The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Given the importance of soil as a supplier of nutrients and water for different ecosystems, understanding soil health and quality is necessary for its preservation. Microorganisms, due to their high abundance and their relationship with the degradation of organic matter and biogeochemical cycles, have a rapid response to environmental changes and thus are a discriminating factor that can be used as bioindicators of soil health. However, 97% of microorganisms are unculturable, leaving a gap in their taxonomic and functional knowledge. The development of metagenomics has reduced this problem through the direct extraction of DNA from soil, allowing the characterization of such non-culturable microorganisms, this technique can be considered one of the most impactful in soil health, given that it allows for an exploration of the biodiversity, the community structure, and the potential functions of the microbial communities from distinct environments. In addition to this, metagenomics have had an impact in different areas such as “OneHealth” or EcoGenomics allowing the formation of international projects. The aim of this paper is to show how metagenomics can be used as a technique to assess soil quality and health through the taxonomic and functional identification of the microorganisms present in the soil.

A bacterial (16S rRNA) and fungal (ITS rRNA) taxonomic characterization was carried out using metabarcoding along an altitudinal gradient in the western range of the Valle del Cauca, Colombia. This study encompassed Tropical Dry Forests, Andean, and Páramo ecosystems in Laguna de Sonso (900 m.a.s.l), Yotoco (1,800 m.a.s.l), Bosque del Duende (2,400 m.a.s.l), and Páramo del Duende (3,200 m.a.s.l). The physicochemical analyses revealed soils with high organic matter (>10%), non-compacted, extremely acidic pH levels (4.4) at higher altitudes, and slightly to moderately acidic pH in lower areas (5.5–6.1). 59 plant families were identified, with Araceae, Lauraceae, and Fabaceae being the most abundant. The most abundant bacterial taxonomic assignments were Acidobacteriota and Proteobacteria phyla, while for fungi, it was Ascomycota and Basidiomycota. Alpha diversity analysis showed high community diversity, whereas beta diversity reflected composition differences among locations and their heterogeneity. The most abundant functional predictions for bacteria were chemoheterotrophic activity and nitrogen cycle involvement. At the same time, for fungi, it was ecological guilds related to pathogenic activity in both animals and plants, endophytes, and epiphytic saprotrophs. The PLS-PM analysis revealed an indirect influence of altitude on microbial abundance and diversity.

Medicinal plants maintain structures and diversities of bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) that can interact to promote growth and therapeutic properties. Therefore, the purpose of this research was to evaluate the microbiome of Lippia alba and Petiveria alliacea, species known for their high potential for medicinal benefits in Colombia. To achieve this, rhizosphere soils and roots were sampled from five departments in Colombia: Boyacá, Cundinamarca, Tolima, Putumayo, and Valle del Cauca. The results revealed that the dominant bacterial groups in both plants were primarily Proteobacteria, Acidobacteriota, and Actinobacteriota, with the first phylum showing the highest number of differentially abundant genera between the sampling points. In fungi, Ascomycota tended to dominate in most of the sampled locations, while Mortierellomycota was particularly abundant in roots of P. alliacea in Valle. Furthermore, the study of AMF indicated differentiation in the colonization for both plants, with the genera Glomus and Paraglomus being predominant. Differences in the Shannon diversity index were recorded between sampling types within these sampling points, possibly influenced by local and environmental factors. Our findings reveal that the microbiomes of both medicinal plants exhibit distinct community assemblies, which could be a significant factor for their future therapeutic use.

The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.

Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, F_ST = 0.115 (p < 0.001) and F_IT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.