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IntroductionThe ecosystem services provided by soil microbial communities are critical for the resilience of agroecosystems, ensuring environmental conservation and food security. Long-term experiments comparing contrasting crop rotations are valuable tools for monitoring microbial responses, but they rarely include all crop phases within a single year. Therefore, the long-term agronomic impact may be masked by the immediate effect of the crop evaluated. In this study, we compared different crop rotations based on the Intensification Sequence Index (ISI), which considers the soil occupation time, and analyzed the impact of cover crops and two nitrogen fertilization strategies.Material and methodsWe used an experiment initiated in 2006 with the following crop rotations: Soybean-Soybean, Maize-Wheat/Soybean, and Maize-Soybean-Wheat/Soybean. Soil samples were taken after the harvest of each summer crop phase (i.e., Soybean, Maize, Wheat/Soybean), and the soil prokaryotic community was monitored using 16S rRNA gene sequencing.Results and discussionWe observed that ISI and crop phase were the main predictors of microbial community composition, explaining 14.7% and 13.0% of the variation, respectively. Nitrogen fertilization had a minor effect (3.12%) and was detected only after maize sampling; cover crops had no significant effect. However, the presence of cover crops showed higher alpha diversity and an increased abundance of Proteobacteria. Maize enriched the abundance of certain taxa of Planctomycetes and Verrucomicrobia, while Soybean increased the abundance of Bacteroidetes and Proteobacteria. Comparatively, Soybean enriched Mucilaginibacter and Geobacter, while Wheat/Soybean enriched Brevundimonas and Roseimicrobium.ConclusionOur results demonstrate that crop phase is as important as the long-term legacy of crop rotations in shaping the microbial community and that specific taxa responses are highly dependent on the crop phase surveyed.

Fungi are essential players in the maintenance of global coffee productivity, but their taxonomic and functional diversity in tropical and subtropical soils of Latin America remains largely unexplored. To address this concern, soil fungi were surveyed in six farms in three traditional coffee-growing regions of Colombia (Cauca, Magdalena, and Risaralda). Five farms were organic and newly established (30 years old) with higher shade cover. We used amplicon sequencing and functional prediction based on the FUNGuild annotation tool. Fungal community composition diverged among farms, with Mortierella (Mortierellomycota) and Saitozyma (Basidiomycota) among the most prevalent genera. Functional prediction revealed the predominance of saprotroph-symbiotroph and pathotroph fungi. The endophyte and litter decomposer Mortierella genus was dominant within the saprotrophs and symbiotrophs. The pathotroph community was characterized by insect pathogen species belonging to the Metarhizium (Ascomycota) genus. Indeed, M. anisopliae and M. marquandii were identified as indicator species in the conventional long-term shaded farm. This study revealed that coffee plantations studied sustain a diverse fungal community and nurture potentially beneficial species. Further studies are needed to elucidate how particular management practices can nourish beneficial fungi, suppress detrimental species, and promote more sustainable coffee production.

The transformation of the semiarid steppe soil after 5 years of intensive irrigated agriculture in Northern Patagonia was analyzed in an on-farm study. The private grower venture used conservative practices, including no-till to maintain soil structure, high crop rotation and cover crops. To characterize steppe soil changes by irrigated agriculture, we analyzed the enzymatic activities involved in the biogeochemical cycles (carbon, nitrogen, phosphorus and sulfur), the whole soil fatty acids profile, the state of soil aggregation, and the bacterial and fungal microbiota through DNA sequencing methods. After 5 years of management, irrigated agriculture soil increased organic matter (25–33%), enzymatic activities -Cellobiose-hydrolase (60–250%), Phosphatase (35–60%), Xylanase (101–185%), Aryl-sulphatase (32–100%), Chitinase (85%), β-Glucosidase (61–128%), Leucine-aminopeptidase (138%)—depending on soil series, and macro-aggregate formation at the expense of the abundance of micro-aggregates in the first 0–5 cm of soil. Whole soil fatty acids profiles changed, enhancing mono-unsaturated, branched, cyclic and methylated fatty acids. Microbial communities showed significant differences between irrigated agriculture sites and pristine valleys. The richness-based alpha-diversity established increased bacterial communities but decreased fungal communities in cultivated soil. Indicators selected using the LEfSe method revealed the bacterial taxa Acidothermus, Conexibacter and Thermoleophilum, associated with semiarid steppe soil while Asticcacaulis, Aquicella and Acromobacter with irrigated agriculture. Ascomycota Phylum changed its community composition, being both taxa Aspergillus and Alternaria reduced while Stagonospora and Metarhizium were enhanced in irrigated agriculture. Taxa belonging to Acidobacteria, Chloroflexi, and Betaproteobacteria, that were enriched in irrigated agriculture soils, were associated with higher capture of C but smaller values of aggregation, while taxa abundant on steppe soils belonging to Actinobacteria, Alphaproteobacteria, and Firmicutes were positively associated with soil aggregation but negatively with C uptake.