The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli, ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis, Flavobacterium terrae, Niastella vici, and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.

Background: Analyzing interactions between vegetation and environmental factors at regional scales provide information for the understanding of species assemblages. Hypotheses: Environmental restrictions at higher elevations produce a decreasing species richness pattern along an elevational gradient and the climatic variables related to temperature and precipitation are the main filters of species distribution. Objectives: (1) To identify the different assemblages of tree species occurring in a biodiversity hotspot; (2) to analyze the pattern of tree species richness along an elevational gradient; and (3) to analyze the environmental filters that determine the species distribution. Study site: Serranías Meridionales of Jalisco in western Mexico. Period of study: 2016-2018. Methods: Thirty-three rectangular 0.1 ha plots were established for vegetation and environmental characterization. Cluster and canonical correspondence analyses were conducted to analyze tree species composition. We defined three groups of variables (climatic, relief and soil) to evaluate the influence of environmental filters. We used generalized linear models to assess the contribution of each group to the spatial variation in species richness. Results: A total of 63 tree species were recorded. The cluster analysis defined eight groups within three forest types. The species richness showed a hump-shaped pattern along the elevational gradient and the climatic and soil variables explained a considerable amount of variation in the species richness. Conclusions: The tree species richness in the Serranías Meridionales de Jalisco is dominated by a striking number of Pinus and Quercus species. This biodiversity hotspot is an important site for the understanding of tree ecological diversification in Mexico.

Rivers are important sites for carbon (C) transport and critical components of the global C cycle that is currently not well constrained. However, little is known about C species’ longitudinal and temporal changes in large tropical rivers. The Usumacinta River is Mexico’s main lotic system and the tenth largest in North America. Being a tropical river, it has a strong climatic seasonality. This study aims to evaluate how organic (DOC and POC) and inorganic (DIC and PIC) carbon change spatially and seasonally along the Usumacinta River (medium and lower basin) in rainy (RS-2017) and dry (DS-2018) seasons and to estimate C fluxes into the southern Gulf of Mexico. Concentrations of DOC, POC, DIC, and PIC ranged from 0.88 to 7.11 mg L⁻¹, 0.21 to 3.78 mg L⁻¹, 15.59 to 48.27 mg L⁻¹, and 0.05 to 1.51 mg L⁻¹, respectively. DOC was the dominant organic species (DOC/POC > 1). It was ~doubled in RS and showed a longitudinal increase, probably through exchange with wetlands and floodplains. Particulate carbon showed a positive relationship with the total suspended solids, suggesting that in RS, it derived from surface erosion and runoff in the watershed. DIC is reported for the first time as the highest concentration measured in tropical rivers in America. It was higher in the dry season without a longitudinal trend. The C mass inflow–outflow balance in the RS suggested net retention (DOC and POC sink) in floodplains. In contrast, in the DS, the balance suggested that floodplains supply (C source) autochthonous DOC and POC. The lower Usumacinta River basin is a sink for DIC in both seasons. Finally, the estimated annual C export for the Usumacinta-Grijalva River was 2.88 (2.65 to 3.14) Tg yr⁻¹, of which DIC was the largest transported fraction (85%), followed by DOC (10%), POC (4%), and PIC (<1%). This investigation is the first to present the C loads in a Mexican river.