conrad, 2009; Xu et al, 2012; Alves et al, 2018; Nelkner et al, 2019 for overview). Incorporation of carbon from organic substrates into AOA cells has also been reported in ocean waters (Ouverney and Fuhrman, 2000; Ingalls et al, 2006; Hansman et al, 2009), and other studies were unable to detect autotrophic carbon assimilation in populations actively growing in wastewater treatment plants (Mussmann et al, 2011; Sauder et al, 2017).…”

Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota

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