Microorganism community structure: A characterisation of agrosystems from Madeira Archipelago

Abstract

Microbial diversity profoundly influences soil ecosystem functions, making it vital to monitor community dynamics to comprehend its structure. Our study focused on six agrosystems in Madeira Archipelago, analysing bacteria, archaea, fungi and AMF through classical microbiology and molecular techniques. Despite distinct edaphoclimatic conditions and management practices, bacterial structures exhibited similarities, with Alphaproteobacteria at 18%-20%, Bacilli at 11%-18% and Clostridia at 9%-14%. The predominance of copiothrophic groups suggested that soil nutrient content was the driver of these communities. Regarding archaea, the communities changed among sites, and it was evident that agrosystems provided niches for methanogens. The Crenarchaeota varied between 15% and 29%, followed by two classes of Euryarchaeota, Methanomicrobia (17%-25%) and Methanococci (4%-32%). Fungal communities showed consistent composition at the class level but had differing diversity indices due to management practices and soil texture. Sordaryomycetes (21%-28%) and Agaricomycetes (15%-23%) were predominant. Conversely, AMF communities appeared to be also influenced by the agrosystem, with Glomus representing over 50% of the community in all agrosystems. These insights into microbial groups' susceptibilities to environmental conditions are crucial for maintaining healthy soil and predicting climate change effects on agrosystems' productivity, resilience and sustainability. Additionally, our findings enable the development of more robust prediction models for agricultural practices.

FIGURE 1

Sampled agrosystems from the Madeira Archipelago.

FIGURE 2

Variation in total bacteria, fungi, nitrogen‐fixing, and denitrifying bacteria abundance for the 2 years. Boxes with different letters indicate a significant difference among them (ANOVA, p ≤ 0.05). The letter ‘a’ corresponds to the lowest values.

FIGURE 3

UpSet plot showing how many unique T‐RFs of bacteria, archaea, fungi and AMF are shared between and among agrosystems.

FIGURE 4

Relative abundance (%) of T‐RFs, identified at a class level, for Bacteria (left) and Archaea (right) communities.

FIGURE 5

Relative abundance (%) of T‐RFs, identified at the class level, observed for Fungal (left) communities, and T‐RFs, identified at a genus level, observed for AMF (right) communities.

FIGURE 6

Variation in the T‐RF Richness (R), Shannon–Winner diversity (H′) and Corrected Evenness (E′) of Bacteria and Archaea by agrosystem. Different letters above the boxes indicate a significant difference between them (ANOVA, p ≤ 0.05). The letter ‘a’ refers to the lowest values.

FIGURE 7

Variation in the Species Richness (R), Shannon–Winner diversity (H′), and Corrected Evenness (E′), of Fungi and AMF by agrosystem. Different letters above the boxes indicate a significant difference between them (ANOVA, p ≤ 0.05). The letter ‘a’ refers to the lowest values.

FIGURE 8

Dendrogram of the beta‐diversity (compositional dissimilarity between sites).

FIGURE 9

Venn diagram with the percentage of shared T‐RFs among different management practices and soil textures. Figures (A) to (D) are for bacterial communities. Figures (E) to (H) are for archaeal communities. (A) and (E) cultivated crops: vegetables (veg), banana, vine, apple; (B) and (F) cropping system: monoculture (mono) and polyculture (poly); (C) and (G) mode of production: transition to organic farming (T‐OF), organic farming (OF), traditional (T); (D) and (H) soil texture: silt loam, silt clay loam, silt clay.

FIGURE 10

Venn diagram showing the percentage of shared T‐RFs among different management practices and soil textures. Figures (A) to (D) are for fungal communities. Figures (E) to (H) are for AMF communities. (A) and (E) cultivated crops: vegetables (veg), banana, vine, apple; (B) and (F) cropping system: monoculture (mono) and polyculture (poly); (C) and (G) mode of production: transition to organic farming (T‐OF), organic farming (OF), traditional (T); (D) and (H) soil texture: silt loam, silt clay loam, silt clay.