Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State

Arbuscular mycorrhizal interaction associated with a botanical garden in the tropics of Mexico

Botanical gardens, areas for vegetation conservation, have become important reservoirs of beneficial soil microbiota, mainly as a source of microbial inoculum for agricultural purposes. Shrubby mycorrhizal fungi (AMF), an important genetic resource of tropical soils, have a high potential for agricultural production, generally used as inoculant medium that provides better yield, productivity and physiological response to crops. This research study explores the presence of AMF in a botanical garden, composed of four areas: cactarium collection, epiphytes and ornamental collection, tropical forest area and coastal zone. Each area is composed of plants representative of its ecosystem. For the study, a random systematic model was used, with nine samples per site at a depth of 20 cm. A physicochemical characterization of the soils was developed. The extraction of AMF spores was carried out by wet sieving and centrifugation in 60% sucrose. The spores were identified by taxon. The results indicate a total of 379 AMF spores identified in the study area. The highest spore incidence was recorded in the tropical forest area with a total of 161 (53.67±5.51) spores extracted, followed by the coastal zone and cactus collection area with 78 (26.00±9.64) and 73 (24.33±4.73) spores in total. In the study two taxa were identified, Glomeraceae and Gigasporaceae. The taxon Glomeraceae is also considered to be the most representative (highest abundance and frequency) of the study. In conclusion, botanical gardens, by their extructure (plant composition) and management can be taken into account as important ecosystems reservoirs and source of viable microbial genetic material for the bioprospecting of beneficial soil genotic resources (rhizophiles and endophylls) for use in modern agriculture and sustainable food production systems.

Making partners in the city: impact of urban soil P enrichment on the partnership between an invasive herb and arbuscular mycorrhizal fungi in a tropical city

The mutualistic relationship between plants and arbuscular mycorrhizal (AM) fungi is essential for optimal plant nutrition, enabling plants to better withstand biotic and abiotic stressors and enhancing survival, reproduction, and colonization of new environments. Activities, such as soil enrichment or compaction, may decrease the benefits of AM fungi for plants, potentially reducing interactions in urban environments. Here, we examine this prediction by studying how urbanization alters AM interactions with the invasive herb Ruellia nudiflora (Acanthaceae). We collected soil and plants from deep urban sites (DUS; e.g., sidewalks), open urban sites (OUS; parks), and rural sites (RS) to analyse soil nutrient content, plant morphology, AM colonization rates, spore density, richness, and diversity. Contrary to predicted, DUS had the lowest soil nutrient concentration, except for phosphorus, reducing AM colonization. This supports the prediction of reduced AM interactions in urban environments. We also found that potassium affects the AM association. Urban plants had smaller and more compact root systems compared to their rural counterparts, but there were no discernible differences in AM fungi communities between urban and rural environments. Phosphorus enrichment in sidewalks is the main driver of reductionof R. nudiflora-AM fungi interactions in Mérida. More studies are needed to gain a better understanding of how AM fungi contribute to plant colonization in urban environments.

Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens

During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.

Insights into the Chemical Diversity of Selected Fungi from the Tza Itzá Cenote of the Yucatan Peninsula

Cenotes are habitats with unique physical, chemical, and biological features. Unexplored microorganisms from these sinkholes represent a potential source of bioactive molecules. Thus, a series of cultivable fungi (Aspergillus spp. NCA257, NCA264, and NCA276, Stachybotrys sp. NCA252, and Cladosporium sp. NCA273) isolated from the cenote Tza Itzá were subjected to chemical, coculture, and metabolomic analyses. Nineteen compounds were obtained and tested for their antimicrobial potential against ESKAPE pathogens, Mycobacterium tuberculosis, and nontuberculous mycobacteria. In particular, phenylspirodrimanes from Stachybotrys sp. NCA252 showed significant activity against MRSA, MSSA, and mycobacterial strains. On the other hand, the absolute configuration of the new compound 17-deoxy-aspergillin PZ (1) isolated from Aspergillus sp. NCA276 was established via single-crystal X-ray crystallography. Also, the chemical analysis of the cocultures between Aspergillus and Cladosporium strains revealed the production of metabolites that were not present or were barely detected in the monocultures. Finally, molecular networking analysis of the LC-MS-MS/MS data for each fungus was used as a tool for the annotation of additional compounds, increasing the chemical knowledge on the corresponding fungal strains. Overall, this is the first systematic chemical study on fungi isolated from a sinkhole in Mexico.

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery

Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.

Diversity and Structure of Soil Fungal Communities across Experimental Everglades Tree Islands

Fungi play prominent roles in ecosystem services (e.g., nutrient cycling, decomposition) and thus have increasingly garnered attention in restoration ecology. However, it is unclear how most management decisions impact fungal communities, making it difficult to protect fungal diversity and utilize fungi to improve restoration success. To understand the effects of restoration decisions and environmental variation on fungal communities, we sequenced soil fungal microbiomes from 96 sites across eight experimental Everglades tree islands approximately 15 years after restoration occurred. We found that early restoration decisions can have enduring consequences for fungal communities. Factors experimentally manipulated in 2003–2007 (e.g., type of island core) had significant legacy effects on fungal community composition. Our results also emphasized the role of water regime in fungal diversity, composition, and function. As the relative water level decreased, so did fungal diversity, with an approximately 25% decline in the driest sites. Further, as the water level decreased, the abundance of the plant pathogen–saprotroph guild increased, suggesting that low water may increase plant-pathogen interactions. Our results indicate that early restoration decisions can have long-term consequences for fungal community composition and function and suggest that a drier future in the Everglades could reduce fungal diversity on imperiled tree islands.