Abstract
Agriculture is fundamental for food production, and microbiomes support agriculture through multiple essential ecosystem services. Despite the importance of individual (i.e., niche specific) agricultural microbiomes, microbiome interactions across niches are not well-understood. To observe the linkages between nearby agricultural microbiomes, multiple approaches (16S, 18S, and ITS) were used to inspect a broad coverage of niche microbiomes. Here we examined agricultural microbiome responses to 3 different nitrogen treatments (0, 150, and 300 kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches (rumen, faecal, white clover leaf, white clover root, rye grass leaf, and rye grass root). Nitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive. Nitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should be considered when management is applied to a single agricultural niche.
Highlights
A farm is a collection of interlinked ecological habitats split by locations, including above-ground, below-ground, and animal-associated niches each harbouring unique microbiomes
Microbiomes from phyllosphere and rhizosphere provide benefits to host growth and wellbeing (Adesemoye et al, 2009), for instance helping with nutrient acquisition from soil, defence against plant-pathogens or adapting to environmental stresses (Mendes et al, 2013; Turner et al, 2013; Muller et al, 2016)
From samples across farm niches, an average of 111588, 102169, and 98632 raw reads (16S, 18S, and internal transcribed spacer (ITS), respectively) per sample were generated with details listed in Supplementary Table 1
Summary
A farm is a collection of interlinked ecological habitats split by locations, including above-ground, below-ground, and animal-associated niches each harbouring unique microbiomes. Microbiomes from phyllosphere (above-ground parts associated with plants) and rhizosphere (below-ground parts associated with roots) provide benefits to host growth and wellbeing (Adesemoye et al, 2009), for instance helping with nutrient acquisition from soil, defence against plant-pathogens or adapting to environmental stresses (Mendes et al, 2013; Turner et al, 2013; Muller et al, 2016). These benefits are seen in animal microbiomes through nutrient acquisition mediated by gut microbiomes (Flint et al, 2008)
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