It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil – their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.
Background During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood. Results Using shotgun metagenomic (DNA) and metatranscriptomic (RNA) sequencing data from ten wastewater treatment plants in Switzerland, we were able to assess the entire wastewater microbiome, including the often neglected microeukaryotes (protists). In the latter group, we found a surprising richness and relative abundance of active parasites, particularly in the inflow. Using network analysis, we tracked these taxa across the various treatment compartments and linked their removal to trophic interactions. Conclusions Our results indicate that the combination of DNA and RNA data is essential for assessing the full spectrum of taxa present in wastewater. In particular, we shed light on an important but poorly understood function of wastewater treatment – parasite removal.
Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly.To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots.Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response.Our results indicate a central role of root caps in microbiome assembly with ripple-on effects affecting higher trophic levels and microbiome composition on older root zones.
The soil alpine microbiome is dependent on season and elevation, yet there is limited understanding of how complex communities are differentially shaped by abiotic and biotic factors. Here we investigated the spring-to-summer dynamics of soil microbiomes in alpine grasslands, focussing on soil food web interactions. To this end, we conducted a survey along altitudinal transects in three mountains in the Alps, in spring at snowmelt and in the following summer, recorded vegetation and topographic, climatic and edaphic parameters for 158 soil samples. By using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified by nutrition guilds. Our results show: (i) that biotic interactions could explain more variation of the microbial communities than topographic and edaphic variables, more for consumers than for preys, and this effect was stronger in summer than in spring; (ii) a seasonal dynamic in biotic interactions: the consumers' pressure on preys increases from spring to summer, resulting in a higher diversity and evenness of preys. In alpine grasslands, consumers effectively contribute to maintain the diverse soil bacterial and fungal community essential for ecosystem functioning.
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