18S rRNA gene amplicon sequencing combined with culture‐based surveys of maize rhizosphere protists reveal dominant, plant‐enriched and culturable community members

Abstract

Summary Protists play important roles in shaping the microbial community of the rhizosphere and defining these roles will require the study of protist isolates. However, there is still a limited understanding of how well protist isolation efforts can capture the diversity and composition of rhizosphere protistan communities. Here, we report a simultaneous isolation and 18S rRNA gene amplicon sequencing survey describing the protist diversity of maize rhizospheres in two climatically and pedologically distinct sites. We demonstrated that the maize rhizosphere exerted significant and site‐dependent effects on the protistan community structure and defined a set of core and rhizosphere‐enriched protists. From the same root samples, we generated a library of 103 protist isolates representing 46 18S rRNA gene sequence variants from six eukaryotic supergroups. While cultured isolates represented a small proportion of total protist diversity recovered by sequencing, they included taxa enriched in rhizosphere soils across all samples, encompassing 9% of all core sequence variants. The isolation approach also captured 17 protists not detected through 18S rRNA gene amplicon sequencing. This study demonstrated that maize roots select for distinct protistan communities, and established a diverse protist culture collection that can be used for future research linking protists to rhizosphere status and plant health.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize–cabbage rotation

“…This result is unsurprising because microbial communities including fungi are known to be influenced by crops and land use history, including crop rotations. This is also the case with eukaryotic communities; for instance, protist communities were changed by fertilization 44 and depth 45 , and unique communities of eukaryotes 46 – 49 , including protists 50 – 53 and nematodes 54 , 55 , were formed in different types of soils, including agricultural soils. Furthermore, the taxonomic variations in β-diversities were almost comparable among the three different growth stages of crops except for prokaryotic variations in field_2 soils cropping maize at the early stage (Fig.…”

The potential of Pseudomonas fluorescens SBW25 to produce viscosin enhances wheat root colonization and shapes root-associated microbial communities in a plant genotype-dependent manner in soil systems

“…In the Sheriff cultivar, we observed a decrease in the Cercozoa Group-Te in the SBW25 WT-treated rhizoplane. Group-Te is found in the rhizosphere of multiple crops and model plants, e.g., maize, Arabidopsis, and potato ( 64 , 65 ), but the ecology of this organism is unknown. While the overall findings support the resilience of the microbial communities in the Heerup rhizoplane, the diversity estimates showed a differential pattern for the bacterial and the protist community, respectively, with no difference in the protist diversity measure upon inoculation with either strain of SBW25.…”

The potential ofPseudomonas fluorescensSBW25 to produce viscosin enhances wheat root colonization and shapes root-associated microbial communities in a plant genotype dependent manner in soil systems

“…Group-Te is found in the rhizosphere of multiple crops and model plants, e.g. maize, Arabidopsis, potato (65, 66), but the ecology of this organism is unknown. While the overall findings support a resilience of the microbial communities in the Heerup rhizoplane, the diversity estimates showed a differential pattern for the bacterial and the protist community, respectively, with no difference in the protist diversity measure upon inoculation with either strain of SBW25.…”

“…Group-Te is found in the rhizosphere of multiple crops and model plants, e.g. maize, Arabidopsis, potato [66,67], but the ecology of this organism is unknown. In contrast to the Sheriff cultivar, SBW25 WT did not result in any changes of any protist ASVs in the rhizoplane of the Heerup cultivar, in line with our results of the bacterial community.…”