Microbial diversity and physicochemical characteristics of tropical karst soils in the northeastern Yucatan peninsula, Mexico

Abstract Shallow karst soils can support productive forests, but their microbiota has been poorly studied in tropical areas where they accomplish relevant biogeochemical functions. Therefore, we studied the bacterial, archaeal, and fungal communities of Rendzic Leptosols from a tropical sub-humid area in the Peninsula of Yucatan (Mexico), aiming to know these microorganisms and the physicochemical characteristics that shape their communities. The soils were moderately alkaline (pH ~8.4), with a high content of organic-C (17–29%) and a clay fraction >43%. The microbial component was estimated at 2.8 × 107 16S rDNA gene copies/g (Bacteria/Archaea) and 9.3 × 104 ITS copies/g (Fungi). The microbial communities were divergent among subsites, possibly due to soil microheterogeneity, and less than 1.5% of the phylotypes were observed in at least 65% of the samples. These shared microorganisms were affiliated to phyla often found in forest soils such as Acidobacteria, Actinobacteria, Rokubacteria, and Mortierellomycota, which are reported as effective organic matter transformers. N-fixing bacteria (Bradyrhizobium) and nitrifiers (Thaumarchaeota and Nitrospira) were also detected. pH was the main factor associated with the bacterial and archaeal community structure. The functional prediction suggests that soil microorganisms have a high potential for carbon metabolism and the biosynthesis of antibiotics, besides polymer and pollutant degradation, such as phenolic substances and PAHs. Consequently, these shallow black soils harbor a diverse biosphere that can readily transform litter material and fix-N to increase the C- and N-soil pools, supporting thus a productive low forest.